From 3b7344076d3a3d21fdebb071855c591a86f23e38 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Jun 2019 20:48:44 +0200 Subject: [PATCH 001/793] adding easyconfigs: PRISMS-PF-2.1.1-foss-2019a.eb, p4est-2.2-foss-2019a.eb, deal.II-9.1.1-foss-2019a.eb --- .../d/deal.II/deal.II-9.1.1-foss-2019a.eb | 45 ++++++++++++++++++ .../p/PRISMS-PF/PRISMS-PF-2.1.1-foss-2019a.eb | 33 +++++++++++++ .../p/p4est/p4est-2.2-foss-2019a.eb | 47 +++++++++++++++++++ 3 files changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-foss-2019a.eb create mode 100644 easybuild/easyconfigs/p/PRISMS-PF/PRISMS-PF-2.1.1-foss-2019a.eb create mode 100644 easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb diff --git a/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-foss-2019a.eb b/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-foss-2019a.eb new file mode 100644 index 00000000000..e4990e2bda0 --- /dev/null +++ b/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-foss-2019a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'deal.II' +version = '9.1.1' + +homepage = 'https://www.dealii.org' +description = """deal.II is a C++ program library targeted at the computational solution of + partial differential equations using adaptive finite elements.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['https://github.com/dealii/dealii/releases/download/v%(version)s/'] +sources = ['dealii-%(version)s.tar.gz'] +checksums = ['fc5b483f7fe58dfeb52d05054011280f115498e337af3e085bf272fd1fd81276'] + +builddependencies = [('CMake', '3.13.3')] + +dependencies = [ + ('Boost', '1.70.0'), + ('GSL', '2.5'), + ('HDF5', '1.10.5'), + ('METIS', '5.1.0'), + ('netCDF', '4.6.2'), + ('p4est', '2.2'), + ('PETSc', '3.11.1'), + ('zlib', '1.2.11'), +] + +configopts = "-DCMAKE_BUILD_TYPE=Release " +configopts += "-DDEAL_II_WITH_LAPACK=ON -DDEAL_II_WITH_MPI=ON " +configopts += "-DDEAL_II_WITH_BOOST=ON -DBOOST_DIR=$EBROOTBOOST" +configopts += "-DDEAL_II_WITH_GSL=ON -DGSL_DIR=$EBROOTBOOST" +configopts += "-DDEAL_II_WITH_HDF5=ON -DHDF5_DIR=$EBROOTBOOST" +configopts += "-DDEAL_II_WITH_METIS=ON -DMETIS_DIR=$EBROOTBOOST" +configopts += "-DDEAL_II_WITH_NETCDF=ON -DNETCDF_DIR=$EBROOTBOOST" +configopts += "-DDEAL_II_WITH_P4EST=ON -DP4EST_DIR=$EBROOTP4EST" +configopts += "-DDEAL_II_WITH_PETSC=ON -DPETSC_DIR=$EBROOTBOOST" +configopts += "-DDEAL_II_WITH_ZLIB=ON -DZLIB_DIR=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ['lib/libdeal_II.%s' % SHLIB_EXT], + 'dirs': ['include/deal.II', 'lib/cmake', 'lib/pkgconfig', 'share/deal.II'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/PRISMS-PF/PRISMS-PF-2.1.1-foss-2019a.eb b/easybuild/easyconfigs/p/PRISMS-PF/PRISMS-PF-2.1.1-foss-2019a.eb new file mode 100644 index 00000000000..5e30567763c --- /dev/null +++ b/easybuild/easyconfigs/p/PRISMS-PF/PRISMS-PF-2.1.1-foss-2019a.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMakeCp' + +name = 'PRISMS-PF' +version = '2.1.1' + +homepage = 'https://prisms-center.github.io/phaseField' +description = """PRISMS-PF is a powerful, massively parallel finite element code for conducting phase field and + other related simulations of microstructural evolution.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['https://github.com/prisms-center/phaseField/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fd76b105d28791c5be5e624cacca9db4c453fbba26727c829ef3f0810f02fffe'] + +builddependencies = [('CMake', '3.13.3')] + +dependencies = [ + ('p4est', '2.2'), + ('deal.II', '9.1.1'), +] + +configopts = "-DCMAKE_PREFIX_PATH=$EBROOTDEALII" +buildopts = 'release' + +files_to_copy = ['applications', 'include', (['libprisms_pf*.a'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libprisms_pf.a', 'lib/libprisms_pf_debug.a'], + 'dirs': ['applications', 'include'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb b/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb new file mode 100644 index 00000000000..c2d29a78764 --- /dev/null +++ b/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'p4est' +version = '2.2' + +homepage = 'http://www.p4est.org' +description = """p4est is a C library to manage a collection (a forest) of multiple +connected adaptive quadtrees or octrees in parallel.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +# disable architecture-specific optimisations to fix failing sc_test_dmatrix test +# cfr. https://github.com/cburstedde/libsc/issues/15 +toolchainopts = {'openmp': True, 'usempi': True, 'optarch': False} + +source_urls = [ + 'https://github.com/cburstedde/p4est/archive', + 'https://github.com/cburstedde/libsc/archive/', +] +sources = [ + 'v%(version)s.tar.gz', + {'download_filename': '5282025.tar.gz', 'filename': 'libsc-2.2.tar.gz'}, +] +checksums = ['7df0e9a161b6ea680324dfdbc0ffc6e0d0a6c9c9b0ea5b37c973e71a054226c2'] + +dependencies = [ + ('zlib', '1.2.11'), + ('METIS', '5.1.0') +] + +builddependencies = [ + ('Autotools', '20180311') +] + +preconfigopts = "rmdir sc && mv %(builddir)s/libsc-* sc && " +preconfigopts += "echo '%(version)s' >> .tarball-version && ./bootstrap && " +configopts = "--enable-openmp --enable-mpi --with-metis " +configopts += "--with-blas=$EBROOTOPENBLAS/lib/libopenblas.a --with-lapack=$EBROOTOPENBLAS/lib/libopenblas.a" + +runtest = 'check VERBOSE=1' + +sanity_check_paths = { + 'files': ['bin/p4est_simple', 'bin/p4est_step1', 'bin/p4est_step2', 'bin/p4est_step3', 'bin/p4est_step4', + 'lib/libp4est-%%(version)s.%s' % SHLIB_EXT, 'lib/libp4est.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' From ac65f13da7670951c049b6eac451039588e3383f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Jun 2019 22:35:01 +0200 Subject: [PATCH 002/793] add missing checksum in p4est easyconfig --- easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb b/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb index c2d29a78764..99c7f47225b 100644 --- a/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb +++ b/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb @@ -20,7 +20,10 @@ sources = [ 'v%(version)s.tar.gz', {'download_filename': '5282025.tar.gz', 'filename': 'libsc-2.2.tar.gz'}, ] -checksums = ['7df0e9a161b6ea680324dfdbc0ffc6e0d0a6c9c9b0ea5b37c973e71a054226c2'] +checksums = [ + '7df0e9a161b6ea680324dfdbc0ffc6e0d0a6c9c9b0ea5b37c973e71a054226c2', # v2.2.tar.gz + 'c32682c7542ecf2c115150bf79c7b9ac379cb6396179878575d7b228cc0295c5', # libsc-2.2.tar.gz +] dependencies = [ ('zlib', '1.2.11'), From ac246899f0c71351a61a4c76b6c619ef70a11b85 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Sep 2020 13:18:33 +0200 Subject: [PATCH 003/793] use https in homepage for p4est --- easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb b/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb index 99c7f47225b..20a5323912e 100644 --- a/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb +++ b/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'p4est' version = '2.2' -homepage = 'http://www.p4est.org' +homepage = 'https://www.p4est.org' description = """p4est is a C library to manage a collection (a forest) of multiple connected adaptive quadtrees or octrees in parallel.""" From 2548bacdf12cbfe7d62f79699497180513814c28 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Sep 2020 13:20:46 +0200 Subject: [PATCH 004/793] fix PETSc dep in deal.II easyconfig --- easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-foss-2019a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-foss-2019a.eb b/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-foss-2019a.eb index e4990e2bda0..06af00f0bdd 100644 --- a/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-foss-2019a.eb +++ b/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-foss-2019a.eb @@ -22,7 +22,7 @@ dependencies = [ ('METIS', '5.1.0'), ('netCDF', '4.6.2'), ('p4est', '2.2'), - ('PETSc', '3.11.1'), + ('PETSc', '3.11.1', '-Python-3.7.2'), ('zlib', '1.2.11'), ] From bf2486e7b750dfd8b20fece4966125bd9781df53 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 10 Sep 2021 09:50:19 +0200 Subject: [PATCH 005/793] adding easyconfigs: Chemaxon_Marvin-21.14.eb --- .../Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb diff --git a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb b/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb new file mode 100644 index 00000000000..b54cae19c1b --- /dev/null +++ b/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb @@ -0,0 +1,69 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +# rpm file extension does not look to be known yet: Unknown file type for file *.rpm (at easybuild/tools/filetools.py) +# easyblock = 'Rpm' +easyblock = 'Binary' + +name = 'Chemaxon_Marvin' +version = '21.14' + +homepage = 'https://chemaxon.com/products/marvin' +description = """Marvin suite is a chemically intelligent desktop toolkit built +to help you draw, edit, publish, render, import and export your chemical structures +and as well as allowing you to convert between various chemical and graphical file +formats. It is free for individual, academic and non-commercial use.""" + +# NOTE not in the license list of EB +# software_license = 'Proprietary: Personal, Commercial or Academic' +software_license_urls = ['https://www.chemaxon.com/marvin/license.html'] +docurls = [ + 'https://docs.chemaxon.com/display/docs/marvinsketch-user-s-guide.md', + 'https://docs.chemaxon.com/display/docs/marvinview-user-s-guide.md', + 'https://docs.chemaxon.com/display/docs/file-formats.md', +] + +toolchain = SYSTEM + +sources = ['marvin_linux_%(version)s.rpm'] +checksums = ['3102f30479a365758fd14ca5efcdacfe0624db80a35b146ba9a5d07e948bd8dc'] + + +osdependencies = [('rpm', 'cpio')] # for extracting rpm-files + +dependencies = [ + ('Java', '11'), +] + +extract_sources = False + +install_cmd = 'rpm2cpio ' + sources[0] + ' | cpio -idmv && ' +install_cmd += 'cd opt/chemaxon/marvinsuite/ && ' +install_cmd += 'chmod -x bin/*.bat && ' +install_cmd += 'cp -ar . %(installdir)s/' + +# plugins directory is empty +sanity_check_paths = { + 'files': ["bin/cxcalc", "bin/cxtrain", "bin/evaluate", "bin/molconvert", + "bin/msketch", "bin/mview", "EULA.html", "README"], + 'dirs': ['lib'] +} + +sanity_check_commands = ["molconvert"] + +# You need a key/license file to fully activate Chemaxon Marvin +# +# COMMERCIAL +# For commercial use please contact sales@chemaxon.com +# NON-COMMERCIAL +# For personal use get a key to be renewed every 2 months at https://chemaxon.com/products/marvin/download +# For academic use get a key for research or educational purposes at https://chemaxon.com/academic-license +# +# The license file "license.cxl" has to be placed in $HOME/.chemaxon/ + +moduleclass = 'chem' From 323c0b438e12959c6f965d294a75269d2772b64e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 10 Sep 2021 10:37:55 +0200 Subject: [PATCH 006/793] Clarify where to get download files and license + Clarify why *easyblock = "Rpm"* cannot be used --- .../easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb b/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb index b54cae19c1b..d7523baf6be 100644 --- a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb +++ b/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb @@ -6,8 +6,8 @@ # ## -# rpm file extension does not look to be known yet: Unknown file type for file *.rpm (at easybuild/tools/filetools.py) -# easyblock = 'Rpm' +# Cannot use *easyblock = 'Rpm'* because the RPM misses some fields: +# Summary and License fields must be present in package: (main package) easyblock = 'Binary' name = 'Chemaxon_Marvin' @@ -30,10 +30,10 @@ docurls = [ toolchain = SYSTEM +# Download and license at https://chemaxon.com/products/marvin sources = ['marvin_linux_%(version)s.rpm'] checksums = ['3102f30479a365758fd14ca5efcdacfe0624db80a35b146ba9a5d07e948bd8dc'] - osdependencies = [('rpm', 'cpio')] # for extracting rpm-files dependencies = [ From e9d6f7a596bccab420556aa164dd5fbe2bae492c Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Thu, 16 Sep 2021 12:53:22 +0200 Subject: [PATCH 007/793] adding easyconfigs: pyqstem-1.0.3-foss-2020b.eb, pyqstem-1.0.3-fosscuda-2020b.eb --- .../p/pyqstem/pyqstem-1.0.3-foss-2020b.eb | 41 +++++++++++++++++++ .../p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb | 41 +++++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb new file mode 100644 index 00000000000..37f0e99e6cf --- /dev/null +++ b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb @@ -0,0 +1,41 @@ +easyblock = "PythonPackage" + +name = 'pyqstem' +version = '1.0.3' + +homepage = 'https://github.com/jacobjma/PyQSTEM' +description = """QSTEM is a program for quantitative image simulation in electron +microscopy, including TEM, STEM and CBED image simulation. + +This project interfaces the QSTEM code with Python and the Atomic +Simulation Environment (ASE) to provide a single environment for +building models, simulating and analysing images.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('pyqstem-1.0.3-Remove-unused-scipy-import.patch', 1), +] +checksums = [ + '612c4c95531ea9239c91e6f8b9e29a954ac873dd8584b6a57512dcfb6263ff0a', # pyqstem-1.0.3.tar.gz + # pyqstem-1.0.3-Remove-unused-scipy-import.patch + 'de1e6615057648c4d1f857f58d751699c1b292b4fe0c0f8b2f0b300e99f91d59', +] + +dependencies = [ + ('Python', '3.8.6'), + ('scikit-image', '0.18.1'), + ('ASE', '3.22.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb new file mode 100644 index 00000000000..bfd19a0d087 --- /dev/null +++ b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb @@ -0,0 +1,41 @@ +easyblock = "PythonPackage" + +name = 'pyqstem' +version = '1.0.3' + +homepage = 'https://github.com/jacobjma/PyQSTEM' +description = """QSTEM is a program for quantitative image simulation in electron +microscopy, including TEM, STEM and CBED image simulation. + +This project interfaces the QSTEM code with Python and the Atomic +Simulation Environment (ASE) to provide a single environment for +building models, simulating and analysing images.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('pyqstem-1.0.3-Remove-unused-scipy-import.patch', 1), +] +checksums = [ + '612c4c95531ea9239c91e6f8b9e29a954ac873dd8584b6a57512dcfb6263ff0a', # pyqstem-1.0.3.tar.gz + # pyqstem-1.0.3-Remove-unused-scipy-import.patch + 'de1e6615057648c4d1f857f58d751699c1b292b4fe0c0f8b2f0b300e99f91d59', +] + +dependencies = [ + ('Python', '3.8.6'), + ('scikit-image', '0.18.1'), + ('ASE', '3.22.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'phys' From b7c1ad949a02b83b8e0b017d752c189fd664dca5 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 26 Oct 2021 15:54:01 +0200 Subject: [PATCH 008/793] Add sanity_pip_check to both .eb files. --- easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb | 1 + easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb index 37f0e99e6cf..9894375dcc0 100644 --- a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb @@ -32,6 +32,7 @@ dependencies = [ download_dep_fail = True use_pip = True +sanity_pip_check = True sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb index bfd19a0d087..73aa35a300a 100644 --- a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb @@ -32,6 +32,7 @@ dependencies = [ download_dep_fail = True use_pip = True +sanity_pip_check = True sanity_check_paths = { 'files': [], From 21cac071134c4b2a75a3aa87c706f4fdcaa97529 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 26 Oct 2021 15:57:31 +0200 Subject: [PATCH 009/793] Add version suffix because of ASE dependency. --- .../pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb | 44 +++++++++++++++++++ ...pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb | 44 +++++++++++++++++++ 2 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb create mode 100644 easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb new file mode 100644 index 00000000000..2e18fed82c8 --- /dev/null +++ b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb @@ -0,0 +1,44 @@ +easyblock = "PythonPackage" + +name = 'pyqstem' +version = '1.0.3' +_aseversion = '3.22.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://github.com/jacobjma/PyQSTEM' +description = """QSTEM is a program for quantitative image simulation in electron +microscopy, including TEM, STEM and CBED image simulation. + +This project interfaces the QSTEM code with Python and the Atomic +Simulation Environment (ASE) to provide a single environment for +building models, simulating and analysing images.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('pyqstem-1.0.3-Remove-unused-scipy-import.patch', 1), +] +checksums = [ + '612c4c95531ea9239c91e6f8b9e29a954ac873dd8584b6a57512dcfb6263ff0a', # pyqstem-1.0.3.tar.gz + # pyqstem-1.0.3-Remove-unused-scipy-import.patch + 'de1e6615057648c4d1f857f58d751699c1b292b4fe0c0f8b2f0b300e99f91d59', +] + +dependencies = [ + ('Python', '3.8.6'), + ('scikit-image', '0.18.1'), + ('ASE', _aseversion), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb new file mode 100644 index 00000000000..b6a80dcfb0c --- /dev/null +++ b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb @@ -0,0 +1,44 @@ +easyblock = "PythonPackage" + +name = 'pyqstem' +version = '1.0.3' +_aseversion = '3.22.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://github.com/jacobjma/PyQSTEM' +description = """QSTEM is a program for quantitative image simulation in electron +microscopy, including TEM, STEM and CBED image simulation. + +This project interfaces the QSTEM code with Python and the Atomic +Simulation Environment (ASE) to provide a single environment for +building models, simulating and analysing images.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('pyqstem-1.0.3-Remove-unused-scipy-import.patch', 1), +] +checksums = [ + '612c4c95531ea9239c91e6f8b9e29a954ac873dd8584b6a57512dcfb6263ff0a', # pyqstem-1.0.3.tar.gz + # pyqstem-1.0.3-Remove-unused-scipy-import.patch + 'de1e6615057648c4d1f857f58d751699c1b292b4fe0c0f8b2f0b300e99f91d59', +] + +dependencies = [ + ('Python', '3.8.6'), + ('scikit-image', '0.18.1'), + ('ASE', _aseversion), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'phys' From a8c092a7c72944a2f5b9de5b7312b2874028548b Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 26 Oct 2021 16:01:19 +0200 Subject: [PATCH 010/793] Remove old versions of files that were accidentally preserved. --- .../p/pyqstem/pyqstem-1.0.3-foss-2020b.eb | 42 ------------------- .../p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb | 42 ------------------- 2 files changed, 84 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb delete mode 100644 easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb deleted file mode 100644 index 9894375dcc0..00000000000 --- a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = "PythonPackage" - -name = 'pyqstem' -version = '1.0.3' - -homepage = 'https://github.com/jacobjma/PyQSTEM' -description = """QSTEM is a program for quantitative image simulation in electron -microscopy, including TEM, STEM and CBED image simulation. - -This project interfaces the QSTEM code with Python and the Atomic -Simulation Environment (ASE) to provide a single environment for -building models, simulating and analysing images.""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - ('pyqstem-1.0.3-Remove-unused-scipy-import.patch', 1), -] -checksums = [ - '612c4c95531ea9239c91e6f8b9e29a954ac873dd8584b6a57512dcfb6263ff0a', # pyqstem-1.0.3.tar.gz - # pyqstem-1.0.3-Remove-unused-scipy-import.patch - 'de1e6615057648c4d1f857f58d751699c1b292b4fe0c0f8b2f0b300e99f91d59', -] - -dependencies = [ - ('Python', '3.8.6'), - ('scikit-image', '0.18.1'), - ('ASE', '3.22.0'), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb deleted file mode 100644 index 73aa35a300a..00000000000 --- a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = "PythonPackage" - -name = 'pyqstem' -version = '1.0.3' - -homepage = 'https://github.com/jacobjma/PyQSTEM' -description = """QSTEM is a program for quantitative image simulation in electron -microscopy, including TEM, STEM and CBED image simulation. - -This project interfaces the QSTEM code with Python and the Atomic -Simulation Environment (ASE) to provide a single environment for -building models, simulating and analysing images.""" - -toolchain = {'name': 'fosscuda', 'version': '2020b'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - ('pyqstem-1.0.3-Remove-unused-scipy-import.patch', 1), -] -checksums = [ - '612c4c95531ea9239c91e6f8b9e29a954ac873dd8584b6a57512dcfb6263ff0a', # pyqstem-1.0.3.tar.gz - # pyqstem-1.0.3-Remove-unused-scipy-import.patch - 'de1e6615057648c4d1f857f58d751699c1b292b4fe0c0f8b2f0b300e99f91d59', -] - -dependencies = [ - ('Python', '3.8.6'), - ('scikit-image', '0.18.1'), - ('ASE', '3.22.0'), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'phys' From 57d80ed0298fcd9cd0c13ee0dd378f64c88da4ba Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 17 Jan 2022 17:13:15 +0100 Subject: [PATCH 011/793] adding easyconfigs: NAMD-2.14-foss-2021a-CUDA-11.3.1.eb --- .../NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..ba107970cf1 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,37 @@ +name = 'NAMD' +version = '2.14' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': False, 'openmp': False, 'pic': True} + +source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/946183/'] +sources = [{'filename': 'NAMD_%(version)s_Source.tar.gz'}] +patches = [ + "%(name)s-%(version)s_Linux-POWER-cuda.patch", + "%(name)s-%(version)s-use_system_mremap_decl.patch" +] +checksums = [ + '34044d85d9b4ae61650ccdba5cda4794088c3a9075932392dd0752ef8c049235', # NAMD_2.14_Source.tar.gz + 'db4aeb482dfa805c859ea18940026395763169e0257401ee5341ca550029031c', # NAMD-2.14_Linux-POWER-cuda.patch + 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch +] + +# support for GCC 8+ on POWER +dependencies = [ + ('Tcl', '8.6.11'), + ('CUDA', '11.3.1', '', True), +] + +builddependencies = [ + ('tcsh', '6.22.04'), +] + +charm_arch = "multicore-linux-%(arch)s" +charm_extra_cxxflags = '-fpermissive' + +moduleclass = 'chem' From 4f7df0034e369e25fde8ee4d44713d21c95d33a2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 9 Mar 2022 17:02:53 +0200 Subject: [PATCH 012/793] adding easyconfigs: dm-reverb-0.7.0-foss-2021b.eb and patches: dm-reverb-0.7.0_eb-build-environment.patch --- .../d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb | 41 ++ ...dm-reverb-0.7.0_eb-build-environment.patch | 687 ++++++++++++++++++ 2 files changed, 728 insertions(+) create mode 100644 easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0_eb-build-environment.patch diff --git a/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb new file mode 100644 index 00000000000..52279474a01 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb @@ -0,0 +1,41 @@ +name = 'dm-reverb' +version = '0.7.0' + +homepage = 'https://github.com/deepmind/reverb' +description = """ +Reverb is an efficient and easy-to-use data storage and transport system +designed for machine learning research. Reverb is primarily used as an +experience replay system for distributed reinforcement learning algorithms but +the system also supports multiple data structure representations such as FIFO, +LIFO, and priority queues.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/deepmind/reverb/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +patches = ['dm-reverb-0.7.0_eb-build-environment.patch'] +checksums = [ + '11fd16db4dab60cc3e827fe8311921797c8e0371e55a2e0f2798ae7d9aabe47c', # v0.7.0.tar.gz + 'eb75e3ec778a1cafafd93d5dbd0d7530ea785c0378e0ee1ef2321ce7599aa7f0', # dm-reverb-0.7.0_eb-build-environment.patch +] + +builddependencies = [ + ('Bazel', '3.7.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('TensorFlow', '2.7.1'), + ('Abseil', '20210324.2'), + ('dm-tree', '0.1.6'), + ('gRPC', '1.44.0'), + ('protobuf', '3.17.3'), + ('snappy', '1.1.9'), + ('zlib', '1.2.11'), +] + +sanity_pip_check = True + +options = {'modulename': 'reverb'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0_eb-build-environment.patch b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0_eb-build-environment.patch new file mode 100644 index 00000000000..a1d6297a79c --- /dev/null +++ b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0_eb-build-environment.patch @@ -0,0 +1,687 @@ +Refactor the build environment to use dependencies from EasyBuild +* fix detection of Python installation +* disable toolchain definitions with gcc-7 +* use C++11 ABI as it is used in protobuf from EB +* define a single local repo using files from EB for the following dependencies: + * local com_google_protobuf replaces protobuf_archive, protobuf_protoc and + external com_google_protobuf + * local zlib replaces zlib_includes and external zlib + * local snappy replaces snappy_includes + * local pybind11 replaces http archive source + * local com_github_grpc_grpc replaces http archive source + * local com_google_absl replaces http archive source +author: Alex Domingo (Vrije Universiteit Brussel) +diff --git a/WORKSPACE.orig b/WORKSPACE +index 5d47f95..6d587ab 100644 +--- a/WORKSPACE.orig ++++ b/WORKSPACE +@@ -13,8 +13,15 @@ workspace(name = "reverb") + # + # *WARNING* If using the REVERB_PROTOC_VERSION environment variable, sha256 + # checking is disabled. Use at your own risk. +-PROTOC_VERSION = "3.9.0" +-PROTOC_SHA256 = "15e395b648a1a6dda8fd66868824a396e9d3e89bc2c8648e3b9ab9801bea5d55" ++#PROTOC_VERSION = "3.9.0" ++#PROTOC_SHA256 = "15e395b648a1a6dda8fd66868824a396e9d3e89bc2c8648e3b9ab9801bea5d55" ++ ++load( ++ "//reverb/cc/platform/default:repo.bzl", ++ "cc_tf_configure", ++) ++ ++cc_tf_configure() + + load("@bazel_tools//tools/build_defs/repo:http.bzl", "http_archive") + +@@ -28,72 +35,6 @@ http_archive( + ], + ) + +-http_archive( +- name = "com_google_absl", +- sha256 = "35f22ef5cb286f09954b7cc4c85b5a3f6221c9d4df6b8c4a1e9d399555b366ee", # SHARED_ABSL_SHA +- strip_prefix = "abseil-cpp-997aaf3a28308eba1b9156aa35ab7bca9688e9f6", +- urls = [ +- "https://storage.googleapis.com/mirror.tensorflow.org/github.com/abseil/abseil-cpp/archive/997aaf3a28308eba1b9156aa35ab7bca9688e9f6.tar.gz", +- "https://github.com/abseil/abseil-cpp/archive/997aaf3a28308eba1b9156aa35ab7bca9688e9f6.tar.gz", +- ], +-) +- + # Note that the Python dependencies are not tracked by bazel here, but + # in setup.py. + +-## Begin GRPC related deps +-http_archive( +- name = "com_github_grpc_grpc", +- patch_cmds = [ +- """sed -i.bak 's/"python",/"python3",/g' third_party/py/python_configure.bzl""", +- """sed -i.bak 's/PYTHONHASHSEED=0/PYTHONHASHSEED=0 python3/g' bazel/cython_library.bzl""", +- ], +- sha256 = "39bad059a712c6415b168cb3d922cb0e8c16701b475f047426c81b46577d844b", +- strip_prefix = "grpc-reverb_fix", +- urls = [ +- # Patched version of GRPC / boringSSL to make it compile with old TF GCC compiler +- "https://github.com/qstanczyk/grpc/archive/reverb_fix.tar.gz", +- ], +-) +- +- +-load("@com_github_grpc_grpc//bazel:grpc_deps.bzl", "grpc_deps") +- +-grpc_deps() +- +-load("@com_github_grpc_grpc//bazel:grpc_extra_deps.bzl", "grpc_extra_deps") +- +-grpc_extra_deps() +- +- +-load("@upb//bazel:workspace_deps.bzl", "upb_deps") +- +-upb_deps() +- +-load( +- "@build_bazel_rules_apple//apple:repositories.bzl", +- "apple_rules_dependencies", +-) +- +-apple_rules_dependencies() +- +-load( +- "@build_bazel_apple_support//lib:repositories.bzl", +- "apple_support_dependencies", +-) +- +-apple_support_dependencies() +-## End GRPC related deps +- +-load( +- "//reverb/cc/platform/default:repo.bzl", +- "cc_tf_configure", +- "reverb_protoc_deps", +- "reverb_python_deps", +-) +- +-cc_tf_configure() +- +-reverb_python_deps() +- +-reverb_protoc_deps(version = PROTOC_VERSION, sha256 = PROTOC_SHA256) +diff --git a/reverb/cc/platform/default/BUILD.orig b/reverb/cc/platform/default/BUILD +index 372653e..897c346 100644 +--- a/reverb/cc/platform/default/BUILD.orig ++++ b/reverb/cc/platform/default/BUILD +@@ -18,7 +18,7 @@ reverb_cc_library( + srcs = ["snappy.cc"], + deps = [ + "//reverb/cc/platform:snappy_hdr", +- "@com_google_absl//absl/strings", ++ "@com_google_absl//:absl", + ] + reverb_tf_deps(), + alwayslink = 1, + ) +@@ -30,7 +30,7 @@ reverb_cc_library( + "//reverb/cc/checkpointing:interface", + "//reverb/cc/platform:checkpointing_hdr", + "//reverb/cc/platform:tfrecord_checkpointer", +- "@com_google_absl//absl/strings", ++ "@com_google_absl//:absl", + ], + alwayslink = 1, + ) +@@ -48,7 +48,7 @@ reverb_cc_library( + "//reverb/cc/platform:status_macros", + "//reverb/cc/platform:tfrecord_checkpointer", + "//reverb/cc/support:periodic_closure", +- "@com_google_absl//absl/strings", ++ "@com_google_absl//:absl", + ] + reverb_grpc_deps(), + alwayslink = 1, + ) +@@ -60,7 +60,7 @@ reverb_cc_library( + "status_matchers.h", + ], + deps = [ +- "@com_google_absl//absl/status", ++ "@com_google_absl//:absl", + ], + ) + +@@ -68,7 +68,7 @@ reverb_cc_library( + name = "status_matchers", + hdrs = ["status_matchers.h"], + deps = [ +- "@com_google_absl//absl/status", ++ "@com_google_absl//:absl", + ], + ) + +@@ -77,8 +77,7 @@ reverb_cc_library( + srcs = ["thread.cc"], + deps = [ + "//reverb/cc/platform:thread_hdr", +- "@com_google_absl//absl/memory", +- "@com_google_absl//absl/strings", ++ "@com_google_absl//:absl", + ], + alwayslink = 1, + ) +@@ -101,7 +100,7 @@ reverb_cc_library( + hdrs = ["hash_map.h"], + deps = [ + ":hash", +- "@com_google_absl//absl/container:flat_hash_map", ++ "@com_google_absl//:absl", + ], + ) + +@@ -110,7 +109,7 @@ reverb_cc_library( + hdrs = ["hash_set.h"], + deps = [ + ":hash", +- "@com_google_absl//absl/container:flat_hash_set", ++ "@com_google_absl//:absl", + ], + ) + +diff --git a/reverb/cc/platform/default/repo.bzl.orig b/reverb/cc/platform/default/repo.bzl +index 1daac52..f6d55e3 100644 +--- a/reverb/cc/platform/default/repo.bzl.orig ++++ b/reverb/cc/platform/default/repo.bzl +@@ -91,13 +91,13 @@ def _find_python_solib_path(repo_ctx): + version = exec_result.stdout.splitlines()[-1] + basename = "lib{}.so".format(version) + exec_result = repo_ctx.execute( +- ["{}-config".format(version), "--configdir"], ++ ["{}-config".format(version), "--prefix"], + quiet = True, + ) + if exec_result.return_code != 0: + fail("Could not locate python shared library path:\n{}" + .format(exec_result.stderr)) +- solib_dir = exec_result.stdout.splitlines()[-1] ++ solib_dir = "{}/{}".format(exec_result.stdout.splitlines()[-1], "lib") + full_path = repo_ctx.path("{}/{}".format(solib_dir, basename)) + if not full_path.exists: + fail("Unable to find python shared library file:\n{}/{}" +@@ -125,64 +125,121 @@ cc_library( + ) + + def _nsync_includes_repo_impl(repo_ctx): +- tf_include_path = _find_tf_include_path(repo_ctx) +- repo_ctx.symlink(tf_include_path + "/external", "nsync_includes") ++ nsync_root = repo_ctx.os.environ.get("EBROOTNSYNC") ++ repo_ctx.symlink(nsync_root, "nsync") + repo_ctx.file( + "BUILD", + content = """ + cc_library( + name = "includes", +- hdrs = glob(["nsync_includes/nsync/public/*.h"]), +- includes = ["nsync_includes"], ++ hdrs = glob(["nsync/**/*.h"]), ++ includes = ["nsync/include"], + visibility = ["//visibility:public"], + ) + """, + executable = False, + ) + +-def _zlib_includes_repo_impl(repo_ctx): +- tf_include_path = _find_tf_include_path(repo_ctx) +- repo_ctx.symlink( +- tf_include_path + "/external/zlib", +- "zlib", +- ) ++def _zlib_repo_impl(repo_ctx): ++ zlib_root = repo_ctx.os.environ.get("EBROOTZLIB") ++ repo_ctx.symlink(zlib_root, "zlib") + repo_ctx.file( + "BUILD", + content = """ + cc_library( ++ name = "libz", ++ srcs = ["zlib/lib/libz.so"], ++ visibility = ["//visibility:public"], ++) ++cc_library( + name = "includes", + hdrs = glob(["zlib/**/*.h"]), +- includes = ["zlib"], ++ includes = ["zlib/include"], + visibility = ["//visibility:public"], + ) + """, + executable = False, + ) + +-def _snappy_includes_repo_impl(repo_ctx): +- tf_include_path = _find_tf_include_path(repo_ctx) +- repo_ctx.symlink( +- tf_include_path + "/external/snappy", +- "snappy", +- ) ++def _snappy_repo_impl(repo_ctx): ++ snappy_root = repo_ctx.os.environ.get("EBROOTSNAPPY") ++ repo_ctx.symlink(snappy_root, "snappy") + repo_ctx.file( + "BUILD", + content = """ + cc_library( ++ name = "libsnappy", ++ srcs = ["snappy/lib/libsnappy.so"], ++ visibility = ["//visibility:public"], ++) ++cc_library( + name = "includes", +- hdrs = glob(["snappy/*.h"]), +- includes = ["snappy"], ++ hdrs = glob(["snappy/**/*.h"]), ++ includes = ["snappy/include"], + visibility = ["//visibility:public"], + ) + """, + executable = False, + ) + +-def _protobuf_includes_repo_impl(repo_ctx): +- tf_include_path = _find_tf_include_path(repo_ctx) +- repo_ctx.symlink(tf_include_path, "tf_includes") ++def _pybind11_includes_repo_impl(repo_ctx): ++ pybind_root = repo_ctx.os.environ.get("EBROOTPYBIND11") ++ repo_ctx.symlink("{}/include".format(pybind_root), "include") ++ repo_ctx.symlink(Label("//third_party:pybind11.BUILD"), "BUILD") ++ ++def _protobuf_repo_impl(repo_ctx): ++ protobuf_root = repo_ctx.os.environ.get("EBROOTPROTOBUF") ++ repo_ctx.symlink(protobuf_root, "protobuf") + repo_ctx.symlink(Label("//third_party:protobuf.BUILD"), "BUILD") + ++def _absl_repo_impl(repo_ctx): ++ absl_root = repo_ctx.os.environ.get("EBROOTABSEIL") ++ repo_ctx.symlink(absl_root, "absl") ++ repo_ctx.file( ++ "BUILD", ++ content = """ ++cc_library( ++ name = "absl", ++ hdrs = glob(["absl/**/*.h", "absl/**/*.inc"]), ++ srcs = glob(["absl/lib/*.so"]), ++ includes = ["absl/include"], ++ visibility = ["//visibility:public"], ++) ++""", ++ executable = False, ++ ) ++ ++def _grpc_repo_impl(repo_ctx): ++ grpc_root = repo_ctx.os.environ.get("EBROOTGRPC") ++ repo_ctx.symlink(grpc_root, "grpc") ++ repo_ctx.file( ++ "BUILD", ++ content = """ ++cc_library( ++ name = "grpc++", ++ hdrs = glob(["grpc/**/*.h"]), ++ srcs = glob(["grpc/lib/*.so"]), ++ includes = ["grpc/include"], ++ visibility = ["//visibility:public"], ++) ++cc_library( ++ name = "grpc++_codegen_proto", ++ hdrs = glob([ ++ "grpc/include/*/impl/codegen/*.h", ++ "grpc/include/*/impl/codegen/security/*.h", ++ ]), ++ includes = ["grpc/include"], ++ visibility = ["//visibility:public"], ++) ++filegroup( ++ name = "grpc_cpp_plugin", ++ srcs = ["grpc/bin/grpc_cpp_plugin"], ++ visibility = ["//visibility:public"], ++) ++""", ++ executable = False, ++ ) ++ + def _tensorflow_includes_repo_impl(repo_ctx): + tf_include_path = _find_tf_include_path(repo_ctx) + repo_ctx.symlink(tf_include_path, "tensorflow_includes") +@@ -200,11 +257,11 @@ cc_library( + ), + includes = ["tensorflow_includes"], + deps = [ +- "@com_google_absl//absl/container:flat_hash_map", ++ "@com_google_absl//:absl", + "@eigen_archive//:includes", +- "@protobuf_archive//:includes", +- "@zlib_includes//:includes", +- "@snappy_includes//:includes", ++ "@com_google_protobuf//:includes", ++ "@zlib//:includes", ++ "@snappy//:includes", + ], + visibility = ["//visibility:public"], + ) +@@ -226,7 +283,12 @@ def _tensorflow_solib_repo_impl(repo_ctx): + cc_library( + name = "framework_lib", + srcs = ["tensorflow_solib/libtensorflow_framework.so.2"], +- deps = ["@python_includes", "@python_includes//:numpy_includes"], ++ deps = [ ++ "@python_includes", ++ "@python_includes//:numpy_includes", ++ "@zlib//:libz", ++ "@snappy//:libsnappy", ++ ], + visibility = ["//visibility:public"], + ) + """, +@@ -275,17 +337,29 @@ def cc_tf_configure(): + ) + make_nsync_repo(name = "nsync_includes") + make_zlib_repo = repository_rule( +- implementation = _zlib_includes_repo_impl, ++ implementation = _zlib_repo_impl, + ) +- make_zlib_repo(name = "zlib_includes") ++ make_zlib_repo(name = "zlib") + make_snappy_repo = repository_rule( +- implementation = _snappy_includes_repo_impl, ++ implementation = _snappy_repo_impl, + ) +- make_snappy_repo(name = "snappy_includes") ++ make_snappy_repo(name = "snappy") ++ make_pybind11_repo = repository_rule( ++ implementation = _pybind11_includes_repo_impl, ++ ) ++ make_pybind11_repo(name = "pybind11") + make_protobuf_repo = repository_rule( +- implementation = _protobuf_includes_repo_impl, ++ implementation = _protobuf_repo_impl, ++ ) ++ make_protobuf_repo(name = "com_google_protobuf") ++ make_absl_repo = repository_rule( ++ implementation = _absl_repo_impl, + ) +- make_protobuf_repo(name = "protobuf_archive") ++ make_absl_repo(name = "com_google_absl") ++ make_grpc_repo = repository_rule( ++ implementation = _grpc_repo_impl, ++ ) ++ make_grpc_repo(name = "com_github_grpc_grpc") + make_tfinc_repo = repository_rule( + implementation = _tensorflow_includes_repo_impl, + ) +@@ -298,65 +372,3 @@ def cc_tf_configure(): + implementation = _python_includes_repo_impl, + ) + make_python_inc_repo(name = "python_includes") +- +-def reverb_python_deps(): +- http_archive( +- name = "pybind11", +- urls = [ +- "https://storage.googleapis.com/mirror.tensorflow.org/github.com/pybind/pybind11/archive/v2.4.3.tar.gz", +- "https://github.com/pybind/pybind11/archive/v2.4.3.tar.gz", +- ], +- sha256 = "1eed57bc6863190e35637290f97a20c81cfe4d9090ac0a24f3bbf08f265eb71d", +- strip_prefix = "pybind11-2.4.3", +- build_file = clean_dep("//third_party:pybind11.BUILD"), +- ) +- +- http_archive( +- name = "absl_py", +- sha256 = "603febc9b95a8f2979a7bdb77d2f5e4d9b30d4e0d59579f88eba67d4e4cc5462", +- strip_prefix = "abseil-py-pypi-v0.9.0", +- urls = [ +- "https://storage.googleapis.com/mirror.tensorflow.org/github.com/abseil/abseil-py/archive/pypi-v0.9.0.tar.gz", +- "https://github.com/abseil/abseil-py/archive/pypi-v0.9.0.tar.gz", +- ], +- ) +- +-def _reverb_protoc_archive(ctx): +- version = ctx.attr.version +- sha256 = ctx.attr.sha256 +- +- override_version = ctx.os.environ.get("REVERB_PROTOC_VERSION") +- if override_version: +- sha256 = "" +- version = override_version +- +- urls = [ +- "https://github.com/protocolbuffers/protobuf/releases/download/v%s/protoc-%s-linux-x86_64.zip" % (version, version), +- ] +- ctx.download_and_extract( +- url = urls, +- sha256 = sha256, +- ) +- +- ctx.file( +- "BUILD", +- content = """ +-filegroup( +- name = "protoc_bin", +- srcs = ["bin/protoc"], +- visibility = ["//visibility:public"], +-) +-""", +- executable = False, +- ) +- +-reverb_protoc_archive = repository_rule( +- implementation = _reverb_protoc_archive, +- attrs = { +- "version": attr.string(mandatory = True), +- "sha256": attr.string(mandatory = True), +- }, +-) +- +-def reverb_protoc_deps(version, sha256): +- reverb_protoc_archive(name = "protobuf_protoc", version = version, sha256 = sha256) +diff --git a/reverb/cc/platform/default/build_rules.bzl.orig b/reverb/cc/platform/default/build_rules.bzl +index fa8560f..6bf3694 100644 +--- a/reverb/cc/platform/default/build_rules.bzl.orig ++++ b/reverb/cc/platform/default/build_rules.bzl +@@ -90,12 +90,12 @@ def reverb_cc_proto_library(name, srcs = [], deps = [], **kwargs): + srcs = srcs, + outs = gen_srcs + gen_hdrs, + tools = dep_srcs + [ +- "@protobuf_protoc//:protoc_bin", ++ "@com_google_protobuf//:protoc_bin", + "@tensorflow_includes//:protos", + ], + cmd = """ + OUTDIR=$$(echo $(RULEDIR) | sed -E -e 's#reverb(/.*|$$)##') +- $(location @protobuf_protoc//:protoc_bin) \ ++ $(location @com_google_protobuf//:protoc_bin) \ + --proto_path=external/tensorflow_includes/tensorflow_includes/ \ + --proto_path=. \ + --cpp_out=$$OUTDIR {}""".format( +@@ -165,12 +165,12 @@ def reverb_py_proto_library(name, srcs = [], deps = [], **kwargs): + srcs = srcs, + outs = gen_srcs, + tools = proto_deps + [ +- "@protobuf_protoc//:protoc_bin", ++ "@com_google_protobuf//:protoc_bin", + "@tensorflow_includes//:protos", + ], + cmd = """ + OUTDIR=$$(echo $(RULEDIR) | sed -E -e 's#reverb(/.*|$$)##') +- $(location @protobuf_protoc//:protoc_bin) \ ++ $(location @com_google_protobuf//:protoc_bin) \ + --proto_path=external/tensorflow_includes/tensorflow_includes/ \ + --proto_path=. \ + --python_out=$$OUTDIR {}""".format( +@@ -227,14 +227,14 @@ def reverb_cc_grpc_library( + srcs = srcs, + outs = gen_srcs + gen_hdrs + gen_mocks, + tools = proto_src_deps + [ +- "@protobuf_protoc//:protoc_bin", ++ "@com_google_protobuf//:protoc_bin", + "@tensorflow_includes//:protos", +- "@com_github_grpc_grpc//src/compiler:grpc_cpp_plugin", ++ "@com_github_grpc_grpc//:grpc_cpp_plugin", + ], + cmd = """ + OUTDIR=$$(echo $(RULEDIR) | sed -e 's#reverb/.*##') +- $(location @protobuf_protoc//:protoc_bin) \ +- --plugin=protoc-gen-grpc=$(location @com_github_grpc_grpc//src/compiler:grpc_cpp_plugin) \ ++ $(location @com_google_protobuf//:protoc_bin) \ ++ --plugin=protoc-gen-grpc=$(location @com_github_grpc_grpc//:grpc_cpp_plugin) \ + --proto_path=external/tensorflow_includes/tensorflow_includes/ \ + --proto_path=. \ + --grpc_out={} {}""".format( +@@ -544,6 +544,8 @@ def reverb_tf_ops_visibility(): + + def reverb_tf_deps(): + return [ ++ "@zlib//:libz", ++ "@snappy//:libsnappy", + "@tensorflow_includes//:includes", + "@tensorflow_solib//:framework_lib", + ] +@@ -552,24 +554,4 @@ def reverb_grpc_deps(): + return ["@com_github_grpc_grpc//:grpc++"] + + def reverb_absl_deps(): +- return [ +- # We purposefully don't include absl::flat_hash_{map,set} so that users +- # are forced to use platform:hash_{map,set}, which uses a safer hasher. +- "@com_google_absl//absl/base", +- "@com_google_absl//absl/base:core_headers", +- "@com_google_absl//absl/functional:bind_front", +- "@com_google_absl//absl/memory", +- "@com_google_absl//absl/numeric:int128", +- "@com_google_absl//absl/random", +- "@com_google_absl//absl/random:distributions", +- "@com_google_absl//absl/status", +- "@com_google_absl//absl/status:statusor", +- "@com_google_absl//absl/strings", +- "@com_google_absl//absl/strings:cord", +- "@com_google_absl//absl/strings:str_format", +- "@com_google_absl//absl/synchronization", +- "@com_google_absl//absl/time", +- "@com_google_absl//absl/types:optional", +- "@com_google_absl//absl/types:span", +- "@com_google_absl//absl/flags:flag", +- ] ++ return ["@com_google_absl//:absl"] +diff --git a/third_party/protobuf.BUILD.orig b/third_party/protobuf.BUILD +index b8e9496..7d601a5 100644 +--- a/third_party/protobuf.BUILD.orig ++++ b/third_party/protobuf.BUILD +@@ -1,10 +1,10 @@ + _CHECK_VERSION = """ +-PROTOC_VERSION=$$($(location @protobuf_protoc//:protoc_bin) --version \ ++PROTOC_VERSION=$$($(location protobuf/bin/protoc) --version \ + | cut -d' ' -f2 | sed -e 's/\\./ /g') + PROTOC_VERSION=$$(printf '%d%03d%03d' $${PROTOC_VERSION}) + TF_PROTO_VERSION=$$(grep '#define PROTOBUF_MIN_PROTOC_VERSION' \ +- $(location tf_includes/google/protobuf/port_def.inc) | cut -d' ' -f3) +-if [ "$${PROTOC_VERSION}" -ne "$${TF_PROTO_VERSION}" ]; then ++ $(location protobuf/include/google/protobuf/port_def.inc) | cut -d' ' -f3) ++if [ "$${PROTOC_VERSION}" -lt "$${TF_PROTO_VERSION}" ]; then + echo !!!!!!!!!!!!!!!!!!!!!!!!!!!!! 1>&2 + echo Your protoc version does not match the tensorflow proto header \ + required version: "$${PROTOC_VERSION}" vs. "$${TF_PROTO_VERSION}" 1>&2 +@@ -20,9 +20,9 @@ genrule( + name = "compare_protobuf_version", + outs = ["versions_compared"], + srcs = [ +- "tf_includes/google/protobuf/port_def.inc", ++ "protobuf/include/google/protobuf/port_def.inc", + ], +- tools = ["@protobuf_protoc//:protoc_bin"], ++ tools = ["protobuf/bin/protoc"], + cmd = _CHECK_VERSION, + ) + +@@ -30,11 +30,45 @@ cc_library( + name = "includes", + data = [":versions_compared"], + hdrs = glob([ +- "tf_includes/google/protobuf/*.h", +- "tf_includes/google/protobuf/*.inc", +- "tf_includes/google/protobuf/**/*.h", +- "tf_includes/google/protobuf/**/*.inc", ++ "protobuf/include/google/protobuf/*.h", ++ "protobuf/include/google/protobuf/*.inc", ++ "protobuf/include/google/protobuf/**/*.h", ++ "protobuf/include/google/protobuf/**/*.inc", + ]), +- includes = ["tf_includes"], ++ includes = ["protobuf/include"], ++ visibility = ["//visibility:public"], ++) ++cc_library( ++ name = "protobuf_headers", ++ data = [":versions_compared"], ++ hdrs = glob([ ++ "protobuf/include/google/protobuf/*.h", ++ "protobuf/include/google/protobuf/*.inc", ++ "protobuf/include/google/protobuf/**/*.h", ++ "protobuf/include/google/protobuf/**/*.inc", ++ ]), ++ includes = ["protobuf/include"], ++ visibility = ["//visibility:public"], ++) ++cc_library( ++ name = "protobuf_lite", ++ srcs = ["protobuf/lib/libprotobuf-lite.so"], ++ visibility = ["//visibility:public"], ++) ++cc_library( ++ name = "protobuf", ++ srcs = ["protobuf/lib/libprotobuf.so"], ++ visibility = ["//visibility:public"], ++ deps = [":protobuf_lite"], ++) ++cc_library( ++ name = "protoc_lib", ++ srcs = ["protobuf/lib/libprotoc.so"], ++ visibility = ["//visibility:public"], ++ deps = [":protobuf"], ++) ++filegroup( ++ name = "protoc_bin", ++ srcs = ["protobuf/bin/protoc"], + visibility = ["//visibility:public"], + ) +diff --git a/reverb/cc/opensource/opensource_only.files.orig b/reverb/cc/opensource/opensource_only.files +index 375df63..d74bec1 100644 +--- a/reverb/cc/opensource/opensource_only.files.orig ++++ b/reverb/cc/opensource/opensource_only.files +@@ -1,8 +1,5 @@ + reverb/third_party/BUILD.oss + reverb/third_party/protobuf.BUILD.oss + reverb/third_party/pybind11.BUILD.oss +-reverb/third_party/toolchains/preconfig/ubuntu16.04/gcc7_manylinux2010/BUILD.oss +-reverb/third_party/toolchains/preconfig/ubuntu16.04/gcc7_manylinux2010/cc_toolchain_config.bzl.oss +-reverb/third_party/toolchains/preconfig/ubuntu16.04/gcc7_manylinux2010/dummy_toolchain.bzl.oss + reverb/platform/default/BUILD.oss + reverb/pip_package/BUILD.oss +diff --git a/third_party/opensource_only.files.orig b/third_party/opensource_only.files +index e1f9e12..f3e999c 100644 +--- a/third_party/opensource_only.files.orig ++++ b/third_party/opensource_only.files +@@ -6,6 +6,3 @@ reverb/pip_package/setup.py: + third_party/BUILD: + third_party/protobuf.BUILD: + third_party/pybind11.BUILD: +-third_party/toolchains/preconfig/ubuntu16.04/gcc7_manylinux2010/BUILD: +-third_party/toolchains/preconfig/ubuntu16.04/gcc7_manylinux2010/cc_toolchain_config.bzl: +-third_party/toolchains/preconfig/ubuntu16.04/gcc7_manylinux2010/dummy_toolchain.bzl: +diff --git a/.bazelrc.orig b/.bazelrc +index f4b08d3..89f82dd 100644 +--- a/.bazelrc.orig ++++ b/.bazelrc +@@ -13,7 +13,7 @@ build:manylinux2010 --crosstool_top=//third_party/toolchains/preconfig/ubuntu16. + + build -c opt + build --cxxopt="-std=c++14" +-build --cxxopt="-D_GLIBCXX_USE_CXX11_ABI=0" ++build --cxxopt="-D_GLIBCXX_USE_CXX11_ABI=1" + build --auto_output_filter=subpackages + build --copt="-Wall" --copt="-Wno-sign-compare" + build --linkopt="-lrt -lm" From 99c487735e62ceec71b088f80fcbd4ec8fcedcc6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Apr 2022 12:51:21 +0100 Subject: [PATCH 013/793] adding easyconfigs: Scoary-1.6.16-foss-2021a.eb, ETE-3.1.2-foss-2021a.eb --- .../easyconfigs/e/ETE/ETE-3.1.2-foss-2021a.eb | 34 +++++++++++++++++ .../s/Scoary/Scoary-1.6.16-foss-2021a.eb | 38 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb diff --git a/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021a.eb b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021a.eb new file mode 100644 index 00000000000..05d4d90ee50 --- /dev/null +++ b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'ETE' +version = '3.1.2' + +homepage = 'http://etetoolkit.org' +description = """A Python framework for the analysis and visualization of trees""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://pypi.python.org/packages/source/e/ete3'] +sources = ['ete3-%(version)s.tar.gz'] +checksums = ['4fc987b8c529889d6608fab1101f1455cb5cbd42722788de6aea9c7d0a8e59e9'] + +dependencies = [ + ('lxml', '4.6.3'), + ('Python', '3.9.5'), + ('PyQt5', '5.15.4'), + ('SciPy-bundle', '2021.05'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'ete3'} + +sanity_check_paths = { + 'files': ['bin/ete3'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb new file mode 100644 index 00000000000..412551c4fc9 --- /dev/null +++ b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'Scoary' +version = '1.6.16' + +homepage = 'https://github.com/AdmiralenOla/Scoary' +description = "Microbial pan-GWAS using the output from Roary" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Tkinter', '%(pyver)s'), + ('ETE', '3.1.2'), +] + +exts_list = [ + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + (name, version, { + 'source_tmpl': 'scoary-%(version)s.tar.gz', + 'checksums': ['f433343422c5805a70a20f7fe83851490ae3cdf07745c65680de5feea40a6dca'], + 'modulename': False, + }), +] + + +sanity_check_paths = { + 'files': ['bin/scoary', 'bin/scoary_GUI', 'bin/vcf2scoary'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 57a9e0110a0becccbcb0eb7f5541a39f1307b450 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Apr 2022 15:10:54 +0100 Subject: [PATCH 014/793] Add missing sanity_pip_check --- easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb index 412551c4fc9..d3a039e9601 100644 --- a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb +++ b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb @@ -29,10 +29,11 @@ exts_list = [ }), ] - sanity_check_paths = { 'files': ['bin/scoary', 'bin/scoary_GUI', 'bin/vcf2scoary'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_pip_check = True + moduleclass = 'bio' From 7759425f0ef22774b4967c87825dd87a3bbff6ad Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Apr 2022 15:32:06 +0100 Subject: [PATCH 015/793] Add other missing pip boilerplate --- easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb index d3a039e9601..58b68198536 100644 --- a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb +++ b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb @@ -18,6 +18,9 @@ dependencies = [ ('ETE', '3.1.2'), ] +download_dep_fail = True +use_pip = True + exts_list = [ ('argparse', '1.4.0', { 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], From 2741fae7c06171aeba482a3cbd2419f679d3bd53 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Apr 2022 15:57:46 +0100 Subject: [PATCH 016/793] download_dep_fail not required... --- easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb index 58b68198536..6e3329bd511 100644 --- a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb +++ b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb @@ -18,7 +18,6 @@ dependencies = [ ('ETE', '3.1.2'), ] -download_dep_fail = True use_pip = True exts_list = [ From 1ffa5b8d47834a6282ebd99d3766bb13f16d3380 Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Mon, 16 May 2022 10:24:35 +0200 Subject: [PATCH 017/793] adding easyconfigs: OpenMM-7.7.0-foss-2021a.eb --- .../o/OpenMM/OpenMM-7.7.0-foss-2021a.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb new file mode 100644 index 00000000000..5f7e08ce1ce --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb @@ -0,0 +1,69 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.7.0' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-7.5.0_fix_path_to_nvcc.patch'] +checksums = [ + '51970779b8dc639ea192e9c61c67f70189aa294575acb915e14be1670a586c25', # 7.7.0.tar.gz + '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c', # OpenMM-7.5.0_fix_path_to_nvcc.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), +] + +separate_build_dir = True + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('CUDA', '11.2.1', '', True), + ('SWIG', '4.0.2'), +] + +# Flags for CUDA-enabled build +configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" + +#pretestopts = "export OPENMM_CUDA_COMPILER=nvcc && CTEST_OUTPUT_ON_FAILURE=1" +# defining OPENMM_CUDA_COMPILER=nvcc on pretestops causes 1 test to fail: https://github.com/openmm/openmm/issues/3373 +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/__init__.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m openmm.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From a92b0043c1075f8b5605a8b7ae7721db363cb115 Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Mon, 16 May 2022 16:45:11 +0200 Subject: [PATCH 018/793] Update cuda version --- easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb index 5f7e08ce1ce..6221e22818b 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb @@ -34,7 +34,7 @@ separate_build_dir = True dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), - ('CUDA', '11.2.1', '', True), + ('CUDA', '11.3.1', '', True), ('SWIG', '4.0.2'), ] From ce79d418a7b1683af9024b71704a163fa3760567 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 18 May 2022 11:04:04 +0100 Subject: [PATCH 019/793] adding easyconfigs: Mmg-5.6.0-gompi-2021a.eb --- .../m/Mmg/Mmg-5.6.0-gompi-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb diff --git a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb new file mode 100644 index 00000000000..5f1a28b4c64 --- /dev/null +++ b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'Mmg' +version = '5.6.0' + +homepage = 'https://www.mmgtools.org/' +description = """ +Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries: +the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional +triangulation and generation of a triangulation from a set of points or from given boundary edges +the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation +and isovalue discretization the mmg3d application and the libmmg3d library: adaptation and optimization +of a tetrahedral mesh and implicit domain meshing the libmmg library gathering the libmmg2d, +libmmgs and libmmg3d libraries.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://github.com/MmgTools/mmg/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['bbf9163d65bc6e0f81dd3acc5a51e4a8c47a7fdae849abc26277e01154fe2437'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +dependencies = [('SCOTCH', '6.1.0')] + +separate_build_dir = True + +configopts = '-DUSE_SCOTCH=ON ' +configopts += '-DLIBMMG2D_SHARED=ON -DLIBMMG3D_SHARED=ON -DLIBMMGS_SHARED=ON -DLIBMMG_SHARED=ON ' + +sanity_check_paths = { + 'files': ['bin/%s_O3' % x for x in ['mmg2d', 'mmg3d', 'mmgs']] + + ['lib/lib%s.%s' % (x, y) for x in ['mmg2d', 'mmg3d', 'mmgs', 'mmg'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include/mmg/%s' % x for x in ['mmg2d', 'mmg3d', 'mmgs']] +} + +moduleclass = 'math' From b6920bb0ca97e7faa96e1a10ff3df9780fb6bcbf Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Fri, 20 May 2022 21:10:27 +0200 Subject: [PATCH 020/793] Add comment for the changes to the pretestopts, fix comment spacing --- .../OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..88ef97aa375 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,69 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.7.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-7.5.0_fix_path_to_nvcc.patch'] +checksums = [ + '51970779b8dc639ea192e9c61c67f70189aa294575acb915e14be1670a586c25', # 7.7.0.tar.gz + '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c', # OpenMM-7.5.0_fix_path_to_nvcc.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), +] + +separate_build_dir = True + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('CUDA', '11.3.1', '', True), + ('SWIG', '.4.0.2'), +] + +# Flags for CUDA-enabled build +configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" + +# defining OPENMM_CUDA_COMPILER=nvcc on pretestops causes 1 test to fail: https://github.com/openmm/openmm/issues/3373 +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/__init__.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m openmm.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From 8a6fecb0035d4f0b7e3e3fb3a97c7a69a4b491f1 Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Fri, 20 May 2022 21:41:56 +0200 Subject: [PATCH 021/793] Incorrectly made SWIG module hidden --- .../easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb index 88ef97aa375..d52bab5ca43 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb @@ -36,7 +36,7 @@ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('CUDA', '11.3.1', '', True), - ('SWIG', '.4.0.2'), + ('SWIG', '4.0.2'), ] # Flags for CUDA-enabled build From 8c0cb82a3e7eea58b56dc3d6936d4ff448045803 Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Sat, 21 May 2022 10:37:41 +0200 Subject: [PATCH 022/793] Rename easyconfig with incorrect suffix --- .../OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb | 69 ------------------- 1 file changed, 69 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb deleted file mode 100644 index d52bab5ca43..00000000000 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb +++ /dev/null @@ -1,69 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics -# Update to 7.5.1 -# J. Sassmannshausen / GSTT - -easyblock = 'CMakeMake' - -name = 'OpenMM' -version = '7.7.0' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'https://openmm.org' -description = "OpenMM is a toolkit for molecular simulation." - -toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'opt': True} - -source_urls = ['https://github.com/openmm/openmm/archive/'] -sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-7.5.0_fix_path_to_nvcc.patch'] -checksums = [ - '51970779b8dc639ea192e9c61c67f70189aa294575acb915e14be1670a586c25', # 7.7.0.tar.gz - '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c', # OpenMM-7.5.0_fix_path_to_nvcc.patch -] - -builddependencies = [ - ('CMake', '3.20.1'), - ('Doxygen', '1.9.1'), -] - -separate_build_dir = True - -dependencies = [ - ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05'), - ('CUDA', '11.3.1', '', True), - ('SWIG', '4.0.2'), -] - -# Flags for CUDA-enabled build -configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" - -# defining OPENMM_CUDA_COMPILER=nvcc on pretestops causes 1 test to fail: https://github.com/openmm/openmm/issues/3373 -pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" -local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" -runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern - -preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' -preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' - -# required to install the python API -installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' - -sanity_check_paths = { - 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/__init__.py'], - 'dirs': [] -} - -sanity_check_commands = ["python -m openmm.testInstallation"] - -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', - 'OPENMM_INCLUDE_PATH': 'include', - 'OPENMM_LIB_PATH': 'lib', -} - -moduleclass = 'bio' From 894d7acc7af2c6ebdb59456349823465825fee27 Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Sat, 21 May 2022 20:44:22 +0200 Subject: [PATCH 023/793] Re submit the fix for the lint --- .../OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..d52bab5ca43 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,69 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.7.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-7.5.0_fix_path_to_nvcc.patch'] +checksums = [ + '51970779b8dc639ea192e9c61c67f70189aa294575acb915e14be1670a586c25', # 7.7.0.tar.gz + '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c', # OpenMM-7.5.0_fix_path_to_nvcc.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), +] + +separate_build_dir = True + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('CUDA', '11.3.1', '', True), + ('SWIG', '4.0.2'), +] + +# Flags for CUDA-enabled build +configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" + +# defining OPENMM_CUDA_COMPILER=nvcc on pretestops causes 1 test to fail: https://github.com/openmm/openmm/issues/3373 +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/__init__.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m openmm.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From f804d20305771baccac5578c30a3b3980fe38b6c Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Mon, 23 May 2022 08:59:52 +0200 Subject: [PATCH 024/793] Restore the good EasyConfig as I deleted the wrong one by mistake... --- .../o/OpenMM/OpenMM-7.7.0-foss-2021a.eb | 69 ------------------- 1 file changed, 69 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb deleted file mode 100644 index 6221e22818b..00000000000 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb +++ /dev/null @@ -1,69 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics -# Update to 7.5.1 -# J. Sassmannshausen / GSTT - -easyblock = 'CMakeMake' - -name = 'OpenMM' -version = '7.7.0' - -homepage = 'https://openmm.org' -description = "OpenMM is a toolkit for molecular simulation." - -toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'opt': True} - -source_urls = ['https://github.com/openmm/openmm/archive/'] -sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-7.5.0_fix_path_to_nvcc.patch'] -checksums = [ - '51970779b8dc639ea192e9c61c67f70189aa294575acb915e14be1670a586c25', # 7.7.0.tar.gz - '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c', # OpenMM-7.5.0_fix_path_to_nvcc.patch -] - -builddependencies = [ - ('CMake', '3.20.1'), - ('Doxygen', '1.9.1'), -] - -separate_build_dir = True - -dependencies = [ - ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05'), - ('CUDA', '11.3.1', '', True), - ('SWIG', '4.0.2'), -] - -# Flags for CUDA-enabled build -configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" - -#pretestopts = "export OPENMM_CUDA_COMPILER=nvcc && CTEST_OUTPUT_ON_FAILURE=1" -# defining OPENMM_CUDA_COMPILER=nvcc on pretestops causes 1 test to fail: https://github.com/openmm/openmm/issues/3373 -pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" -local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" -runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern - -preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' -preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' - -# required to install the python API -installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' - -sanity_check_paths = { - 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/__init__.py'], - 'dirs': [] -} - -sanity_check_commands = ["python -m openmm.testInstallation"] - -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', - 'OPENMM_INCLUDE_PATH': 'include', - 'OPENMM_LIB_PATH': 'lib', -} - -moduleclass = 'bio' From 1e99ae552d5767f214ff9f96d87db5f006380c4a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Jun 2022 20:56:19 +0200 Subject: [PATCH 025/793] adding easyconfigs: tokenizers-0.12.1-GCCcore-10.3.0.eb --- .../tokenizers-0.12.1-GCCcore-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/t/tokenizers/tokenizers-0.12.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/t/tokenizers/tokenizers-0.12.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/tokenizers/tokenizers-0.12.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..ea5fce7f67c --- /dev/null +++ b/easybuild/easyconfigs/t/tokenizers/tokenizers-0.12.1-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'tokenizers' +version = '0.12.1' + +homepage = 'https://github.com/huggingface/tokenizers' +description = "Fast State-of-the-Art Tokenizers optimized for Research and Production" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['070746f86efa6c873db341e55cf17bb5e7bdd5450330ca8eca542f5c3dab2c66'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Rust', '1.60.0'), +] + +dependencies = [ + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From dcaf15510d7ee82f3c88ca50ae669cb88a1a1be1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Jun 2022 21:01:56 +0200 Subject: [PATCH 026/793] {lib}[foss/2021a] flair-NLP v0.11.3, gensim v4.2.0, Hyperopt v0.2.7, SentencePiece v0.1.96 w/ Python 3.9.5 --- .../flair-NLP/flair-NLP-0.11.3-foss-2021a.eb | 95 +++++++++++++++++++ .../g/gensim/gensim-4.2.0-foss-2021a.eb | 30 ++++++ .../h/Hyperopt/Hyperopt-0.2.7-foss-2021a.eb | 35 +++++++ .../SentencePiece-0.1.96-GCC-10.3.0.eb | 65 +++++++++++++ 4 files changed, 225 insertions(+) create mode 100644 easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a.eb create mode 100644 easybuild/easyconfigs/g/gensim/gensim-4.2.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a.eb b/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a.eb new file mode 100644 index 00000000000..dd85efe2e48 --- /dev/null +++ b/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a.eb @@ -0,0 +1,95 @@ +easyblock = 'PythonBundle' + +name = 'flair-NLP' +version = '0.11.3' + +homepage = 'https://github.com/flairNLP/flair' +description = "A very simple framework for state-of-the-art NLP" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('PyTorch', '1.10.0'), + ('tqdm', '4.61.2'), + ('matplotlib', '3.4.2'), + ('scikit-learn', '0.24.2'), + ('lxml', '4.6.3'), + ('gensim', '4.2.0'), + ('Hyperopt', '0.2.7'), + ('BeautifulSoup', '4.10.0'), + ('SentencePiece', '0.1.96'), + ('tokenizers', '0.12.1'), +] + +use_pip = True + +exts_list = [ + ('bpemb', '0.3.3', { + 'checksums': ['ad86ba9b1623ecc3be6fcc5ba4408e23a30e118b7e1d683d292f4be788798ffe'], + }), + ('conllu', '4.4.2', { + 'checksums': ['d5ba2f9ebf5c9af86d560e11681a172f6cd8a934967baa6839ba9a0648919c10'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('Deprecated', '1.2.13', { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), + ('ftfy', '6.1.1', { + 'checksums': ['bfc2019f84fcd851419152320a6375604a0f1459c281b5b199b2cd0d2e727f8f'], + }), + ('gdown', '4.4.0', { + 'checksums': ['18fc3a4da4a2273deb7aa29c7486be4df3919d904158ad6a6a3e25c8115470d7'], + }), + ('huggingface_hub', '0.7.0', { + 'checksums': ['8154dc2fad84b32a4bca18372a647d9381ed8550a80b11050758357b8fcea639'], + }), + ('Janome', '0.4.2', { + 'checksums': ['14c31bbfc11724da299b4b71a06bccb3af9a105e7c912bc38a22132d8991ec97'], + }), + ('overrides', '3.1.0', { + 'checksums': ['30f761124579e59884b018758c4d7794914ef02a6c038621123fec49ea7599c6'], + }), + ('importlib_metadata', '3.10.1', { + 'checksums': ['c9356b657de65c53744046fa8f7358afe0714a1af7d570c00c3835c2d724a7c1'], + }), + ('konoha', '4.6.5', { + 'checksums': ['c83023e3bda68aa910bfc115c6ab72d10b2b9478093253b4e17a20b0acf6bb7f'], + }), + ('langdetect', '1.0.9', { + 'checksums': ['cbc1fef89f8d062739774bd51eda3da3274006b3661d199c2655f6b3f6d605a0'], + }), + ('mpld3', '0.5.8', { + 'checksums': ['1a167dbef836dd7c66d8aa71c06a32d50bffa18725f304d93cb74fdb3545043b'], + }), + ('pptree', '3.1', { + 'checksums': ['4dd0ba2f58000cbd29d68a5b64bac29bcb5a663642f79404877c0059668a69f6'], + }), + ('segtok', '1.5.11', { + 'checksums': ['8ab2dd44245bcbfec25b575dc4618473bbdf2af8c2649698cd5a370f42f3db23'], + }), + ('sqlitedict', '2.0.0', { + 'checksums': ['23a370416f4e1e962daa293382f3a8dbc4127e6a0abc06a5d4e58e6902f05d17'], + }), + ('transformers', '4.19.2', { + 'checksums': ['e19a4ff07458eda143c738e5259caf48449fcf078a63d6b1bd1aa806543440a3'], + }), + ('Wikipedia-API', '0.5.4', { + 'checksums': ['5173d4db641cdb78d96f2b052df2232bcdc00cf32a424c43402958a40f783992'], + 'modulename': 'wikipediaapi', + }), + ('flair', version, { + # can't use PyPI source tarball, because requirements.txt is missing; + # see also https://github.com/flairNLP/flair/issues/2759 + 'source_urls': ['https://github.com/flairNLP/flair/archive/refs/tags'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['c780320d6d85075e25638a7157a16409f46bc9496db31fbbaa92aeac448f1cf9'], + 'preinstallopts': "sed -i 's/==/>=/g' requirements.txt && ", + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gensim/gensim-4.2.0-foss-2021a.eb b/easybuild/easyconfigs/g/gensim/gensim-4.2.0-foss-2021a.eb new file mode 100644 index 00000000000..2270b2977d2 --- /dev/null +++ b/easybuild/easyconfigs/g/gensim/gensim-4.2.0-foss-2021a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'gensim' +version = '4.2.0' + +homepage = 'https://radimrehurek.com/gensim' +description = """Gensim is a Python library for topic modelling, document indexing and similarity retrieval with + large corpora.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # for numpy, pandas +] + +use_pip = True + +exts_list = [ + ('smart_open', '6.0.0', { + 'checksums': ['d60106b96f0bcaedf5f1cd46ff5524a1c3d02d5653425618bb0fa66e158d22b0'], + }), + (name, version, { + 'checksums': ['995ebd2970a31d47c100aaac10212f47e2bf12e2b06536d38883c951ff34eef1'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2021a.eb b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2021a.eb new file mode 100644 index 00000000000..9cc986b48f5 --- /dev/null +++ b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2021a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'Hyperopt' +version = '0.2.7' + +homepage = 'http://hyperopt.github.io/hyperopt/' +description = """hyperopt is a Python library for optimizing over awkward search spaces with real-valued, + discrete, and conditional dimensions.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('networkx', '2.5.1'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '2.0.0', { + 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], + }), + ('py4j', '0.10.9.5', { + 'checksums': ['276a4a3c5a2154df1860ef3303a927460e02e97b047dc0a47c1c3fb8cce34db6'], + }), + ('hyperopt', version, { + 'checksums': ['1bf89ae58050bbd32c7307199046117feee245c2fd9ab6255c7308522b7ca149'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.3.0.eb new file mode 100644 index 00000000000..c4db4aa9a4d --- /dev/null +++ b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.3.0.eb @@ -0,0 +1,65 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Bundle' + +name = 'SentencePiece' +version = '0.1.96' + +homepage = 'https://github.com/google/sentencepiece' +description = "Unsupervised text tokenizer for Neural Network-based text generation." +github_account = 'google' + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('gperftools', '2.9.1'), +] + +default_component_specs = { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['5198f31c3bb25e685e9e68355a3bf67a1db23c9e8bdccc33dc015f496a44df7a'], +} + +components = [ + (name, version, { + 'easyblock': 'CMakeMake', + 'separate_build_dir': True, + 'start_dir': '%(namelower)s-%(version)s', + }), + ('sentencepiece', version, { + 'easyblock': 'PythonPackage', + 'start_dir': '%(namelower)s-%(version)s/python', + 'prebuildopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ', + 'preinstallopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ', + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + }), +] + +postinstallcmds = ['cp -a %(builddir)s/%(namelower)s-%(version)s/{data,doc} %(installdir)s/'] + +sanity_check_paths = { + 'files': ['bin/spm_%s' % x for x in ['decode', 'encode', 'export_vocab', 'normalize', 'train']] + + ['lib/libsentencepiece.%s' % SHLIB_EXT, 'lib/libsentencepiece_train.%s' % SHLIB_EXT] + + ['include/sentencepiece_processor.h', 'include/sentencepiece_trainer.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'data', 'doc'], +} + +sanity_check_commands = [ + 'spm_train --help', + "python -c 'import sentencepiece'", +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'lib' From a8ba288f3cbe8f590458ff691db99e9a7de97f1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jun 2022 20:38:17 +0200 Subject: [PATCH 027/793] {lib}[foss/2021a] flair-NLP v0.11.3 w/ Python 3.9.5 + CUDA 11.3.1 --- ...flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..1ad8d95623e --- /dev/null +++ b/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,97 @@ +easyblock = 'PythonBundle' + +name = 'flair-NLP' +version = '0.11.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/flairNLP/flair' +description = "A very simple framework for state-of-the-art NLP" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('PyTorch', '1.10.0', versionsuffix), + ('tqdm', '4.61.2'), + ('matplotlib', '3.4.2'), + ('scikit-learn', '0.24.2'), + ('lxml', '4.6.3'), + ('gensim', '4.2.0'), + ('Hyperopt', '0.2.7'), + ('BeautifulSoup', '4.10.0'), + ('SentencePiece', '0.1.96'), + ('tokenizers', '0.12.1'), +] + +use_pip = True + +exts_list = [ + ('bpemb', '0.3.3', { + 'checksums': ['ad86ba9b1623ecc3be6fcc5ba4408e23a30e118b7e1d683d292f4be788798ffe'], + }), + ('conllu', '4.4.2', { + 'checksums': ['d5ba2f9ebf5c9af86d560e11681a172f6cd8a934967baa6839ba9a0648919c10'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('Deprecated', '1.2.13', { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), + ('ftfy', '6.1.1', { + 'checksums': ['bfc2019f84fcd851419152320a6375604a0f1459c281b5b199b2cd0d2e727f8f'], + }), + ('gdown', '4.4.0', { + 'checksums': ['18fc3a4da4a2273deb7aa29c7486be4df3919d904158ad6a6a3e25c8115470d7'], + }), + ('huggingface_hub', '0.7.0', { + 'checksums': ['8154dc2fad84b32a4bca18372a647d9381ed8550a80b11050758357b8fcea639'], + }), + ('Janome', '0.4.2', { + 'checksums': ['14c31bbfc11724da299b4b71a06bccb3af9a105e7c912bc38a22132d8991ec97'], + }), + ('overrides', '3.1.0', { + 'checksums': ['30f761124579e59884b018758c4d7794914ef02a6c038621123fec49ea7599c6'], + }), + ('importlib_metadata', '3.10.1', { + 'checksums': ['c9356b657de65c53744046fa8f7358afe0714a1af7d570c00c3835c2d724a7c1'], + }), + ('konoha', '4.6.5', { + 'checksums': ['c83023e3bda68aa910bfc115c6ab72d10b2b9478093253b4e17a20b0acf6bb7f'], + }), + ('langdetect', '1.0.9', { + 'checksums': ['cbc1fef89f8d062739774bd51eda3da3274006b3661d199c2655f6b3f6d605a0'], + }), + ('mpld3', '0.5.8', { + 'checksums': ['1a167dbef836dd7c66d8aa71c06a32d50bffa18725f304d93cb74fdb3545043b'], + }), + ('pptree', '3.1', { + 'checksums': ['4dd0ba2f58000cbd29d68a5b64bac29bcb5a663642f79404877c0059668a69f6'], + }), + ('segtok', '1.5.11', { + 'checksums': ['8ab2dd44245bcbfec25b575dc4618473bbdf2af8c2649698cd5a370f42f3db23'], + }), + ('sqlitedict', '2.0.0', { + 'checksums': ['23a370416f4e1e962daa293382f3a8dbc4127e6a0abc06a5d4e58e6902f05d17'], + }), + ('transformers', '4.19.2', { + 'checksums': ['e19a4ff07458eda143c738e5259caf48449fcf078a63d6b1bd1aa806543440a3'], + }), + ('Wikipedia-API', '0.5.4', { + 'checksums': ['5173d4db641cdb78d96f2b052df2232bcdc00cf32a424c43402958a40f783992'], + 'modulename': 'wikipediaapi', + }), + ('flair', version, { + # can't use PyPI source tarball, because requirements.txt is missing; + # see also https://github.com/flairNLP/flair/issues/2759 + 'source_urls': ['https://github.com/flairNLP/flair/archive/refs/tags'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['c780320d6d85075e25638a7157a16409f46bc9496db31fbbaa92aeac448f1cf9'], + 'preinstallopts': "sed -i 's/==/>=/g' requirements.txt && ", + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 75b46a40a55ff45d3b4561bfcfb8e8f25f20b006 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 7 Jun 2022 17:49:13 +0200 Subject: [PATCH 028/793] adding easyconfigs: MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb --- ...Estimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb diff --git a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb new file mode 100644 index 00000000000..0e578acd269 --- /dev/null +++ b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'MultilevelEstimators' +version = '0.1.0' +local_julia_ver = '1.7.2' +versionsuffix = "-Julia-%s" % local_julia_ver + +homepage = 'https://github.com/PieterjanRobbe/MultilevelEstimators.jl' +description = "The Julia module for Multilevel Monte Carlo methods" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +dependencies = [ + ('Python', '3.9.6'), + ('Julia', local_julia_ver, '-linux-%s' % ARCH, True), +] + +postinstallcmds = [ + "cd %(installdir)s && mkdir pkgs", + """export JULIA_DEPOT_PATH=%%(installdir)s/pkgs && + julia -e 'using Pkg;Pkg.add(url="%s")' """ % homepage +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["pkgs"] +} + +modextrapaths = {'JULIA_DEPOT_PATH': 'pkgs'} + +moduleclass = 'lib' From fd21fd2caa58f12bfebb710a88f5d2118ad8c158 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 7 Jun 2022 20:40:03 +0200 Subject: [PATCH 029/793] Removed trailing whitespace --- .../MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb index 0e578acd269..ca021785912 100644 --- a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb @@ -17,7 +17,7 @@ dependencies = [ postinstallcmds = [ "cd %(installdir)s && mkdir pkgs", - """export JULIA_DEPOT_PATH=%%(installdir)s/pkgs && + """export JULIA_DEPOT_PATH=%%(installdir)s/pkgs && julia -e 'using Pkg;Pkg.add(url="%s")' """ % homepage ] From 891504d787ece5b15caf2824a5ee850bbdde0da8 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 24 Jun 2022 10:35:48 +0200 Subject: [PATCH 030/793] Add a link where to find download files once logged in --- .../easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb b/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb index d7523baf6be..adadbfe31a0 100644 --- a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb +++ b/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb @@ -31,6 +31,8 @@ docurls = [ toolchain = SYSTEM # Download and license at https://chemaxon.com/products/marvin +# Once logged in download files can be found here: +# https://chemaxon.com/products/marvin/download#download sources = ['marvin_linux_%(version)s.rpm'] checksums = ['3102f30479a365758fd14ca5efcdacfe0624db80a35b146ba9a5d07e948bd8dc'] From fd4b8c78a2dbc42649ab7d1f14e4bbdcc9e4dd89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 11:14:22 +0200 Subject: [PATCH 031/793] adding easyconfigs: Boost.MPI-1.77.0-gompi-2021b.eb --- .../Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb new file mode 100644 index 00000000000..f0d6e24166d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb @@ -0,0 +1,28 @@ +easyblock = 'EB_Boost' + +name = 'Boost.MPI' +version = '1.77.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['5347464af5b14ac54bb945dc68f1dd7c56f0dad7262816b956138fc53bcc0131'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), + ('ICU', '69.1'), +] + +configopts = '--without-libraries=python' + +boost_mpi = True +tagged_layout = True + +moduleclass = 'devel' From 4264534fa65657d9a60c7fd9f183ea328194fed6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 11:20:38 +0200 Subject: [PATCH 032/793] adding easyconfigs: SISSO++-1.1-foss-2021b.eb --- .../s/SISSO++/SISSO++-1.1-foss-2021b.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/s/SISSO++/SISSO++-1.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SISSO++/SISSO++-1.1-foss-2021b.eb b/easybuild/easyconfigs/s/SISSO++/SISSO++-1.1-foss-2021b.eb new file mode 100644 index 00000000000..53ebb6d4cad --- /dev/null +++ b/easybuild/easyconfigs/s/SISSO++/SISSO++-1.1-foss-2021b.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakeMake' + +name = 'SISSO++' +version = '1.1' + +homepage = 'https://gitlab.com/sissopp_developers/sissopp' +description = "C++ implementation of SISSO with built in Python bindings for an efficient python interface" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://gitlab.com/sissopp_developers/sissopp/-/archive/v%(version)s/'] +sources = [{ + 'git_config': { + 'url': 'https://gitlab.com/sissopp_developers/', + 'repo_name': 'sissopp', + 'recursive': True, + 'commit': 'v%(version)s', + }, + 'filename': SOURCE_TAR_GZ, +}] +patches = ['SISSO++-1.1_cmake-mpi-fix.patch'] +checksums = [ + None, # SISSO++-1.1.tar.gz + '614f13ef34dc1d1b2fe0e9868cdcf576a0dacb336759f5295115131d15e9c35a', +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('Boost.Python', '1.77.0'), + ('Boost.MPI', '1.77.0'), + ('Clp', '1.17.7'), + ('NLopt', '2.7.0'), + ('pybind11', '2.7.1'), + ('fmt', '7.1.1'), + ('googletest', '1.11.0'), +] + +preconfigopts = "export BOOST_ROOT=$EBROOTBOOSTMPI && " +configopts = "-DEXTERNAL_BOOST=ON -DBUILD_PYTHON=ON -DPYTHON_INSTDIR=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/sisso++', 'lib/libsisso.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import sissopp'"] + +modextrapaths = {'PYTHONPATH': ''} + +moduleclass = 'math' From 72c10836b64162fb32399acb6c42ee32c4ae7c28 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 12:24:04 +0200 Subject: [PATCH 033/793] add patch file for SISSO++ --- .../s/SISSO++/SISSO++-1.1_cmake-mpi-fix.patch | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/s/SISSO++/SISSO++-1.1_cmake-mpi-fix.patch diff --git a/easybuild/easyconfigs/s/SISSO++/SISSO++-1.1_cmake-mpi-fix.patch b/easybuild/easyconfigs/s/SISSO++/SISSO++-1.1_cmake-mpi-fix.patch new file mode 100644 index 00000000000..d91c3e3fe6d --- /dev/null +++ b/easybuild/easyconfigs/s/SISSO++/SISSO++-1.1_cmake-mpi-fix.patch @@ -0,0 +1,19 @@ +workaround for $MPI_CXX_LIBRARIES being empty and CMake tripping over that with: +CMake Error at CMakeLists.txt:252 (list): + list GET given empty list +author: Kenneth Hoste (HPC-UGent) +--- sissopp/CMakeLists.txt.orig 2022-06-23 17:17:12.083398990 +0200 ++++ sissopp/CMakeLists.txt 2022-06-23 17:17:26.326311818 +0200 +@@ -248,9 +248,9 @@ + # Check MPI + find_package(MPI REQUIRED) + include_directories(${MPI_CXX_INCLUDE_DIRS}) +-set(MPI_LIBRARIES, ${MPI_CXX_LIBRARIES}) +-list(GET MPI_CXX_LIBRARIES 0 MPI_LIBRARY) +-get_filename_component(MPI_DIR ${MPI_LIBRARY} DIRECTORY) ++#set(MPI_LIBRARIES, ${MPI_CXX_LIBRARIES}) ++#list(GET MPI_CXX_LIBRARIES 0 MPI_LIBRARY) ++#get_filename_component(MPI_DIR ${MPI_LIBRARY} DIRECTORY) + + # Build libnlopt + if(BUILD_PARAMS) From 72ab1ca18f2e461b9468ef42928315b12e00ebf5 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 27 Jun 2022 14:38:22 +0100 Subject: [PATCH 034/793] set JUPYTER_PATH in modextrapaths for IRkernel 1.x --- .../IRkernel-1.1-foss-2019b-R-3.6.2-Python-3.7.4.eb | 7 ++++--- .../IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb | 7 ++++--- .../IRkernel-1.1-fosscuda-2019b-R-3.6.2-Python-3.7.4.eb | 7 ++++--- .../IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb | 7 ++++--- .../i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb | 7 ++++--- 5 files changed, 20 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2019b-R-3.6.2-Python-3.7.4.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2019b-R-3.6.2-Python-3.7.4.eb index fe42a2e870a..515926174ff 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2019b-R-3.6.2-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2019b-R-3.6.2-Python-3.7.4.eb @@ -44,7 +44,10 @@ exts_list = [ }), ] -modextrapaths = {'R_LIBS_SITE': ''} +modextrapaths = { + 'R_LIBS_SITE': '', + 'JUPYTER_PATH': '%(name)s' +} # IPython notebook looks for the json kernel file in kernels/IRkernel local_kerneldir = '%(installdir)s/IRkernel' @@ -53,8 +56,6 @@ postinstallcmds = [ 'cp %s/kernelspec/* %s/kernels/ir' % (local_kerneldir, local_kerneldir) ] -modextravars = {'JUPYTER_PATH': local_kerneldir} - sanity_check_paths = { 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], 'dirs': [name], diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb index db893db1a39..68c33b16ff9 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb @@ -45,7 +45,10 @@ exts_list = [ }), ] -modextrapaths = {'R_LIBS_SITE': ''} +modextrapaths = { + 'R_LIBS_SITE': '', + 'JUPYTER_PATH': '%(name)s' +} # IPython notebook looks for the json kernel file in kernels/IRkernel # We start the kernel with default bitmapType 'cairo'. This is a more sensible default @@ -58,8 +61,6 @@ postinstallcmds = [ ' %s/kernels/ir/kernel.json') % local_kerneldir ] -modextravars = {'JUPYTER_PATH': local_kerneldir} - sanity_check_paths = { 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], 'dirs': [name], diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-fosscuda-2019b-R-3.6.2-Python-3.7.4.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-fosscuda-2019b-R-3.6.2-Python-3.7.4.eb index 32f9762476c..c9b0e435d6c 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-fosscuda-2019b-R-3.6.2-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-fosscuda-2019b-R-3.6.2-Python-3.7.4.eb @@ -44,7 +44,10 @@ exts_list = [ }), ] -modextrapaths = {'R_LIBS_SITE': ''} +modextrapaths = { + 'R_LIBS_SITE': '', + 'JUPYTER_PATH': '%(name)s' +} # IPython notebook looks for the json kernel file in kernels/IRkernel local_kerneldir = '%(installdir)s/IRkernel' @@ -53,8 +56,6 @@ postinstallcmds = [ 'cp %s/kernelspec/* %s/kernels/ir' % (local_kerneldir, local_kerneldir) ] -modextravars = {'JUPYTER_PATH': local_kerneldir} - sanity_check_paths = { 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], 'dirs': [name], diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb index 51142541134..6aba48fcb51 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb @@ -45,7 +45,10 @@ exts_list = [ }), ] -modextrapaths = {'R_LIBS_SITE': ''} +modextrapaths = { + 'R_LIBS_SITE': '', + 'JUPYTER_PATH': '%(name)s' +} # IPython notebook looks for the json kernel file in kernels/IRkernel # We start the kernel with default bitmapType 'cairo'. This is a more sensible default @@ -58,8 +61,6 @@ postinstallcmds = [ ' %s/kernels/ir/kernel.json') % local_kerneldir ] -modextravars = {'JUPYTER_PATH': local_kerneldir} - sanity_check_paths = { 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], 'dirs': [name], diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb index 4f72aab2b80..33da48260c8 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb @@ -45,7 +45,10 @@ exts_list = [ }), ] -modextrapaths = {'R_LIBS_SITE': ''} +modextrapaths = { + 'R_LIBS_SITE': '', + 'JUPYTER_PATH': '%(name)s' +} # IPython notebook looks for the json kernel file in kernels/IRkernel # We start the kernel with default bitmapType 'cairo'. This is a more sensible default @@ -58,8 +61,6 @@ postinstallcmds = [ ' %s/kernels/ir/kernel.json') % local_kerneldir ] -modextravars = {'JUPYTER_PATH': local_kerneldir} - sanity_check_paths = { 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], 'dirs': [name], From 18042c5467e8d4ead2e2162853f2123e9bebfccb Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Thu, 30 Jun 2022 14:10:07 +0200 Subject: [PATCH 035/793] adding easyconfigs: Beast-2.6.7-GCC-10.3.0.eb, beagle-lib-3.1.2-GCC-10.3.0.eb, pocl-1.8-GCC-10.3.0.eb --- .../b/Beast/Beast-2.6.7-GCC-10.3.0.eb | 39 ++++++++++++++++ .../beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb | 35 +++++++++++++++ .../easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb | 44 +++++++++++++++++++ 3 files changed, 118 insertions(+) create mode 100644 easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb new file mode 100644 index 00000000000..09bab325f65 --- /dev/null +++ b/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'Tarball' + +name = 'Beast' +version = '2.6.7' + +homepage = 'http://beast2.org' +description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular + sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using + strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies + but is also a framework for testing evolutionary hypotheses without conditioning on a single + tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted + proportional to its posterior probability. """ + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] +sources = ['BEAST.v%(version)s.Linux.tgz'] +checksums = ['05dcc619c2e10163f2c1089ec66149f6e53ec5a0583cd2cb8ffdccbbdb1d8183'] + +dependencies = [ + # this is not mandatory but beagle-lib is recommended by developers + # beagle-lib will also load the required java dependency + # if you remove this you should add the java dependency + ('beagle-lib', '3.1.2'), +] + +builddependencies = [ + ('Autotools', '20210128'), + ('pkg-config', '0.29.2'), +] + +sanity_check_paths = { + 'files': ['bin/beast'], + 'dirs': [] +} + +sanity_check_commands = ["beast -help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb new file mode 100644 index 00000000000..d665b15fb9b --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'beagle-lib' +version = '3.1.2' + +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275'] + +builddependencies = [ + ('Autotools', '20210128'), +] + +dependencies = [ + ('Java', '11', '', True), + ('pkg-config', '0.29.2'), + ('pocl', '1.8'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--with-opencl=$EBROOTPOCL --with-cuda=$EBROOTCUDA " + +sanity_check_paths = { + 'files': ['include/libhmsbeagle-1/libhmsbeagle/%s' % x for x in ['beagle.h', 'platform.h']] + + ['lib/libhmsbeagle%s.%s' % (x, SHLIB_EXT) for x in ['-cpu', '-cpu-sse', '-jni', '']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb new file mode 100644 index 00000000000..4075c55b03b --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeNinja' + +name = 'pocl' +version = '1.8' + +homepage = 'https://portablecl.org' +description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['pocl-%(version)s_fix-header-install.patch'] +checksums = [ + '0f63377ae1826e16e90038fc8e7f65029be4ff6f9b059f6907174b5c0d1f8ab2', # v1.8.tar.gz + '97dc45437ae7464bda9f13088720482804b8a19a4e71067196daa86af487222d', # pocl-1.8_fix-header-install.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Clang', '12.0.1'), + ('hwloc', '2.4.1'), + ('libtool', '2.4.6'), + ('libxml2', '2.9.10'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON" + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From f666cec3d36caa76cf6460f31de9e09d3ab7e9d0 Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Mon, 25 Jul 2022 09:32:14 +0200 Subject: [PATCH 036/793] Remove cuda from beagle-lib configopts --- .../easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb index d665b15fb9b..388390b27a1 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb @@ -24,7 +24,7 @@ dependencies = [ ] preconfigopts = "./autogen.sh && " -configopts = "--with-opencl=$EBROOTPOCL --with-cuda=$EBROOTCUDA " +configopts = "--with-opencl=$EBROOTPOCL " sanity_check_paths = { 'files': ['include/libhmsbeagle-1/libhmsbeagle/%s' % x for x in ['beagle.h', 'platform.h']] + From 5ccb86a252382048a49aa99639d4cf8fa5955522 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 28 Jul 2022 18:24:54 +0200 Subject: [PATCH 037/793] adding easyconfigs: magma-2.6.2-foss-2022a-CUDA-11.7.0.eb --- .../magma-2.6.2-foss-2022a-CUDA-11.7.0.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..1e6b82478d4 --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'magma' +version = '2.6.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://icl.cs.utk.edu/magma/' +description = """The MAGMA project aims to develop a dense linear algebra library similar to + LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://icl.cs.utk.edu/projectsfiles/%(name)s/downloads/'] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version_major_minor)s.1_allow-all-sms.patch'] +checksums = [ + '75b554dab00903e2d10b972c913e50e7f88cbc62f3ae432b5a086c7e4eda0a71', # %(name)s-%(version)s.tar.gz + # %(name)s-%(version_major_minor)s.1_allow-all-sms.patch + 'b89285bac007b68e88e3b5ddbb7f94dbc8a9d77590e58c352e477574d8dca738', +] + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('CUDA', '11.7.0', '', True), +] + +# make sure both static and shared libs are built +configopts = [ + '-DBUILD_SHARED_LIBS=ON -DGPU_TARGET="%(cuda_sm_space_sep)s" ', + '-DBUILD_SHARED_LIBS=OFF -DGPU_TARGET="%(cuda_sm_space_sep)s" ', +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = [ + '3.5', + '5.0', + '6.0', + '7.0', + '7.5', + '%(cuda_cc_space_sep)s', + '8.6', +] + +sanity_check_paths = { + 'files': ['lib/libmagma.so', 'lib/libmagma.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' From 57ef1cb4d548bba79d597905435ee8c51c956ae3 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 28 Jul 2022 18:32:37 +0200 Subject: [PATCH 038/793] adding easyconfigs: PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb --- .../PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb | 116 ++++++++++++++++++ 1 file changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..d868b1a890d --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,116 @@ +name = 'PyTorch' +version = '1.12.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] + +patches = [ + '%(name)s-1.7.0_avoid-nan-in-test-torch.patch', + '%(name)s-1.7.0_disable-dev-shm-test.patch', + '%(name)s-1.8.1_dont-use-gpu-ccc-in-test.patch', + '%(name)s-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + '%(name)s-1.10.0_fix-test-dataloader-fixed-affinity.patch', + '%(name)s-1.10.0_skip_cmake_rpath.patch', + '%(name)s-1.11.0_increase-distributed-test-timeout.patch', + '%(name)s-1.11.0_skip_failing_ops_tests.patch', + '%(name)s-1.11.0_fix_skip_jit_cuda_fuser.patch', + '%(name)s-1.11.0_fix_sharded_imports.patch', + '%(name)s-1.11.0_increase_test_tolerances_TF32.patch', + '%(name)s-1.11.0_increase_c10d_gloo_timeout.patch', + '%(name)s-1.11.0_disable_failing_jit_cuda_fuser_tests.patch', +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('hypothesis', '6.46.7'), +] +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.10.4'), + ('protobuf', '3.19.4'), + ('protobuf-python', '3.19.4'), + ('pybind11', '2.9.2'), + ('SciPy-bundle', '2022.05'), + ('typing-extensions', '4.3.0'), + ('PyYAML', '6.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '5.0.1'), + ('Pillow', '9.1.1'), + ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', True), + ('magma', '2.6.2', '-CUDA-%(cudaver)s'), + ('NCCL', '2.12.12', '-CUDA-%(cudaver)s'), + ('expecttest', '0.1.3'), +] + +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = [ + '3.5', + '3.7', + '5.2', + '6.0', + '6.1', + '7.0', + '7.2', + '7.5', + '8.0', + '8.6', +] + +custom_opts = ['USE_CUPTI_SO=1'] + +excluded_tests = { + '': [ + # Bad tests: https://github.com/pytorch/pytorch/issues/60260 + 'distributed/elastic/utils/distributed_test', + 'distributed/elastic/multiprocessing/api_test', + # These tests fail on A10s at the very least, they time out forever no matter how long the timeout is. + # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html + # 'distributed/test_distributed_fork', + 'distributed/test_distributed_spawn', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + 'test_optim', + # Test from this suite timeout often. The process group backend is deprecated anyway + # 'distributed/rpc/test_process_group_agent', + # This test fails constently when run as part of the test suite, but succeeds when run interactively + 'test_model_dump', + # These tests appear flaky, possibly related to number of GPUs that are used + 'distributed/fsdp/test_fsdp_memory', + 'distributed/fsdp/test_fsdp_overlap', + ] +} + +runtest = "cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s" + +# several tests are known to be flaky, and fail in some contexts (like having multiple GPUs available), +# so we allow up to 10 (out of ~90k) tests to fail before treating the installation to be faulty +max_failed_tests = 10 + +# The readelf sanity check command can be taken out once the TestRPATH test from +# https://github.com/pytorch/pytorch/pull/68912 is accepted, since it is then checked as part of the PyTorch test suite +local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT +sanity_check_commands = [ + "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, +] + +tests = ['%(name)s-check-cpp-extension.py'] + +moduleclass = 'devel' From a8e8b2050770261d6be07609e789b194c7a40ea2 Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 29 Jul 2022 10:46:40 +0200 Subject: [PATCH 039/793] Make EasyConfig more similar to magma-2.6.2-foss-2021b-CUDA-11.4.1 in terms of syntax/order --- .../magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb | 17 ++++------------- 1 file changed, 4 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb index 1e6b82478d4..b15aaf2ae7d 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb @@ -27,21 +27,12 @@ dependencies = [ ('CUDA', '11.7.0', '', True), ] +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6'] + # make sure both static and shared libs are built configopts = [ - '-DBUILD_SHARED_LIBS=ON -DGPU_TARGET="%(cuda_sm_space_sep)s" ', - '-DBUILD_SHARED_LIBS=OFF -DGPU_TARGET="%(cuda_sm_space_sep)s" ', -] - -# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) -cuda_compute_capabilities = [ - '3.5', - '5.0', - '6.0', - '7.0', - '7.5', - '%(cuda_cc_space_sep)s', - '8.6', + '-DBUILD_SHARED_LIBS=%s -DGPU_TARGET="%%(cuda_sm_space_sep)s" ' % local_shared for local_shared in ('ON', 'OFF') ] sanity_check_paths = { From 07bfd803c614e20cd98bd56026bd2745d79050eb Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 1 Aug 2022 15:04:41 +0200 Subject: [PATCH 040/793] Removed some patches for tests, as we don't want to keep maintaining these - lines change with every PT version etc - and we now have the ability to allow for a small number of failed test. Set allowed number of failing tests at 20 (14 fail on my current system). --- .../PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb | 26 ++++++++++++++----- 1 file changed, 19 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb index d868b1a890d..08c753b7af7 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb @@ -17,7 +17,6 @@ sources = [{ 'recursive': True, }, }] - patches = [ '%(name)s-1.7.0_avoid-nan-in-test-torch.patch', '%(name)s-1.7.0_disable-dev-shm-test.patch', @@ -26,13 +25,26 @@ patches = [ '%(name)s-1.10.0_fix-test-dataloader-fixed-affinity.patch', '%(name)s-1.10.0_skip_cmake_rpath.patch', '%(name)s-1.11.0_increase-distributed-test-timeout.patch', - '%(name)s-1.11.0_skip_failing_ops_tests.patch', - '%(name)s-1.11.0_fix_skip_jit_cuda_fuser.patch', - '%(name)s-1.11.0_fix_sharded_imports.patch', - '%(name)s-1.11.0_increase_test_tolerances_TF32.patch', '%(name)s-1.11.0_increase_c10d_gloo_timeout.patch', '%(name)s-1.11.0_disable_failing_jit_cuda_fuser_tests.patch', ] +checksums = [ + None, # PyTorch-1.12.0.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch + 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', # PyTorch-1.10.0_skip_cmake_rpath.patch + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch + 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', +] builddependencies = [ ('CMake', '3.23.1'), @@ -101,8 +113,8 @@ excluded_tests = { runtest = "cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s" # several tests are known to be flaky, and fail in some contexts (like having multiple GPUs available), -# so we allow up to 10 (out of ~90k) tests to fail before treating the installation to be faulty -max_failed_tests = 10 +# so we allow up to 20 (out of ~90k) tests to fail before treating the installation to be faulty +max_failed_tests = 20 # The readelf sanity check command can be taken out once the TestRPATH test from # https://github.com/pytorch/pytorch/pull/68912 is accepted, since it is then checked as part of the PyTorch test suite From 3835bb496a1e484250eea6533b1bc142db659e64 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 1 Aug 2022 15:08:54 +0200 Subject: [PATCH 041/793] Typing-extensions removed as explicit dependency, as 4.2.0 is already part of Python-3.10.4-GCCcore-11.3.0.eb --- .../p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb index 08c753b7af7..9a48694ea1f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb @@ -58,7 +58,6 @@ dependencies = [ ('protobuf-python', '3.19.4'), ('pybind11', '2.9.2'), ('SciPy-bundle', '2022.05'), - ('typing-extensions', '4.3.0'), ('PyYAML', '6.0'), ('MPFR', '4.1.0'), ('GMP', '6.2.1'), From 6e09e1180386364fa5819105642f7b785768a55f Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 3 Aug 2022 14:43:26 +0100 Subject: [PATCH 042/793] Tests added, following PR #15622 --- .../easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb index 5f1a28b4c64..2339f816add 100644 --- a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb @@ -17,7 +17,13 @@ toolchain = {'name': 'gompi', 'version': '2021a'} source_urls = ['https://github.com/MmgTools/mmg/archive'] sources = ['v%(version)s.tar.gz'] -checksums = ['bbf9163d65bc6e0f81dd3acc5a51e4a8c47a7fdae849abc26277e01154fe2437'] +patches = ['mmg-%(version)s_remove_ci_tests.patch'] + +checksums = [ + 'bbf9163d65bc6e0f81dd3acc5a51e4a8c47a7fdae849abc26277e01154fe2437', # v5.6.0.tar.gz + '99de7437fb9d036c786b7f1526da93d4aa1d28e728fe7279f4c9204bbbb9f734', # mmg-5.6.0_remove_ci_tests.patch + +] builddependencies = [ ('CMake', '3.20.1'), @@ -28,9 +34,15 @@ dependencies = [('SCOTCH', '6.1.0')] separate_build_dir = True -configopts = '-DUSE_SCOTCH=ON ' +# CI tests require downloading of data that might not be available in the future. +# Sticking to tests included in the source with help of patch +configopts = '-DUSE_SCOTCH=ON -DBUILD_TESTING=ON -DONLY_VERY_SHORT_TESTS=ON ' +configopts += '-DTEST_LIBMMG2D=ON -DTEST_LIBMMG3D=ON -DTEST_LIBMMGS=ON ' configopts += '-DLIBMMG2D_SHARED=ON -DLIBMMG3D_SHARED=ON -DLIBMMGS_SHARED=ON -DLIBMMG_SHARED=ON ' +pretestopts = 'export CTEST_PARALLEL_LEVEL=%(parallel)s &&' +runtest = 'test' + sanity_check_paths = { 'files': ['bin/%s_O3' % x for x in ['mmg2d', 'mmg3d', 'mmgs']] + ['lib/lib%s.%s' % (x, y) for x in ['mmg2d', 'mmg3d', 'mmgs', 'mmg'] for y in ['a', SHLIB_EXT]], From 0125c8e66dca61d894285e99b20ec6bef557eae2 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 3 Aug 2022 14:51:44 +0100 Subject: [PATCH 043/793] binutils removed --- easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb index 2339f816add..80a0bcb4e5e 100644 --- a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb @@ -27,7 +27,6 @@ checksums = [ builddependencies = [ ('CMake', '3.20.1'), - ('binutils', '2.36.1'), ] dependencies = [('SCOTCH', '6.1.0')] From 1b6fc26b3057b6cd0f7771dad09448d803c03209 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 5 Aug 2022 21:23:47 +0200 Subject: [PATCH 044/793] Add WRF and WPS --- .../t/tcsh/tcsh-6.24.01-GCCcore-11.3.0.eb | 45 +++ .../t/time/time-1.9-GCCcore-11.3.0.eb | 27 ++ .../w/WPS/WPS-4.4-foss-2022a-dmpar.eb | 38 +++ ...WPS-4.4_netCDF-Fortran_separate_path.patch | 91 ++++++ .../w/WRF/WRF-4.4-foss-2022a-dmpar.eb | 51 ++++ ...WRF-4.4_netCDF-Fortran_separate_path.patch | 266 ++++++++++++++++++ 6 files changed, 518 insertions(+) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.24.01-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/time/time-1.9-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.4-foss-2022a-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.4_netCDF-Fortran_separate_path.patch create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.4_netCDF-Fortran_separate_path.patch diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.24.01-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.01-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..27ca241e481 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.01-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.24.01' + +homepage = 'https://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [ + 'https://astron.com/pub/%(namelower)s', + 'https://astron.com/pub/%(namelower)s/old', + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5659a1b973b1f947e36238cb17a00210ac4cff3b496f8f851acd77172ab91d7e'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('ncurses', '6.3')] + +postinstallcmds = ["ln -s tcsh %(installdir)s/bin/csh"] + +sanity_check_paths = { + 'files': ["bin/tcsh", "bin/csh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/time/time-1.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d0b426f3ff8 --- /dev/null +++ b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'time' +version = '1.9' + +homepage = 'https://www.gnu.org/software/time/' +description = """The `time' command runs another program, then displays information about the resources used by that + program, collected by the system while the program was running.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['fbacf0c81e62429df3e33bda4cee38756604f18e01d977338e23306a3e3b521e'] + +builddependencies = [('binutils', '2.38')] + +postinstallcmds = ["ln -s %(installdir)s/bin/%(name)s %(installdir)s/bin/gtime"] + +sanity_check_paths = { + 'files': ['bin/gtime', 'bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["time echo test"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.4-foss-2022a-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.4-foss-2022a-dmpar.eb new file mode 100644 index 00000000000..f42560bc809 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.4-foss-2022a-dmpar.eb @@ -0,0 +1,38 @@ +name = 'WPS' +version = '4.4' + +homepage = 'http://www.wrf-model.org' +description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is + a next-generation mesoscale numerical weather prediction system designed to serve both operational + forecasting and atmospheric research needs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/wrf-model/WPS/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WPS-%(version)s_netCDF-Fortran_separate_path.patch', +] +checksums = [ + 'fe9c8d8a9a4abbf800b30e6cbb378604c6040e4536f5594b8e2dae43e942e2b3', # v4.4.tar.gz + '751bb744bf8e5386b3bcf9c3c92dbd06183acf4007d061a3c10da808387bb0a8', # WPS-4.4_netCDF-Fortran_separate_path.patch +] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +builddependencies = [ + ('Perl', '5.34.1'), +] + +dependencies = [ + ('WRF', '4.4', versionsuffix), + ('JasPer', '2.0.33'), + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.4_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WPS/WPS-4.4_netCDF-Fortran_separate_path.patch new file mode 100644 index 00000000000..71d67030c7e --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.4_netCDF-Fortran_separate_path.patch @@ -0,0 +1,91 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since 2013; it was committed by +# @boegel then. Adapted by @andreas-h to accomodate WPSv4 and foss toolchain +# +# updated for WPS v4.1 by Kenneth Hoste (HPC-UGent) +# updated for WPS v4.2 by Åke Sandgren (HPC2N) +# updated for WPS v4.4 by Maxim Masterov (SURF) + +diff -Nru WPS-4.4.orig/arch/Config.pl WPS-4.4/arch/Config.pl +--- WPS-4.4.orig/arch/Config.pl 2022-08-05 20:46:38.790818000 +0200 ++++ WPS-4.4/arch/Config.pl 2022-08-05 20:47:19.544741000 +0200 +@@ -42,6 +42,7 @@ + if(substr( $ARGV[0], 1, 8 ) eq "netcdff=") + { + $sw_netcdff_lib = substr( $ARGV[0], 9); ++ $sw_netcdff_lib =~ s/!/ /g ; + } + if(substr( $ARGV[0], 1, 6 ) eq "phdf5=") + { +diff -Nru WPS-4.4.orig/arch/preamble WPS-4.4/arch/preamble +--- WPS-4.4.orig/arch/preamble 2022-08-05 20:46:38.792313000 +0200 ++++ WPS-4.4/arch/preamble 2022-08-05 20:47:40.331112000 +0200 +@@ -39,7 +39,7 @@ + -I$(WRF_DIR)/external/io_grib1 \ + -I$(WRF_DIR)/external/io_int \ + -I$(WRF_DIR)/inc \ +- -I$(NETCDF)/include ++ -I$(NETCDF)/include -I$(NETCDFF)/include + + WRF_LIB = -L$(WRF_DIR)/external/io_grib1 -lio_grib1 \ + -L$(WRF_DIR)/external/io_grib_share -lio_grib_share \ +diff -Nru WPS-4.4.orig/configure WPS-4.4/configure +--- WPS-4.4.orig/configure 2022-08-05 20:46:38.790086000 +0200 ++++ WPS-4.4/configure 2022-08-05 20:48:51.938951000 +0200 +@@ -138,9 +138,14 @@ + echo "Will use NETCDF in dir: $NETCDF" + # for 3.6.2 and greater there might be a second library, libnetcdff.a . Check for this and use + # if available +- NETCDFF=" " +- if [ -f "$NETCDF/lib/libnetcdff.a" ] ; then +- NETCDFF="-lnetcdff" ++ USENETCDFF=" " ++ # for netCDF 4.2 and greater, the Fortran library is a seperate install ++ if [ -z "$NETCDFF" ] ++ then ++ NETCDFF=$NETCDF ++ fi ++ if [ -f "$NETCDFF/lib/libnetcdff.a" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-lnetcdff" + fi + else + echo "Will configure for use without NetCDF" +@@ -239,7 +244,7 @@ + fi + + # Found perl, so proceed with configuration +-perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$NETCDFF -os=$os -mach=$mach -wrfdir=$wrf_dir -grib2dir=$grib2dir ++perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$USENETCDFF -os=$os -mach=$mach -wrfdir=$wrf_dir + + + #Checking cross-compiling capability for some particular environment +@@ -405,9 +410,9 @@ + end program + EOF + FFLAGS=`grep ^FFLAGS configure.wps | cut -d"=" -f2-` +- cp $NETCDF/include/netcdf.inc . ++ cp $NETCDFF/include/netcdf.inc . + FC=`grep ^SFC configure.wps | cut -d"=" -f2-` +- $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib $NETCDFF -lnetcdf > /dev/null 2>&1 ++ $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib -lnetcdf $USENETCDFF > /dev/null 2>&1 + if [ -f "fort_netcdf" ] ; then + ./fort_netcdf > /dev/null 2>&1 + if [ $? = 0 ]; then +diff -Nru WPS-4.4.orig/util/src/Makefile WPS-4.4/util/src/Makefile +--- WPS-4.4.orig/util/src/Makefile 2022-08-05 20:46:38.503642000 +0200 ++++ WPS-4.4/util/src/Makefile 2022-08-05 20:52:25.200578000 +0200 +@@ -41,11 +41,11 @@ + write_met_module.o misc_definitions_module.o met_data_module.o + $(SFC) $(LDFLAGS) -o $@ elev_angle.o cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o met_data_module.o \ +- -L$(NETCDF)/lib -I$(NETCDF)/include -lnetcdf ++ -L$(NETCDFF)/lib -I$(NETCDFF)/include -lnetcdff + + elev_angle.o: elev_angle.F cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o +- $(SFC) -c elev_angle.F -I$(NETCDF)/include ++ $(SFC) -c elev_angle.F -I$(NETCDFF)/include + + calc_ecmwf_p.exe: calc_ecmwf_p.o cio.o module_debug.o module_stringutil.o gridinfo_module.o read_met_module.o \ + write_met_module.o module_date_pack.o misc_definitions_module.o met_data_module.o constants_module.o diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb new file mode 100644 index 00000000000..f5772f50f24 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb @@ -0,0 +1,51 @@ +name = 'WRF' +version = '4.4' +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +homepage = 'https://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +source_urls = ['https://github.com/wrf-model/WRF/archive/'] +# sources = ['v%(version)s.tar.gz'] +sources = [{ + 'filename': 'v4.4.tar.gz', + 'git_config': { + 'url': 'https://github.com/wrf-model', + 'repo_name': 'WRF', + 'tag': 'v4.4', + 'clone_into': 'WRF-4.4', + 'recursive': True, + }, +}] +patches = [ + 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', +] +checksums = [ + '92f87fd769867a12dc0bda9778a2ec5319249bc335cbda87043a873d9139088d', # v4.4.tar.gz + '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch +] + +# csh is used by WRF install scripts +builddependencies = [ + ('Autotools', '20220317'), + ('tcsh', '6.24.01'), + ('time', '1.9'), + ('Perl', '5.34.1'), +] + +dependencies = [ + ('JasPer', '2.0.33'), + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), +] + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-4.4_netCDF-Fortran_separate_path.patch new file mode 100644 index 00000000000..34e03618a66 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4_netCDF-Fortran_separate_path.patch @@ -0,0 +1,266 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since WRF3.5; it was committed by +# @boegel then. Adapted by @andreas-h to accomodate WRFv4 and foss toolchain +# +# updated for WPS v4.4 by Maxim Masterov (SURF) + +diff -Nru WRF-4.4.orig/arch/Config.pl WRF-4.4/arch/Config.pl +--- WRF-4.4.orig/arch/Config.pl 2022-08-05 12:50:41.026673000 +0200 ++++ WRF-4.4/arch/Config.pl 2022-08-05 12:53:16.487608000 +0200 +@@ -11,6 +11,7 @@ + select((select(STDOUT), $|=1)[0]); + $sw_perl_path = perl ; + $sw_netcdf_path = "" ; ++$sw_netcdff_path = "" ; # for netCDF 4.2 and greater, Fortran lib might be in a different path + $sw_pnetcdf_path = "" ; + $sw_netcdfpar_path = "" ; + $sw_hdf5_path=""; +@@ -95,6 +96,10 @@ + } + } + } ++ if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" ) ++ { ++ $sw_netcdff_path = substr( $ARGV[0], 9 ) ; ++ } + if ( substr( $ARGV[0], 1, 8 ) eq "pnetcdf=" ) + { + $sw_pnetcdf_path = substr( $ARGV[0], 9 ) ; +@@ -126,6 +131,7 @@ + if ( substr( $ARGV[0], 1, 11 ) eq "USENETCDFF=" ) + { + $sw_usenetcdff = substr( $ARGV[0], 12 ) ; ++ $sw_usenetcdff =~ s/!/ /g ; + } + if ( substr( $ARGV[0], 1, 10 ) eq "USENETCDF=" ) + { +@@ -610,6 +616,7 @@ + { + $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ; + $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ; ++ $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ; + $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ; + $_ =~ s/CONFIGURE_NETCDFPAR_PATH/$sw_netcdfpar_path/g ; + $_ =~ s/CONFIGURE_HDF5_PATH/$sw_hdf5_path/g ; +@@ -678,7 +685,7 @@ + } elsif ( $sw_os eq "Interix" ) { + $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } else { +- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdff_path/lib -L$sw_netcdf_path/lib64 $sw_usenetcdff $sw_usenetcdf : ; + } + } + else +diff -Nru WRF-4.4.orig/arch/configure.defaults WRF-4.4/arch/configure.defaults +--- WRF-4.4.orig/arch/configure.defaults 2022-08-05 12:50:41.028943000 +0200 ++++ WRF-4.4/arch/configure.defaults 2022-08-05 12:53:38.767002000 +0200 +@@ -1636,6 +1636,7 @@ + + LIB_EXTERNAL = \ + ../external/io_netcdf/libwrfio_nf.a CONFIGURE_NETCDF_PATH/lib/libnetcdf.lib \ ++ CONFIGURE_NETCDFF_PATH/lib/libnetcdff.lib \ + ../external/wavelet/libWavelet.a ../external/wavelet/lib_wavelet.a + ESMF_IO_LIB = ../external/esmf_time_f90/libesmf_time.a + LIB_BUNDLED = \ +diff -Nru WRF-4.4.orig/arch/conf_tokens WRF-4.4/arch/conf_tokens +--- WRF-4.4.orig/arch/conf_tokens 2022-08-05 12:50:41.028607000 +0200 ++++ WRF-4.4/arch/conf_tokens 2022-08-05 12:53:57.832914000 +0200 +@@ -5,6 +5,7 @@ + CONFIGURE_DMPARALLEL + CONFIGURE_RWORDSIZE + CONFIGURE_NETCDF_FLAG ++CONFIGURE_NETCDFF_FLAG + CONFIGURE_GRIB2_FLAG + CONFIGURE_NETCDF_LIB_PATH + CONFIGURE_GRIB2_LIB +@@ -13,4 +14,5 @@ + CONFIGURE_WRFIO_NF + CONFIGURE_WRFIO_GRIB2 + CONFIGURE_NETCDF_PATH ++CONFIGURE_NETCDFF_PATH + CONFIGURE_GRIB2_INC +diff -Nru WRF-4.4.orig/arch/postamble WRF-4.4/arch/postamble +--- WRF-4.4.orig/arch/postamble 2022-08-05 12:50:41.031770000 +0200 ++++ WRF-4.4/arch/postamble 2022-08-05 12:54:52.759085000 +0200 +@@ -53,6 +53,7 @@ + -I$(WRF_SRC_ROOT_DIR)/phys \ + -I$(WRF_SRC_ROOT_DIR)/wrftladj \ + -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \ ++ -I$(NETCDFPATH)/include -I$(NETCDFFPATH)/include \ + -I$(NETCDFPATH)/include \ + CONFIGURE_RTTOV_INC CONFIGURE_CTSM_INC + REGISTRY = Registry +@@ -63,6 +64,7 @@ + ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS + CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE + NETCDFPATH = CONFIGURE_NETCDF_PATH ++NETCDFFPATH = CONFIGURE_NETCDFF_PATH + HDF5PATH = CONFIGURE_HDF5_PATH + WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH + RTTOVPATH = CONFIGURE_RTTOV_PATH +@@ -94,7 +96,7 @@ + + wrfio_nf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \ +- make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ ++ make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ + CC="$(SCC)" CFLAGS="$(CFLAGS)" \ + FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + +@@ -105,7 +107,7 @@ + + wrfio_pnf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_pnetcdf ; \ +- make $(J) NETCDFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ ++ make $(J) NETCDFPATH="$(PNETCDFPATH)" NETCDFFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ + FC="$(FC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + + wrfio_grib_share : +diff -Nru WRF-4.4.orig/configure WRF-4.4/configure +--- WRF-4.4.orig/configure 2022-08-05 12:50:41.453325000 +0200 ++++ WRF-4.4/configure 2022-08-05 12:57:14.821614000 +0200 +@@ -222,9 +222,13 @@ + if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" -o -f "$NETCDF/lib/libnetcdff.dll.a" ] ; then + USENETCDFF="-lnetcdff" + else +- USENETCDFF=" " ++ if [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-L$NETCDFF/lib64!-lnetcdff" # ! will be replaced with space ++ else ++ USENETCDFF=" " ++ fi + fi +- if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib/libnetcdf.dll.a" ] ; then ++ if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then + USENETCDF="-lnetcdf" + else + USENETCDF=" " +@@ -566,7 +570,7 @@ + srch=`grep -i "^#ARCH.*$os" arch/configure.defaults | grep -i "$mach"` + if [ -n "$srch" ] ; then + $PERL arch/Config.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \ +- -netcdf=$NETCDF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ ++ -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ + -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \ + -time=$FORTRAN_COMPILER_TIMER -tfl="$TFL" -cfl="$CFL" -config_line="$config_line" \ + -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -dep_lib_path="$DEP_LIB_PATH" +@@ -648,14 +652,14 @@ + echo "If you wish to change the default options, edit the file:" + echo " arch/configure.defaults" + +-if test -n "$NETCDF" ; then +- if [ ! -f $NETCDF/include/netcdf.inc ] ; then ++if test -n "$NETCDFF" ; then ++ if [ ! -f $NETCDFF/include/netcdf.inc ] ; then + echo +- echo "Error : Not found $NETCDF/include/netcdf.inc" ++ echo "Error : Not found $NETCDFF/include/netcdf.inc" + echo " Please check this installation of NetCDF and re-run this configure script" + exit -1 + fi +- grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null ++ grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null + configure_aaaa=$? ; export configure_aaaa + if [ $configure_aaaa -a -z "$WRFIO_NCD_NO_LARGE_FILE_SUPPORT" ] ; then + echo "NetCDF users note:" +diff -Nru WRF-4.4.orig/external/io_netcdf/makefile WRF-4.4/external/io_netcdf/makefile +--- WRF-4.4.orig/external/io_netcdf/makefile 2022-08-05 12:50:41.676471000 +0200 ++++ WRF-4.4/external/io_netcdf/makefile 2022-08-05 15:32:21.053573000 +0200 +@@ -3,9 +3,9 @@ + OBJSL = wrf_io.o field_routines.o module_wrfsi_static.o + OBJS = $(OBJSL) + CODE = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf +-LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -lnetcdf ++LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -L$(NETCDFFPATH)/lib -L$(NETCDFFPATH)/lib64 -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -24,7 +24,7 @@ + $(RANLIB) $@ + + wrf_io.o: wrf_io.F90 $(CODE) +- grep nf_format_64bit $(NETCDFPATH)/include/netcdf.inc ;\ ++ grep nf_format_64bit $(NETCDFFPATH)/include/netcdf.inc ;\ + a=$$? ; export a ; \ + if [ $$a -a "$$WRFIO_NCD_LARGE_FILE_SUPPORT" = "1" ] ; then \ + $(CPP1) -DWRFIO_NCD_LARGE_FILE_SUPPORT -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ; \ +@@ -43,14 +43,14 @@ + x=`echo "$(FC)" | awk '{print $$1}'` ; export x ; \ + if [ $$x = "gfortran" ] ; then \ + echo removing external declaration of iargc for gfortran ; \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ + else \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ + fi + $(FC) -c $(FFLAGS) diffwrf.f + @if [ \( -f ../../frame/wrf_debug.o \) -a \( -f ../../frame/module_wrf_error.o \) -a \( -f $(ESMF_MOD_DEPENDENCE) \) -a \( -f ../../frame/clog.o \) ] ; then \ + echo "diffwrf io_netcdf is being built now. " ; \ +- if [ \( -f $(NETCDFPATH)/lib/libnetcdff.a -o -f $(NETCDFPATH)/lib/libnetcdff.so -o -f $(NETCDFPATH)/lib/libnetcdff.dll.a \) ] ; then \ ++ if [ \( -f $(NETCDFFPATH)/lib/libnetcdff.a -o -f $(NETCDFFPATH)/lib/libnetcdff.so -o -f $(NETCDFFPATH)/lib64/libnetcdff.a -o -f $(NETCDFFPATH)/lib64/libnetcdff.so \) ] ; then \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBFFS) ;\ + else \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBS) ;\ +diff -Nru WRF-4.4.orig/external/io_pnetcdf/Makefile WRF-4.4/external/io_pnetcdf/Makefile +--- WRF-4.4.orig/external/io_pnetcdf/Makefile 2022-08-05 12:50:41.688872000 +0200 ++++ WRF-4.4/external/io_pnetcdf/Makefile 2022-08-05 13:00:28.273185000 +0200 +@@ -9,8 +9,8 @@ + ext_pnc_put_var_td.code \ + ext_pnc_put_var_ti.code \ + transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = -L$(NETCDFPATH)/lib -lpnetcdf ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = -L$(NETCDFFPATH)/lib -lpnetcdf + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -25,15 +25,15 @@ + $(RANLIB) libwrfio_pnf.a + + wrf_io.o: wrf_io.F90 $(CODE) +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f + $(FC) $(FFLAGS) -c wrf_io.f + + module_wrfsi_static.o: module_wrfsi_static.F90 +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f + $(FC) $(FFLAGS) -c module_wrfsi_static.f + + field_routines.o: field_routines.F90 wrf_io.o +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f + $(FC) $(FFLAGS) -c field_routines.f + + superclean: +diff -Nru WRF-4.4.orig/Makefile WRF-4.4/Makefile +--- WRF-4.4.orig/Makefile 2022-08-05 12:50:40.979120000 +0200 ++++ WRF-4.4/Makefile 2022-08-05 13:03:38.672102000 +0200 +@@ -923,7 +923,7 @@ + @ echo '--------------------------------------' + ( cd frame ; $(MAKE) $(J) LLIST="$(LINKLIST)" framework ; \ + cd ../external/io_netcdf ; \ +- $(MAKE) NETCDFPATH="$(NETCDFPATH)" \ ++ $(MAKE) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" \ + FC="$(FC) $(FCBASEOPTS) $(PROMOTION) $(FCDEBUG) $(OMP)" RANLIB="$(RANLIB)" \ + CPP="$(CPP)" LDFLAGS="$(LDFLAGS)" TRADFLAG="$(TRADFLAG)" ESMF_IO_LIB_EXT="$(ESMF_IO_LIB_EXT)" \ + LIB_LOCAL="$(LIB_LOCAL)" \ +@@ -1070,9 +1070,9 @@ + # rule used by configure to test if this will compile with netcdf4 + nc4_test: + if [ $(USENETCDFPAR) -eq 0 ] ; then \ +- ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ ++ ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib64 -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ + else \ +- ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(DM_CC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ ++ ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(DM_CC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib64 -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ + fi + + # rule used by configure to test if Fortran 2003 IEEE signaling is available From ff9d2f1f6fb14ea00fe8159fe432e31af8f93038 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 8 Aug 2022 14:19:50 +0200 Subject: [PATCH 045/793] Fix checksum --- easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb index f5772f50f24..170cb7b35b9 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb @@ -27,7 +27,7 @@ patches = [ 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', ] checksums = [ - '92f87fd769867a12dc0bda9778a2ec5319249bc335cbda87043a873d9139088d', # v4.4.tar.gz + '5332c78f5ea8d1a4475c7cd749e8f22a40b4cc5290bdf0c1c9fb051c8e6e9037', # v4.4.tar.gz '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch ] From 0e1b1f0583615fbac0453f9716a82fb41e1286a5 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 8 Aug 2022 17:14:54 +0200 Subject: [PATCH 046/793] Update WRF-4.4-foss-2022a-dmpar.eb --- easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb index 170cb7b35b9..8fdfe98201a 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb @@ -27,7 +27,6 @@ patches = [ 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', ] checksums = [ - '5332c78f5ea8d1a4475c7cd749e8f22a40b4cc5290bdf0c1c9fb051c8e6e9037', # v4.4.tar.gz '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch ] From 840c2593870ff11da7dc7d8a2a0fbf34122140fd Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 8 Aug 2022 17:32:37 +0200 Subject: [PATCH 047/793] Update WRF-4.4-foss-2022a-dmpar.eb --- easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb index 8fdfe98201a..b59ecf9d60f 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb @@ -26,9 +26,11 @@ sources = [{ patches = [ 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', ] -checksums = [ - '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch -] +# The problem: sources from git clone have different checksum every time +# checksums = [ +# '0d68df19766ad03041126c1531cb115e2d2a69043df96314fd30d897cfca9e4c', # v4.4.tar.gz +# '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch +# ] # csh is used by WRF install scripts builddependencies = [ From a6e7ab092747b48cb412b7b6a9f7f45fe516b7da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 9 Aug 2022 13:06:26 +0200 Subject: [PATCH 048/793] Update easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb Co-authored-by: SebastianAchilles --- .../easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb index b15aaf2ae7d..2ed04d457b6 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb @@ -36,7 +36,7 @@ configopts = [ ] sanity_check_paths = { - 'files': ['lib/libmagma.so', 'lib/libmagma.a'], + 'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'], 'dirs': ['include'], } From e6b1ccccd867ad20e44ee44fe3b5c8dc26b27e4a Mon Sep 17 00:00:00 2001 From: Maxim Date: Tue, 9 Aug 2022 21:42:02 +0200 Subject: [PATCH 049/793] Update easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb index b59ecf9d60f..b2412e3eb97 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb @@ -27,10 +27,10 @@ patches = [ 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', ] # The problem: sources from git clone have different checksum every time -# checksums = [ -# '0d68df19766ad03041126c1531cb115e2d2a69043df96314fd30d897cfca9e4c', # v4.4.tar.gz -# '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch -# ] +checksums = [ + None, # v4.4.tar.gz + '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch +] # csh is used by WRF install scripts builddependencies = [ From bb8536851f88f810d5a922e2eefe06de44f598a1 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 9 Aug 2022 14:39:56 +0200 Subject: [PATCH 050/793] adding easyconfigs: netCDF-Fortran-4.6.0-iimpi-2022a.eb, netCDF-4.9.0-iimpi-2022a.eb --- .../netCDF-Fortran-4.6.0-iimpi-2022a.eb | 28 +++++++++++ .../n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 48 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-iimpi-2022a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-iimpi-2022a.eb new file mode 100644 index 00000000000..6ccd8e61271 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-iimpi-2022a.eb @@ -0,0 +1,28 @@ +name = 'netCDF-Fortran' +version = '4.6.0' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8194aa70e400c0adfc456127c1d97af2c6489207171d13b10cd754a16da8b0ca'] + +builddependencies = [ + ('M4', '1.4.19'), +] + +dependencies = [ + ('netCDF', '4.9.0'), + ('bzip2', '1.0.8'), +] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb new file mode 100644 index 00000000000..b13202347f8 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -0,0 +1,48 @@ +name = 'netCDF' +version = '4.9.0' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'netCDF-%(version)s_fix-lib-name.patch', + 'netCDF-%(version)s_fix-linking-errors.patch', +] +checksums = [ + '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6', # v4.9.0.tar.gz + 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a', # netCDF-4.9.0_fix-lib-name.patch + '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15', # netCDF-4.9.0_fix-linking-errors.patch +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.23.1'), + ('Doxygen', '1.9.4'), +] + +dependencies = [ + ('HDF5', '1.13.1'), + ('cURL', '7.83.0'), + ('Szip', '2.1.1'), + ('zstd', '1.5.2'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF", + "-DBUILD_SHARED_LIBS=ON", +] + +# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " + +runtest = 'test' + +moduleclass = 'data' From 1acfc6c5de84bb2bb7e0bc2e47736e54f158cdab Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 18 Aug 2022 18:43:52 +0200 Subject: [PATCH 051/793] Add netCDF-4.9.0_skip-nasa-test.patch to netCDF-4.9.0-iimpi-2022a.eb --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb index b13202347f8..e8aeb8b93a8 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -14,11 +14,13 @@ sources = ['v%(version)s.tar.gz'] patches = [ 'netCDF-%(version)s_fix-lib-name.patch', 'netCDF-%(version)s_fix-linking-errors.patch', + 'netCDF-%(version)s_skip-nasa-test.patch', ] checksums = [ '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6', # v4.9.0.tar.gz 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a', # netCDF-4.9.0_fix-lib-name.patch '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15', # netCDF-4.9.0_fix-linking-errors.patch + '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a', # netCDF-4.9.0_skip-nasa-test.patch ] builddependencies = [ From 00d382d19f7a68eebee0c2a5490fe5c35a2c8f04 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 10:29:26 +0100 Subject: [PATCH 052/793] adding easyconfigs: dbus-glib-0.112-GCCcore-11.2.0.eb --- .../dbus-glib-0.112-GCCcore-11.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..2b0e0d55ab9 --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'dbus-glib' +version = '0.112' + +homepage = 'https://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk to one another.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] +checksums = ['7d550dccdfcd286e33895501829ed971eeb65c614e73aadb4a08aeef719b143a'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('Python', '3.9.6', '-bare'), # Python is needed for building against GLib. +] + +dependencies = [ + ('GLib', '2.69.1'), + ('DBus', '1.13.18'), + ('expat', '2.4.1'), +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' From 272c32b0058a9c744041dcd549814ca340280367 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 10:33:12 +0100 Subject: [PATCH 053/793] adding easyconfigs: enchant-2-2.3.3-GCCcore-11.2.0.eb --- .../enchant-2-2.3.3-GCCcore-11.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..025a3fe29b1 --- /dev/null +++ b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb @@ -0,0 +1,44 @@ +# Updated from enchant-1.6.1-intel-2017a.eb +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'enchant-2' +version = '2.3.3' + +homepage = 'https://github.com/AbiWord/enchant' +description = """Enchant aims to provide a simple but comprehensive abstraction for dealing +with different spell checking libraries in a consistent way. A client, such +as a text editor or word processor, need not know anything about a specific +spell-checker, and since all back-ends are plugins, new spell-checkers can +be added without needing any change to the program using Enchant.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/AbiWord/enchant/releases/download/v%(version)s'] +sources = ['enchant-%(version)s.tar.gz'] +checksums = [ + '3da12103f11cf49c3cf2fd2ce3017575c5321a489e5b9bfa81dd91ec413f3891' +] + +builddependencies = [ + ('Autotools', '20210726'), + ('binutils', '2.37'), + ('M4', '1.4.19'), +] + +preconfigopts = "autoreconf -vfi && " + +dependencies = [ + ('hunspell', '1.7.0'), +] + +buildopts = "LIBTOOL='libtool --tag=CC'" + +sanity_check_paths = { + 'files': ['bin/enchant-2', 'bin/enchant-lsmod-2', + 'lib/libenchant-2.a', 'lib/libenchant-2.%s' % SHLIB_EXT], + 'dirs': ['include/enchant-2', 'lib/enchant-2'], +} + +moduleclass = 'tools' From d74d9289492bbd7460c3614888fe4413a940c45f Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 10:35:05 +0100 Subject: [PATCH 054/793] adding easyconfigs: hunspell-1.7.0-GCCcore-11.2.0.eb --- .../hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..857561f81b8 --- /dev/null +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'hunspell' +version = '1.7.0' + +homepage = 'http://hunspell.github.io/' +description = """Hunspell is a spell checker and morphological analyzer +library and program designed for languageswith rich morphology and +complex word compounding or character encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/hunspell/hunspell/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['bb27b86eb910a8285407cf3ca33b62643a02798cf2eef468c0a74f6c3ee6bc8a'] + +builddependencies = [ + ('Autotools', '20210726'), + ('binutils', '2.37'), + ('M4', '1.4.19'), +] + +preconfigopts = "autoreconf -vfi && " + +sanity_check_paths = { + 'files': ['bin/hunspell', 'lib/libhunspell-%(version_major_minor)s.a', + 'lib/libhunspell-%%(version_major_minor)s.%s' % SHLIB_EXT, 'lib/pkgconfig/hunspell.pc'], + 'dirs': ['include/hunspell'], +} + +moduleclass = 'tools' From 561bc7295b6ed7fd85482b3b6a5f5e0a3d3501e5 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 10:37:55 +0100 Subject: [PATCH 055/793] adding easyconfigs: GConf-3.2.6-GCCcore-11.2.0.eb --- .../g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b78028c24b1 --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'GConf' +version = '3.2.6' + +# The homeage is no longer reachable! +# homepage = 'https://developer.gnome.org/gconf/' +# The project was depricated with the move to Gnome-3 +# Possible alternative, although 6 years old: +homepage = 'https://gitlab.gnome.org/iainl/gconf' +description = """GConf is a system for storing application preferences. + It is intended for user preferences; not configuration + of something like Apache, or arbitrary data storage.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +patches = [ + '%(name)s-%(version)s_call-dbus_g_thread_init.patch', + '%(name)s-%(version)s_fix_wrong_return_value.patch', + '%(name)s-%(version)s_gconf-path-max-hurd.patch', + '%(name)s-%(version)s_readd_gconf_engine_key_is_writable.patch', +] +checksums = [ + '1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c', # GConf-3.2.6.tar.xz + 'ed55bff5bc239115ae27b8520a923ae0d5cab6cb15ca9921a8c23b939306489f', # GConf-3.2.6_call-dbus_g_thread_init.patch + 'f8f7745c3648953098eb56af0f64adc69d8c0b0e78c8db351746a2b4c58e8bb4', # GConf-3.2.6_fix_wrong_return_value.patch + 'ee5524c3cb985088bbe4884531ddc48ba22d2fced2a34865304c77e194a55bde', # GConf-3.2.6_gconf-path-max-hurd.patch + # GConf-3.2.6_readd_gconf_engine_key_is_writable.patch + 'b95dfc2f0474d9162fc686f26cd4d3da5c9b01a9c609dc0a4f2b2bd901d497f3', +] + +builddependencies = [ + ('binutils', '2.37'), + ('GObject-Introspection', '1.68.0'), +] + +dependencies = [ + ('GLib', '2.69.1'), + ('dbus-glib', '0.112'), + ('libxml2', '2.9.10'), + ('GTK3', '3.24.31'), + ('intltool', '0.51.0'), +] + +configopts = '--disable-orbit ' + +local_check_filelist = ['bin/gconf%s' % x for x in ['-merge-tree', 'tool-2']] +local_check_filelist += ['bin/gsettings-%s-convert' % x for x in ['data', 'schema']] +local_check_filelist += ['lib/libgconf-2.%s' % x for x in ['a', 'so']] + +sanity_check_paths = { + 'files': local_check_filelist, + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' From 845936e6bcea7ee1bcc45d3f89d0f4b6e36f9473 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 11:01:48 +0100 Subject: [PATCH 056/793] adding easyconfigs: libwpe-1.13.3-GCCcore-11.2.0.eb --- .../l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..90c0db43eef --- /dev/null +++ b/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb @@ -0,0 +1,43 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'libwpe' +version = '1.13.3' + +homepage = 'https://webkit.org/wpe' +description = """WPE is the reference WebKit port for embedded and +low-consumption computer devices. It has been designed from the +ground-up with performance, small footprint, accelerated content +rendering, and simplicity of deployment in mind, bringing the +excellence of the WebKit engine to countless platforms and target devices.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://wpewebkit.org/releases'] +sources = ['%(name)s-%(version)s.tar.xz'] + +checksums = [ + '05f871922f6ca750c5689a38a346c3fba130417d3490dd52362b4fe22f334e96', # libwpe-1.13.3.tar.xz +] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('CMake', '3.22.1'), + ('Meson', '0.58.2'), +] + +dependencies = [ + ('glew', '2.2.0', '-egl'), +] + +parallel = 2 + +sanity_check_paths = { + 'files': ['lib/libwpe-1.0.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 361535d2431a52cbef706d6fd0782593f9f5b56a Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 11:03:40 +0100 Subject: [PATCH 057/793] adding easyconfigs: Wayland-1.20.0-GCCcore-11.2.0.eb --- .../Wayland/Wayland-1.20.0-GCCcore-11.2.0.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..6036be672fc --- /dev/null +++ b/easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.2.0.eb @@ -0,0 +1,59 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'Bundle' + +name = 'Wayland' +version = '1.20.0' + +homepage = 'https://wayland.freedesktop.org/' +description = """ +Wayland is a project to define a protocol for a compositor to talk to + its clients as well as a library implementation of the protocol. The + compositor can be a standalone display server running on Linux kernel + modesetting and evdev input devices, an X application, or a wayland + client itself. The clients can be traditional applications, X servers + (rootless or fullscreen) or other display servers. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('CMake', '3.21.1'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), + ('binutils', '2.37'), +] + +dependencies = [ + ('libffi', '3.4.2'), + ('expat', '2.4.1'), + ('libxml2', '2.9.10'), +] + +default_easyblock = 'MesonNinja' +default_component_specs = { + 'source_urls': ['https://wayland.freedesktop.org/releases'], + 'sources': [SOURCE_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('wayland', version, { + 'checksums': ['b8a034154c7059772e0fdbd27dbfcda6c732df29cae56a82274f6ec5d7cd8725'], + 'configopts': "-Ddocumentation=false", + }), + ('wayland-protocols', '1.25', { + 'checksums': ['f1ff0f7199d0a0da337217dd8c99979967808dc37731a1e759e822b75b571460'], + 'preconfigopts': "PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH " + }), +] + +_libs = ['lib/libwayland-%s.%s' % (x, SHLIB_EXT) for x in ['client', 'cursor', 'egl', 'server']] +sanity_check_paths = { + 'files': ['bin/wayland-scanner'] + _libs, + 'dirs': ['lib'], +} + +sanity_check_commands = ["wayland-scanner --help", "wayland-scanner --version"] + +moduleclass = 'vis' From f245cb5c529148e665bb7c9d4e292dbda49669e7 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 11:21:20 +0100 Subject: [PATCH 058/793] adding easyconfigs: Waylandpp-1.0.0-GCCcore-11.2.0.eb --- .../Waylandpp-1.0.0-GCCcore-11.2.0.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..327d939ec40 --- /dev/null +++ b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb @@ -0,0 +1,53 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'Waylandpp' +version = '1.0.0' + +homepage = 'https://github.com/NilsBrause/waylandpp' +description = """Wayland is an object oriented display protocol, which +features request and events. Requests can be seen as method calls on +certain objects, whereas events can be seen as signals of an object. +This makes the Wayland protocol a perfect candidate for a C++ binding. + +The goal of this library is to create such a C++ binding for Wayland +using the most modern C++ technology currently available, providing +an easy to use C++ API to Wayland.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/NilsBrause/waylandpp/archive'] +sources = ['%(version)s.tar.gz'] + +checksums = [ + 'b20b45917382c6b87e9380130c9a1a1c563da2f498de5830df12fbce326dd9f5', # 1.0.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('CMake', '3.22.1'), +] + +dependencies = [ + ('pugixml', '1.12.1'), + ('Wayland', '1.20.0'), +] + +parallel = 2 + +sanity_check_paths = { + 'files': ['bin/wayland-scanner++', 'lib//libwayland-client-extra++.%s' % SHLIB_EXT, + 'lib/libwayland-client++.%s' % SHLIB_EXT, + 'lib/libwayland-client-unstable++.%s' % SHLIB_EXT, + 'lib/libwayland-cursor++.%s' % SHLIB_EXT, + 'lib/libwayland-egl++.%s' % SHLIB_EXT, + 'lib/libwayland-server-extra++.%s' % SHLIB_EXT, + 'lib/libwayland-server++.%s' % SHLIB_EXT, + 'lib/libwayland-server-unstable++.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From 86c002427aa49cb0a166b121b4ebe81d0575e781 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 11:34:59 +0100 Subject: [PATCH 059/793] adding easyconfigs: wpebackend-fdo-1.13.1-GCCcore-11.2.0.eb --- .../wpebackend-fdo-1.13.1-GCCcore-11.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.13.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.13.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.13.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..e675f510aa1 --- /dev/null +++ b/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.13.1-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MesonNinja' + +name = 'wpebackend-fdo' +version = '1.13.1' + +homepage = 'https://wpewebkit.org/' +description = """WPE WebKit allows embedders to create simple and performant +systems based on Web platform technologies. It is a WebKit port designed with +flexibility and hardware acceleration in mind, leveraging common 3D graphics +APIs for best performance.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://wpewebkit.org/releases'] +sources = ['%(name)s-%(version)s.tar.xz'] +checksums = ['d61ca47ec52d7cd1d6f869f66d6ea247a53092acfad1a8cbab71836a82d3a0ae'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('binutils', '2.37'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('pugixml', '1.12.1'), + ('Waylandpp', '1.0.0'), + ('libepoxy', '1.5.8'), + ('glib-networking', '2.72.1'), + ('libwpe', '1.13.3'), +] + +sanity_check_paths = { + 'files': ['lib/libWPEBackend-fdo-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From f94d60dbb9a69b0dfbe1f2bdf2864093209dd3d8 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 12:26:58 +0100 Subject: [PATCH 060/793] adding easyconfigs: LibSoup-3.0.7-GCC-11.2.0.eb --- .../l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb b/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb new file mode 100644 index 00000000000..33e5fa76118 --- /dev/null +++ b/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'MesonNinja' + +name = 'LibSoup' +version = '3.0.7' + +homepage = 'https://wiki.gnome.org/Projects/libsoup' +description = """libsoup is an HTTP client/server library for GNOME. It +uses GObjects and the glib main loop, to integrate well with GNOME +applications, and also has a synchronous API, for use in threaded +applications.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'cstd': 'gnu11'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ebdf90cf3599c11acbb6818a9d9e3fc9d2c68e56eb829b93962972683e1bf7c8'] + +builddependencies = [ + ('binutils', '2.37'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.68.0'), + ('CMake', '3.22.1'), +] + +dependencies = [ + ('libxml2', '2.9.10'), + ('SQLite', '3.36'), + ('GLib', '2.69.1'), + ('libpsl', '0.21.1'), + ('cURL', '7.78.0'), + ('GnuTLS', '3.7.3'), + ('nghttp2', '1.48.0'), + ('glib-networking', '2.72.1'), + ('Brotli', '1.0.9'), +] + +# uncomment for checking TLS support +osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] + +sanity_check_paths = { + 'files': ['lib/libsoup-3.0.%s' % SHLIB_EXT], + 'dirs': ['include/libsoup-3.0/libsoup/', 'lib/pkgconfig'] +} + +moduleclass = 'lib' From e4bbb8c902b303e9030039694adf6b63332460fe Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 12:38:51 +0100 Subject: [PATCH 061/793] adding easyconfigs: nghttp2-1.48.0-GCC-11.2.0.eb --- .../n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..4b516f19c4b --- /dev/null +++ b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb @@ -0,0 +1,62 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'nghttp2' +version = '1.48.0' + +homepage = 'https://github.com/nghttp2/nghttp2' +description = """ +This is an implementation of the Hypertext Transfer Protocol version 2 in C. + +The framing layer of HTTP/2 is implemented as a reusable C library. +On top of that, we have implemented an HTTP/2 client, server and proxy. +We have also developed load test and benchmarking tools for HTTP/2. + +An HPACK encoder and decoder are available as a public API.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'nghttp2' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] + +checksums = [ + '946a8fa490548b67fc6074553cb225279cc6404bae96cf74551f2ad4453be637', # v1.48.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('CMake', '3.22.1'), + ('CUnit', '2.1-3'), + ('Boost', '1.79.0'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', True), + ('nghttp3', '0.6.0'), + ('Python', '3.9.6'), + ('libxml2', '2.9.10'), + ('Jansson', '2.14'), + ('jemalloc', '5.2.1'), + ('ngtcp2', '0.7.0'), + ('libevent', '2.1.12'), + ('libev', '4.33'), + ('c-ares', '1.18.1'), +] + + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=release ' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libnghttp2.%s' % SHLIB_EXT], + 'dirs': ['include/nghttp2', 'share'], +} + +moduleclass = 'lib' From 87781aecc599bad8f4da9473badbf09b914bb907 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 12:44:05 +0100 Subject: [PATCH 062/793] adding easyconfigs: ngtcp2-0.7.0-GCCcore-11.2.0.eb --- .../n/ngtcp2/ngtcp2-0.7.0-GCCcore-11.2.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..81bcc53c6e2 --- /dev/null +++ b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCCcore-11.2.0.eb @@ -0,0 +1,50 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'ngtcp2' +version = '0.7.0' + +homepage = 'https://github.com/ngtcp2/ngtcp2' +description = """ +'Call it TCP/2. One More Time.' + +ngtcp2 project is an effort to implement RFC9000 QUIC protocol.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'ngtcp2' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] + +checksums = [ + 'b2015c58e6d249bb71c7f7726a1e5ec5ccc78be7d50d82938358fac14ec98ca9', # v0.6.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), + ('CUnit', '2.1-3'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', True), + ('GnuTLS', '3.7.3'), + ('nghttp3', '0.6.0'), +] + +osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=release -DENABLE_GNUTLS=True' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libngtcp2_static.a', 'lib/libngtcp2.%s' % SHLIB_EXT], + 'dirs': ['share/doc/ngtcp2'], +} + +moduleclass = 'lib' From 1077292d28470795781056e1fbec866f70003953 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 15:18:31 +0100 Subject: [PATCH 063/793] Sanity check commands added --- .../e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb index 025a3fe29b1..6af0833119a 100644 --- a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb @@ -35,6 +35,11 @@ dependencies = [ buildopts = "LIBTOOL='libtool --tag=CC'" +sanity_check_commands = [ + 'enchant-2 -h', + 'enchant-lsmod-2 -v', +] + sanity_check_paths = { 'files': ['bin/enchant-2', 'bin/enchant-lsmod-2', 'lib/libenchant-2.a', 'lib/libenchant-2.%s' % SHLIB_EXT], From 45ee59f684a386cfc80db31f0a6ed4d82e2bc3bf Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 15:21:30 +0100 Subject: [PATCH 064/793] Sanity check command added --- .../easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb index 857561f81b8..b37fdbc7121 100644 --- a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb @@ -25,6 +25,10 @@ builddependencies = [ preconfigopts = "autoreconf -vfi && " +sanity_check_commands = [ + 'hunspell -h', +] + sanity_check_paths = { 'files': ['bin/hunspell', 'lib/libhunspell-%(version_major_minor)s.a', 'lib/libhunspell-%%(version_major_minor)s.%s' % SHLIB_EXT, 'lib/pkgconfig/hunspell.pc'], From bb88dd5d72b3b79eb55818e58a0096960affcfae Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 18:04:18 +0100 Subject: [PATCH 065/793] adding easyconfigs: WebKitGTK+-2.37.1-GCC-11.2.0.eb --- .../WebKitGTK+-2.37.1-GCC-11.2.0.eb | 86 +++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..1ede0f20a54 --- /dev/null +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb @@ -0,0 +1,86 @@ +# Updated from WebKitGTK+-2.27.4-GCC-8.3.0.eb with more modules added +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'WebKitGTK+' +version = '2.37.1' + +homepage = 'https://webkitgtk.org/' +description = """WebKitGTK+ is a full-featured port of the WebKit +rendering engine, suitable for projects requiring any kind of web +integration, from hybrid HTML/CSS applications to full-fledged web +browsers. It offers WebKit's full functionality and is useful in a wide +range of systems from desktop computers to embedded systems like phones, +tablets, and televisions.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://webkitgtk.org/releases'] +sources = ['webkitgtk-%(version)s.tar.xz'] +checksums = [ + 'c53326b1751f8c6da3db2f4bfa91c1801755893e287d0e1f6c07344589d4a6a7', # webkitgtk-2.37.1.tar.xz +] + +osdependencies = [ + # Would be better to use the system package due to security reasons + # But we need at least libgcrypt 1.7.0 and Ubuntu 16.04 and RH 7.5 + # are both using a too old version. + # Update: Libcrypt 1.9.3 from EasyBuild added (J.S) + # ('libgcrypt-dev', 'libgcrypt20-dev', 'libgcrypt-devel'), + # libsecret is not actually needed since USE_LIBSECRET option is disabled + # ('libsecret-1-dev', 'libsecret-devel'), +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('Python', '3.9.6'), + ('Perl', '5.34.0', '-minimal'), + ('GObject-Introspection', '1.68.0'), + ('pkg-config', '0.29.2'), + ('ccache', '4.6.1', '', True), +] +dependencies = [ + ('GLib', '2.69.1'), + ('gperf', '3.1'), + ('cairo', '1.16.0'), + ('GTK3', '3.24.31'), + ('LibSoup', '3.0.7'), + ('ATK', '2.36.0'), + ('libgcrypt', '1.9.3'), + ('libwebp', '1.2.0'), + ('libxslt', '1.1.34'), + ('libtasn1', '4.18.0'), + ('GStreamer', '1.18.5'), + ('OpenJPEG', '2.4.0'), + ('Ruby', '3.0.1'), + ('GSL', '2.7'), + ('glew', '2.2.0', '-egl'), + ('libwpe', '1.13.3'), + ('pugixml', '1.12.1'), + ('Wayland', '1.20.0'), + ('Waylandpp', '1.0.0'), + ('wpebackend-fdo', '1.13.1'), + ('enchant-2', '2.3.3'), + ('LittleCMS', '2.12'), + ('GST-plugins-base', '1.18.5'), +] + +# The build takes around 2.5 hours on 24 cores on AMD Rome! +# So be patient! + +# Instead of using a patch file, we are disabling problematic builds in the command line. +# At least this way, if something is not needed it can be turned off, without looking into +# a patch file. +configopts = "-DCMAKE_VERBOSE_MAKEFILE=ON -DPORT=GTK -DCMAKE_FIND_USE_PACKAGE_REGISTRY=FALSE " +configopts += "-DENABLE_GAMEPAD=OFF -DUSE_LIBSECRET=OFF -DUSE_LIBHYPHEN=OFF " +configopts += "-DUSE_WOFF2=OFF -DENABLE_JOURNALD_LOG=OFF -DENABLE_BUBBLEWRAP_SANDBOX=OFF " +configopts += "-DENABLE_INTROSPECTION=OFF -DUSE_LIBNOTIFY=OFF " + +sanity_check_paths = { + 'files': ['bin/WebKitWebDriver', 'lib/libwebkit2gtk-4.1.%s' % SHLIB_EXT, + 'lib/libjavascriptcoregtk-4.1.%s' % SHLIB_EXT], + 'dirs': ['include/webkitgtk-4.1/webkit2', 'libexec/webkit2gtk-4.1'], +} + +moduleclass = 'lib' From 96aabade8a3b104d292fafa6869feedeae386937 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 24 Aug 2022 17:12:52 +0200 Subject: [PATCH 066/793] adding easyconfigs: MATLAB-Engine-2021a-GCCcore-10.2.0.eb, MATLAB-Engine-2021a-GCCcore-11.2.0.eb --- .../MATLAB-Engine-2021a-GCCcore-10.2.0.eb | 32 +++++++++++++++++++ .../MATLAB-Engine-2021a-GCCcore-11.2.0.eb | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..14525297b2f --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'MATLAB-Engine' +version = '2021a' + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('MATLAB', version, '', True), + ('Python', '3.8.6'), +] + +use_pip = False +download_dep_fail = True + +# Since this setup.py does not provide a separate --build-base for the install +# step, both build and install must be performed in a single command. +prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " +buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" + +skipsteps = ['install'] + +# Test that connection with MATLAB can be established successfully +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +options = {'modulename': 'matlab.engine'} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..629c793528c --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'MATLAB-Engine' +version = '2021a' + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('MATLAB', version, '', True), + ('Python', '3.9.6'), +] + +use_pip = False +download_dep_fail = True + +# Since this setup.py does not provide a separate --build-base for the install +# step, both build and install must be performed in a single command. +prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " +buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" + +skipsteps = ['install'] + +# Test that connection with MATLAB can be established successfully +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +options = {'modulename': 'matlab.engine'} + +moduleclass = 'math' From 4038b236aafc832399534ee095d4119d5d8d6c00 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 24 Aug 2022 17:59:45 +0200 Subject: [PATCH 067/793] Add sanity pip check --- .../m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb | 2 ++ .../m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb index 14525297b2f..3418f6ddc56 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb @@ -27,6 +27,8 @@ skipsteps = ['install'] # Test that connection with MATLAB can be established successfully sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] +sanity_pip_check = True + options = {'modulename': 'matlab.engine'} moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb index 629c793528c..9380e93ff8a 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb @@ -27,6 +27,8 @@ skipsteps = ['install'] # Test that connection with MATLAB can be established successfully sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] +sanity_pip_check = True + options = {'modulename': 'matlab.engine'} moduleclass = 'math' From 3339fed38d65f0188b5a635b32c3e0e2e4be1448 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 29 Aug 2022 15:30:09 +0200 Subject: [PATCH 068/793] Add Cartopy and dependencies --- .../c/Cartopy/Cartopy-0.20.3-foss-2022a.eb | 50 +++++++++++++++++++ .../f/Fiona/Fiona-1.8.21-foss-2022a.eb | 48 ++++++++++++++++++ .../p/pyproj/pyproj-3.3.1-GCCcore-11.3.0.eb | 37 ++++++++++++++ .../s/Shapely/Shapely-1.8.2-foss-2022a.eb | 30 +++++++++++ 4 files changed, 165 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb create mode 100644 easybuild/easyconfigs/f/Fiona/Fiona-1.8.21-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/pyproj/pyproj-3.3.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/Shapely/Shapely-1.8.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb new file mode 100644 index 00000000000..f8c63257d0f --- /dev/null +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonBundle' + +name = 'Cartopy' +version = '0.20.3' + +homepage = 'https://scitools.org.uk/cartopy/docs/latest/' +description = """Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('Fiona', '1.8.21'), + ('GDAL', '3.5.0'), + ('GEOS', '3.10.3'), + ('matplotlib', '3.5.2'), + ('pyproj', '3.3.1'), + ('SciPy-bundle', '2022.05'), + ('Shapely', '1.8.2'), + ('lxml', '4.9.1'), + ('Pillow', '9.1.1'), + ('PROJ', '9.0.0'), + ('PyYAML', '6.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('OWSLib', '0.27.2', { + 'checksums': ['e102aa2444dfe0c8439ab1e1776cc0fa47cea28c09b8a28212c893c6017c179b'], + }), + ('pyepsg', '0.4.0', { + 'checksums': ['2d08fad1e7a8b47a90a4e43da485ba95705923425aefc4e2a3efa540dbd470d7'], + }), + ('pykdtree', '1.3.5', { + 'checksums': ['7342f75e731103e653fc1f6b9fdabc2410cf92b6e7b06160804a75786c9b5747'], + }), + ('pyshp', '2.3.1', { + 'modulename': 'shapefile', + 'checksums': ['4caec82fd8dd096feba8217858068bacb2a3b5950f43c048c6dc32a3489d5af1'], + }), + (name, version, { + 'checksums': ['0d60fa2e2fbd77c4d1f6b1f9d3b588966147f07c1b179d2d34570ac1e1b49006'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.21-foss-2022a.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.21-foss-2022a.eb new file mode 100644 index 00000000000..a1a8ffdd7e0 --- /dev/null +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.21-foss-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'Fiona' +version = '1.8.21' + +homepage = 'https://github.com/Toblerity/Fiona' +description = """Fiona is designed to be simple and dependable. It focuses on reading and writing data +in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, +mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using +multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS +packages such as pyproj, Rtree, and Shapely.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('GDAL', '3.5.0'), + ('Shapely', '1.8.2'), # optional for 'calc' extras +] + +use_pip = True + +exts_list = [ + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + (name, version, { + 'checksums': ['3a0edca2a7a070db405d71187214a43d2333a57b4097544a3fcc282066a58bfc'], + 'use_pip_extras': 'calc', + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["fio --help"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pyproj/pyproj-3.3.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pyproj/pyproj-3.3.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d70aee5e640 --- /dev/null +++ b/easybuild/easyconfigs/p/pyproj/pyproj-3.3.1-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'pyproj' +version = '3.3.1' + +homepage = 'https://pyproj4.github.io/pyproj' +description = "Python interface to PROJ4 library for cartographic transformations" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b3d8e14d91cc95fb3dbc03a9d0588ac58326803eefa5bbb0978d109de3304fbe'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('PROJ', '9.0.0'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = "export PROJ_DIR=$EBROOTPROJ && " + +sanity_check_paths = { + 'files': ['bin/pyproj'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['pyproj --help'] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.8.2-foss-2022a.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.8.2-foss-2022a.eb new file mode 100644 index 00000000000..1a79d23c752 --- /dev/null +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.8.2-foss-2022a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'Shapely' +version = '1.8.2' + +homepage = 'https://github.com/Toblerity/Shapely' +description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. +It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['572af9d5006fd5e3213e37ee548912b0341fb26724d6dc8a4e3950c10197ebb6'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # needed by shapely.vectorized + ('GEOS', '3.10.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = [ + "python -c 'import shapely'", + "python -c 'import shapely.vectorized'", +] + +moduleclass = 'math' From c23cfa5d4c3f02ba5aed74915a3a2d7a2de16037 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Aug 2022 16:26:44 +0200 Subject: [PATCH 069/793] adding easyconfigs: spaln-2.4.12-GCC-10.2.0.eb --- .../s/spaln/spaln-2.4.12-GCC-10.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb new file mode 100644 index 00000000000..364c2101be1 --- /dev/null +++ b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'spaln' +version = '2.4.12' + +homepage = 'https://github.com/ogotoh/spaln' +description = """Spaln (space-efficient spliced alignment) is a stand-alone program that maps + and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +# disable use of -march=native, which makes compilation fail due to missing header files like fwd2s1_simd.h; +# see also https://github.com/ogotoh/spaln/issues/56 +toolchainopts = {'optarch': False} + +source_urls = ['https://github.com/ogotoh/spaln/archive/'] +sources = ['ver%(version)s.tar.gz'] +checksums = ['0c5f842131409686dbaad01778960f53f1ebba8dd83d55b454ec4bf1b6bde2af'] + +dependencies = [('zlib', '1.2.11')] + +start_dir = 'src' + +# we need to make sure not to pass --prefix, otherwise the configure script gets stuck in an infinite loop... +prefix_opt = '--exec_prefix=' + +configopts = "--exec_prefix=%(installdir)s/bin --table_dir=%(installdir)s/table --alndbs_dir=%(installdir)s/seqdb " +configopts += "--use_zlib=1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['makdbs', 'makmdm', 'sortgrcd', 'spaln']], + 'dirs': ['seqdb', 'table'], +} + +sanity_check_commands = ["spaln -h 2>&1 | grep 'SPALN version %(version)s'"] + +moduleclass = 'bio' From b8afe74f657367ecbd1e98937b1209e16e3a076e Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 29 Aug 2022 18:58:01 +0200 Subject: [PATCH 070/793] Add sympy and gmpy2 --- .../g/gmpy2/gmpy2-2.1.2-GCC-11.3.0.eb | 25 ++++++++++++ .../s/sympy/sympy-1.10.1-foss-2022a.eb | 40 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.10.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..59aba6600bd --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-GCC-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.1.2' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['da75140bca128ece795895477e53b43773e3748aa90ba6170eae7ca2c74b82d1'] + +dependencies = [ + ('Python', '3.10.4'), + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('MPC', '1.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.10.1-foss-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.10.1-foss-2022a.eb new file mode 100644 index 00000000000..3799a72d02d --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.10.1-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.10.1' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['5939eeffdf9e152172601463626c022a2c27e75cf6278de8d401d50c9d58787b'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('gmpy2', '2.1.2'), +] + +download_dep_fail = True +use_pip = True + +# fix broken test, sympy doesn't actually use gmpy2's Decimal anywhere; +# see https://github.com/sympy/sympy/issues/23061#issuecomment-1052424896 +pretestopts = """sed -i "s@Decimal('0.6')@'0.6'@g" sympy/external/tests/test_pythonmpq.py && """ +runtest = 'python setup.py test' + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/isympy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], +} + +sanity_check_commands = ["isympy --help"] + +moduleclass = 'math' From 5611a5ea008664b69564eb1034cc56c72380c897 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 29 Aug 2022 20:02:55 +0200 Subject: [PATCH 071/793] Update easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Disable DAP remote tests Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb index e8aeb8b93a8..7e7c2186c13 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -38,8 +38,8 @@ dependencies = [ # make sure both static and shared libs are built configopts = [ - "-DBUILD_SHARED_LIBS=OFF", - "-DBUILD_SHARED_LIBS=ON", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", ] # some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests From ec1da3bd9fb2125d6323da3e7f2b895e7f0e94c6 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 30 Aug 2022 14:34:32 +0100 Subject: [PATCH 072/793] Updated to latest version, affiliation updated --- ...0-GCCcore-11.2.0.eb => hunspell-1.7.1-GCCcore-11.2.0.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/h/hunspell/{hunspell-1.7.0-GCCcore-11.2.0.eb => hunspell-1.7.1-GCCcore-11.2.0.eb} (86%) diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.2.0.eb similarity index 86% rename from easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.2.0.eb index b37fdbc7121..db6674f606b 100644 --- a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.2.0.eb @@ -1,10 +1,10 @@ -# Contribution from the Crick HPC team +# Contribution from Imperial College London/UK # uploaded by J. Sassmannshausen easyblock = 'ConfigureMake' name = 'hunspell' -version = '1.7.0' +version = '1.7.1' homepage = 'http://hunspell.github.io/' description = """Hunspell is a spell checker and morphological analyzer @@ -15,7 +15,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/hunspell/hunspell/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['bb27b86eb910a8285407cf3ca33b62643a02798cf2eef468c0a74f6c3ee6bc8a'] +checksums = ['6e3557624c608b3e6525b8bd277706db4f5a857c28fdb3cfa8d0d2b67776da8a'] builddependencies = [ ('Autotools', '20210726'), From 096e4416a32c225224fc56494189d908fffe47d4 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 30 Aug 2022 16:07:38 +0100 Subject: [PATCH 073/793] adding easyconfigs: x13as-1-1-b59-GCCcore-11.2.0.eb and patches: x13as-1-1-b59_makefile.patch --- .../x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb | 51 +++++++++++++++++++ .../x/x13as/x13as-1-1-b59_makefile.patch | 25 +++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..de01155ab14 --- /dev/null +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb @@ -0,0 +1,51 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MakeCp' + +name = 'x13as' +version = '1-1-b59' + +homepage = 'https://www.census.gov/data/software/x13as.About_X-13.html' + +description = """ +X-13ARIMA-SEATS is seasonal adjustment software produced, distributed, +and maintained by the Census Bureau. + +Features of X-13ARIMA-SEATS include: + - Extensive time series modeling and model selection capabilities for + linear regression models with ARIMA errors (regARIMA models); + - The capability to generate ARIMA model-based seasonal adjustment + using a version of the SEATS software originally developed by Victor + Gómez and Agustín Maravall at the Bank of Spain, as well as nonparametric + adjustments from the X-11 procedure; + - Diagnostics of the quality and stability of the adjustments + achieved under the options selected; + - The ability to efficiently process many series at once. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [ + 'https://www2.census.gov/software/x-13arima-seats/x13as/unix-linux/program-archives', +] +sources = ['%(name)s_asciisrc-v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_makefile.patch'] +checksums = [ + '256ee87f326ef6e0ac33a806812d614a5584c6b9e1f2a67ec06af52f2c3be85d', # x13as_asciisrc-v1-1-b59.tar.gz + '5403011b3781a025887f1c2d17a6ebd55e1eee5c2b65c60b90b1940b3f5c3d83', # x13as-v1-1_makefile.patch +] + +builddependencies = [ + ('binutils', '2.37'), +] + +build_cmd = 'make -f makefile.gf' + +files_to_copy = [(["x13as_ascii"], "bin")] + +sanity_check_paths = { + 'files': ['bin/x13as_ascii'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch new file mode 100644 index 00000000000..b1c29383c33 --- /dev/null +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch @@ -0,0 +1,25 @@ +Patch to build with newer versions of gfortran +see: https://salsa.debian.org/science-team/x13as/-/blob/master/debian/rules#L4 +Author: J. Sassmannshausen, Thomas Hayward-Schneider, Jasper Grimm +diff --git a/x13as_asciisrc-v1-1-b59.orig/makefile.gf b/x13as_asciisrc-v1-1-b59/makefile.gf +index e60896e..5dad49c 100644 +--- a/x13as_asciisrc-v1-1-b59.orig/makefile.gf ++++ b/x13as_asciisrc-v1-1-b59/makefile.gf +@@ -4,7 +4,7 @@ LINKER = gfortran + PROGRAM = x13as_ascii + DEST = . + EXTHDRS = +-FFLAGS = -O2 ++FFLAGS = -O2 -std=legacy + HDRS = + LDFLAGS = -s + LDMAP = +@@ -290,7 +290,7 @@ SRCS = aaamain.f abend.f acf.f acfar.f acfdgn.f \ + testodf.f + + $(PROGRAM): $(OBJS) $(LIBS) +- $(LINKER) -static -o $@ $(OBJS) $(LDMAP) $(LIBS) $(LDFLAGS) ++ $(LINKER) -o $@ $(OBJS) $(LDMAP) $(LIBS) $(LDFLAGS) + + clean:; @rm -f $(OBJS) + From 0552d2660bb20501220b432d9057e89ade74609f Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 30 Aug 2022 16:30:32 +0100 Subject: [PATCH 074/793] adding easyconfigs: gawk-5.1.1-GCC-11.2.0.eb --- .../g/gawk/gawk-5.1.1-GCC-11.2.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/gawk/gawk-5.1.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/g/gawk/gawk-5.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/g/gawk/gawk-5.1.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..26a2216bd7c --- /dev/null +++ b/easybuild/easyconfigs/g/gawk/gawk-5.1.1-GCC-11.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gawk' +version = '5.1.1' + +homepage = 'https://www.gnu.org/software/gawk' +description = """The awk utility interprets a special-purpose programming language that makes it possible to handle +simple data-reformatting jobs with just a few lines of code.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6168d8d1dc8f74bd17d9dc22fa9634c49070f232343b744901da15fb4f06bffd'] + +sanity_check_paths = { + 'files': ['bin/gawk'], + 'dirs': [], +} + +sanity_check_commands = ["gawk --help"] + +moduleclass = 'tools' From 704b43a24dfcd0d89b94935515922b6784a34e0d Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 30 Aug 2022 18:33:05 +0100 Subject: [PATCH 075/793] Name of executable changed to x13as as this seems to be the default --- .../x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb | 6 +++--- .../easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch | 10 +++++++--- 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb index de01155ab14..182ad2ee738 100644 --- a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb @@ -32,7 +32,7 @@ sources = ['%(name)s_asciisrc-v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s_makefile.patch'] checksums = [ '256ee87f326ef6e0ac33a806812d614a5584c6b9e1f2a67ec06af52f2c3be85d', # x13as_asciisrc-v1-1-b59.tar.gz - '5403011b3781a025887f1c2d17a6ebd55e1eee5c2b65c60b90b1940b3f5c3d83', # x13as-v1-1_makefile.patch + 'cbde094a2396c256e9ac996cd539806bb0274e569d578ad42c4879f0e02c5ef3', # x13as-v1-1_makefile.patch ] builddependencies = [ @@ -41,10 +41,10 @@ builddependencies = [ build_cmd = 'make -f makefile.gf' -files_to_copy = [(["x13as_ascii"], "bin")] +files_to_copy = [(["x13as"], "bin")] sanity_check_paths = { - 'files': ['bin/x13as_ascii'], + 'files': ['bin/x13as'], 'dirs': [], } diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch index b1c29383c33..96ded45a757 100644 --- a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch @@ -2,11 +2,15 @@ Patch to build with newer versions of gfortran see: https://salsa.debian.org/science-team/x13as/-/blob/master/debian/rules#L4 Author: J. Sassmannshausen, Thomas Hayward-Schneider, Jasper Grimm diff --git a/x13as_asciisrc-v1-1-b59.orig/makefile.gf b/x13as_asciisrc-v1-1-b59/makefile.gf -index e60896e..5dad49c 100644 +index e60896e..cb1b38e 100644 --- a/x13as_asciisrc-v1-1-b59.orig/makefile.gf +++ b/x13as_asciisrc-v1-1-b59/makefile.gf -@@ -4,7 +4,7 @@ LINKER = gfortran - PROGRAM = x13as_ascii +@@ -1,10 +1,10 @@ + # MKMF template makefile for protected mode executables. + FC = gfortran + LINKER = gfortran +-PROGRAM = x13as_ascii ++PROGRAM = x13as DEST = . EXTHDRS = -FFLAGS = -O2 From 1618d63e63da710fbb9a63fbc0d5bb68a836137a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 31 Aug 2022 07:54:34 +0200 Subject: [PATCH 076/793] adding easyconfigs: Amber-22.0-foss-2021b-AmberTools-22.3.eb --- .../Amber-22.0-foss-2021b-AmberTools-22.3.eb | 96 +++++++++++++++++++ 1 file changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb new file mode 100644 index 00000000000..07b04661999 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb @@ -0,0 +1,96 @@ +name = 'Amber' +local_amber_ver = 22 +local_ambertools_ver = 22 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (3, 0) # (AmberTools, Amber) +version = '%s.%s' % (local_amber_ver, patchlevels[1]) +versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing + molecular dynamics and structure prediction.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + '%%(name)s%s.tar.bz2' % local_amber_ver, + {'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, 'alt_location': 'AmberTools'}, +] +patches = [ + {'name': 'AmberTools-20_cmake-locate-netcdf.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-20_fix_xblas_missing_make_dependency.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_CMake-FlexiBLAS.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_DGESVD_workspace_query.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_incorrect_dvout_call.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_incorrect_mexit_calls.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_more_blas_argument_problems.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_multiple_definition.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_potential_use_before_init.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_rism_argument_mismatch.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-22_fix_test_missing_cuda_dir.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-22_fix_missing_error_check_on_test_run.patch', 'alt_location': 'AmberTools'}, + 'Amber-22_reduce_precision_of_kmmd_test.patch', + 'Amber-22_remove_undeclared_redundant_variable.patch', +] +checksums = [ + '3c887ccbad690fc76ff0b120a3448eae023c08e76582aac07900d4a9708ebd16', # Amber22.tar.bz2 + '1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121', # AmberTools22.tar.bz2 + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', + # AmberTools-20_fix_xblas_missing_make_dependency.patch + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', + '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch + # AmberTools-21_fix_DGESVD_workspace_query.patch + '560c73e9d8bd159c609098c63a0256cdee78f49e524d06ea94d16d3146f69bcd', + '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b', # AmberTools-21_fix_incorrect_dvout_call.patch + 'd1de8c596119dcedbb809515816f0c98762306c469e9caf2c0b878d9b0a1095f', # AmberTools-21_fix_incorrect_mexit_calls.patch + # AmberTools-21_fix_more_blas_argument_problems.patch + 'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c', + 'ce30eeaba9feea53aa115e4b0dcc5be943b8a55abe322480c807ca7ea963d83b', # AmberTools-21_fix_multiple_definition.patch + # AmberTools-21_fix_potential_use_before_init.patch + '377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139', + # AmberTools-21_fix_rism_argument_mismatch.patch + '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1', + # AmberTools-21_fix_xray_fftpack_arg_mismatch.patch + '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f', + 'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737', # AmberTools-22_fix_test_missing_cuda_dir.patch + # AmberTools-22_fix_missing_error_check_on_test_run.patch + 'a86eee60bd65c16a849469e303cb99dfc207cbadd2ae9e70b9ff580ced785475', + 'b5855866c63c2ee860a5e6ad6f618ac4dab7072f5caae95769d4b2457d616a8e', # Amber-22_reduce_precision_of_kmmd_test.patch + # Amber-22_remove_undeclared_redundant_variable.patch + 'b94900c2178dd6dbf2824b17074980a3e5e6e71b38c0b2b30e1f147e4e1ac8cb', +] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # mpi4py required for MMPBSA + ('Perl', '5.34.0'), + ('Boost', '1.77.0'), + ('libreadline', '8.1'), + ('matplotlib', '3.4.3'), + ('netCDF', '4.8.1'), + ('netCDF-Fortran', '4.5.3'), + ('PnetCDF', '1.12.3'), + ('Tkinter', '3.9.6'), + ('X11', '20210802'), +] + +# All tests are expected to pass or be skipped +runtest = True + +static = False + +moduleclass = 'chem' From eef360dc8d0f30d27748cef9452087f11dcbaf4a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 31 Aug 2022 11:01:37 +0200 Subject: [PATCH 077/793] update urls to use https --- .../a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb index 07b04661999..234d491d03b 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb @@ -1,12 +1,12 @@ name = 'Amber' local_amber_ver = 22 local_ambertools_ver = 22 -# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +# Patch levels from https://ambermd.org/AmberPatches.php and https://ambermd.org/ATPatches.php patchlevels = (3, 0) # (AmberTools, Amber) version = '%s.%s' % (local_amber_ver, patchlevels[1]) versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0]) -homepage = 'http://ambermd.org/amber.html' +homepage = 'https://ambermd.org/amber.html' description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.""" From 32089ec0fe4e5fb10e681b77f394e0b30aa5543a Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Thu, 1 Sep 2022 09:44:53 +0200 Subject: [PATCH 078/793] Tweak dependencies and settings for Beast and pocl --- easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb | 8 +------- easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb | 2 -- 2 files changed, 1 insertion(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb index 09bab325f65..10b75ac34ee 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb @@ -18,17 +18,11 @@ sources = ['BEAST.v%(version)s.Linux.tgz'] checksums = ['05dcc619c2e10163f2c1089ec66149f6e53ec5a0583cd2cb8ffdccbbdb1d8183'] dependencies = [ + ('Java', '11', '', True), # this is not mandatory but beagle-lib is recommended by developers - # beagle-lib will also load the required java dependency - # if you remove this you should add the java dependency ('beagle-lib', '3.1.2'), ] -builddependencies = [ - ('Autotools', '20210128'), - ('pkg-config', '0.29.2'), -] - sanity_check_paths = { 'files': ['bin/beast'], 'dirs': [] diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb index 4075c55b03b..6caccf9d359 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb @@ -29,8 +29,6 @@ dependencies = [ ('libxml2', '2.9.10'), ] -separate_build_dir = True - # disable attempt to find an ICD loader, always build libOpenCL.so configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " # make sure we use the easybuild Clang From 78dfc7768c743f5c727d48b4b5e2c6aa9894089b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 1 Sep 2022 13:40:44 +0200 Subject: [PATCH 079/793] Add missing patches. --- ...ber-22_reduce_precision_of_kmmd_test.patch | 29 +++++++++++++++++++ ...remove_undeclared_redundant_variable.patch | 26 +++++++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-22_reduce_precision_of_kmmd_test.patch create mode 100644 easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-22_reduce_precision_of_kmmd_test.patch b/easybuild/easyconfigs/a/Amber/Amber-22_reduce_precision_of_kmmd_test.patch new file mode 100644 index 00000000000..981f0df3425 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-22_reduce_precision_of_kmmd_test.patch @@ -0,0 +1,29 @@ +Reduce the number of digits checked for kmmd_pmemd/kmmd_pmemd:gb tests. +Partially ok:ed by Amber devs. They will investigate and come back with +more info. + +Åke Sandgren, 2022-08-25 +diff -ru amber22_src.orig/test/kmmd/kmmd_pmemd/Run.kmmd amber22_src/test/kmmd/kmmd_pmemd/Run.kmmd +--- amber22_src.orig/test/kmmd/kmmd_pmemd/Run.kmmd 2022-04-09 03:11:47.000000000 +0200 ++++ amber22_src/test/kmmd/kmmd_pmemd/Run.kmmd 2022-08-25 10:52:13.397649018 +0200 +@@ -64,7 +64,7 @@ + #cp $output $output.save + + ##diff the test and reference +-../../dacdif -t 2 $output.save $output ++../../dacdif -a 0.03 $output.save $output + + /bin/rm -f mdin mdinfo mdcrd mdfrc restrt logfile tidied*txt *.dat + exit(0) +diff -ru amber22_src.orig/test/kmmd/kmmd_pmemd_gb/Run.kmmd amber22_src/test/kmmd/kmmd_pmemd_gb/Run.kmmd +--- amber22_src.orig/test/kmmd/kmmd_pmemd_gb/Run.kmmd 2022-04-09 03:11:47.000000000 +0200 ++++ amber22_src/test/kmmd/kmmd_pmemd_gb/Run.kmmd 2022-08-25 10:52:20.981592091 +0200 +@@ -64,7 +64,7 @@ + #cp $output $output.save + + ##diff the test and reference +-../../dacdif -t 2 $output.save $output ++../../dacdif -a 0.01 $output.save $output + + /bin/rm -f mdin mdinfo mdcrd mdfrc restrt tidied*txt *.dat + exit(0) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch b/easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch new file mode 100644 index 00000000000..08658942fb5 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch @@ -0,0 +1,26 @@ +Remove the undeclared (and unused) variable i from the private clause +in an OpenMP pragma, which otherwise results in an error: + + 93 | !$omp parallel do private(ihkl,i,f,angle) + | 1 +Error: Symbol i at (1) has no IMPLICIT type + +Bob Dröge, University of Groningen, 2022-08-18 +--- amber22_src.orig/src/pmemd/src/xray/src/xray_non_bulk_impl_cpu.F90 2022-08-18 13:12:24.807724049 +0200 ++++ amber22_src/src/pmemd/src/xray/src/xray_non_bulk_impl_cpu.F90 2022-08-18 13:12:42.039809811 +0200 +@@ -90,7 +90,7 @@ + call check_precondition(size(frac, 2) == size(scatter_type_index)) + call check_precondition(size(hkl, 2) == size(atomic_scatter_factor, 1)) + +- !$omp parallel do private(ihkl,i,f,angle) ++ !$omp parallel do private(ihkl,f,angle) + do ihkl = 1, size(hkl, 2) + + ! Fhkl = SUM( fj * exp(2 * M_PI * i * (h * xj + k * yj + l * zj)) ), +@@ -127,4 +127,4 @@ + end subroutine calc_f_non_bulk + + +-end module xray_non_bulk_impl_cpu_module +\ No newline at end of file ++end module xray_non_bulk_impl_cpu_module From 4a4c348ee4609ddbace5c8234a77c2c71def0fbf Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 2 Sep 2022 16:09:15 +0200 Subject: [PATCH 080/793] Add ESMF for 2022a --- .../e/ESMF/ESMF-8.3.0-foss-2022a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb new file mode 100644 index 00000000000..e7645fa6164 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb @@ -0,0 +1,37 @@ +name = 'ESMF' +version = '8.3.0' + +homepage = 'https://www.earthsystemcog.org/projects/esmf/' +description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing + high-performance, multi-component Earth science modeling applications.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + '0ff43ede83d1ac6beabd3d5e2a646f7574174b28a48d1b9f2c318a054ba268fd', # v8.3.0.tar.gz + '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch +] + +# builddependencies = [('libarchive', '3.6.1')] + +dependencies = [ + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), + ('netCDF-C++4', '4.3.1'), + ('libarchive', '3.6.1'), +] + +# disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour) +prebuildopts = 'ESMF_F90COMPILEOPTS="${ESMF_F90COMPILEOPTS} -fallow-argument-mismatch"' + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' From 70d346f5af9739b963d7989ffb1d378acfa7d87d Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 2 Sep 2022 16:43:43 +0200 Subject: [PATCH 081/793] Update easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb index e7645fa6164..7857718c8b0 100644 --- a/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb @@ -16,8 +16,6 @@ checksums = [ '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch ] -# builddependencies = [('libarchive', '3.6.1')] - dependencies = [ ('netCDF', '4.9.0'), ('netCDF-Fortran', '4.6.0'), From 4d9d0cc0826cd10a1d39e97fe6d7b7f476660ba2 Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 2 Sep 2022 16:59:51 +0200 Subject: [PATCH 082/793] Update ESMF-8.3.0-foss-2022a.eb --- easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb index 7857718c8b0..215115944a2 100644 --- a/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb @@ -16,6 +16,8 @@ checksums = [ '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch ] +builddependencies = [('CMake', '3.23.1')] + dependencies = [ ('netCDF', '4.9.0'), ('netCDF-Fortran', '4.6.0'), From 9acd4fec75feb2b80c2c0a1dabc538f21a3953f5 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 5 Sep 2022 13:48:22 +0200 Subject: [PATCH 083/793] Update easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb index 7e7c2186c13..182023f4691 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -30,7 +30,7 @@ builddependencies = [ ] dependencies = [ - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ('cURL', '7.83.0'), ('Szip', '2.1.1'), ('zstd', '1.5.2'), From 87cd10d6e6a73b48b5cff42aa48960286ef94036 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 5 Sep 2022 14:41:53 +0100 Subject: [PATCH 084/793] Upgraded to 1.21.0, URL for source code upgraded --- ...-GCCcore-11.2.0.eb => Wayland-1.21.0-GCCcore-11.2.0.eb} | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/w/Wayland/{Wayland-1.20.0-GCCcore-11.2.0.eb => Wayland-1.21.0-GCCcore-11.2.0.eb} (82%) diff --git a/easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/Wayland/Wayland-1.21.0-GCCcore-11.2.0.eb similarity index 82% rename from easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/w/Wayland/Wayland-1.21.0-GCCcore-11.2.0.eb index 6036be672fc..15fd8e5d655 100644 --- a/easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/w/Wayland/Wayland-1.21.0-GCCcore-11.2.0.eb @@ -1,8 +1,10 @@ # Author: Jasper Grimm (UoY) +# URL of Wayland download changed to GitLab due to changes upstream +# Author: J. Sassmannshausen (Imperial College London/UK) easyblock = 'Bundle' name = 'Wayland' -version = '1.20.0' +version = '1.21.0' homepage = 'https://wayland.freedesktop.org/' description = """ @@ -39,7 +41,8 @@ default_component_specs = { components = [ ('wayland', version, { - 'checksums': ['b8a034154c7059772e0fdbd27dbfcda6c732df29cae56a82274f6ec5d7cd8725'], + 'source_urls': ['https://gitlab.freedesktop.org/wayland/wayland/-/releases/%(version)s/downloads'], + 'checksums': ['6dc64d7fc16837a693a51cfdb2e568db538bfdc9f457d4656285bb9594ef11ac'], 'configopts': "-Ddocumentation=false", }), ('wayland-protocols', '1.25', { From d501882880bfe28e8911e498c7ac37fa247b1a82 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 5 Sep 2022 14:45:45 +0100 Subject: [PATCH 085/793] Wayland upgraded to 1.21.0 --- .../easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb index 327d939ec40..ba0e31b6d0c 100644 --- a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb @@ -33,7 +33,7 @@ builddependencies = [ dependencies = [ ('pugixml', '1.12.1'), - ('Wayland', '1.20.0'), + ('Wayland', '1.21.0'), ] parallel = 2 From fd13d3e28f22cbf43076f8d567e53052cde5af54 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 5 Sep 2022 15:25:13 +0100 Subject: [PATCH 086/793] Sanity check commands added, pkg-config replaced with pkgconf --- .../d/dbus-glib/dbus-glib-0.112-GCCcore-11.2.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.2.0.eb index 2b0e0d55ab9..18c6be8c2e6 100644 --- a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.2.0.eb @@ -14,7 +14,7 @@ checksums = ['7d550dccdfcd286e33895501829ed971eeb65c614e73aadb4a08aeef719b143a'] builddependencies = [ ('binutils', '2.37'), - ('pkg-config', '0.29.2'), + ('pkgconf', '1.8.0'), ('Python', '3.9.6', '-bare'), # Python is needed for building against GLib. ] @@ -24,6 +24,11 @@ dependencies = [ ('expat', '2.4.1'), ] +sanity_check_commands = [ + 'dbus-binding-tool --version', + 'dbus-binding-tool --help', +] + sanity_check_paths = { 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], 'dirs': ['include', 'share'] From 42f0c6d217f05de81039f961f227c38d263628c8 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 6 Sep 2022 09:39:20 +0100 Subject: [PATCH 087/793] OS dependencies removed, libev added, toolchain changed to GCC, DCMAKE_BUILD_TYPE=release removed as not needed --- ...-0.7.0-GCCcore-11.2.0.eb => ngtcp2-0.7.0-GCC-11.2.0.eb} | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/n/ngtcp2/{ngtcp2-0.7.0-GCCcore-11.2.0.eb => ngtcp2-0.7.0-GCC-11.2.0.eb} (83%) diff --git a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb similarity index 83% rename from easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb index 81bcc53c6e2..6b12dec5b6a 100644 --- a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb @@ -11,7 +11,7 @@ description = """ ngtcp2 project is an effort to implement RFC9000 QUIC protocol.""" -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchain = {'name': 'GCC', 'version': '11.2.0'} toolchainopts = {'pic': True} github_account = 'ngtcp2' @@ -32,13 +32,12 @@ dependencies = [ ('OpenSSL', '1.1', '', True), ('GnuTLS', '3.7.3'), ('nghttp3', '0.6.0'), + ('libev', '4.33'), ] -osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] - separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=release -DENABLE_GNUTLS=True' +configopts = '-DENABLE_GNUTLS=True' runtest = 'check' From 5508f1bec3f8da72c0986c36d83cb0c93fe43435 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 6 Sep 2022 16:58:12 +0200 Subject: [PATCH 088/793] Fix miscomputation in OpenBLAS on POWER --- .../o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb | 5 +++- ...-0.3.12_add-missing-params-for-power.patch | 23 +++++++++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb | 13 +++++++---- ...S-0.3.7_add-missing-params-for-power.patch | 23 +++++++++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.8-GCC-9.2.0.eb | 11 +++++---- .../o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb | 11 +++++---- 6 files changed, 72 insertions(+), 14 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12_add-missing-params-for-power.patch create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_add-missing-params-for-power.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb index f3346d9db0a..a0d4dffee1d 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb @@ -15,7 +15,8 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), - 'OpenBLAS-0.3.7_fix-possible-memory-leak-after-fork.patch', + '%(name)s-0.3.7_fix-possible-memory-leak-after-fork.patch', + '%(name)s-%(version)s_add-missing-params-for-power.patch', '%(name)s-0.3.15_icelake-detection.patch', ] checksums = [ @@ -24,6 +25,8 @@ checksums = [ '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz # OpenBLAS-0.3.7_fix-possible-memory-leak-after-fork.patch '4b3ab7260975ea2cfd7460731c0201b2c1e374cd83ae90d55b8da3e670633ba0', + # OpenBLAS-0.3.12_add-missing-params-for-power.patch + '4454af07290d1fe33e414023a41bb8999d6ee31887e194daa72bd23d46a0072a', '9cc47898ba4ad090011dbb0b29e597a13eeebd49a52d4dc94e975743072724b7', # OpenBLAS-0.3.15_icelake-detection.patch ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12_add-missing-params-for-power.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12_add-missing-params-for-power.patch new file mode 100644 index 00000000000..3bad4d7bca3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12_add-missing-params-for-power.patch @@ -0,0 +1,23 @@ +This fixes inexact calculations on POWER, see https://github.com/xianyi/OpenBLAS/issues/2923 +From https://github.com/xianyi/OpenBLAS/pull/3062 + +Backported by Alexander Grund (TU Dresden) + +--- + param.h | 6 ++++++ + 1 file changed, 6 insertions(+) + +diff --git a/param.h b/param.h +index f3ddde6..35f579b 100644 +--- a/param.h ++++ b/param.h +@@ -2397,6 +2397,9 @@ USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + #define GEMM_DEFAULT_OFFSET_B 65536 + #define GEMM_DEFAULT_ALIGN 0x0ffffUL + ++#define SWITCH_RATIO 16 ++#define GEMM_PREFERED_SIZE 16 ++ + #define SGEMM_DEFAULT_UNROLL_M 16 + #define SGEMM_DEFAULT_UNROLL_N 8 + #define DGEMM_DEFAULT_UNROLL_M 16 diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb index 23c7cb7aea5..58fe90fcc5b 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb @@ -15,16 +15,19 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), - 'OpenBLAS-0.3.7_fix-build-on-arm-tsv110.patch', - 'OpenBLAS-0.3.7_fix-missing-sync-on-power.patch', - 'OpenBLAS-0.3.7_reinit-threads-after-fork.patch', - 'OpenBLAS-0.3.7_fix-possible-memory-leak-after-fork.patch', - 'OpenBLAS-0.3.8_fix-dscal-inline-asm.patch', + '%(name)s-%(version)s_add-missing-params-for-power.patch', + '%(name)s-%(version)s_fix-build-on-arm-tsv110.patch', + '%(name)s-%(version)s_fix-missing-sync-on-power.patch', + '%(name)s-%(version)s_reinit-threads-after-fork.patch', + '%(name)s-%(version)s_fix-possible-memory-leak-after-fork.patch', + '%(name)s-0.3.8_fix-dscal-inline-asm.patch', ] checksums = [ 'bde136122cef3dd6efe2de1c6f65c10955bbb0cc01a520c2342f5287c28f9379', # v0.3.7.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.7_add-missing-params-for-power.patch + '969ac4708092a6862cd9a03541c5c0588b191513d15492b022319daed5a1cd89', '5d5ec94002daefe10a839f621bf083c85fbda6c55c5e486f48375a2891f405c5', # OpenBLAS-0.3.7_fix-build-on-arm-tsv110.patch # OpenBLAS-0.3.7_fix-missing-sync-on-power.patch 'aefe4254caa14612eaf9a203b3f870f3b43724d28da7d7ab484810b4278f198f', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_add-missing-params-for-power.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_add-missing-params-for-power.patch new file mode 100644 index 00000000000..cc556272dd6 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_add-missing-params-for-power.patch @@ -0,0 +1,23 @@ +This fixes inexact calculations on POWER, see https://github.com/xianyi/OpenBLAS/issues/2923 +From https://github.com/xianyi/OpenBLAS/pull/3062 + +Backported by Alexander Grund (TU Dresden) + +--- + param.h | 6 ++++++ + 1 file changed, 6 insertions(+) + +diff --git a/param.h b/param.h +index 6c5e0f107b..6a790ab615 100644 +--- a/param.h ++++ b/param.h +@@ -2239,6 +2239,9 @@ USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + #define GEMM_DEFAULT_OFFSET_B 65536 + #define GEMM_DEFAULT_ALIGN 0x0ffffUL + ++#define SWITCH_RATIO 16 ++#define GEMM_PREFERED_SIZE 16 ++ + #define SGEMM_DEFAULT_UNROLL_M 16 + #define SGEMM_DEFAULT_UNROLL_N 8 + #define DGEMM_DEFAULT_UNROLL_M 16 diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.8-GCC-9.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.8-GCC-9.2.0.eb index 5d292f2abb7..4d8542cb37e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.8-GCC-9.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.8-GCC-9.2.0.eb @@ -15,15 +15,18 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), - 'OpenBLAS-0.3.7_fix-missing-sync-on-power.patch', - 'OpenBLAS-0.3.7_reinit-threads-after-fork.patch', - 'OpenBLAS-0.3.7_fix-possible-memory-leak-after-fork.patch', - 'OpenBLAS-0.3.8_fix-dscal-inline-asm.patch', + '%(name)s-0.3.7_add-missing-params-for-power.patch', + '%(name)s-0.3.7_fix-missing-sync-on-power.patch', + '%(name)s-0.3.7_reinit-threads-after-fork.patch', + '%(name)s-0.3.7_fix-possible-memory-leak-after-fork.patch', + '%(name)s-%(version)s_fix-dscal-inline-asm.patch', ] checksums = [ '8f86ade36f0dbed9ac90eb62575137388359d97d8f93093b38abe166ad7ef3a8', # v0.3.8.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.7_add-missing-params-for-power.patch + '969ac4708092a6862cd9a03541c5c0588b191513d15492b022319daed5a1cd89', # OpenBLAS-0.3.7_fix-missing-sync-on-power.patch 'aefe4254caa14612eaf9a203b3f870f3b43724d28da7d7ab484810b4278f198f', # OpenBLAS-0.3.7_reinit-threads-after-fork.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb index 1658647c8e2..c390c260b68 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb @@ -15,15 +15,18 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), - 'OpenBLAS-0.3.7_fix-missing-sync-on-power.patch', - 'OpenBLAS-0.3.7_reinit-threads-after-fork.patch', - 'OpenBLAS-0.3.7_fix-possible-memory-leak-after-fork.patch', - 'OpenBLAS-0.3.9_fix-lapack_h.patch', + '%(name)s-0.3.7_add-missing-params-for-power.patch', + '%(name)s-0.3.7_fix-missing-sync-on-power.patch', + '%(name)s-0.3.7_reinit-threads-after-fork.patch', + '%(name)s-0.3.7_fix-possible-memory-leak-after-fork.patch', + '%(name)s-%(version)s_fix-lapack_h.patch', ] checksums = [ '17d4677264dfbc4433e97076220adc79b050e4f8a083ea3f853a53af253bc380', # v0.3.9.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.7_add-missing-params-for-power.patch + '969ac4708092a6862cd9a03541c5c0588b191513d15492b022319daed5a1cd89', # OpenBLAS-0.3.7_fix-missing-sync-on-power.patch 'aefe4254caa14612eaf9a203b3f870f3b43724d28da7d7ab484810b4278f198f', # OpenBLAS-0.3.7_reinit-threads-after-fork.patch From 2e91283ebe1b9dbc758cd5383e6821470ca3528d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Sep 2022 10:02:17 +0200 Subject: [PATCH 089/793] {lang}[GCCcore/12.2.0] Perl v5.36.0, libreadline v8.1.2, ncurses v6.3, ... --- .../d/DB/DB-18.1.40-GCCcore-12.2.0.eb | 33 + .../e/expat/expat-2.4.8-GCCcore-12.2.0.eb | 30 + .../g/groff/groff-1.22.4-GCCcore-12.2.0.eb | 27 + .../libreadline-8.1.2-GCCcore-12.2.0.eb | 41 + .../n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb | 47 + .../p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 1939 +++++++++++++++++ 6 files changed, 2117 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7bc947e2ae0 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +name = 'DB' +version = '18.1.40' + +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' + +description = """Berkeley DB enables the development of custom data management + solutions, without the overhead traditionally associated with such custom + projects.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +# use http to allow auto-downloading... +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_doc_install.patch'] +checksums = [ + '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz + '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch +] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('OpenSSL', '1.1', '', True)] + +sanity_check_paths = { + 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', + 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', + 'tuner', 'upgrade', 'verify']] + + ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..df978cec524 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' +name = 'expat' +version = '2.4.8' + +homepage = 'https://libexpat.github.io' + +description = """Expat is an XML parser library written in C. It is a stream-oriented parser +in which an application registers handlers for things the parser might find +in the XML document (like start tags).""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')] +sources = [SOURCE_TAR_BZ2] +checksums = ['a247a7f6bbb21cf2ca81ea4cbb916bfb9717ca523631675f99b3d4a5678dcd16'] + +builddependencies = [('binutils', '2.39')] + +# Since expat 2.2.6, docbook2X is needed to produce manpage of xmlwf. +# Docbook2X needs XML-Parser and XML-Parser needs expat. +# -> circular dependency. "--without-docbook" breaks this circle. +configopts = ['--without-docbook'] + +sanity_check_paths = { + 'files': ['include/expat.h', 'lib/libexpat.a', 'lib/libexpat.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e2b37f3dcd4 --- /dev/null +++ b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'groff' +version = '1.22.4' + +homepage = 'https://www.gnu.org/software/groff' +description = """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands + and produces formatted output.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://ftp.gnu.org/gnu/groff'] +sources = [SOURCE_TAR_GZ] +checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] + +builddependencies = [ + ('binutils', '2.39'), +] + +configopts = '--with-doc=no' + +sanity_check_paths = { + 'files': ['bin/groff', 'bin/nroff', 'bin/troff'], + 'dirs': ['lib/groff', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b164af87b06 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.1.2' + +homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['7589a2381a8419e68654a47623ce7dfcb756815c8fee726b98f90bf668af7bc6'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('ncurses', '6.3'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7fed097a62f --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.3' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['97fc51ac2b085d4cde31ef4d2c3122c21abc217e9090a43a30fc5ec21684e059'] + +builddependencies = [('binutils', '2.39')] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +configopts = [ + # build ncurses: serial build in default paths with shared libraries + local_common_configopts, + # build ncursesw: serial with UTF-8 + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..5e960b5fcac --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -0,0 +1,1939 @@ +name = 'Perl' +version = '5.36.0' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = ['perl-%(version)s.tar.gz'] +checksums = ['e26085af8ac396f62add8a533c3a0ea8c8497d836f0689347ac5abd7b7a4e00a'] + +builddependencies = [ + ('binutils', '2.39'), + ('groff', '1.22.4'), +] + +dependencies = [ + ('zlib', '1.2.12'), # for Net::SSLeay + ('expat', '2.4.8'), # for XML::Parser + ('ncurses', '6.3'), # for Term::ReadLine::Gnu + ('libreadline', '8.1.2'), # for Term::ReadLine::Gnu + ('DB', '18.1.40'), # for DB_File + ('OpenSSL', '1.1', '', True), # required for Net::SSLeay +] + +# !! order of extensions is important !! +# extensions updated on Apr 28th 2022 +exts_list = [ + ('Config::General', '2.65', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': ['4d6d5754be3a9f30906836f0cc10e554c8832e14e7a1341efb15b05d706fc58f'], + }), + ('File::Listing', '6.15', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['46c4fb9f9eb9635805e26b7ea55b54455e47302758a10ed2a0b92f392713770c'], + }), + ('ExtUtils::InstallPaths', '0.012', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['84735e3037bab1fdffa3c2508567ad412a785c91599db3c12593a50a1dd434ed'], + }), + ('ExtUtils::Helpers', '0.026', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['de901b6790a4557cf4ec908149e035783b125bf115eb9640feb1bc1c24c33416'], + }), + ('Test::Harness', '3.44', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7eb591ea6b499ece6745ff3e80e60cee669f0037f9ccbc4e4511425f593e5297'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7d580ff6ace0cbe555bf36b86dc8ea232581530cbeaaea09bccb57b55797f11c'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb'], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287'], + }), + ('Regexp::Common', '2017060201', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + 'checksums': ['ee07853aee06f310e040b6bf1a0199a18d81896d3219b9b35c9630d0eb69089b'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + 'checksums': ['b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df'], + }), + ('Test::Fatal', '0.016', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7283d430f2ba2030b8cd979ae3039d3f1b2ec3dde1a11ca6ae09f992a66f788f'], + }), + ('Test::Warnings', '0.031', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['1e542909fef305e45563e9878ea1c3b0c7cef1b28bb7ae07eba2e1efabec477b'], + }), + ('File::ShareDir', '1.118', { + 'source_tmpl': 'File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['3bb2a20ba35df958dc0a4f2306fc05d903d8b8c4de3c8beefce17739d281c958'], + }), + ('File::ShareDir::Install', '0.14', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['8f9533b198f2d4a9a5288cbc7d224f7679ad05a7a8573745599789428bc5aea0'], + }), + ('IPC::System::Simple', '1.30', { + 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', + 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['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], + 'checksums': ['c8b362b860172a4076acee00438f52b86464f2c500702cfcf7527811ff9a683e'], + }), + ('XSLoader', '0.24', { + 'source_tmpl': 'XSLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAPER'], + 'checksums': ['e819a35a6b8e55cb61b290159861f0dc00fe9d8c4f54578eb24f612d45c8d85f'], + }), + ('AutoLoader', '5.74', { + 'source_tmpl': 'AutoLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['2fac75b05309f71a6871804cd25e1a3ba0a28f43f294fb54528077558da3aff4'], + }), + ('URI::Escape', '5.12', { + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['66abe0eaddd76b74801ecd28ec1411605887550fc0a45ef6aa744fdad768d9b3'], + }), + ('Set::IntervalTree', '0.12', { + 'source_tmpl': 'Set-IntervalTree-%(version)s.tar.gz', + 'source_urls': 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['https://cpan.metacpan.org/authors/id/M/MR/MRDVT'], + 'checksums': ['d58667f64381a105f375226f592d0af71068e640a5a9f4d5ecf27c90feb32676'], + }), + ('Config::Simple', '4.58', { + 'source_tmpl': 'Config-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHERZODR'], + 'checksums': ['dd9995706f0f9384a15ccffe116c3b6e22f42ba2e58d8f24ed03c4a0e386edb4'], + }), + ('Business::ISBN', '3.007', { + 'source_tmpl': 'Business-ISBN-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['50cc4686dd21c9537b49a231d71711e814ebd2f19aa4ca331baf92ff2de5ce19'], + }), + ('Business::ISBN::Data', '20210112.006', { + 'source_tmpl': 'Business-ISBN-Data-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['98c2cfb266b5fdd016989abaa471d9dd4c1d593c508a6f01f66d184d5fee8bae'], + }), + ('common::sense', '3.75', { + 'source_tmpl': 'common-sense-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], + }), + ('IO::Compress::Bzip2', '2.201', { + 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['f6c55c4e39cfaa3219965dd3b36c9de1edee9a82a10a9cadeb3b74a9ceeeaaad'], + }), + ('JSON::XS', '4.03', { + 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['515536f45f2fa1a7e88c8824533758d0121d267ab9cb453a1b5887c8a56b9068'], + }), + ('List::MoreUtils::XS', '0.430', { + 'source_tmpl': 'List-MoreUtils-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['e8ce46d57c179eecd8758293e9400ff300aaf20fefe0a9d15b9fe2302b9cb242'], + }), + ('Authen::NTLM', '1.09', { + 'source_tmpl': 'NTLM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NB/NBEBOUT'], + 'checksums': ['c823e30cda76bc15636e584302c960e2b5eeef9517c2448f7454498893151f85'], + }), + ('Types::Serialiser', '1.01', { + 'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['f8c7173b0914d0e3d957282077b366f0c8c70256715eaef3298ff32b92388a80'], + }), + ('XML::SAX::Expat', '0.51', { + 'source_tmpl': 'XML-SAX-Expat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BJ/BJOERN'], + 'checksums': ['4c016213d0ce7db2c494e30086b59917b302db8c292dcd21f39deebd9780c83f'], + }), + ('Inline', '0.86', { + 'source_tmpl': 'Inline-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], + }), + ('Sys::Info::Base', '0.7807', { + 'source_tmpl': 'Sys-Info-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['132362b0046e8dc4f12e1560903623a88a8871d09bf1c29d93d48d3f4a582acb'], + }), + ('Sys::Info', '0.7811', { + 'source_tmpl': 'Sys-Info-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['566482bff3427c198d7955468ed945a8e736c4a2925151fdef96801ef8a401e1'], + }), + ('HTML::Template', '2.97', { + 'source_tmpl': 'HTML-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAMTREGAR/'], + 'checksums': ['6547af61f3aa85793f8616190938d677d7995fb3b720c16258040bc935e2129f'], + }), + ('MIME::Charset', '1.013.1', { + 'source_tmpl': 'MIME-Charset-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI/'], + 'checksums': ['1bb7a6e0c0d251f23d6e60bf84c9adefc5b74eec58475bfee4d39107e60870f0'], + }), + ('Unicode::LineBreak', '2019.001', { + 'source_tmpl': 'Unicode-LineBreak-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI/'], + 'checksums': ['486762e4cacddcc77b13989f979a029f84630b8175e7fef17989e157d4b6318a'], + }), + ('String::Print', '0.94', { + 'source_tmpl': 'String-Print-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['9b3cd677adb7a40cb183bd6c60db80d96adcabd5aae27e324e3ee37e3275229b'], + }), + ('Log::Report', '1.33', { + 'source_tmpl': 'Log-Report-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['49624da338fd7d57288fa22a47241476fb5ce2f6008181f786c7830fe5af01ff'], + }), + ('Log::Report::Optional', '1.07', { + 'source_tmpl': 'Log-Report-Optional-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['b2658b53176df5afa5d02789368715c86b98c8d04ecd930252bcd7f832cc6224'], + }), + ('Sys::Info::Driver::Unknown', '0.79', { + 'source_tmpl': 'Sys-Info-Driver-Unknown-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'], + }), + ('Sys::Info::Driver::Linux', '0.7905', { + 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], + }), + ('Unix::Processors', '2.046', { + 'source_tmpl': 'Unix-Processors-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER/'], + 'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'], + }), + ('local::lib', '2.000029', { + 'source_tmpl': 'local-lib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], + 'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'], + }), + ('Module::Path', '0.19', { + 'source_tmpl': 'Module-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'], + 'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'], + }), +] + +moduleclass = 'lang' From fec5d05b3b12cd2be260119458ed5fd10269ec52 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 8 Sep 2022 15:27:17 +0100 Subject: [PATCH 090/793] adding easyconfigs: x13as-1-1-b59-GCCcore-10.2.0.eb --- .../x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..b3b916d6405 --- /dev/null +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb @@ -0,0 +1,51 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MakeCp' + +name = 'x13as' +version = '1-1-b59' + +homepage = 'https://www.census.gov/data/software/x13as.About_X-13.html' + +description = """ +X-13ARIMA-SEATS is seasonal adjustment software produced, distributed, +and maintained by the Census Bureau. + +Features of X-13ARIMA-SEATS include: + - Extensive time series modeling and model selection capabilities for + linear regression models with ARIMA errors (regARIMA models); + - The capability to generate ARIMA model-based seasonal adjustment + using a version of the SEATS software originally developed by Victor + Gómez and Agustín Maravall at the Bank of Spain, as well as nonparametric + adjustments from the X-11 procedure; + - Diagnostics of the quality and stability of the adjustments + achieved under the options selected; + - The ability to efficiently process many series at once. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'https://www2.census.gov/software/x-13arima-seats/x13as/unix-linux/program-archives', +] +sources = ['%(name)s_asciisrc-v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_makefile.patch'] +checksums = [ + '256ee87f326ef6e0ac33a806812d614a5584c6b9e1f2a67ec06af52f2c3be85d', # x13as_asciisrc-v1-1-b59.tar.gz + 'cbde094a2396c256e9ac996cd539806bb0274e569d578ad42c4879f0e02c5ef3', # x13as-v1-1_makefile.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + +build_cmd = 'make -f makefile.gf' + +files_to_copy = [(["x13as"], "bin")] + +sanity_check_paths = { + 'files': ['bin/x13as'], + 'dirs': [], +} + +moduleclass = 'tools' From 84e4dfebfed5596f4d75ed040285e958155f81d0 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 8 Sep 2022 15:30:47 +0100 Subject: [PATCH 091/793] Patchfile added --- .../x/x13as/x13as-1-1-b59_makefile.patch | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch new file mode 100644 index 00000000000..96ded45a757 --- /dev/null +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch @@ -0,0 +1,29 @@ +Patch to build with newer versions of gfortran +see: https://salsa.debian.org/science-team/x13as/-/blob/master/debian/rules#L4 +Author: J. Sassmannshausen, Thomas Hayward-Schneider, Jasper Grimm +diff --git a/x13as_asciisrc-v1-1-b59.orig/makefile.gf b/x13as_asciisrc-v1-1-b59/makefile.gf +index e60896e..cb1b38e 100644 +--- a/x13as_asciisrc-v1-1-b59.orig/makefile.gf ++++ b/x13as_asciisrc-v1-1-b59/makefile.gf +@@ -1,10 +1,10 @@ + # MKMF template makefile for protected mode executables. + FC = gfortran + LINKER = gfortran +-PROGRAM = x13as_ascii ++PROGRAM = x13as + DEST = . + EXTHDRS = +-FFLAGS = -O2 ++FFLAGS = -O2 -std=legacy + HDRS = + LDFLAGS = -s + LDMAP = +@@ -290,7 +290,7 @@ SRCS = aaamain.f abend.f acf.f acfar.f acfdgn.f \ + testodf.f + + $(PROGRAM): $(OBJS) $(LIBS) +- $(LINKER) -static -o $@ $(OBJS) $(LDMAP) $(LIBS) $(LDFLAGS) ++ $(LINKER) -o $@ $(OBJS) $(LDMAP) $(LIBS) $(LDFLAGS) + + clean:; @rm -f $(OBJS) + From 4a1f2679da64809757a836e0bae27cc1a33efedc Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 12 Sep 2022 09:58:58 +0100 Subject: [PATCH 092/793] Name of module class changed to math --- easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb index b3b916d6405..0687aee7c0e 100644 --- a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb @@ -48,4 +48,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'tools' +moduleclass = 'math' From e46ec84730ad2d59b75aa2106e161db4e15bd443 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 12 Sep 2022 10:03:02 +0100 Subject: [PATCH 093/793] Name of module class changed to math --- easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb index 182ad2ee738..4359434e6cf 100644 --- a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb @@ -48,4 +48,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'tools' +moduleclass = 'math' From c939ac06512b432390c45eb98ee35ba32ebfba04 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 12 Sep 2022 16:10:51 +0200 Subject: [PATCH 094/793] configure recent pocl versions to -DLLC_HOST_CPU=native to avoid CPU auto-detection --- easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb | 4 +++- easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb | 4 +++- easybuild/easyconfigs/p/pocl/pocl-1.5-GCC-9.3.0.eb | 4 +++- easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb | 4 +++- easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb | 4 +++- easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb | 4 +++- easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb | 4 +++- 7 files changed, 21 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb index c8b6eda3b49..032f249a058 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb @@ -34,7 +34,9 @@ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " # make sure we use the easybuild Clang -configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config" +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb b/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb index 42495666e3e..2939fcf0e31 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb @@ -34,7 +34,9 @@ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so, enable CUDA configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 -DENABLE_CUDA=1 " # make sure we use the easybuild Clang -configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config" +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.5-GCC-9.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.5-GCC-9.3.0.eb index 9868608073f..3a67d21dcc9 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.5-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.5-GCC-9.3.0.eb @@ -34,7 +34,9 @@ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " # make sure we use the easybuild Clang -configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config" +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb index 7f2991f31f8..949bd6168a8 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb @@ -30,7 +30,9 @@ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " # make sure we use the easybuild Clang -configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON" +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb b/easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb index d5d54b8902c..b6ff23250e3 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb @@ -30,7 +30,9 @@ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so, enable CUDA configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 -DENABLE_CUDA=1 " # make sure we use the easybuild Clang -configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON" +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb b/easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb index 4dc3a0dc23e..257dcb0f4d9 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb @@ -30,7 +30,9 @@ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " # make sure we use the easybuild Clang -configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON" +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb index 8dff6865a13..0c7f9416308 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb @@ -34,7 +34,9 @@ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " # make sure we use the easybuild Clang -configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON" +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], From 7c6aac356fa03c85fb293950850e4659d4739e3d Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 12 Sep 2022 21:10:48 +0200 Subject: [PATCH 095/793] adding easyconfigs: IPython-8.5.0-GCCcore-11.3.0.eb, libsodium-1.0.18-GCCcore-11.3.0.eb, OpenPGM-5.2.122-GCCcore-11.3.0.eb, ZeroMQ-4.3.4-GCCcore-11.3.0.eb --- .../i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb | 180 ++++++++++++++++++ .../libsodium-1.0.18-GCCcore-11.3.0.eb | 33 ++++ .../OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb | 45 +++++ .../z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb | 40 ++++ 4 files changed, 298 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4697bcfaf93 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,180 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '8.5.0' + +homepage = 'https://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('ZeroMQ', '4.3.4'), + ('lxml', '4.9.1'), + ('BeautifulSoup', '4.10.0'), +] + +use_pip = True + +exts_list = [ + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'checksums': ['097bdf5cd87576fd066179c9f7f208004f7a6864ee1b20f37d346c0bcb099f84'], + }), + ('pickleshare', '0.7.5', { + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('prompt_toolkit', '3.0.31', { + 'checksums': ['9ada952c9d1787f52ff6d5f3484d0b4df8952787c087edf6a1f7c2cb1ea88148'], + }), + ('traitlets', '5.2.0', { + 'checksums': ['60474f39bf1d39a11e0233090b99af3acee93bbc2281777e61dd8c87da8a0014'], + }), + ('parso', '0.8.3', { + 'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0'], + }), + ('jedi', '0.18.1', { + 'checksums': ['74137626a64a99c8eb6ae5832d99b3bdd7d29a3850fe2aa80a4126b2a7d949ab'], + }), + ('testpath', '0.6.0', { + 'checksums': ['2f1b97e6442c02681ebe01bd84f531028a7caea1af3825000f52345c30285e0f'], + }), + ('Send2Trash', '1.8.0', { + 'checksums': ['d2c24762fd3759860a0aff155e45871447ea58d2be6bdd39b5c8f966a0c99c2d'], + }), + ('bleach', '5.0.1', { + 'checksums': ['0d03255c47eb9bd2f26aa9bb7f2107732e7e8fe195ca2f64709fcf3b0a4a085c'], + }), + ('pandocfilters', '1.5.0', { + 'checksums': ['0b679503337d233b4339a817bfc8c50064e2eff681314376a47cb582305a7a38'], + }), + ('pyzmq', '23.2.1', { + 'modulename': 'zmq', + 'checksums': ['2b381aa867ece7d0a82f30a0c7f3d4387b7cf2e0697e33efaa5bed6c5784abcd'], + }), + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), + ('jupyter_core', '4.10.0', { + 'checksums': ['a6de44b16b7b31d7271130c71a6792c4040f077011961138afed5e5e73181aec'], + }), + ('fastjsonschema', '2.16.1', { + 'checksums': ['d6fa3ffbe719768d70e298b9fb847484e2bdfdb7241ed052b8d57a9294a8c334'], + }), + ('nbformat', '5.4.0', { + 'checksums': ['44ba5ca6acb80c5d5a500f1e5b83ede8cbe364d5a495c4c8cf60aaf1ba656501'], + }), + ('mistune', '0.8.1', { + 'checksums': ['4c0f66924ce28f03b95b210ea57e57bd0b59f479edd91c2fa4fe59331eae4a82'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('async_generator', '1.10', { + 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], + }), + ('nest_asyncio', '1.5.5', { + 'checksums': ['e442291cd942698be619823a17a86a5759eabe1f8613084790de189fe9e16d65'], + }), + ('nbclient', '0.6.3', { + 'checksums': ['b80726fc1fb89a0e8f8be1e77e28d0026b1e8ed90bc143c8a0c7622e4f8cdd9e'], + }), + ('tinycss2', '1.1.1', { + 'checksums': ['b2e44dd8883c360c35dd0d1b5aad0b610e5156c2cb3b33434634e539ead9d8bf'], + }), + ('nbconvert', '6.5.3', { + 'checksums': ['10ed693c4cfd3c63583c87ca5c3a2f6ed874145103595f3824efcc8dfcb7522c'], + }), + ('tornado', '6.2', { + 'checksums': ['9b630419bde84ec666bfd7ea0a4cb2a8a651c2d5cccdbdd1972a0c859dfc3c13'], + }), + ('terminado', '0.13.0', { + 'checksums': ['713531ccb5db7d4f544651f14050da79809030f00d1afa21462088cf32fb143a'], + }), + ('jupyter_client', '7.3.1', { + 'checksums': ['05d4ff6a0ade25138c6bb0fbeac7ddc26b5fe835e7dd816b64b4a45b931bdc0b'], + }), + ('backcall', '0.2.0', { + 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'], + }), + ('executing', '1.0.0', { + 'checksums': ['98daefa9d1916a4f0d944880d5aeaf079e05585689bebd9ff9b32e31dd5e1017'], + }), + ('asttokens', '2.0.8', { + 'checksums': ['c61e16246ecfb2cde2958406b4c8ebc043c9e6d73aaa83c941673b35e5d3a76b'], + }), + ('pure_eval', '0.2.2', { + 'checksums': ['2b45320af6dfaa1750f543d714b6d1c520a1688dec6fd24d339063ce0aaa9ac3'], + }), + ('stack_data', '0.5.0', { + 'checksums': ['715c8855fbf5c43587b141e46cc9d9339cc0d1f8d6e0f98ed0d01c6cb974e29f'], + }), + ('ipykernel', '6.13.0', { + 'checksums': ['0e28273e290858393e86e152b104e5506a79c13d25b951ac6eca220051b4be60'], + }), + ('prometheus_client', '0.11.0', { + 'checksums': ['3a8baade6cb80bcfe43297e33e7623f3118d660d41387593758e2fb1ea173a86'], + }), + ('ipywidgets', '7.6.3', { + 'checksums': ['9f1a43e620530f9e570e4a493677d25f08310118d315b00e25a18f12913c41f0'], + }), + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('jupyter_packaging', '0.12.0', { + 'checksums': ['b27455d60adc93a7baa2e0b8f386be81b932bb4e3c0116046df9ed230cd3faac'], + }), + ('jupyterlab_pygments', '0.1.2', { + 'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'], + }), + ('jupyterlab_widgets', '3.0.3', { + 'checksums': ['c767181399b4ca8b647befe2d913b1260f51bf9d8ef9b7a14632d4c1a7b536bd'], + }), + ('argon2-cffi', '20.1.0', { + 'modulename': 'argon2', + 'checksums': ['d8029b2d3e4b4cea770e9e5a0104dd8fa185c1724a0f01528ae4826a6d25f97d'], + }), + ('notebook', '6.4.0', { + 'checksums': ['9c4625e2a2aa49d6eae4ce20cbc3d8976db19267e32d2a304880e0c10bf8aef9'], + }), + ('widgetsnbextension', '3.5.1', { + 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], + }), + ('matplotlib-inline', '0.1.2', { + 'checksums': ['f41d5ff73c9f5385775d5c0bc13b424535c8402fe70ea8210f93e11f3683993e'], + }), + ('debugpy', '1.4.1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['84ff51b8b5c847d5421324ca419db1eec813a4dd2bbf19dbbbe132e2ab2b2fc6'], + }), +] + +modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/IPython', + 'share/jupyter' + ], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e62a803500d --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.18' + +homepage = 'https://doc.libsodium.org/' + +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['6f504490b342a4f8a4c4a02fc9b866cbef8622d5df4e5452b46be121e46636c1'] + +builddependencies = [ + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0563e14c45a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'https://code.google.com/p/openpgm/' + +description = """ + OpenPGM is an open source implementation of the Pragmatic General Multicast + (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable + and scalable multicast protocol that enables receivers to detect loss, request + retransmission of lost data, or notify an application of unrecoverable loss. + PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception + responsibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] +sources = ['libpgm-%(version)s.tar.gz'] +patches = [ + 'OpenPGM-5.2.122-pkgconfig_includes.patch', + 'OpenPGM-5.2.122-python3-compliant.patch' +] +checksums = [ + '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-5.2.122.tar.gz + '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # OpenPGM-5.2.122-pkgconfig_includes.patch + 'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618', # OpenPGM-5.2.122-python3-compliant.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('Python', '3.10.4'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0d05aef4ded --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.3.4' + +homepage = 'https://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('libsodium', '1.0.18'), + ('util-linux', '2.38'), +] + +# Compialtion warnings in GCC 11, cf. https://github.com/zeromq/libzmq/issues/4178 +# Needto disable warnings as errors. +configopts = '--with-pic --with-pgm --with-libsodium --disable-Werror' + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' From bf3948c68d80222e7340b9818d05c95686dfe185 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 14 Sep 2022 15:35:35 +0200 Subject: [PATCH 096/793] make template_easyconfig_test aware of patches with dicts --- test/easyconfigs/easyconfigs.py | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 0fb05afe876..f190f2cba33 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1333,21 +1333,29 @@ def template_easyconfig_test(self, spec): # make sure all patch files are available specdir = os.path.dirname(spec) + basedir = os.path.dirname(os.path.dirname(specdir)) specfn = os.path.basename(spec) for idx, patch in enumerate(ec['patches']): - if isinstance(patch, (tuple, list)): - patch = patch[0] + patch_dir = specdir + if isinstance(patch, str): + patch_name = patch + elif isinstance(patch, (tuple, list)): + patch_name = patch[0] + elif isinstance(patch, dict): + patch_name = patch['name'] + if patch['alt_location']: + patch_dir = os.path.join(basedir, letter_dir_for(patch_name), patch_name) # only check actual patch files, not other files being copied via the patch functionality - patch_full = os.path.join(specdir, patch) - if patch.endswith('.patch'): + patch_full = os.path.join(patch_dir, patch_name) + if patch_name.endswith('.patch'): msg = "Patch file %s is available for %s" % (patch_full, specfn) self.assertTrue(os.path.isfile(patch_full), msg) # verify checksum for each patch file - if idx < len(patch_checksums) and (os.path.exists(patch_full) or patch.endswith('.patch')): + if idx < len(patch_checksums) and (os.path.exists(patch_full) or patch_name.endswith('.patch')): checksum = patch_checksums[idx] - error_msg = "Invalid checksum for patch file %s in %s: %s" % (patch, ec_fn, checksum) + error_msg = "Invalid checksum for patch file %s in %s: %s" % (patch_name, ec_fn, checksum) res = verify_checksum(patch_full, checksum) self.assertTrue(res, error_msg) From f1d1a11248619a3ca73105827971387b2e905ceb Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 14 Sep 2022 15:55:10 +0200 Subject: [PATCH 097/793] patch_dir for patch in alt_location is in alt_locataion, not patch_name --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f190f2cba33..297025bec2b 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1344,7 +1344,7 @@ def template_easyconfig_test(self, spec): elif isinstance(patch, dict): patch_name = patch['name'] if patch['alt_location']: - patch_dir = os.path.join(basedir, letter_dir_for(patch_name), patch_name) + patch_dir = os.path.join(basedir, letter_dir_for(alt_location), alt_location) # only check actual patch files, not other files being copied via the patch functionality patch_full = os.path.join(patch_dir, patch_name) From 03c3c85e9b7b9cb401f6cd24f873a3f5cb1eab7b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 14 Sep 2022 15:59:03 +0200 Subject: [PATCH 098/793] Fix typo: alt_location -> patch['alt_location'] --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 297025bec2b..7e40d102230 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1344,7 +1344,7 @@ def template_easyconfig_test(self, spec): elif isinstance(patch, dict): patch_name = patch['name'] if patch['alt_location']: - patch_dir = os.path.join(basedir, letter_dir_for(alt_location), alt_location) + patch_dir = os.path.join(basedir, letter_dir_for(patch['alt_location']), patch['alt_location']) # only check actual patch files, not other files being copied via the patch functionality patch_full = os.path.join(patch_dir, patch_name) From 34cae5483945e9da678188b1ed282ca212e48db2 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 14 Sep 2022 16:27:05 +0200 Subject: [PATCH 099/793] Update chksum for AmberTools-20_fix_missing_MPI_LIBRARY_error.patch --- .../a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb index 234d491d03b..e09a0fe8d70 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb @@ -40,7 +40,7 @@ checksums = [ '1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121', # AmberTools22.tar.bz2 '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch - '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', + '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', # AmberTools-20_fix_xblas_missing_make_dependency.patch 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch From 5912119214d0e7e40830b157e5dac5dd412b7c20 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 14 Sep 2022 21:45:45 +0200 Subject: [PATCH 100/793] adding easyconfigs: NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb --- .../NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..89e4a5835bb --- /dev/null +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb @@ -0,0 +1,65 @@ +easyblock = 'ConfigureMake' + +name = 'NVSHMEM' +version = '2.5.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/nvshmem' +description = """NVSHMEM is a parallel programming interface based on OpenSHMEM that provides +efficient and scalable communication for NVIDIA GPU clusters. NVSHMEM creates a +global address space for data that spans the memory of multiple GPUs and can be +accessed with fine-grained GPU-initiated operations, CPU-initiated operations, +and operations on CUDA streams. +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +# You need to download the source manully from https://developer.nvidia.com/nvshmem-downloads +sources = ['%(namelower)s_src_%(version)s-19.txz'] +checksums = ['dd800b40f1d296e1d3ed2a9885adcfe745c3e57582bc809860e87bd32abcdc60'] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('UCX-CUDA', '1.12.1', versionsuffix), + ('NCCL', '2.12.12', versionsuffix), +] + +skipsteps = ['configure'] + +prebuildopts = 'export NVSHMEM_USE_GDRCOPY=1 && ' +prebuildopts += 'export GDRCOPY_HOME=${EBROOTGDRCOPY} && ' + +prebuildopts += 'export MPI_HOME=${EBROOTOPENMPI} && ' +prebuildopts += 'export NVSHMEM_MPI_SUPPORT=1 && ' +prebuildopts += 'export NVSHMEMTEST_USE_MPI_LAUNCHER=1 && ' + +prebuildopts += 'export NCCL_HOME=${EBROOTNCCL} && ' +prebuildopts += 'export NVSHMEM_USE_NCCL=1 && ' + +prebuildopts += 'export NVSHMEM_BUILDDIR=%(builddir)s && ' +prebuildopts += 'export NVSHMEM_EXAMPLES_BUILDDIR=${NVSHMEM_BUILDDIR}/examples/obj && ' +prebuildopts += 'export NVSHMEM_OTHERTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/othertest/obj && ' +prebuildopts += 'export NVSHMEM_TEST_BUILDDIR=${NVSHMEM_BUILDDIR}/test/obj && ' +prebuildopts += 'export NVSHMEM_PERFTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/perftest/obj && ' + +prebuildopts += 'export NVSHMEM_PREFIX=%(installdir)s && ' +prebuildopts += 'export NVSHMEM_EXAMPLES_INSTALL=${NVSHMEM_PREFIX}/examples && ' +prebuildopts += 'export NVSHMEM_OTHERTEST_INSTALL=${NVSHMEM_PREFIX}/othertest && ' +prebuildopts += 'export NVSHMEM_PERFTEST_INSTALL=${NVSHMEM_PREFIX}/perftest && ' +prebuildopts += 'export NVSHMEM_TEST_INSTALL=${NVSHMEM_PREFIX}/test && ' + +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['lib/libnvshmem.a', 'lib/nvshmem_bootstrap_mpi.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +modextravars = {'NVSHMEM_HOME': '%(installdir)s'} + +moduleclass = 'devel' From e17c8a4ad9c8b7189651a207f71e127b9ff42275 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 16 Sep 2022 10:09:49 +0100 Subject: [PATCH 101/793] Corrected version of Wayland to 1.21.0 --- .../easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb index 1ede0f20a54..9026c3b2c20 100644 --- a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb @@ -58,7 +58,7 @@ dependencies = [ ('glew', '2.2.0', '-egl'), ('libwpe', '1.13.3'), ('pugixml', '1.12.1'), - ('Wayland', '1.20.0'), + ('Wayland', '1.21.0'), ('Waylandpp', '1.0.0'), ('wpebackend-fdo', '1.13.1'), ('enchant-2', '2.3.3'), From a8c0b09f919023448521989f3750615396e6688a Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 16 Sep 2022 10:19:01 +0100 Subject: [PATCH 102/793] Missing GLib-2.69.1 added, sanity check command corrected --- .../e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb index 6af0833119a..3f4b2a24826 100644 --- a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb @@ -30,13 +30,14 @@ builddependencies = [ preconfigopts = "autoreconf -vfi && " dependencies = [ - ('hunspell', '1.7.0'), + ('hunspell', '1.7.1'), + ('GLib', '2.69.1'), ] buildopts = "LIBTOOL='libtool --tag=CC'" sanity_check_commands = [ - 'enchant-2 -h', + 'enchant-2 -v', 'enchant-lsmod-2 -v', ] From efde57cb097195438513c94ec4208f548cb9ad8a Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 16 Sep 2022 10:32:35 +0100 Subject: [PATCH 103/793] Missing freeglut added --- .../easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb index ba0e31b6d0c..c59f1cf7ccc 100644 --- a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb @@ -34,8 +34,12 @@ builddependencies = [ dependencies = [ ('pugixml', '1.12.1'), ('Wayland', '1.21.0'), + ('freeglut', '3.2.1'), ] +# Required to find EGL +#osdependencies = [('libegl-dev', 'libegl-devel')] + parallel = 2 sanity_check_paths = { From c4c1a9b5ba47224454f3d4eb3502fa2e520eed03 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 16 Sep 2022 16:25:43 +0200 Subject: [PATCH 104/793] add download_instructions --- .../n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb index 89e4a5835bb..5e8b6ae2658 100644 --- a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb @@ -14,7 +14,10 @@ and operations on CUDA streams. toolchain = {'name': 'gompi', 'version': '2022a'} -# You need to download the source manully from https://developer.nvidia.com/nvshmem-downloads +download_instructions = """The sources of NVSHMEM can be downloaded at Nvidia's webpage when you have signed up for +their (free) developer program: +https://developer.nvidia.com/nvshmem-downloads""" + sources = ['%(namelower)s_src_%(version)s-19.txz'] checksums = ['dd800b40f1d296e1d3ed2a9885adcfe745c3e57582bc809860e87bd32abcdc60'] From dad7ad6a6e4e6df9bdca82c712dbdf1bf8cfea09 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 16 Sep 2022 16:28:48 +0200 Subject: [PATCH 105/793] update download_instructions --- .../n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb index 5e8b6ae2658..52e0be373d1 100644 --- a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb @@ -14,7 +14,7 @@ and operations on CUDA streams. toolchain = {'name': 'gompi', 'version': '2022a'} -download_instructions = """The sources of NVSHMEM can be downloaded at Nvidia's webpage when you have signed up for +download_instructions = """The sources of NVSHMEM can be downloaded at NVIDIA's webpage when you have signed up for their (free) developer program: https://developer.nvidia.com/nvshmem-downloads""" From f8283428783661c6f944e8930c2767626e0905a7 Mon Sep 17 00:00:00 2001 From: guacke Date: Fri, 16 Sep 2022 17:26:01 +0200 Subject: [PATCH 106/793] adding easyconfigs: Avogadro2-1.97.0-linux-x86_64.eb --- .../Avogadro2-1.97.0-linux-x86_64.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb diff --git a/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb b/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb new file mode 100644 index 00000000000..0e2449a1bdf --- /dev/null +++ b/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb @@ -0,0 +1,30 @@ +easyblock = 'Binary' + +name = 'Avogadro2' +version = '1.97.0' +versionsuffix = '-linux-x86_64' + +homepage = 'https://two.avogadro.cc/index.html' +description = """ + Avogadro is an advanced molecule editor and visualizer designed for cross-platform + use in computational chemistry, molecular modeling, bioinformatics, materials science, + and related areas. It offers flexible high quality rendering and + a powerful plugin architecture. +""" + +toolchain = SYSTEM + +sources = [{ + 'source_urls' : ['https://github.com/OpenChemistry/avogadroapp/releases/download/1.97.0'], + 'filename': 'avogadro2', + 'download_filename': 'Avogadro2-x86_64.AppImage' +}] + +checksums = ['cc522dbdaa6e5386cb7101d382c5730f0d1ff71f2e70eb10f7e55f4ca052c89d'] + +sanity_check_paths = { + 'files' : ['avogadro2'], + 'dirs' : [], +} + +moduleclass = 'vis' From e9e653af905a4de4daa8d0e85a4e041133acd0ef Mon Sep 17 00:00:00 2001 From: guacke Date: Fri, 16 Sep 2022 18:27:49 +0200 Subject: [PATCH 107/793] Style fixes. --- .../Avogadro2-1.97.0-linux-x86_64.eb | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb b/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb index 0e2449a1bdf..eacd093cbd5 100644 --- a/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb @@ -6,25 +6,24 @@ versionsuffix = '-linux-x86_64' homepage = 'https://two.avogadro.cc/index.html' description = """ - Avogadro is an advanced molecule editor and visualizer designed for cross-platform - use in computational chemistry, molecular modeling, bioinformatics, materials science, - and related areas. It offers flexible high quality rendering and - a powerful plugin architecture. + Avogadro is an advanced molecule editor and visualizer designed for cross-platform + use in computational chemistry, molecular modeling, bioinformatics, materials science, + and related areas. """ toolchain = SYSTEM sources = [{ - 'source_urls' : ['https://github.com/OpenChemistry/avogadroapp/releases/download/1.97.0'], - 'filename': 'avogadro2', - 'download_filename': 'Avogadro2-x86_64.AppImage' + 'source_urls': ['https://github.com/OpenChemistry/avogadroapp/releases/download/1.97.0'], + 'filename': 'avogadro2', + 'download_filename': 'Avogadro2-x86_64.AppImage' }] checksums = ['cc522dbdaa6e5386cb7101d382c5730f0d1ff71f2e70eb10f7e55f4ca052c89d'] sanity_check_paths = { - 'files' : ['avogadro2'], - 'dirs' : [], + 'files': ['avogadro2'], + 'dirs': [], } -moduleclass = 'vis' +moduleclass = 'vis' \ No newline at end of file From d36b8d9745ec9593612d00f6b4004f9dd507741d Mon Sep 17 00:00:00 2001 From: guacke Date: Fri, 16 Sep 2022 18:41:34 +0200 Subject: [PATCH 108/793] Style fixes. --- .../easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb b/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb index eacd093cbd5..0e2597cebb9 100644 --- a/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb @@ -26,4 +26,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'vis' \ No newline at end of file +moduleclass = 'vis' From ed3095735a1eaff3e992f9d0c19f0a57da170ace Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Sep 2022 20:27:23 +0200 Subject: [PATCH 109/793] Remove AmberTools-20 patch file from Amber, it's now located in AmberTools only. --- ...ols-20_fix_missing_MPI_LIBRARY_error.patch | 21 ------------------- 1 file changed, 21 deletions(-) delete mode 100644 easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch diff --git a/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch b/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch deleted file mode 100644 index 8d96ce176c0..00000000000 --- a/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch +++ /dev/null @@ -1,21 +0,0 @@ -When using "usempi" there will be no MPI_xxx_LIBRARIES set and that causes -import_libraries to error out. We know it is correct so comment out that -FATAL_ERROR. - -Åke Sandgren, 2021-06-16 -diff -ru amber20_src.orig/cmake/LibraryTracking.cmake amber20_src/cmake/LibraryTracking.cmake ---- amber20_src.orig/cmake/LibraryTracking.cmake 2021-04-25 02:51:44.000000000 +0200 -+++ amber20_src/cmake/LibraryTracking.cmake 2021-06-16 13:30:26.568317368 +0200 -@@ -170,9 +170,9 @@ - - cmake_parse_arguments(IMP_LIBS "" "" "LIBRARIES;INCLUDES" ${ARGN}) - -- if("${IMP_LIBS_LIBRARIES}" STREQUAL "") -- message(FATAL_ERROR "Incorrect usage. At least one LIBRARY should be provided.") -- endif() -+ #if("${IMP_LIBS_LIBRARIES}" STREQUAL "") -+ # message(FATAL_ERROR "Incorrect usage. At least one LIBRARY should be provided.") -+ #endif() - - if(NOT "${IMP_LIBS_UNPARSED_ARGUMENTS}" STREQUAL "") - message(FATAL_ERROR "Incorrect usage. Extra arguments provided.") From 99b7331dd4785187f3ece14a5f756ef271c7dae2 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Sat, 17 Sep 2022 08:53:30 +0200 Subject: [PATCH 110/793] Update easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb | 44 ++++++++++--------- 1 file changed, 23 insertions(+), 21 deletions(-) diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb index 52e0be373d1..5c22660ad0b 100644 --- a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb @@ -34,27 +34,29 @@ dependencies = [ skipsteps = ['configure'] -prebuildopts = 'export NVSHMEM_USE_GDRCOPY=1 && ' -prebuildopts += 'export GDRCOPY_HOME=${EBROOTGDRCOPY} && ' - -prebuildopts += 'export MPI_HOME=${EBROOTOPENMPI} && ' -prebuildopts += 'export NVSHMEM_MPI_SUPPORT=1 && ' -prebuildopts += 'export NVSHMEMTEST_USE_MPI_LAUNCHER=1 && ' - -prebuildopts += 'export NCCL_HOME=${EBROOTNCCL} && ' -prebuildopts += 'export NVSHMEM_USE_NCCL=1 && ' - -prebuildopts += 'export NVSHMEM_BUILDDIR=%(builddir)s && ' -prebuildopts += 'export NVSHMEM_EXAMPLES_BUILDDIR=${NVSHMEM_BUILDDIR}/examples/obj && ' -prebuildopts += 'export NVSHMEM_OTHERTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/othertest/obj && ' -prebuildopts += 'export NVSHMEM_TEST_BUILDDIR=${NVSHMEM_BUILDDIR}/test/obj && ' -prebuildopts += 'export NVSHMEM_PERFTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/perftest/obj && ' - -prebuildopts += 'export NVSHMEM_PREFIX=%(installdir)s && ' -prebuildopts += 'export NVSHMEM_EXAMPLES_INSTALL=${NVSHMEM_PREFIX}/examples && ' -prebuildopts += 'export NVSHMEM_OTHERTEST_INSTALL=${NVSHMEM_PREFIX}/othertest && ' -prebuildopts += 'export NVSHMEM_PERFTEST_INSTALL=${NVSHMEM_PREFIX}/perftest && ' -prebuildopts += 'export NVSHMEM_TEST_INSTALL=${NVSHMEM_PREFIX}/test && ' +prebuildopts = 'export %s &&' % ' '.join([ + 'NVSHMEM_USE_GDRCOPY=1', + 'GDRCOPY_HOME=${EBROOTGDRCOPY}', + + 'MPI_HOME=${EBROOTOPENMPI}', + 'NVSHMEM_MPI_SUPPORT=1', + 'NVSHMEMTEST_USE_MPI_LAUNCHER=1', + + 'NCCL_HOME=${EBROOTNCCL}', + 'NVSHMEM_USE_NCCL=1', + + 'NVSHMEM_BUILDDIR=%(builddir)s', + 'NVSHMEM_EXAMPLES_BUILDDIR=${NVSHMEM_BUILDDIR}/examples/obj', + 'NVSHMEM_OTHERTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/othertest/obj', + 'NVSHMEM_TEST_BUILDDIR=${NVSHMEM_BUILDDIR}/test/obj', + 'NVSHMEM_PERFTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/perftest/obj', + + 'NVSHMEM_PREFIX=%(installdir)s', + 'NVSHMEM_EXAMPLES_INSTALL=${NVSHMEM_PREFIX}/examples', + 'NVSHMEM_OTHERTEST_INSTALL=${NVSHMEM_PREFIX}/othertest', + 'NVSHMEM_PERFTEST_INSTALL=${NVSHMEM_PREFIX}/perftest', + 'NVSHMEM_TEST_INSTALL=${NVSHMEM_PREFIX}/test', +]) preinstallopts = prebuildopts From 8837734e2629fb17cec68918e9720302e2e8e050 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 19 Sep 2022 17:10:09 +0200 Subject: [PATCH 111/793] skip flaky test in PyTorch 1.9 --- .../p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 3 +++ .../PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 3 +++ .../p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 3 +++ ....0_skip-autograd-thread_shutdown-test.patch | 18 ++++++++++++++++++ 4 files changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb index 68f81ba8ce2..000f5a2c4f2 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -28,6 +28,7 @@ patches = [ 'PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch', 'PyTorch-1.9.0_fix-kineto-crash.patch', 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch', 'PyTorch-1.9.0_skip-lstm-serialization-test.patch', ] checksums = [ @@ -49,6 +50,8 @@ checksums = [ 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', '1ed5e125f7922ea577d43053a6652aedc21cc036157e101c0e3b9aee9029d3b0', # PyTorch-1.9.0_fix-kineto-crash.patch 'a4733b6b16a0db4ee5f85f2b103abc29bd711cfc5253f8dd8494d2b0c1509516', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + # PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch + '94957de0fd5bcbea37482cb6d0d12b4608dccf50a10da0836e151b414954ccc3', # PyTorch-1.9.0_skip-lstm-serialization-test.patch '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index b4662e2722d..12f72390950 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -37,6 +37,7 @@ patches = [ 'PyTorch-1.9.0_increase-test-cuda-tolerance.patch', 'PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch', 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + 'PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch', 'PyTorch-1.9.0_skip-lstm-serialization-test.patch', 'PyTorch-1.9.0_skip-nccl-error-tests.patch', ] @@ -73,6 +74,8 @@ checksums = [ '725922f0000d51c03f726a34b249db8f53eee7e5c67417774a5113de954f5a5c', # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch + '94957de0fd5bcbea37482cb6d0d12b4608dccf50a10da0836e151b414954ccc3', # PyTorch-1.9.0_skip-lstm-serialization-test.patch '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', '9634fb34fedff4589b9175a4e4c3f278b60d4dcbc7b36b0f19604748d32074f0', # PyTorch-1.9.skip-nccl-error-tests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index e7070b8d189..0982b4f230d 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -36,6 +36,7 @@ patches = [ 'PyTorch-1.9.0_increase-test-cuda-tolerance.patch', 'PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch', 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + 'PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch', 'PyTorch-1.9.0_skip-lstm-serialization-test.patch', 'PyTorch-1.9.0_skip-nccl-error-tests.patch', ] @@ -72,6 +73,8 @@ checksums = [ '725922f0000d51c03f726a34b249db8f53eee7e5c67417774a5113de954f5a5c', # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch + '94957de0fd5bcbea37482cb6d0d12b4608dccf50a10da0836e151b414954ccc3', # PyTorch-1.9.0_skip-lstm-serialization-test.patch '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', '9634fb34fedff4589b9175a4e4c3f278b60d4dcbc7b36b0f19604748d32074f0', # PyTorch-1.9.skip-nccl-error-tests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch new file mode 100644 index 00000000000..cfb52a911e0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch @@ -0,0 +1,18 @@ +This test is flaky due to a race condition. +See https://github.com/pytorch/pytorch/issues/85259 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_autograd.py b/test/test_autograd.py +index 19fe8777d5..bb25e3ef53 100644 +--- a/test/test_autograd.py ++++ b/test/test_autograd.py +@@ -4339,7 +4339,7 @@ class TestAutograd(TestCase): + b.data = a + self.assertTrue(b_id_saved == id(b)) + +- @unittest.skipIf(IS_WINDOWS, "Skipping because doesn't work for windows") ++ @unittest.skip("Skipping due to possible race condition") + def test_thread_shutdown(self): + code = """import torch + from torch.autograd import Function From bfb6b70236547b9cff46f2d8f1b578a2e589f851 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 19 Sep 2022 18:44:44 +0200 Subject: [PATCH 112/793] Add UCX-CUDA as dependency --- .../easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb index 2ed04d457b6..a81d983d6e3 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb @@ -25,6 +25,7 @@ builddependencies = [ ] dependencies = [ ('CUDA', '11.7.0', '', True), + ('UCX-CUDA', '1.12.1', versionsuffix), ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) @@ -36,7 +37,7 @@ configopts = [ ] sanity_check_paths = { - 'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'], + 'files': ['lib/libmagma.so', 'lib/libmagma.a'], 'dirs': ['include'], } From 13a229157d19415bfddfbc22796d08b5675152fb Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 19 Sep 2022 16:52:39 -0700 Subject: [PATCH 113/793] {bio}[GCC/11.2.0] AGAT 0.9.2 --- .../a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb new file mode 100644 index 00000000000..97dd5d374f3 --- /dev/null +++ b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb @@ -0,0 +1,57 @@ +# easybuild easyconfig +# +# John Dey Fred Hutchinson Cancer Center +# +easyblock = 'Bundle' + +name = 'AGAT' +version = '0.9.2' + +homepage = 'https://agat.readthedocs.io/en/latest/' +description = """AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations + in any GTF/GFF format.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Perl', '5.34.0'), + ('BioPerl', '1.7.8'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('File::Share', '0.27', { + 'source_tmpl': 'File-Share-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['d6e8f4b55ebd38e0bb45e44392e3fa27dc1fde16abc5d1ff53e157e19a5755be'], + }), + ('Sort::Naturally', '1.03', { + 'source_tmpl': 'Sort-Naturally-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['eaab1c5c87575a7826089304ab1f8ffa7f18e6cd8b3937623e998e865ec1e746'], + }), + ('Term::ProgressBar', '2.22', { + 'source_tmpl': 'Term-ProgressBar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': ['2642ecca5b0b038c14812bcad3a9611ff7911dc59c9104d220797f837a880c49'], + }), + (name, version, { + 'modulename': 'AGAT::Utilities', + 'source_urls': ['https://github.com/NBISweden/AGAT/archive/refs/tags'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['998e32a3cb5e941efd324daf9ee4e0a71d605d06999922f083170b7a9f059899'], + }), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/%(name)s'], +} + +moduleclass = 'bio' From 2e62c073e28d4821a2ef282fd766a4792b397996 Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 20 Sep 2022 11:50:34 +0200 Subject: [PATCH 114/793] adding easyconfigs: libcint-5.1.6-foss-2022a.eb --- .../l/libcint/libcint-5.1.6-foss-2022a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcint/libcint-5.1.6-foss-2022a.eb diff --git a/easybuild/easyconfigs/l/libcint/libcint-5.1.6-foss-2022a.eb b/easybuild/easyconfigs/l/libcint/libcint-5.1.6-foss-2022a.eb new file mode 100644 index 00000000000..6b4b19e2832 --- /dev/null +++ b/easybuild/easyconfigs/l/libcint/libcint-5.1.6-foss-2022a.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'libcint' +version = '5.1.6' + +homepage = 'https://github.com/sunqm/libcint' +description = """libcint is an open source library for analytical Gaussian integrals.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/sunqm/libcint/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-4.4.0_remove_pyscftest.patch'] +checksums = [ + 'c111d82140e2e8415775e73f571a16456c9deadd36d58795edd170035b06f8a5', # v5.1.6.tar.gz + '6449297a6aee30fef3d6a268aa892dea8dd5c3ca9669a50ae694ab9bcf17842d', # libcint-4.4.0_remove_pyscftest.patch +] + +builddependencies = [ + ('CMake', '3.23.1'), + # Python with numpy only required for 'make test' + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +separate_build_dir = False # Must use the same directory for tests + +configopts = '-DWITH_RANGE_COULOMB=on -DWITH_COULOMB_ERF=on -DWITH_F12=on -DENABLE_TEST=on' + +buildopts = "VERBOSE=1" + +runtest = 'test ' + +sanity_check_paths = { + 'files': ['include/cint.h', 'lib/libcint.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'chem' From 095470f83e7906758f162be7c38941eb201aa5ca Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 20 Sep 2022 12:38:30 +0200 Subject: [PATCH 115/793] Add Guile and deps --- .../g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb | 45 +++++++++++++++++++ .../g/gc/gc-8.2.2-GCCcore-11.3.0.eb | 42 +++++++++++++++++ .../libunistring-1.0-GCCcore-11.3.0.eb | 31 +++++++++++++ 3 files changed, 118 insertions(+) create mode 100644 easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0feea67dfc8 --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '3.0.8' + +homepage = 'https://www.gnu.org/software/guile/' + +description = """ + Guile is a programming language, designed to help programmers create flexible + applications that can be extended by users or other programmers with plug-ins, + modules, or scripts. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f25ae0c26e911af1b5005292d4f56621879f74d6958b30741cf67d8b6feb2016'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] + +dependencies = [ + ('gc', '8.2.2'), + ('GMP', '6.2.1'), + ('libffi', '3.4.2'), + ('libunistring', '1.0'), +] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s guile guile%(version_major)s"] + +sanity_check_paths = { + 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', + 'bin/guile-snarf', 'bin/guile-tools', + 'include/guile/%(version_major_minor)s/libguile.h', + 'lib/libguile-%(version_major_minor)s.a', + 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/guile/%(version_major_minor)s/libguile', + 'lib/guile/%(version_major_minor)s/ccache'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0539f756059 --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '8.2.2' +local_libatomic_version = '7.6.14' + +homepage = 'https://hboehm.info/gc/' +description = """The Boehm-Demers-Weiser conservative garbage collector can be used as a +garbage collecting replacement for C malloc or C++ new. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [ + 'https://github.com/ivmai/bdwgc/releases/download/v%(version)s/', # preferred for gc-%(version)s.tar.gz + 'https://hboehm.info/gc/gc_source/', # alternate for gc-%(version)s.tar.gz + 'https://github.com/ivmai/libatomic_ops/releases/download/v%s/' % local_libatomic_version, +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-%s.tar.gz' % local_libatomic_version, +] +checksums = [ + 'f30107bcb062e0920a790ffffa56d9512348546859364c23a14be264b38836a0', # gc-8.2.2.tar.gz + '390f244d424714735b7050d056567615b3b8f29008a663c262fb548f1802d292', # libatomic_ops-7.6.14.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), +] + +preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && ' + +configopts = "--enable-static" + +sanity_check_paths = { + 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, + 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], + 'dirs': ['include/gc', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a6849817c91 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '1.0' + +homepage = 'https://www.gnu.org/software/libunistring/' + +description = """This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['5bab55b49f75d77ed26b257997e919b693f29fd4a1bc22e0e6e024c246c72741'] + +builddependencies = [ + ('binutils', '2.38'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' From 4ceccfc979768c33859d99f8a56213811111d634 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 20 Sep 2022 17:45:08 +0200 Subject: [PATCH 116/793] Add --with-versioned-syms to ncurses 6.2 and 6.3 --- easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb index 816870478e9..04fddafce58 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb @@ -20,7 +20,7 @@ checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] builddependencies = [('binutils', '2.36.1')] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # default build local_common_configopts, diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb index d0f89800315..2ef2ac3431c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] builddependencies = [('binutils', '2.35')] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb index da6d4c2d78d..3608131b4d7 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb @@ -20,7 +20,7 @@ checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] builddependencies = [('binutils', '2.36.1')] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb index 15191562f91..8c1f8604b30 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb @@ -20,7 +20,7 @@ checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] builddependencies = [('binutils', '2.37')] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb index a5329b525e9..cee6bdc8b98 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb @@ -20,7 +20,7 @@ checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] builddependencies = [('binutils', '2.34')] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, From d389fc024851212db53face5674112233eb24785 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 20 Sep 2022 17:47:33 +0200 Subject: [PATCH 117/793] Add --with-versioned-syms to 6.3 --- easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb index 26666e64a97..232a2cfedab 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb @@ -20,7 +20,7 @@ checksums = ['97fc51ac2b085d4cde31ef4d2c3122c21abc217e9090a43a30fc5ec21684e059'] builddependencies = [('binutils', '2.38')] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb index 843c52c75d9..4b9fc292bde 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb @@ -20,7 +20,7 @@ checksums = ['97fc51ac2b085d4cde31ef4d2c3122c21abc217e9090a43a30fc5ec21684e059'] builddependencies = [('binutils', '2.38')] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, From 12016618ef7f89ae78b0554263c5a21f3dcc38f1 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 20 Sep 2022 18:24:15 +0200 Subject: [PATCH 118/793] ADD CDO --- .../c/CDO/CDO-2.0.6-gompi-2022a.eb | 46 +++++++++++++++++++ .../e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb | 44 ++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb new file mode 100644 index 00000000000..caccb37e498 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '2.0.6' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'cstd': 'c++17', 'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/27276/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ef120dea9032b1be80a4cfa201958c3b910107205beb6674195675f1ee8ed402'] + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('cURL', '7.83.0'), + ('ecCodes', '2.27.0'), + ('FFTW', '3.3.10'), + ('HDF5', '1.12.2'), + ('libxml2', '2.9.13'), + ('netCDF', '4.9.0'), + ('PROJ', '9.0.0'), + ('Szip', '2.1.1'), + ('UDUNITS', '2.2.28'), + ('util-linux', '2.38'), +] + +# Build libcdi +configopts = "--enable-cdi-lib " + +# Use dependencies from EasyBuild +configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw3 --with-hdf5=$EBROOTHDF5 " +configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP " +configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX " + +sanity_check_paths = { + 'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb new file mode 100644 index 00000000000..742bdb55b84 --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.27.0' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': False} + +source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/'] +sources = ['eccodes-%(version)s-Source.tar.gz'] +checksums = ['ede5b3ffd503967a5eac89100e8ead5e16a881b7585d02f033584ed0c4269c99'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('netCDF', '4.9.0'), + ('JasPer', '2.0.33'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), +] + +# Python bindings are provided by a separate package 'eccodes-python' +configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON -DENABLE_PYTHON=OFF " +configopts += "-DENABLE_JPG=ON -DENABLE_JPG_LIBJASPER=ON " +configopts += "-DENABLE_ECCODES_THREADS=ON" # multi-threading with pthreads + +local_exes = ['%s_%s' % (a, b) + for a in ['bufr', 'grib', 'gts', 'metar'] + for b in ['compare', 'copy', 'dump', 'filter', 'get', 'ls']] +local_exes += ['codes_%s' % c for c in ['count', 'info', 'split_file']] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_exes] + + ['lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' From 954022bebd993c28d9c3eecd34b3e3baf57d1295 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Sep 2022 11:43:18 +0200 Subject: [PATCH 119/793] adding easyconfigs: TELEMAC-MASCARET-8p3r1-foss-2021b.eb --- .../TELEMAC-MASCARET-8p3r1-foss-2021b.eb | 85 +++++++++++++++++++ 1 file changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb diff --git a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb new file mode 100644 index 00000000000..bd10f9de826 --- /dev/null +++ b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb @@ -0,0 +1,85 @@ +easyblock = 'Binary' + +name = 'TELEMAC-MASCARET' +version = '8p3r1' + +homepage = 'http://www.opentelemac.org' +description = """TELEMAC-MASCARET is an integrated suite of solvers for use in the field of free-surface flow. Having +been used in the context of many studies throughout the world, it has become one of the major standards in its field.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'extra_fcflags': "-fallow-invalid-boz"} + +source_urls = ['https://gitlab.pam-retd.fr/otm/telemac-mascaret/-/archive/v%(version)s/'] +sources = ['telemac-mascaret-v%(version)s.tar.gz'] +checksums = ['e37ae6b7eefca0e544c6431308e43828d439be08701356814dd1e04ca762fb7d'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # provides numpy, scipy + ('matplotlib', '3.4.3'), + ('HDF5', '1.12.1'), + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.2'), + ('MUMPS', '5.4.1', '-metis'), +] + +extract_sources = True +unpack_options = '--strip-components=1' + +buildininstalldir = True + +install_cmd = "export HOMETEL=$PWD && " +# add Python scripts to $PATH and $PYTHONPATH +install_cmd += "export PATH=$HOMETEL/scripts/python3/:$PATH && " +install_cmd += "export PYTHONPATH=$HOMETEL/scripts/python3:$PYTHONPATH && " +# force python to flush its output +install_cmd += "export PYTHONUNBUFFERED=1 && " + +# export LD_LIBRARY_PATH=$HOMETEL/builds/$USETELCFG/wrap_api/lib:$LD_LIBRARY_PATH +# export PYTHONPATH=$HOMETEL/builds/$USETELCFG/wrap_api/lib:$PYTHONPATH + +install_cmd += "cp $HOMETEL/configs/systel.edf.cfg $HOMETEL/configs/systel.easybuild.cfg && " +install_cmd += "sed -i 's/S9.gfortran/easybuild/g' $HOMETEL/configs/systel.easybuild.cfg && " +# strip out use of AED, GOTM, MED (optional dependencies) +install_cmd += "sed -i 's/\(^[a-z]*_aed:\).*/\\1/g' $HOMETEL/configs/systel.easybuild.cfg && " +install_cmd += "sed -i 's/\(^[a-z]*_gotm:\).*/\\1/g' $HOMETEL/configs/systel.easybuild.cfg && " +install_cmd += "sed -i 's/\(^[a-z]*_med:\).*/\\1/g' $HOMETEL/configs/systel.easybuild.cfg && " +# replace -O2 with desired compiler options +install_cmd += 'sed -i "s/-O2/$F90FLAGS/g" $HOMETEL/configs/systel.easybuild.cfg && ' +# fix linker option for BLAS +install_cmd += 'sed -i "s/ -lblas/ $LIBBLAS/g" $HOMETEL/configs/systel.easybuild.cfg && ' +# downgrade Fortran compiler error to warning +install_cmd += "sed -i 's/^fflags_gfo:/fflags_gfo: -fallow-invalid-boz/g' $HOMETEL/configs/systel.easybuild.cfg && " +install_cmd += "export SYSTELCFG=$HOMETEL/configs/systel.easybuild.cfg && " +install_cmd += "export USETELCFG=easybuild && " + +install_cmd += "export SCALAPACKHOME=$EBROOTSCALAPACK && " +install_cmd += "export METISHOME=$EBROOTMETIS && " +install_cmd += "export SCOTCHHOME=$EBROOTSCOTCH && " +install_cmd += "export MUMPSHOME=$EBROOTMUMPS && " +install_cmd += "export HDF5HOME=$EBROOTHDF5 && " +install_cmd += "config.py && compile_telemac.py -j %(parallel)s" + +sanity_check_paths = { + 'files': [], + 'dirs': ['scripts/python3'], +} + +sanity_check_commands = [ + "tmpdir=$(mktemp -d) && cp -a %(installdir)s/examples/telemac2d/gouttedo $tmpdir/ && " + "cd $tmpdir/gouttedo && telemac2d.py t2d_gouttedo.cas", +] + +modextrapaths = { + 'LD_LIBRARY_PATH': 'builds/easybuild/lib', + 'PATH': 'scripts/python3', + 'PYTHONPATH': 'scripts/python3', +} + +modextravars = { + 'SYSTELCFG': '%(installdir)s/configs/systel.easybuild.cfg', + 'USETELCFG': 'easybuild', +} + +moduleclass = 'geo' From 0b891aeee1dc31e126d9c4cdbfdd66dc644db125 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Sep 2022 11:53:49 +0200 Subject: [PATCH 120/793] enhance sanity check for TELEMAC --- .../t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb index bd10f9de826..69b187c36e0 100644 --- a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb @@ -62,7 +62,8 @@ install_cmd += "export HDF5HOME=$EBROOTHDF5 && " install_cmd += "config.py && compile_telemac.py -j %(parallel)s" sanity_check_paths = { - 'files': [], + 'files': ['builds/easybuild/bin/telemac2d', 'builds/easybuild/bin/telemac3d', + 'builds/easybuild/lib/libtelemac2d.%s' % SHLIB_EXT, 'builds/easybuild/lib/libtelemac3d.%s' % SHLIB_EXT], 'dirs': ['scripts/python3'], } From da879364bc7f8c8db0050fca3a8a822ddac6ee0f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Sep 2022 11:55:57 +0200 Subject: [PATCH 121/793] enhance sanity check command to make sure that TELEMAC example test case directory is writable --- .../t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb index 69b187c36e0..5b6623b4774 100644 --- a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb @@ -68,7 +68,7 @@ sanity_check_paths = { } sanity_check_commands = [ - "tmpdir=$(mktemp -d) && cp -a %(installdir)s/examples/telemac2d/gouttedo $tmpdir/ && " + "tmpdir=$(mktemp -d) && cp -a %(installdir)s/examples/telemac2d/gouttedo $tmpdir/ && chmod -R u+w $tmpdir && " "cd $tmpdir/gouttedo && telemac2d.py t2d_gouttedo.cas", ] From 70219f9f76ca4815c07aed9a49d983262e928ead Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 21 Sep 2022 11:58:09 +0200 Subject: [PATCH 122/793] Add SuiteSparse --- ...iteSparse-5.13.0-foss-2022a-METIS-5.1.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022a-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022a-METIS-5.1.0.eb new file mode 100644 index 00000000000..8409675b853 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022a-METIS-5.1.0.eb @@ -0,0 +1,31 @@ +name = 'SuiteSparse' +version = '5.13.0' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['59c6ca2959623f0c69226cf9afb9a018d12a37fab3a8869db5f6d7f83b6b147d'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.1.0'), +] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " +# remove broken symlink +prebuildopts += "rm GraphBLAS/CUDA/test/graphblascuda_test && " + +moduleclass = 'numlib' From c65d481876888907a1ea92c95c626eab69a2eec1 Mon Sep 17 00:00:00 2001 From: robogast Date: Wed, 21 Sep 2022 12:45:06 +0200 Subject: [PATCH 123/793] adding easyconfigs: OpenEXR-3.1.5-GCCcore-11.3.0.eb, libwebp-1.2.4-GCCcore-11.3.0.eb, OpenCV-4.6.0-foss-2022a-contrib.eb --- .../l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb | 47 ++++++++ .../OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 114 ++++++++++++++++++ .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 40 ++++++ 3 files changed, 201 insertions(+) create mode 100644 easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..fe7ccf159ab --- /dev/null +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'libwebp' +version = '1.2.4' + +homepage = 'https://developers.google.com/speed/webp/' +description = """WebP is a modern image format that provides superior +lossless and lossy compression for images on the web. Using WebP, +webmasters and web developers can create smaller, richer images that +make the web faster.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('giflib', '5.2.1'), +] + +configopts = '--enable-libwebpmux' + +sanity_check_paths = { + 'files': [ + 'include/webp/decode.h', + 'include/webp/demux.h', + 'include/webp/encode.h', + 'include/webp/mux.h', + 'include/webp/mux_types.h', + 'include/webp/types.h', + 'lib/%(name)s.a', + 'lib/libwebpdemux.a', + 'lib/libwebpmux.a', + 'lib/%(name)s.so', + 'lib/libwebpdemux.so', + 'lib/libwebpmux.so' + ], + 'dirs': ['lib/'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb new file mode 100644 index 00000000000..a5dbf2bbda5 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -0,0 +1,114 @@ +name = 'OpenCV' +version = '4.6.0' +versionsuffix = '-contrib' + +homepage = 'https://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products. + Includes extra modules for OpenCV from the contrib repository.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [ + { + 'source_urls': ['https://github.com/%(namelower)s/%(namelower)s/archive/'], + 'download_filename': '%(version)s.zip', + 'filename': SOURCELOWER_ZIP + }, + { + 'source_urls': ['https://github.com/%(namelower)s/opencv_contrib/archive/'], + 'download_filename': '%(version)s.zip', + 'filename': '%(namelower)s_contrib-%(version)s.zip' + }, + { + 'source_urls': ['https://raw.githubusercontent.com/%(namelower)s/opencv_3rdparty/a56b6ac6f030c312b2dce17430eef13aed9af274/ippicv'], # noqa: E501 + 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', + 'extract_cmd': 'cp %s %(builddir)s' + }, +] + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('zlib', '1.2.12'), + ('FFmpeg', '5.0.1'), + ('freetype', '2.12.1'), + ('HarfBuzz', '4.2.1'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('libwebp', '1.2.4'), + ('OpenEXR', '3.1.5'), + ('JasPer', '2.0.33'), + ('Java', '17', '', True), + ('ant', '1.10.12', '-Java-%(javaver)s', True), + ('GLib', '2.72.1'), + ('GTK4', '4.7.0'), + ('HDF5', '1.13.1'), +] + +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = " ".join([ + "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules", + "-DFREETYPE_FOUND=ON", + "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/", + "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES_XXXXX=ON", + "-DHARFBUZZ_FOUND=ON", + "-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz", + "-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON", + "-DBUILD_opencv_python2=OFF", + "-DCPU_BASELINE=DETECT", +]) +enhance_sanity_check = True + +sanity_check_paths = { + 'files': [ + 'lib64/libopencv_aruco.so', + 'lib64/libopencv_bgsegm.so', + 'lib64/libopencv_bioinspired.so', + 'lib64/libopencv_ccalib.so', + 'lib64/libopencv_datasets.so', + 'lib64/libopencv_dnn_objdetect.so', + 'lib64/libopencv_dnn_superres.so', + 'lib64/libopencv_dpm.so', + 'lib64/libopencv_face.so', + 'lib64/libopencv_freetype.so', + 'lib64/libopencv_fuzzy.so', + 'lib64/libopencv_hdf.so', + 'lib64/libopencv_hfs.so', + 'lib64/libopencv_img_hash.so', + 'lib64/libopencv_line_descriptor.so', + 'lib64/libopencv_optflow.so', + 'lib64/libopencv_phase_unwrapping.so', + 'lib64/libopencv_plot.so', + 'lib64/libopencv_quality.so', + 'lib64/libopencv_reg.so', + 'lib64/libopencv_rgbd.so', + 'lib64/libopencv_saliency.so', + 'lib64/libopencv_shape.so', + 'lib64/libopencv_stereo.so', + 'lib64/libopencv_structured_light.so', + 'lib64/libopencv_superres.so', + 'lib64/libopencv_surface_matching.so', + 'lib64/libopencv_text.so', + 'lib64/libopencv_tracking.so', + 'lib64/libopencv_videostab.so', + 'lib64/libopencv_xfeatures2d.so', + 'lib64/libopencv_ximgproc.so', + 'lib64/libopencv_xobjdetect.so', + 'lib64/libopencv_xphoto.so' + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..bc16062bde2 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '3.1.5' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' + +sanity_check_paths = { + 'files': [ + 'lib/libIex.so', + 'lib/libIlmThread.so', + 'lib/libImath.so', + 'lib/libOpenEXR.so', + 'lib/libOpenEXRUtil.so', + 'bin/exrenvmap', + 'bin/exrheader', + 'bin/exrmakepreview', + 'bin/exrmaketiled', + 'bin/exrmultipart', + 'bin/exrmultiview', + 'bin/exrstdattr' + ], + 'dirs': ['include/%(name)s', 'share'], +} + +moduleclass = 'vis' From d9fbc970ce10066118d95b9bd6f80933b2da9d74 Mon Sep 17 00:00:00 2001 From: robogast Date: Wed, 21 Sep 2022 12:59:37 +0200 Subject: [PATCH 124/793] injected checksums, removed OpenCV CPU_BASELINE configopt --- .../easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb | 1 + .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 6 +++++- .../easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 1 + 3 files changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb index fe7ccf159ab..6fd104e1260 100644 --- a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['7bf5a8a28cc69bcfa8cb214f2c3095703c6b73ac5fba4d5480c205331d9494df'] builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index a5dbf2bbda5..ab2050076ac 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -28,6 +28,11 @@ sources = [ 'extract_cmd': 'cp %s %(builddir)s' }, ] +checksums = [ + '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359', # opencv-4.6.0.zip + '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3', # opencv_contrib-4.6.0.zip + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz +] builddependencies = [ ('CMake', '3.23.1'), @@ -67,7 +72,6 @@ configopts = " ".join([ "-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", "-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON", "-DBUILD_opencv_python2=OFF", - "-DCPU_BASELINE=DETECT", ]) enhance_sanity_check = True diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb index bc16062bde2..6d2db3b7ccc 100644 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['93925805c1fc4f8162b35f0ae109c4a75344e6decae5a240afdfce25f8a433ec'] builddependencies = [ ('binutils', '2.38'), From 16172d66bfc91d25cceade9a48cf45b9fb97c374 Mon Sep 17 00:00:00 2001 From: maximm Date: Wed, 21 Sep 2022 13:00:17 +0200 Subject: [PATCH 125/793] adding easyconfigs: ncdu-1.17-GCC-11.3.0.eb --- .../n/ncdu/ncdu-1.17-GCC-11.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncdu/ncdu-1.17-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/n/ncdu/ncdu-1.17-GCC-11.3.0.eb b/easybuild/easyconfigs/n/ncdu/ncdu-1.17-GCC-11.3.0.eb new file mode 100644 index 00000000000..c3f1012fa69 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdu/ncdu-1.17-GCC-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'ncdu' +version = '1.17' + +homepage = 'https://dev.yorhel.nl/ncdu' +description = """Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a + remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular + desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like + environment with ncurses installed.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://dev.yorhel.nl/download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['810745a8ed1ab3788c87d3aea4cc1a14edf6ee226f764bcc383e024ba56adbf1'] + +dependencies = [('ncurses', '6.3')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'tools' From 184d5dd288100bc0f5ae347ed62ce6daf4414fd2 Mon Sep 17 00:00:00 2001 From: robogast Date: Wed, 21 Sep 2022 13:45:09 +0200 Subject: [PATCH 126/793] Downgraded OpenCV deps FFMpeg, HDF5, Java --- .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index ab2050076ac..0d6357a5ca6 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -41,7 +41,7 @@ dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('zlib', '1.2.12'), - ('FFmpeg', '5.0.1'), + ('FFmpeg', '4.4.2'), ('freetype', '2.12.1'), ('HarfBuzz', '4.2.1'), ('libjpeg-turbo', '2.1.3'), @@ -50,11 +50,11 @@ dependencies = [ ('libwebp', '1.2.4'), ('OpenEXR', '3.1.5'), ('JasPer', '2.0.33'), - ('Java', '17', '', True), + ('Java', '11', '', True), ('ant', '1.10.12', '-Java-%(javaver)s', True), ('GLib', '2.72.1'), ('GTK4', '4.7.0'), - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ] # XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz From 0d386aa360df7b9cf7f85635fd6c0ca2c1576c06 Mon Sep 17 00:00:00 2001 From: robogast Date: Wed, 21 Sep 2022 13:49:46 +0200 Subject: [PATCH 127/793] Re-pinned OpenCV FFmpeg to v5.0.1 --- .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index 0d6357a5ca6..295bc7ccf2b 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -41,7 +41,7 @@ dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('zlib', '1.2.12'), - ('FFmpeg', '4.4.2'), + ('FFmpeg', '5.0.1'), ('freetype', '2.12.1'), ('HarfBuzz', '4.2.1'), ('libjpeg-turbo', '2.1.3'), From eb13f84ac50c1fbebdd31ab64f0d7a92e4742de8 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Wed, 21 Sep 2022 12:53:06 +0100 Subject: [PATCH 128/793] adding easyconfigs: Automake-1.16.5.eb --- .../easyconfigs/a/Automake/Automake-1.16.5.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb new file mode 100644 index 00000000000..5598e22e1d9 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'Automake' +version = '1.16.5' + +homepage = 'https://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['07bd24ad08a64bc17250ce09ec56e921d6343903943e99ccf63bbf0705e34605'] + +dependencies = [ + ('Autoconf', '2.71'), +] + +osdependencies = [ + 'perl-Thread-Queue', +] + +preconfigopts = "export PERL='/usr/bin/env perl' && " + +sanity_check_paths = { + 'files': ['bin/aclocal', 'bin/automake'], + 'dirs': [] +} + +sanity_check_commands = [ + "aclocal --help", + "automake --help", +] + +moduleclass = 'devel' From 10c73ef83017c0123bc87c09c2afe8ad80cda609 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 21 Sep 2022 12:56:25 +0100 Subject: [PATCH 129/793] Jansson version corrected --- easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb index 4b516f19c4b..4d87ace9817 100644 --- a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb @@ -39,7 +39,7 @@ dependencies = [ ('nghttp3', '0.6.0'), ('Python', '3.9.6'), ('libxml2', '2.9.10'), - ('Jansson', '2.14'), + ('Jansson', '2.13.1'), ('jemalloc', '5.2.1'), ('ngtcp2', '0.7.0'), ('libevent', '2.1.12'), From 8719c35ac7163f53da9562abcd79b2462f5366ba Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Wed, 21 Sep 2022 12:59:08 +0100 Subject: [PATCH 130/793] adding easyconfigs: libtool-2.4.7.eb --- .../easyconfigs/l/libtool/libtool-2.4.7.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.7.eb diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.7.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.7.eb new file mode 100644 index 00000000000..493b1c143ee --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.7.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.7' + +homepage = 'https://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['04e96c2404ea70c590c546eba4202a4e12722c640016c12b9b2f1ce3d481e9a8'] + +dependencies = [ + ('M4', '1.4.18'), +] + +sanity_check_paths = { + 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], + 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], +} + +moduleclass = 'lib' From 50f2d3e230b994a3210247845eebb521afcc6021 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 21 Sep 2022 15:11:41 +0200 Subject: [PATCH 131/793] Add NCO --- .../l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb | 37 ++++++++++++++++ .../easyconfigs/n/NCO/NCO-5.1.0-foss-2022a.eb | 44 +++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/NCO/NCO-5.1.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..237260a43f7 --- /dev/null +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libdap' +version = '3.20.11' + +homepage = 'https://www.opendap.org/software/libdap' +description = """A C++ SDK which contains an implementation of DAP 2.0 and + DAP4.0. This includes both Client- and Server-side support classes.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.opendap.org/pub/source/'] +sources = [SOURCE_TAR_GZ] +checksums = ['850debf6ee6991350bf31051308093bee35ddd2121e4002be7e130a319de1415'] + +builddependencies = [ + ('binutils', '2.38'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('cURL', '7.83.0'), + ('libxml2', '2.9.13'), + ('libtirpc', '1.3.2'), + ('PCRE', '8.45'), + ('util-linux', '2.38'), +] + +configopts = 'TIRPC_LIBS="-ltirpc"' + +sanity_check_paths = { + 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.1.0-foss-2022a.eb b/easybuild/easyconfigs/n/NCO/NCO-5.1.0-foss-2022a.eb new file mode 100644 index 00000000000..81047083a23 --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-5.1.0-foss-2022a.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '5.1.0' + +homepage = "https://github.com/nco/nco" +description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, +including DAP, HDF4, and HDF5.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/nco/nco/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['6f0ba812e0684881a85ebf3385117761cffbba36ba842889cc96f111157f89c2'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.28'), + ('expat', '2.4.8'), + ('ANTLR', '2.7.7', '-Java-11'), + ('libdap', '3.20.11'), + ('GSL', '2.7'), + ('netCDF', '4.9.0'), + ('ESMF', '8.3.0'), # ncremap needs ESMF_RegridWeightGen +] + +configopts = "--enable-nco_cplusplus" + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +sanity_check_commands = [ + "ncks -O -7 --cnk_dmn time,10 " + "%(builddir)s/%(namelower)s-%(version)s/data/in.nc %(builddir)s/%(namelower)s-%(version)s/data/in4.cdl" +] + +moduleclass = 'tools' From eb337668e75daacdd7eccb209c76e5a148b338b3 Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 21 Sep 2022 15:16:54 +0200 Subject: [PATCH 132/793] use SHLIB_EXT for shared lib extension in sanity_check_paths --- .../easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb index a81d983d6e3..de1fa80521a 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb @@ -37,7 +37,7 @@ configopts = [ ] sanity_check_paths = { - 'files': ['lib/libmagma.so', 'lib/libmagma.a'], + 'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'], 'dirs': ['include'], } From f8f562e66cc7066424c34d7daaf1873a27661100 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 21 Sep 2022 16:38:44 +0100 Subject: [PATCH 133/793] adding easyconfigs: ruamel.yaml-0.17.21-GCCcore-10.3.0.eb --- .../ruamel.yaml-0.17.21-GCCcore-10.3.0.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e7b90307fb9 --- /dev/null +++ b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-10.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'ruamel.yaml' +version = '0.17.21' + +homepage = 'https://sourceforge.net/projects/ruamel-yaml' +description = "ruamel.yaml is a YAML 1.2 loader/dumper package for Python." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True + +exts_list = [ + ('ruamel.yaml.clib', '0.2.6', { + 'checksums': ['4ff604ce439abb20794f05613c374759ce10e3595d1867764dd1ae675b85acbd'], + 'modulename': False, + }), + (name, version, { + 'checksums': ['8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af'], + }), + ('configobj', '5.0.6', { + 'checksums': ['a2f5650770e1c87fb335af19a9b7eb73fc05ccf22144eb68db7d00cd2bcb0902'], + }), + ('ruamel.yaml.base', '0.3.0', { + 'checksums': ['bee661f95a842c3e90f83560f3a87ad3f9548ed4874af98f36b32aaf8a27462a'], + }), + ('ruamel.yaml.convert', '0.3.2', { + 'checksums': ['065ed9492a3189291d5bc0256709afc0231b52e4a01376fc91cf1757560ac9c4'], + }), + ('ruamel.yaml.cmd', '0.5.10', { + 'checksums': ['043c149c5517cfd0c7d02bd934224e1c9b0053a05e292a14f1b1a7f15bf0a943'], + }), +] + +sanity_check_paths = { + 'files': ['bin/yaml'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["yaml --help"] + +sanity_pip_check = True + +moduleclass = 'lang' From 9be8026ac8f947ee7754d5f365870a64590861cc Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 21 Sep 2022 16:41:39 +0100 Subject: [PATCH 134/793] adding easyconfigs: imgaug-0.4.0-foss-2021a.eb --- .../i/imgaug/imgaug-0.4.0-foss-2021a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021a.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021a.eb new file mode 100644 index 00000000000..b7fac2d92c5 --- /dev/null +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021a.eb @@ -0,0 +1,35 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. + +easyblock = 'PythonPackage' + +name = 'imgaug' +version = '0.4.0' + +homepage = 'https://imgaug.readthedocs.io/en/latest/' +description = """ This python library helps you with augmenting images for your machine learning projects. + It converts a set of input images into a new, much larger set of slightly altered images. """ + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('Pillow', '8.2.0'), + ('matplotlib', '3.4.2'), + ('scikit-image', '0.18.3'), + ('OpenCV', '4.5.3', '-contrib'), + ('Shapely', '1.8a1'), + ('imageio', '2.10.5'), +] + +sources = [SOURCE_TAR_GZ] +patches = ['imgaug-0.4.0_openvc_requirement.patch'] +checksums = [ + '46bab63ed38f8980630ff721a09ca2281b7dbd4d8c11258818b6ebcc69ea46c7', # imgaug-0.4.0.tar.gz + '2ff0b66ba38fdcf5f267a3d0ad1dc2710fee3c2f8cd3d086c56ea538a2a9ffc8', # imgaug-0.4.0_openvc_requirement.patch +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'lib' From 2f0c9a08a15784d70cb130b7443805338b2eca1e Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 21 Sep 2022 18:01:35 +0200 Subject: [PATCH 135/793] Added exception for FFmpeg versions for Paraview and OpenFOAM --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 0fb05afe876..da15318ca58 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -493,6 +493,8 @@ def check_dep_vars(self, gen, dep, dep_vars): 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], + # ParaView 5.10.x requires FFmpeg 4.x + 'FFmpeg': [(r'4\.4\.', [r'ParaView-5\.10\.', 'OpenFOAM-v2206'])], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], From ec2c696406bfb08928e199c00ba914e604f20406 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 21 Sep 2022 18:37:05 +0100 Subject: [PATCH 136/793] Missing gettext added --- .../easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.2.0.eb index db6674f606b..96a79ee0df8 100644 --- a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.2.0.eb @@ -23,6 +23,10 @@ builddependencies = [ ('M4', '1.4.19'), ] +dependencies = [ + ('gettext', '0.21'), +] + preconfigopts = "autoreconf -vfi && " sanity_check_commands = [ From a248ec88f183f7c09928cb3286da28ab9e646769 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 22 Sep 2022 09:46:31 +0100 Subject: [PATCH 137/793] adding easyconfigs: expecttest-0.1.3-GCCcore-11.2.0.eb --- .../expecttest-0.1.3-GCCcore-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..8eab7bea399 --- /dev/null +++ b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'expecttest' +version = '0.1.3' + +homepage = 'https://github.com/ezyang/expecttest' +description = """This library implements expect tests (also known as "golden" tests). Expect tests are a method of + writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and + the test framework automatically populates the expected output. If the output of the test changes, you can rerun + the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['83057695811d94128aed13ed094a070db90e0a92ea40071f8ee073cbab57149a'] + +builddependencies = [ + ('binutils', '2.37'), +] +dependencies = [ + ('Python', '3.9.6'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' From b53ad6aea6fd2aac2e4de798ceee7287980b34eb Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 22 Sep 2022 11:12:41 +0200 Subject: [PATCH 138/793] adding easyconfigs: netcdf4-python-1.6.1-foss-2022a.eb --- .../netcdf4-python-1.6.1-foss-2022a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb new file mode 100644 index 00000000000..e4909b8b62d --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.6.1' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('netCDF', '4.9.0'), + ('cURL', '7.83.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cftime', '1.6.2', { + 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], + }), + (name, version, { + 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + 'ba8dc5d65293a99f1afb8c2acf588d903fdfdc1963a62545b677fa2734262a78', # netCDF4-1.6.1.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' From 2e2208b9b3b48639fe927fcb1bd44711cbe05788 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 22 Sep 2022 12:31:20 +0200 Subject: [PATCH 139/793] Add TurboVNC --- .../TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb | 71 +++++++++++++++++++ .../TurboVNC-3.0.1_fix-libX11-libs.patch | 21 ++++++ 2 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1_fix-libX11-libs.patch diff --git a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..23252bd15dd --- /dev/null +++ b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb @@ -0,0 +1,71 @@ +easyblock = 'CMakeMake' + +name = 'TurboVNC' +version = '3.0.1' + +homepage = 'https://www.turbovnc.org' +description = """TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide + peak performance for 3D and video workloads.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/TurboVNC/turbovnc/archive'] +sources = ['%(version)s.tar.gz'] +patches = ['TurboVNC-%(version)s_fix-libX11-libs.patch'] +checksums = [ + 'f0bd45e4e6f8cb8a52b5ccdef70fbc28ba8776591554c166db113eedc914dd86', # 3.0.1.tar.gz + '11acc18ae10355c7c6816fad0a68ed55fbcb7a04efd30740c619a1d82ecbd4c2', # TurboVNC-3.0.1_fix-libX11-libs.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Java', '11', '', True), + ('X11', '20220504'), + ('pixman', '0.40.0'), + ('libjpeg-turbo', '2.1.3'), + ('Mesa', '22.0.3'), + ('libGLU', '9.0.2'), + ('libglvnd', '1.4.0'), + # OS dependency should be preferred if the OS version is more recent then this version, + # it's nice to have an up to date OpenSSL for security reasons + # ('OpenSSL', '1.1'), +] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), + ('pam-devel', 'libpam0g-dev'), +] + +configopts = "-DTVNC_BUILDJAVA=0 -DTVNC_SYSTEMX11=1 " +configopts += "-DX11_X11_LIB=$EBROOTX11/lib/libX11.%s " % SHLIB_EXT +configopts += "-DX11_Xau_LIB=$EBROOTX11/lib/libXau.%s " % SHLIB_EXT +configopts += "-DX11_SM_LIB=$EBROOTX11/lib/libSM.%s " % SHLIB_EXT +configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libICE.%s " % SHLIB_EXT +configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libXext.%s " % SHLIB_EXT +configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libICE.%s " % SHLIB_EXT +configopts += "-DX11_Pixman_LIB=$EBROOTPIXMAN/lib/libpixman-1.%s.0 " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_egl_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_opengl_LIBRARY=$EBROOTLIBGLVND/lib/libOpenGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glx_LIBRARY=$EBROOTLIBGLVND/lib/libGLX.%s " % SHLIB_EXT + +# if installdir starts with /opt, i.e. /opt/xxx, CMake will set SYSCONFDIR to /etc/opt/xxx instead of /opt/xxx/etc +# https://cmake.org/cmake/help/latest/module/GNUInstallDirs.html +# the solution is to define CMAKE_INSTALL_SYSCONFDIR explicitly +configopts += "-DCMAKE_INSTALL_SYSCONFDIR=%(installdir)s/etc " + +# remove etc/turbovncserver-security.conf, to avoid errors like: +# (EE) Fatal server error: +# (EE) ERROR: .../TurboVNC/2.2.3-GCCcore-8.2.0/etc/turbovncserver-security.conf must be owned by you or by root +postinstallcmds = ["rm -rf %(installdir)s/etc/turbovncserver-security.conf"] + +sanity_check_paths = { + 'files': ['bin/vncserver', 'bin/vncpasswd', 'bin/Xvnc'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1_fix-libX11-libs.patch b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1_fix-libX11-libs.patch new file mode 100644 index 00000000000..877631a18ff --- /dev/null +++ b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1_fix-libX11-libs.patch @@ -0,0 +1,21 @@ +# fix location of libXfont2.so and libfontenc.so +# don't derive location of libpixman-1.so from path to libX11.so +# author: Kenneth Hoste (HPC-UGent) +# +# updated to v3.0.1 by maxim-masterov (SURF) + +diff -Nru turbovnc-3.0.1.orig/unix/Xvnc/CMakeLists.txt turbovnc-3.0.1/unix/Xvnc/CMakeLists.txt +--- turbovnc-3.0.1.orig/unix/Xvnc/CMakeLists.txt 2022-09-22 11:31:39.142872000 +0200 ++++ turbovnc-3.0.1/unix/Xvnc/CMakeLists.txt 2022-09-22 11:33:07.984771000 +0200 +@@ -96,9 +96,8 @@ + if(TVNC_SYSTEMX11) + include_directories(${X11_X11_INCLUDE_PATH} ${X11_Xau_INCLUDE_PATH} + ${X11_Xdmcp_INCLUDE_PATH} ${X11_Xkbfile_INCLUDE_PATH}) +- string(REGEX REPLACE "X11" "Xfont2" X11_Xfont2_LIB ${X11_X11_LIB}) +- string(REGEX REPLACE "X11" "fontenc" X11_Fontenc_LIB ${X11_X11_LIB}) +- string(REGEX REPLACE "X11" "pixman-1" X11_Pixman_LIB ${X11_X11_LIB}) ++ string(REGEX REPLACE "libX11" "libXfont2" X11_Xfont2_LIB ${X11_X11_LIB}) ++ string(REGEX REPLACE "libX11" "libfontenc" X11_Fontenc_LIB ${X11_X11_LIB}) + else() + include_directories(${CMAKE_CURRENT_BINARY_DIR}/X_include) + set(X11_Xau_LIB Xau) From 4a40622848ecd414a86a51fd59842a3d175b8896 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 22 Sep 2022 12:57:12 +0200 Subject: [PATCH 140/793] Remove OpenSSL as OS dependency --- .../easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb index 23252bd15dd..9c572a880b6 100644 --- a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb @@ -30,13 +30,10 @@ dependencies = [ ('Mesa', '22.0.3'), ('libGLU', '9.0.2'), ('libglvnd', '1.4.0'), - # OS dependency should be preferred if the OS version is more recent then this version, - # it's nice to have an up to date OpenSSL for security reasons - # ('OpenSSL', '1.1'), + ('OpenSSL', '1.1', '', True), ] osdependencies = [ - ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ('pam-devel', 'libpam0g-dev'), ] From c3f9130e7f2cc24e66b88b8b0bafb4710b43df6a Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 22 Sep 2022 13:14:25 +0200 Subject: [PATCH 141/793] adding easyconfigs: likwid-5.2.2-GCC-11.3.0.eb --- .../l/likwid/likwid-5.2.2-GCC-11.3.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.2-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.2-GCC-11.3.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..2febcdf589c --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.2-GCC-11.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '5.2.2' + +homepage = 'https://github.com/RRZE-HPC/likwid' + +description = """ +Likwid stands for Like I knew what I am doing. This project contributes easy +to use command line tools for Linux to support programmers in developing high +performance multi threaded programs. +""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7dda6af722e04a6c40536fc9f89766ce10f595a8569b29e80563767a6a8f940e'] + +builddependencies = [ + ('Perl', '5.34.1'), +] + +dependencies = [ + ('hwloc', '2.7.1'), +] + +skipsteps = ['configure'] + +# include_GCC.mk is using ifort by default. +# Changing it to gfortran, to be consistent with GCC toolchain +prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ +prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ +prebuildopts += """ make/include_GCC.mk && """ + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' +buildopts += 'FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +buildopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' + +maxparallel = 1 + +installopts = buildopts + 'INSTALL_CHOWN="" ' + +sanity_check_paths = { + 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', + 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', + 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, + 'lib/liblikwid.%s' % SHLIB_EXT, 'include/likwid.mod'], + 'dirs': ['man/man1'] +} + +moduleclass = 'tools' From 78fcd2dda89e6cac6e6916a94bb4503ee06ea373 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 22 Sep 2022 18:53:02 +0200 Subject: [PATCH 142/793] Add wxWidgets and deps --- .../s/SDL2/SDL2-2.0.22-GCCcore-11.3.0.eb | 26 +++++++ .../w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb | 78 +++++++++++++++++++ 2 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.0.22-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.22-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.22-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..218bf61aeec --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.22-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.0.22' + +homepage = 'https://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['fe7cbf3127882e3fc7259a75a0cb585620272c51745d3852ab9dd87960697f2e'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('X11', '20220504'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..f4c078710de --- /dev/null +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb @@ -0,0 +1,78 @@ +easyblock = 'ConfigureMake' + +name = 'wxWidgets' +version = '3.2.1' + +homepage = 'https://www.wxwidgets.org' +description = """wxWidgets is a C++ library that lets developers create +applications for Windows, Mac OS X, Linux and other platforms with a +single code base. It has popular language bindings for Python, Perl, +Ruby and many other languages, and unlike other cross-platform toolkits, +wxWidgets gives applications a truly native look and feel because it +uses the platform's native API rather than emulating the GUI.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +# wxWidgets now contain three submodules: catch, nanosvg and pcre +sources = [{ + 'git_config': { + 'url': 'https://github.com/wxWidgets/', + 'repo_name': 'wxWidgets', + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [ + ('gettext', '0.21'), + ('pkgconf', '1.8.0'), + ('Python', '3.10.4'), +] + +dependencies = [ + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), + ('libjpeg-turbo', '2.1.3'), + ('XZ', '5.2.5'), + ('jbigkit', '2.1'), + ('LibTIFF', '4.3.0'), + ('expat', '2.4.8'), + ('GTK3', '3.24.33'), + ('X11', '20220504'), + ('Mesa', '22.0.3'), + ('libGLU', '9.0.2'), + ('SDL2', '2.0.22'), + ('cairo', '1.17.4'), + ('GST-plugins-base', '1.20.2'), + ('GLib', '2.72.1'), +] + +local_cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' + +preconfigopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +configopts = '--enable-intl --enable-ipv6 ' +# Options required by wxPython +configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' +# Note: the configure step might claim to find OpenGL headers in +# /usr/include, but it will still use the ones from the Mesa dependency above +configopts += '--with-opengl ' +configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' +configopts += '--enable-mediactrl --enable-display --enable-geometry ' +configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' +configopts += '--enable-autoidman --with-sdl ' +configopts += '--disable-webview --disable-webviewwebkit ' +configopts += '--disable-tests ' + + +prebuildopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +sanity_check_paths = { + 'files': ['bin/wx-config', 'bin/wxrc'], + 'dirs': ['include/wx-%(version_major_minor)s/wx', 'lib', 'share'], +} + +moduleclass = 'vis' From 31be407cee5520158566119340b2006fc5c10dea Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 22 Sep 2022 21:49:15 +0000 Subject: [PATCH 143/793] adding easyconfigs: Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb --- .../Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0973b977079 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'Pillow-SIMD' +version = '9.2.0' + +homepage = 'https://github.com/uploadcare/pillow-simd' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1c3b4bce334fbb234be506cd3146a93714f9de43032aaf807ff47a20d6b42c95'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), + ('LibTIFF', '4.3.0'), + ('freetype', '2.12.1') +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'], +} + +sanity_pip_check = True + +moduleclass = 'vis' From e519f27f87a3c856f790193512bef68cca5fe5b0 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 22 Sep 2022 21:53:07 +0000 Subject: [PATCH 144/793] adding easyconfigs: torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb --- ...rchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..c2820fcd722 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,23 @@ +name = 'torchvision' +version = '0.13.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c32fab734e62c7744dadeb82f7510ff58cc3bca1189d17b16aa99b08afc42249'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('Python', '3.10.4'), + ('Pillow-SIMD', '9.2.0'), + ('PyTorch', '1.12.0', '-CUDA-%(cudaver)s'), +] + +moduleclass = 'vis' From a9dd768833abb2fd849a0401aea1a43b894cc793 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 22 Sep 2022 22:19:20 +0000 Subject: [PATCH 145/793] adding easyconfigs: tensorboard-2.10.0-foss-2022a.eb --- .../tensorboard-2.10.0-foss-2022a.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb new file mode 100644 index 00000000000..329c77c8106 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'tensorboard' +version = '2.10.0' + +homepage = 'https://github.com/tensorflow/tensorboard' +description = """TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs +and graphs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('protobuf-python', '3.19.4'), +] + +exts_list = [ + ('absl-py', '1.2.0', { + 'modulename': 'absl', + 'checksums': ['f568809938c49abbda89826223c992b630afd23c638160ad7840cfe347710d97'], + }), + ('cachetools', '5.2.0', { + 'checksums': ['6a94c6402995a99c3970cc7e4884bb60b4a8639938157eeed436098bf9831757'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('google-auth', '2.11.1', { + 'modulename': 'google.auth', + 'checksums': ['516e6623038b81430dd062a1a25ecd24f173d7c15cdf4e48a9e78bc87e97aeec'], + }), + ('oauthlib', '3.2.1', { + 'checksums': ['1565237372795bf6ee3e5aba5e2a85bd5a65d0e2aa5c628b9a97b7d7a0da3721'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('google-auth-oauthlib', '0.4.6', { + 'checksums': ['a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a'], + }), + ('grpcio', '1.49.1', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['d4725fc9ec8e8822906ae26bb26f5546891aa7fbc3443de970cc556d43a5c99f'], + }), + ('importlib_metadata', '4.12.0', { + 'checksums': ['637245b8bab2b6502fcbc752cc4b7a6f6243bb02b31c5c26156ad103d3d45670'], + }), + ('Markdown', '3.4.1', { + 'checksums': ['3b809086bb6efad416156e00a0da66fe47618a5d6918dd688f53f40c8e4cfeff'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('tensorboard_plugin_wit', '1.8.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('Werkzeug', '2.2.2', { + 'checksums': ['7ea2d48322cc7c0f8b3a215ed73eabd7b5d75d0b50e31ab006286ccff9e00b8f'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['76c91a5e8959cd2208cc32cb17a0cb002badabb66a06ac2af02a7810f49a59e3'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From f92c831a18daa4dd3ec59ba6ee6d040b65134870 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 22 Sep 2022 22:27:53 +0000 Subject: [PATCH 146/793] adding easyconfigs: PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb --- ...-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..ff7163f6c19 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Lightning' +version = '1.7.7' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorchlightning.ai' +description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', versionsuffix), + ('tqdm', '4.64.0'), + ('tensorboard', '2.10.0'), + ('typing-extensions', '4.3.0'), +] + + +exts_list = [ + ('fsspec', '2022.8.2', { + 'checksums': ['7f12b90964a98a7e921d27fb36be536ea036b73bf3b724ac0b0bd7b8e39c7c18'], + }), + + ('pyDeprecate', '0.3.2', { + 'modulename': 'deprecate', + 'checksums': ['d481116cc5d7f6c473e7c4be820efdd9b90a16b594b350276e9e66a6cb5bdd29'], + }), + ('torchmetrics', '0.9.3', { + 'checksums': ['4ebfd2466021db26397636966ee1a195d3b340ba5d71bb258e764340dfc2476f'], + }), + ('pytorch-lightning', version, { + 'checksums': ['27c2dd01a18db2415168e3fa3775ccb5a1fa1e2961a50439ad9365507fe9d4ae'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 21cfa6c6e5d8250afe071f4e79c9896736a9f1ec Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 23 Sep 2022 09:15:03 +0200 Subject: [PATCH 147/793] adding easyconfigs: GPAW-22.8.0-foss-2021b.eb, GPAW-22.8.0-intel-2021b.eb, ASE-3.22.1-foss-2021b.eb, ASE-3.22.1-intel-2021b.eb, spglib-python-1.16.3-foss-2021b.eb, spglib-python-1.16.3-intel-2021b.eb and patches: GPAW-22.8.0-Remove-MPI-compiler-hack.patch --- .../a/ASE/ASE-3.22.1-foss-2021b.eb | 47 +++++++++++++++++ .../a/ASE/ASE-3.22.1-intel-2021b.eb | 47 +++++++++++++++++ ...GPAW-22.8.0-Remove-MPI-compiler-hack.patch | 35 +++++++++++++ .../g/GPAW/GPAW-22.8.0-foss-2021b.eb | 50 +++++++++++++++++++ .../g/GPAW/GPAW-22.8.0-intel-2021b.eb | 49 ++++++++++++++++++ .../spglib-python-1.16.3-foss-2021b.eb | 27 ++++++++++ .../spglib-python-1.16.3-intel-2021b.eb | 27 ++++++++++ 7 files changed, 282 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-intel-2021b.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Remove-MPI-compiler-hack.patch create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2021b.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.3-foss-2021b.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.3-intel-2021b.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2021b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2021b.eb new file mode 100644 index 00000000000..eb2f5708e31 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2021b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Flask', '2.0.2'), + ('matplotlib', '3.4.3'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '1.16.3'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.6.1', { + 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], + }), + ('ase', version, { + 'checksums': ['004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-intel-2021b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-intel-2021b.eb new file mode 100644 index 00000000000..d490b91739e --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-intel-2021b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Flask', '2.0.2'), + ('matplotlib', '3.4.3'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '1.16.3'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.6.1', { + 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], + }), + ('ase', version, { + 'checksums': ['004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Remove-MPI-compiler-hack.patch b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Remove-MPI-compiler-hack.patch new file mode 100644 index 00000000000..da9d3311269 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Remove-MPI-compiler-hack.patch @@ -0,0 +1,35 @@ +Author: Jakob Schiøtz +Date: Thu Jan 27 11:55:07 CET 2022 + +This patch removes the part of setup.py responsible for replacing the +normal compiler with an MPI aware compiler, as that is already done +correctly by the EasyBuild system. + +--- setup.old 2022-01-26 14:37:48.522572258 +0100 ++++ setup.py 2022-01-26 14:39:55.973416534 +0100 +@@ -104,25 +104,6 @@ + if platform_id: + os.environ['_PYTHON_HOST_PLATFORM'] = get_platform() + '-' + platform_id + +-if compiler is not None: +- # A hack to change the used compiler and linker: +- try: +- # distutils is deprecated and will be removed in 3.12 +- from distutils.sysconfig import get_config_vars +- except ImportError: +- from sysconfig import get_config_vars +- +- # If CC is set then the following hack will not work +- assert not os.environ.get('CC'), 'Please unset CC' +- +- vars = get_config_vars() +- for key in ['CC', 'LDSHARED']: +- if key in vars: +- value = vars[key].split() +- # first argument is the compiler/linker. Replace with mpicompiler: +- value[0] = compiler +- vars[key] = ' '.join(value) +- + for flag, name in [(noblas, 'GPAW_WITHOUT_BLAS'), + (nolibxc, 'GPAW_WITHOUT_LIBXC'), + (fftw, 'GPAW_WITH_FFTW'), diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2021b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2021b.eb new file mode 100644 index 00000000000..e3d8e921b48 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2021b.eb @@ -0,0 +1,50 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '22.8.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), + ('GPAW-22.8.0-Remove-MPI-compiler-hack.patch', 0), +] +checksums = [ + '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c', # gpaw-22.8.0.tar.gz + # GPAW-20.1.0-Add-Easybuild-configuration-files.patch + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', + '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e', # GPAW-22.8.0-Remove-MPI-compiler-hack.patch +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('ASE', '3.22.1'), + ('libxc', '5.1.6'), + ('PyYAML', '5.4.1'), + ('libvdwxc', '0.4.0'), + ('GPAW-setups', '0.9.20000', '', True), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2021b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2021b.eb new file mode 100644 index 00000000000..1ca56803196 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2021b.eb @@ -0,0 +1,49 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '22.8.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), + ('GPAW-22.8.0-Remove-MPI-compiler-hack.patch', 0), +] +checksums = [ + '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c', # gpaw-22.8.0.tar.gz + # GPAW-20.1.0-Add-Easybuild-configuration-files.patch + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', + '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e', # GPAW-22.8.0-Remove-MPI-compiler-hack.patch +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('ASE', '3.22.1'), + ('libxc', '5.1.6'), + ('PyYAML', '5.4.1'), + ('GPAW-setups', '0.9.20000', '', True), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.3-foss-2021b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.3-foss-2021b.eb new file mode 100644 index 00000000000..d13be3c325e --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.3-foss-2021b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.16.3' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['ff1420967d64c2d4f0d747886116a6836d9b473454cdd73d560dbfe973a8a038'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'spglib'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.3-intel-2021b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.3-intel-2021b.eb new file mode 100644 index 00000000000..eaa79870a2b --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.3-intel-2021b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.16.3' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." + +toolchain = {'name': 'intel', 'version': '2021b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['ff1420967d64c2d4f0d747886116a6836d9b473454cdd73d560dbfe973a8a038'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'spglib'} + +moduleclass = 'chem' From bd9e4676ee714e90d78d33be8edd48b97109daee Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 23 Sep 2022 13:26:13 +0200 Subject: [PATCH 148/793] Added exception for FFmpeg versions for Paraview and OpenFOAM --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 0fb05afe876..da15318ca58 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -493,6 +493,8 @@ def check_dep_vars(self, gen, dep, dep_vars): 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], + # ParaView 5.10.x requires FFmpeg 4.x + 'FFmpeg': [(r'4\.4\.', [r'ParaView-5\.10\.', 'OpenFOAM-v2206'])], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], From ad6224a33d7921928d9faa3047427c50c5d495c2 Mon Sep 17 00:00:00 2001 From: robogast Date: Fri, 23 Sep 2022 13:26:35 +0200 Subject: [PATCH 149/793] re-added some nice templates from OpenCV/2021b easyconfig --- .../OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 50 +++++-------------- 1 file changed, 13 insertions(+), 37 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index 295bc7ccf2b..dc22d0ca82d 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -2,6 +2,9 @@ name = 'OpenCV' version = '4.6.0' versionsuffix = '-contrib' +# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake +local_ippicv_hash = 'a56b6ac6f030c312b2dce17430eef13aed9af274' + homepage = 'https://opencv.org/' description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide @@ -23,7 +26,7 @@ sources = [ 'filename': '%(namelower)s_contrib-%(version)s.zip' }, { - 'source_urls': ['https://raw.githubusercontent.com/%(namelower)s/opencv_3rdparty/a56b6ac6f030c312b2dce17430eef13aed9af274/ippicv'], # noqa: E501 + 'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', 'extract_cmd': 'cp %s %(builddir)s' }, @@ -73,45 +76,18 @@ configopts = " ".join([ "-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON", "-DBUILD_opencv_python2=OFF", ]) + enhance_sanity_check = True +local_contrib_libs = [ + 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', + 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', + 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', + 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' +] + sanity_check_paths = { - 'files': [ - 'lib64/libopencv_aruco.so', - 'lib64/libopencv_bgsegm.so', - 'lib64/libopencv_bioinspired.so', - 'lib64/libopencv_ccalib.so', - 'lib64/libopencv_datasets.so', - 'lib64/libopencv_dnn_objdetect.so', - 'lib64/libopencv_dnn_superres.so', - 'lib64/libopencv_dpm.so', - 'lib64/libopencv_face.so', - 'lib64/libopencv_freetype.so', - 'lib64/libopencv_fuzzy.so', - 'lib64/libopencv_hdf.so', - 'lib64/libopencv_hfs.so', - 'lib64/libopencv_img_hash.so', - 'lib64/libopencv_line_descriptor.so', - 'lib64/libopencv_optflow.so', - 'lib64/libopencv_phase_unwrapping.so', - 'lib64/libopencv_plot.so', - 'lib64/libopencv_quality.so', - 'lib64/libopencv_reg.so', - 'lib64/libopencv_rgbd.so', - 'lib64/libopencv_saliency.so', - 'lib64/libopencv_shape.so', - 'lib64/libopencv_stereo.so', - 'lib64/libopencv_structured_light.so', - 'lib64/libopencv_superres.so', - 'lib64/libopencv_surface_matching.so', - 'lib64/libopencv_text.so', - 'lib64/libopencv_tracking.so', - 'lib64/libopencv_videostab.so', - 'lib64/libopencv_xfeatures2d.so', - 'lib64/libopencv_ximgproc.so', - 'lib64/libopencv_xobjdetect.so', - 'lib64/libopencv_xphoto.so' - ], + 'files': ['lib64/libopencv_%s.%s' % (l, SHLIB_EXT) for l in local_contrib_libs], 'dirs': [], } From a873082eeb9df75e358a3009eb6e9ea6bdc55946 Mon Sep 17 00:00:00 2001 From: robogast Date: Fri, 23 Sep 2022 13:44:22 +0200 Subject: [PATCH 150/793] re-added templates to OpenEXR, libwebp ec's --- .../l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb | 17 ++++------------- .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 19 +++++++------------ 2 files changed, 11 insertions(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb index 6fd104e1260..51de3daf755 100644 --- a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb @@ -29,20 +29,11 @@ configopts = '--enable-libwebpmux' sanity_check_paths = { 'files': [ - 'include/webp/decode.h', - 'include/webp/demux.h', - 'include/webp/encode.h', - 'include/webp/mux.h', - 'include/webp/mux_types.h', - 'include/webp/types.h', - 'lib/%(name)s.a', - 'lib/libwebpdemux.a', - 'lib/libwebpmux.a', - 'lib/%(name)s.so', - 'lib/libwebpdemux.so', - 'lib/libwebpmux.so' + *['include/webp/%s' % f for f in ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h']], + *['lib/lib%s.a' % l for l in ['webp', 'webpdemux', 'webpmux']], + *['lib/lib%s.%s' % (l, SHLIB_EXT) for l in ['webp', 'webpdemux', 'webpmux']], ], - 'dirs': ['lib/'], + 'dirs': ['lib/'] } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb index 6d2db3b7ccc..77a049dd6b3 100644 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -20,20 +20,15 @@ builddependencies = [ configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' +local_libs, local_bins = [ + ['Iex', 'IlmThread', 'Imath', 'OpenEXR', 'OpenEXRUtil'], + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] +] + sanity_check_paths = { 'files': [ - 'lib/libIex.so', - 'lib/libIlmThread.so', - 'lib/libImath.so', - 'lib/libOpenEXR.so', - 'lib/libOpenEXRUtil.so', - 'bin/exrenvmap', - 'bin/exrheader', - 'bin/exrmakepreview', - 'bin/exrmaketiled', - 'bin/exrmultipart', - 'bin/exrmultiview', - 'bin/exrstdattr' + *['lib/lib%s.%s' % (lib, SHLIB_EXT) for lib in local_libs], + *['bin/exr%s' % bin for bin in local_bins] ], 'dirs': ['include/%(name)s', 'share'], } From 9920070ea2cf9a2f820746237965d0a85e0af165 Mon Sep 17 00:00:00 2001 From: Jef Scheepers Date: Fri, 23 Sep 2022 14:10:44 +0200 Subject: [PATCH 151/793] add python-irodsclient --- .../python-irodsclient-1.1.4.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4.eb diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4.eb new file mode 100644 index 00000000000..9876e55d90f --- /dev/null +++ b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonBundle' +name = 'python-irodsclient' +version = '1.1.4' +homepage = 'https://github.com/irods/python-irodsclient' +description = "A python API for iRODS" +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True +# order is important! +exts_list = [ + ('defusedxml', '0.7.1', {}), + ('prettytable', '3.3.0', {}), + ('python-irodsclient', '1.1.4', {'modulename':'irods'}) +] + +sanity_pip_check = True +moduleclass = 'tools' + From 06cdc6f61197ce2e58ee7e05984ed70d8124c2f4 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 23 Sep 2022 14:17:36 +0200 Subject: [PATCH 152/793] adding easyconfigs: matplotlib-3.5.2-intel-2022a.eb --- .../matplotlib-3.5.2-intel-2022a.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb new file mode 100644 index 00000000000..2bf90cc74a0 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.5.2' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('cppy', '1.2.1') +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('libpng', '1.6.37'), + ('freetype', '2.12.1'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '9.1.1'), + ('Qhull', '2020.2') +] + +use_pip = True +sanity_pip_check = True + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >setup.cfg && " + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('fonttools', '4.34.0', { + 'modulename': 'fontTools', + 'source_tmpl': SOURCE_ZIP, + 'checksums': ['73d3fab85790f076d56db431bfdf9ce51b566816ff74d51e050e11ab1ffa8f8b'], + }), + ('Cycler', '0.11.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['9c87405839a19696e837b3b818fed3f5f69f16f1eec1a1ad77e043dcea9c772f'], + }), + ('kiwisolver', '1.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['ab8a15c2750ae8d53e31f77a94f846d0a00772240f1c12817411fa2344351f86'], + }), + (name, version, { + 'preinstallopts': _fix_setup + _include_path, + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['48cf850ce14fa18067f2d9e0d646763681948487a8080ec0af2686468b4607a2'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' From dafc83c8bc187f651b9c094aed5920cf79bcf34c Mon Sep 17 00:00:00 2001 From: easybuild Date: Fri, 23 Sep 2022 13:40:15 +0000 Subject: [PATCH 153/793] adding easyconfigs: umap-learn-0.5.3-foss-2021a.eb --- .../umap-learn/umap-learn-0.5.3-foss-2021a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb new file mode 100644 index 00000000000..449a1fd265a --- /dev/null +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb @@ -0,0 +1,44 @@ +# Author: Denis Krišťák (INUITS) +# This is a contribution from HPCNow! (http://hpcnow.com) +# Update: Erica Bianco +# License:: GPL-v3.0 +easyblock = "PythonBundle" + +name = 'umap-learn' +version = '0.5.3' + +homepage = 'https://umap-learn.readthedocs.io/en/latest/' +description = """Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique + that can be used for visualisation similarly to t-SNE, but also for general non-linear + dimension reduction.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('scikit-learn', '0.24.2'), + ('numba', '0.53.1'), + ('LLVM', '11.1.0'), + ('tqdm', '4.61.1'), +] + +use_pip = True +download_dep_fail = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('pynndescent', '0.5.7', { + 'checksums': ['ecb395255fa36a748b5870b4ba0300ea0f7da8b1964864b8edd62577a84dfd7d'], + }), + (name, version, { + 'modulename': 'umap', + 'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 80dd609251242b16344fc3a70a2fafb06f161812 Mon Sep 17 00:00:00 2001 From: Jef Scheepers Date: Fri, 23 Sep 2022 16:54:25 +0200 Subject: [PATCH 154/793] Add python and gcccore version to filename This will be easier to tell versions apart (colleagues asked me to soon make a version with gcccore 10.3.0). I tried to follow the example of other files in the repo. --- ...eb => python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/python-irodsclient/{python-irodsclient-1.1.4.eb => python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb} (100%) diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb similarity index 100% rename from easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4.eb rename to easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb From c9bd54fff8d08483d912fd32ae6f5f9fc4cf88c3 Mon Sep 17 00:00:00 2001 From: Jef Scheepers Date: Fri, 23 Sep 2022 16:58:35 +0200 Subject: [PATCH 155/793] add checksums --- ...lient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb | 51 +++++++++++-------- 1 file changed, 29 insertions(+), 22 deletions(-) mode change 100644 => 100755 easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb old mode 100644 new mode 100755 index 9876e55d90f..f8e17945770 --- a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb +++ b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb @@ -1,22 +1,29 @@ -easyblock = 'PythonBundle' -name = 'python-irodsclient' -version = '1.1.4' -homepage = 'https://github.com/irods/python-irodsclient' -description = "A python API for iRODS" -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -dependencies = [ - ('Python', '3.9.6'), -] - -use_pip = True -# order is important! -exts_list = [ - ('defusedxml', '0.7.1', {}), - ('prettytable', '3.3.0', {}), - ('python-irodsclient', '1.1.4', {'modulename':'irods'}) -] - -sanity_pip_check = True -moduleclass = 'tools' - +easyblock = 'PythonBundle' +name = 'python-irodsclient' +version = '1.1.4' +homepage = 'https://github.com/irods/python-irodsclient' +description = "A python API for iRODS" +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True +# order is important! +exts_list = [ + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('prettytable', '3.3.0', { + 'checksums': ['118eb54fd2794049b810893653b20952349df6d3bc1764e7facd8a18064fa9b0'], + }), + (name, version, { + 'modulename': 'irods', + 'checksums': ['f427699739911042dc35a7fbd92f7ba87db9fad3977423c2fa2ab61a0ffebe43'], + }), +] + +sanity_pip_check = True +moduleclass = 'tools' + From dab93d8e3991b7251f6f01d746fa4dc0f3f50389 Mon Sep 17 00:00:00 2001 From: Jef Scheepers Date: Fri, 23 Sep 2022 17:01:46 +0200 Subject: [PATCH 156/793] Improve style Also switched module type to lib (more appropriate for python library) --- ...thon-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb index f8e17945770..a039002b7e6 100755 --- a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb +++ b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb @@ -1,8 +1,11 @@ easyblock = 'PythonBundle' + name = 'python-irodsclient' version = '1.1.4' + homepage = 'https://github.com/irods/python-irodsclient' description = "A python API for iRODS" + toolchain = {'name': 'GCCcore', 'version': '11.2.0'} dependencies = [ @@ -10,7 +13,8 @@ dependencies = [ ] use_pip = True -# order is important! +sanity_pip_check = True + exts_list = [ ('defusedxml', '0.7.1', { 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], @@ -24,6 +28,5 @@ exts_list = [ }), ] -sanity_pip_check = True -moduleclass = 'tools' +moduleclass = 'lib' From a4620aee58528ac877274c58586475445027a871 Mon Sep 17 00:00:00 2001 From: Jef Scheepers Date: Fri, 23 Sep 2022 17:08:51 +0200 Subject: [PATCH 157/793] Remove blank line at end of file Apparently style requirement --- .../python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb index a039002b7e6..3286483e5bc 100755 --- a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb +++ b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb @@ -28,5 +28,4 @@ exts_list = [ }), ] -moduleclass = 'lib' - +moduleclass = 'lib' \ No newline at end of file From 930d392f1bea57ad451eb6e498671da53961feee Mon Sep 17 00:00:00 2001 From: Jef Scheepers Date: Fri, 23 Sep 2022 17:15:27 +0200 Subject: [PATCH 158/793] add python version suffix --- .../python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb index 3286483e5bc..5a022f20b13 100755 --- a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb +++ b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb @@ -2,6 +2,7 @@ easyblock = 'PythonBundle' name = 'python-irodsclient' version = '1.1.4' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/irods/python-irodsclient' description = "A python API for iRODS" @@ -28,4 +29,5 @@ exts_list = [ }), ] -moduleclass = 'lib' \ No newline at end of file +moduleclass = 'lib' + From b1bf3645b4d2b35d7aee08b8ec13515b69c39a5d Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 23 Sep 2022 20:16:58 +0200 Subject: [PATCH 159/793] adding easyconfigs: FDS-6.7.9-intel-2022a.eb --- .../f/FDS/FDS-6.7.9-intel-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-6.7.9-intel-2022a.eb diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.7.9-intel-2022a.eb b/easybuild/easyconfigs/f/FDS/FDS-6.7.9-intel-2022a.eb new file mode 100644 index 00000000000..ba9526d4281 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.7.9-intel-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = '6.7.9' + +homepage = 'https://pages.nist.gov/fds-smv' +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} + +source_urls = ['https://github.com/firemodels/fds/archive/'] +sources = ['FDS%(version)s.tar.gz'] +checksums = ['b6889471a56d0ebf07dfc93bbd35600b7c9ea13f194478c9f797cb653624ecd2'] + +unpack_options = '--strip-components=1' + +start_dir = 'Build' + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +buildopts = 'impi_intel_linux_openmp &&' +buildopts += 'cd %(installdir)s/Build && mv fds_impi_intel_linux_openmp fds' + +modextrapaths = {'PATH': 'Build'} + +sanity_check_paths = { +'files': ['Build/fds'], +'dirs': [], +} + +sanity_check_commands = [ + "fds 2>&1 | grep 'MPI Enabled;'", + "fds 2>&1 | grep 'OpenMP Enabled;'", +] + +moduleclass = 'phys' From 9fd620c19fa6392cf59e01e377d5077e3b827e86 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 23 Sep 2022 20:41:22 +0200 Subject: [PATCH 160/793] Added requested changes + fixed style errors --- easybuild/easyconfigs/f/FDS/FDS-6.7.9-intel-2022a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.7.9-intel-2022a.eb b/easybuild/easyconfigs/f/FDS/FDS-6.7.9-intel-2022a.eb index ba9526d4281..f26d9139e84 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-6.7.9-intel-2022a.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-6.7.9-intel-2022a.eb @@ -23,13 +23,13 @@ skipsteps = ['configure', 'install'] buildininstalldir = True buildopts = 'impi_intel_linux_openmp &&' -buildopts += 'cd %(installdir)s/Build && mv fds_impi_intel_linux_openmp fds' +buildopts += 'cd %(installdir)s/Build && ln -s fds_impi_intel_linux_openmp fds' modextrapaths = {'PATH': 'Build'} sanity_check_paths = { -'files': ['Build/fds'], -'dirs': [], + 'files': ['Build/fds'], + 'dirs': [], } sanity_check_commands = [ From bdcf2fa8a7754cc4a57e7b3abf60fbaa39c3cd72 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Sep 2022 21:08:05 +0200 Subject: [PATCH 161/793] {data}[GCC/11.3.0] MariaDB v10.9.3, libaio v0.3.112, LZO v2.10, Judy v1.0.5 --- .../j/Judy/Judy-1.0.5-GCCcore-11.3.0.eb | 34 ++++++++++ .../l/LZO/LZO-2.10-GCCcore-11.3.0.eb | 27 ++++++++ .../l/libaio/libaio-0.3.112-GCCcore-11.3.0.eb | 39 +++++++++++ .../m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb | 65 +++++++++++++++++++ 4 files changed, 165 insertions(+) create mode 100644 easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..32dbb74b6cf --- /dev/null +++ b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Judy' +version = '1.0.5' + +homepage = 'http://judy.sourceforge.net/' +description = "A C library that implements a dynamic array." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://downloads.sourceforge.net/judy'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['Judy-1.0.5_parallel-make.patch'] # fix Make dependencies, so parallel build also works + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] +checksums = [ + 'd2704089f85fdb6f2cd7e77be21170ced4b4375c03ef1ad4cf1075bd414a63eb', # Judy-1.0.5.tar.gz + '14c2eba71088f3db9625dc4605c6d7183d72412d75ef6c9fd9b95186165cf009', # Judy-1.0.5_parallel-make.patch +] + +preconfigopts = "sed -i 's/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/g' configure.ac && " +preconfigopts += "autoreconf -i && " + +configopts = '--enable-shared --enable-static' + +sanity_check_paths = { + 'files': ["include/%(name)s.h", "lib/lib%(name)s.a", "lib/lib%(name)s.la", "lib/lib%%(name)s.%s" % SHLIB_EXT], + 'dirs': ["share/man"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..108c91bc2a7 --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'https://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +source_urls = [homepage + 'download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [('binutils', '2.38')] + +configopts = '--enable-shared' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..024258d1792 --- /dev/null +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'libaio' +version = '0.3.112' +_libversion = '1.0.1' + +homepage = 'https://pagure.io/libaio' +description = "Asynchronous input/output library that uses the kernels native interface." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://pagure.io/%(name)s/archive/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['4410c033237828c9e1205537df3cc94d4956f39164ef6d17a7813c2c787504c4'] + +builddependencies = [('binutils', '2.38')] + +_soname = "libaio.%s.%s" % (SHLIB_EXT, _libversion) + +files_to_copy = [ + (["src/libaio.a", "src/%s" % _soname], "lib"), + (["src/libaio.h"], "include"), +] + +# links to the shared library with generic names +_solinks = [ + "libaio.%s" % SHLIB_EXT, + "libaio.%s.1" % SHLIB_EXT, +] + +postinstallcmds = ["cd %%(installdir)s/lib && ln -s %s %s" % (_soname, l) for l in _solinks] + +sanity_check_paths = { + 'files': ['lib/%s' % l for l in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb new file mode 100644 index 00000000000..0742cb59603 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb @@ -0,0 +1,65 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '10.9.3' + +homepage = 'https://mariadb.org/' +description = """MariaDB is an enhanced, drop-in replacement for MySQL. +Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] +checksums = [ + '9a1e229972fcccc8270e633f68d3fb824da151dcf4f53da1df8d947aca876bee', # mariadb-10.9.3.tar.gz + '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19', # MariaDB-10.1.13-link-rt-for-jemalloc.patch +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('libaio', '0.3.112'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('LZO', '2.10'), # optional + ('lz4', '1.9.3'), # optional + ('XZ', '5.2.5'), # optional + ('jemalloc', '5.3.0'), # optional + ('snappy', '1.1.9'), # needed by RocksDB; optional for InnoDB + ('libxml2', '2.9.13'), # needed by Connect XML + ('Boost', '1.79.0'), # needed by OQGraph + ('Judy', '1.0.5'), # needed by OQGraph + ('PCRE2', '10.40'), + ('OpenSSL', '1.1', '', True), # runtime dep for mysql and PCRE2 for mysqltest +] + +separate_build_dir = True + +configopts = "-DCMAKE_BUILD_TYPE=Release " +configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) +configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we build PCRE2 directly. +configopts += "-DWITH_ZLIB=system " +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co +configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc + +sanity_check_commands = ["mysql --help", "mysqltest --help"] + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, + 'lib/plugin/ha_connect.%s' % SHLIB_EXT, 'lib/plugin/ha_rocksdb.%s' % SHLIB_EXT, + 'lib/plugin/ha_oqgraph.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +modextrapaths = {'PATH': 'scripts'} + +# Ensure that jemalloc does not use transparent hugepages. +# Database workloads with THP can cause memory bloat, potentially hiting OOM errors. +modextravars = {'MALLOC_CONF': 'thp:never'} + +moduleclass = 'data' From 8b7eab255b88438a757613242a0c5e766d48799c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Sep 2022 21:10:48 +0200 Subject: [PATCH 162/793] {bio}[GCC/11.3.0] VEP v107, Archive-Zip v1.68, DBD-mysql v4.050, ... --- .../Archive-Zip-1.68-GCCcore-11.3.0.eb | 32 ++++++++++++++++ .../Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.3.0.eb | 32 ++++++++++++++++ .../Compress-Raw-Zlib-2.202-GCCcore-11.3.0.eb | 31 +++++++++++++++ .../d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb | 29 ++++++++++++++ .../easyconfigs/v/VEP/VEP-107-GCC-11.3.0.eb | 38 +++++++++++++++++++ 5 files changed, 162 insertions(+) create mode 100644 easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.202-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/v/VEP/VEP-107-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ef7187f720d --- /dev/null +++ b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PerlModule' + +name = 'Archive-Zip' +version = '1.68' + +homepage = 'https://metacpan.org/pod/Archive::Zip' +description = "Provide an interface to ZIP archive files." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Perl', '5.34.1'), + ('UnZip', '6.0'), + ('Zip', '3.0'), +] + +options = {'modulename': 'Archive::Zip'} + +sanity_check_paths = { + 'files': ['bin/crc32'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/Archive/Zip'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.3.0.eb new file mode 100644 index 00000000000..68542cd0dae --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PerlModule' + +name = 'Bio-DB-HTS' +version = '3.01' + +homepage = 'https://metacpan.org/release/Bio-DB-HTS' +description = "Read files using HTSlib including BAM/CRAM, Tabix and BCF database files" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/A/AV/AVULLO/'] +sources = ['Bio-DB-HTS-%(version)s.tar.gz'] +checksums = ['12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42'] + +builddependencies = [('pkgconf', '1.8.0')] + +dependencies = [ + ('Perl', '5.34.1'), + ('BioPerl', '1.7.8'), + ('HTSlib', '1.15.1'), +] + +preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB" + +options = {'modulename': 'Bio::DB::HTS'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s', 'man/man3'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.202-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.202-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a52e00e9f4b --- /dev/null +++ b/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.202-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'Compress-Raw-Zlib' +version = '2.202' + +homepage = 'https://metacpan.org/pod/Compress::Raw::Zlib' +description = "Low-Level Interface to zlib or zlib-ng compression library" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['96e20946eb457a32d2d7a0050b922e37b5ada41246bcdc824196d3f7c4da91b7'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Perl', '5.34.1'), + ('zlib', '1.2.12'), +] + +options = {'modulename': 'Compress::Raw::Zlib'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/Compress/Raw/Zlib.pm'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb new file mode 100644 index 00000000000..eb71c16f467 --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.050' + +homepage = 'https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm' +description = "Perl binding for MySQL" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/D/DV/DVEEDEN'] +sources = [SOURCE_TAR_GZ] +checksums = ['4f48541ff15a0a7405f76adc10f81627c33996fbf56c95c26c094444c0928d78'] + +dependencies = [ + ('Perl', '5.34.1'), + ('MariaDB', '10.9.3'), + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', True), +] + +options = {'modulename': 'DBD::mysql'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql.pm' % ARCH], + 'dirs': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql' % ARCH], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/v/VEP/VEP-107-GCC-11.3.0.eb b/easybuild/easyconfigs/v/VEP/VEP-107-GCC-11.3.0.eb new file mode 100644 index 00000000000..c6e1c1413ca --- /dev/null +++ b/easybuild/easyconfigs/v/VEP/VEP-107-GCC-11.3.0.eb @@ -0,0 +1,38 @@ +name = 'VEP' +version = '107' + +homepage = 'https://www.ensembl.org/info/docs/tools/vep' +description = """Variant Effect Predictor (VEP) determines the effect of your + variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, + transcripts, and protein sequence, as well as regulatory regions. + Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently + used routines in VEP.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/Ensembl/ensembl-vep/archive/release/'] +sources = ['%(version)s.tar.gz'] +checksums = ['4531acfe7a0dc3b1aaf0f9bead043cfb20b6df23a3a922a27a693dc532d0f741'] + +dependencies = [ + ('Perl', '5.34.1'), + ('Archive-Zip', '1.68'), + ('DBD-mysql', '4.050'), + ('BioPerl', '1.7.8'), + ('Bio-DB-HTS', '3.01'), + # VEP requires Compress::Raw::Zlib >= 2.103 + ('Compress-Raw-Zlib', '2.202'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", "") + +exts_list = [ + ('Bio::EnsEMBL::XS', '2.3.2', { + 'source_urls': ['https://github.com/Ensembl/ensembl-xs/archive'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['aafc59568cd1042259196575e99cdfeef9c0fb7966e5f915cfaf38c70885ffa5'], + }), +] + +moduleclass = 'bio' From b398277fcae80f11e705309f0b5d49fb63cf8e5d Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 23 Sep 2022 21:39:25 +0200 Subject: [PATCH 163/793] adding easyconfigs: GitPython-3.1.27-GCCcore-11.3.0.eb, buildingspy-4.0.0-foss-2022a.eb --- .../buildingspy-4.0.0-foss-2022a.eb | 48 +++++++++++++++++++ .../GitPython-3.1.27-GCCcore-11.3.0.eb | 33 +++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb b/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb new file mode 100644 index 00000000000..52e6907b217 --- /dev/null +++ b/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'buildingspy' +version = '4.0.0' + +homepage = 'https://simulationresearch.lbl.gov/modelica/buildingspy' +description = 'Python modules for automating Modelica simulations and for running unit test for the Buildings library' + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('GitPython', '3.1.27'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +exts_list = [ + ('Jinja2', '3.1.2', { + 'checksums': ['31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852'], + }), + ('pytidylib', '0.3.2', { + 'modulename': 'tidylib', + 'checksums': ['22b1c8d75970d8064ff999c2369e98af1d0685417eda4c829a5c9f56764b0af3'], + }), + ('simplejson', '3.16.0', { + 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], + }), + ('six', '1.14.0', { + 'checksums': ['236bdbdce46e6e6a3d61a337c0f8b763ca1e8717c03b369e87a7ec7ce1319c0a'], + }), + ('pyfunnel', '0.3.0', { + 'checksums': ['68256e82ecaa3832741dbf5f9c9a3420fcdb6b0c646406169e6c728ad1d47c6c'], + }), + ('Cerberus', '1.3.4', { + 'checksums': ['d1b21b3954b2498d9a79edf16b3170a3ac1021df88d197dc2ce5928ba519237c'], + }), + (name, version, { + 'checksums': ['78ba40360016850259a3b98fb9a7d1aeceac583a6cc6ae4ef8f684ffbd285f4b'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..fd485f5ec39 --- /dev/null +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'GitPython' +version = '3.1.27' + +homepage = 'https://gitpython.readthedocs.org' +description = """ GitPython is a python library used to interact with Git repositories """ + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('git', '2.36.0', '-nodocs'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('smmap', '5.0.0', { + 'checksums': ['c840e62059cd3be204b0c9c9f74be2c09d5648eddd4580d9314c3ecde0b30936'], + }), + ('gitdb', '4.0.9', { + 'checksums': ['bac2fd45c0a1c9cf619e63a90d62bdc63892ef92387424b855792a6cabe789aa'], + }), + (name, version, { + 'modulename': 'git', + }), +] + +moduleclass = 'lib' From 9a705ac2771deced585a414169b299139a75587f Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 23 Sep 2022 21:53:50 +0200 Subject: [PATCH 164/793] Added checksum for GitPython --- .../easyconfigs/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb index fd485f5ec39..dfc6291a3e3 100644 --- a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb @@ -27,6 +27,7 @@ exts_list = [ }), (name, version, { 'modulename': 'git', + 'checksums': ['1c885ce809e8ba2d88a29befeb385fcea06338d3640712b59ca623c220bb5704'], }), ] From 0f74490ab8551514928cee3e88a80de7de3ae6d3 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 23 Sep 2022 22:10:49 +0200 Subject: [PATCH 165/793] Removed download_dep_fail from BuildingsPy --- .../easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb b/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb index 52e6907b217..782819b71f0 100644 --- a/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb +++ b/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb @@ -18,7 +18,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = True exts_list = [ ('Jinja2', '3.1.2', { From c18443739a13ec92928a88a4d3d97ea1d17ba908 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Sep 2022 22:44:34 +0200 Subject: [PATCH 166/793] don't enable separate_build_dir, already done by default by CMakeMake easyblock --- easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb index 6b12dec5b6a..72ff0976e45 100644 --- a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb @@ -35,8 +35,6 @@ dependencies = [ ('libev', '4.33'), ] -separate_build_dir = True - configopts = '-DENABLE_GNUTLS=True' runtest = 'check' From d1372f9c4d5c1a77b2be02d8b4cebf601ff07a67 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Sep 2022 22:49:53 +0200 Subject: [PATCH 167/793] =?UTF-8?q?=20@boegel=20don't=20enable=20separate?= =?UTF-8?q?=5Fbuild=5Fdir=20or=20-DCMAKE=5FBUILD=5FTYPE=3DRelease,=20alrea?= =?UTF-8?q?dy=20done=20by=20default=20by=20CMakeMake=E2=80=A6?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb index 4d87ace9817..a8a803600e1 100644 --- a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb @@ -47,11 +47,6 @@ dependencies = [ ('c-ares', '1.18.1'), ] - -separate_build_dir = True - -configopts = '-DCMAKE_BUILD_TYPE=release ' - runtest = 'check' sanity_check_paths = { From 75a06833f790027e9d73bb8ed5ac0a936f846261 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Sep 2022 23:25:04 +0200 Subject: [PATCH 168/793] remove OS dependency for gnutls, since it's already included as a dependency --- easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb b/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb index 33e5fa76118..f30142975fd 100644 --- a/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb @@ -37,9 +37,6 @@ dependencies = [ ('Brotli', '1.0.9'), ] -# uncomment for checking TLS support -osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] - sanity_check_paths = { 'files': ['lib/libsoup-3.0.%s' % SHLIB_EXT], 'dirs': ['include/libsoup-3.0/libsoup/', 'lib/pkgconfig'] From e2a27e62d945889dccb6fbbb7e1ad2a3f5f69ffe Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 23 Sep 2022 15:04:00 -0700 Subject: [PATCH 169/793] add missing dep: Class::MethodMaker --- easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb index 97dd5d374f3..b9b1b8b9017 100644 --- a/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb @@ -34,6 +34,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], 'checksums': ['eaab1c5c87575a7826089304ab1f8ffa7f18e6cd8b3937623e998e865ec1e746'], }), + ('Class::MethodMaker', '2.24', { + 'source_tmpl': 'Class-MethodMaker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SC/SCHWIGON/class-methodmaker'], + 'checksums': ['5eef58ccb27ebd01bcde5b14bcc553b5347a0699e5c3e921c7780c3526890328'], + }), ('Term::ProgressBar', '2.22', { 'source_tmpl': 'Term-ProgressBar-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], @@ -42,7 +47,7 @@ exts_list = [ (name, version, { 'modulename': 'AGAT::Utilities', 'source_urls': ['https://github.com/NBISweden/AGAT/archive/refs/tags'], - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['998e32a3cb5e941efd324daf9ee4e0a71d605d06999922f083170b7a9f059899'], }), ] From 141db1f6bd5e4f95c69eef70bacbc6d2c15c8413 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 24 Sep 2022 00:07:26 +0200 Subject: [PATCH 170/793] remove commented out lines + hardcoded 'parallel = 2' --- .../w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb index c59f1cf7ccc..26dfe9217da 100644 --- a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb @@ -37,11 +37,6 @@ dependencies = [ ('freeglut', '3.2.1'), ] -# Required to find EGL -#osdependencies = [('libegl-dev', 'libegl-devel')] - -parallel = 2 - sanity_check_paths = { 'files': ['bin/wayland-scanner++', 'lib//libwayland-client-extra++.%s' % SHLIB_EXT, 'lib/libwayland-client++.%s' % SHLIB_EXT, From 5fdb5196322e312af17ee317dfb8acd0771b3b78 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 24 Sep 2022 18:17:22 +0200 Subject: [PATCH 171/793] adding easyconfigs: SuperLU-5.3.0-foss-2020b.eb, SuperLU-5.3.0-foss-2022a.eb, SuperLU-5.3.0-intel-2020b.eb, SuperLU-5.3.0-intel-2022a.eb --- .../s/SuperLU/SuperLU-5.3.0-foss-2020b.eb | 21 +++++++++++++++++++ .../s/SuperLU/SuperLU-5.3.0-foss-2022a.eb | 21 +++++++++++++++++++ .../s/SuperLU/SuperLU-5.3.0-intel-2020b.eb | 21 +++++++++++++++++++ .../s/SuperLU/SuperLU-5.3.0-intel-2022a.eb | 21 +++++++++++++++++++ 4 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2022a.eb diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2020b.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2020b.eb new file mode 100644 index 00000000000..41d145da7ea --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2020b.eb @@ -0,0 +1,21 @@ +name = 'SuperLU' +version = '5.3.0' + +homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the +direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['3e464afa77335de200aeb739074a11e96d9bef6d0b519950cfa6684c4be1f350'] + +builddependencies = [('CMake', '3.18.4')] + +runtest = " test" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2022a.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2022a.eb new file mode 100644 index 00000000000..dd4bf92289b --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2022a.eb @@ -0,0 +1,21 @@ +name = 'SuperLU' +version = '5.3.0' + +homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the +direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['3e464afa77335de200aeb739074a11e96d9bef6d0b519950cfa6684c4be1f350'] + +builddependencies = [('CMake', '3.23.1')] + +runtest = " test" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2020b.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2020b.eb new file mode 100644 index 00000000000..2328a049426 --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2020b.eb @@ -0,0 +1,21 @@ +name = 'SuperLU' +version = '5.3.0' + +homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the +direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['3e464afa77335de200aeb739074a11e96d9bef6d0b519950cfa6684c4be1f350'] + +builddependencies = [('CMake', '3.18.4')] + +runtest = " test" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2022a.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2022a.eb new file mode 100644 index 00000000000..fbc399aa456 --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2022a.eb @@ -0,0 +1,21 @@ +name = 'SuperLU' +version = '5.3.0' + +homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the +direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['3e464afa77335de200aeb739074a11e96d9bef6d0b519950cfa6684c4be1f350'] + +builddependencies = [('CMake', '3.23.1')] + +runtest = " test" + +moduleclass = 'numlib' From 6efd1227ad596d32908e8e0e34c776589f1a0af7 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 25 Sep 2022 17:26:17 +0200 Subject: [PATCH 172/793] use SYSTEM rather than True --- .../easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb index 388390b27a1..dd690af8e5f 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('pkg-config', '0.29.2'), ('pocl', '1.8'), ] From 4481295a98162c673193d25a3a0c9e3f1c872719 Mon Sep 17 00:00:00 2001 From: Jef Scheepers Date: Mon, 26 Sep 2022 09:30:57 +0200 Subject: [PATCH 173/793] remove python version suffix --- ...python-irodsclient-1.1.4-GCCcore-11.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100755 easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0.eb new file mode 100755 index 00000000000..a039002b7e6 --- /dev/null +++ b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'python-irodsclient' +version = '1.1.4' + +homepage = 'https://github.com/irods/python-irodsclient' +description = "A python API for iRODS" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('prettytable', '3.3.0', { + 'checksums': ['118eb54fd2794049b810893653b20952349df6d3bc1764e7facd8a18064fa9b0'], + }), + (name, version, { + 'modulename': 'irods', + 'checksums': ['f427699739911042dc35a7fbd92f7ba87db9fad3977423c2fa2ab61a0ffebe43'], + }), +] + +moduleclass = 'lib' + From 7ad8d1262ddbbe424649f5ae520010ed6598347d Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 26 Sep 2022 09:47:19 +0200 Subject: [PATCH 174/793] adding easyconfigs: scikit-learn-1.1.2-intel-2022a.eb --- .../scikit-learn-1.1.2-intel-2022a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.1.2-intel-2022a.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.1.2-intel-2022a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.1.2-intel-2022a.eb new file mode 100644 index 00000000000..8150d97c93a --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.1.2-intel-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'scikit-learn' +version = '1.1.2' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'sklearn', + 'checksums': ['7c22d1305b16f08d57751a4ea36071e2215efb4c09cb79183faa4e8e82a3dbf8'], + }), + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), +] + +moduleclass = 'data' From 2058ab67438c7dda0c45ca4876de53a63fff1ca8 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 26 Sep 2022 09:50:33 +0200 Subject: [PATCH 175/793] adding easyconfigs: Wannier90-3.1.0-intel-2022a.eb --- .../Wannier90/Wannier90-3.1.0-intel-2022a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2022a.eb diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2022a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2022a.eb new file mode 100644 index 00000000000..ada98a7bdfc --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch +] + +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' From 97b52bacb15c53133e95f2c7a05b8dd6f1eea084 Mon Sep 17 00:00:00 2001 From: robogast Date: Mon, 26 Sep 2022 12:09:26 +0200 Subject: [PATCH 176/793] fixed ec for python2.7 syntax --- .../l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb | 15 ++++++++++----- .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 8 ++++---- 2 files changed, 14 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb index 51de3daf755..fd1a4dccabd 100644 --- a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb @@ -27,12 +27,17 @@ dependencies = [ configopts = '--enable-libwebpmux' +local_headers, local_libs = ( + ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h'], + ['webp', 'webpdemux', 'webpmux'] +) + sanity_check_paths = { - 'files': [ - *['include/webp/%s' % f for f in ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h']], - *['lib/lib%s.a' % l for l in ['webp', 'webpdemux', 'webpmux']], - *['lib/lib%s.%s' % (l, SHLIB_EXT) for l in ['webp', 'webpdemux', 'webpmux']], - ], + 'files': ( + ['include/webp/%s' % header for header in local_headers] + + ['lib/lib%s.a' % lib for lib in local_libs] + + ['lib/lib%s.%s' % (lib, SHLIB_EXT) for lib in local_libs] + ), 'dirs': ['lib/'] } diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb index 77a049dd6b3..fc208f5ca99 100644 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -26,10 +26,10 @@ local_libs, local_bins = [ ] sanity_check_paths = { - 'files': [ - *['lib/lib%s.%s' % (lib, SHLIB_EXT) for lib in local_libs], - *['bin/exr%s' % bin for bin in local_bins] - ], + 'files': ( + ['lib/lib%s.%s' % (lib, SHLIB_EXT) for lib in local_libs] + + ['bin/exr%s' % bin for bin in local_bins] + ), 'dirs': ['include/%(name)s', 'share'], } From cb65d62214b465837309ff726804537868d3d832 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 26 Sep 2022 12:44:01 +0200 Subject: [PATCH 177/793] adding easyconfigs: spglib-python-2.0.0-intel-2022a.eb --- .../spglib-python-2.0.0-intel-2022a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.0-intel-2022a.eb diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.0-intel-2022a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.0-intel-2022a.eb new file mode 100644 index 00000000000..acbc3e85a70 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.0-intel-2022a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '2.0.0' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." + +toolchain = {'name': 'intel', 'version': '2022a'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['cbbd5e1d6096577c58b2fa47a5ea4f433a1932e5bc1cd1b691ea387c1b2e9974'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'spglib'} + +moduleclass = 'chem' From 228df40dd56d3d589724102d61b216a35384be62 Mon Sep 17 00:00:00 2001 From: robogast Date: Mon, 26 Sep 2022 12:46:24 +0200 Subject: [PATCH 178/793] moved temp variables to single letters again --- .../easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb | 6 +++--- .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 2 +- .../easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb index fd1a4dccabd..b78c2f0eccd 100644 --- a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb @@ -34,9 +34,9 @@ local_headers, local_libs = ( sanity_check_paths = { 'files': ( - ['include/webp/%s' % header for header in local_headers] - + ['lib/lib%s.a' % lib for lib in local_libs] - + ['lib/lib%s.%s' % (lib, SHLIB_EXT) for lib in local_libs] + ['include/webp/%s' % h for h in local_headers] + + ['lib/lib%s.a' % s for s in local_libs] + + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] ), 'dirs': ['lib/'] } diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index dc22d0ca82d..48f3aa8178e 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -87,7 +87,7 @@ local_contrib_libs = [ ] sanity_check_paths = { - 'files': ['lib64/libopencv_%s.%s' % (l, SHLIB_EXT) for l in local_contrib_libs], + 'files': ['lib64/libopencv_%s.%s' % (s, SHLIB_EXT) for s in local_contrib_libs], 'dirs': [], } diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb index fc208f5ca99..2f11268c8fd 100644 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -27,8 +27,8 @@ local_libs, local_bins = [ sanity_check_paths = { 'files': ( - ['lib/lib%s.%s' % (lib, SHLIB_EXT) for lib in local_libs] - + ['bin/exr%s' % bin for bin in local_bins] + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + + ['bin/exr%s' % b for b in local_bins] ), 'dirs': ['include/%(name)s', 'share'], } From 8e905ed1097442ec014d9c6bf6e48e5822359958 Mon Sep 17 00:00:00 2001 From: robogast Date: Mon, 26 Sep 2022 13:30:46 +0200 Subject: [PATCH 179/793] W503 fix --- .../easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb | 6 +++--- .../easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb index b78c2f0eccd..0c0b2fbef39 100644 --- a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb @@ -34,9 +34,9 @@ local_headers, local_libs = ( sanity_check_paths = { 'files': ( - ['include/webp/%s' % h for h in local_headers] - + ['lib/lib%s.a' % s for s in local_libs] - + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + ['include/webp/%s' % h for h in local_headers] + + ['lib/lib%s.a' % s for s in local_libs] + + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] ), 'dirs': ['lib/'] } diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb index 2f11268c8fd..d607a01b64d 100644 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -27,8 +27,8 @@ local_libs, local_bins = [ sanity_check_paths = { 'files': ( - ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] - + ['bin/exr%s' % b for b in local_bins] + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + + ['bin/exr%s' % b for b in local_bins] ), 'dirs': ['include/%(name)s', 'share'], } From 8162d3f8a96280aabc6911aa1cd8521e1109b8ac Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 26 Sep 2022 13:45:19 +0200 Subject: [PATCH 180/793] Removed redundant extensions --- .../b/buildingspy/buildingspy-4.0.0-foss-2022a.eb | 9 --------- 1 file changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb b/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb index 782819b71f0..31b0718b8fd 100644 --- a/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb +++ b/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb @@ -20,19 +20,10 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('Jinja2', '3.1.2', { - 'checksums': ['31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852'], - }), ('pytidylib', '0.3.2', { 'modulename': 'tidylib', 'checksums': ['22b1c8d75970d8064ff999c2369e98af1d0685417eda4c829a5c9f56764b0af3'], }), - ('simplejson', '3.16.0', { - 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], - }), - ('six', '1.14.0', { - 'checksums': ['236bdbdce46e6e6a3d61a337c0f8b763ca1e8717c03b369e87a7ec7ce1319c0a'], - }), ('pyfunnel', '0.3.0', { 'checksums': ['68256e82ecaa3832741dbf5f9c9a3420fcdb6b0c646406169e6c728ad1d47c6c'], }), From 981f4dc121a24e5d3028a8dd814dc9396a9c7e7b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 26 Sep 2022 16:44:14 +0200 Subject: [PATCH 181/793] Drop Java dep from ABAQUS, new 2223 hotfix --- .../a/ABAQUS/ABAQUS-2022-hotfix-2214.eb | 2 -- .../a/ABAQUS/ABAQUS-2022-hotfix-2223.eb | 34 +++++++++++++++++++ easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022.eb | 2 -- 3 files changed, 34 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2223.eb diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2214.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2214.eb index 76e2b9c6712..c5076140bfa 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2214.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2214.eb @@ -34,6 +34,4 @@ checksums = [ '88b5c0b182e2dc3e09c14f89be338993cf7edcfeb2f388f405022c63f5512029', ] -dependencies = [('Java', '11')] - moduleclass = 'cae' diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2223.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2223.eb new file mode 100644 index 00000000000..84bf03d99d0 --- /dev/null +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2223.eb @@ -0,0 +1,34 @@ +name = 'ABAQUS' +version = '2022' +local_hotfix = '2223' +versionsuffix = '-hotfix-%s' % local_hotfix + +homepage = 'https://www.simulia.com/products/abaqus_fea.html' +description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit + dynamics FEA.""" + +toolchain = SYSTEM + +sources = [ + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.1-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.2-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.3-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.4-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.5-5.tar', + # hotfixes + '%%(version)s.FP.CFA.%s.Part_SIMULIA_EstPrd.Linux64.tar' % local_hotfix, + '%%(version)s.FP.CFA.%s.Part_SIMULIA_FlexNet.Linux64.tar' % local_hotfix, +] +checksums = [ + '9025c9bc2d0345c13d96e88c1c422b1979a14bf7ba281bd32dfe093c1446945d', # 2022.AM_SIM_Abaqus_Extend.AllOS.1-5.tar + '14c23b3fdfddb723d84a02eb27edc25162e1d27e8fdce053193f72d28ff0a12c', # 2022.AM_SIM_Abaqus_Extend.AllOS.2-5.tar + '561d54d688ea2f2dcf329701e20502642aecf5526eb56db3a586cbcadfbf20fb', # 2022.AM_SIM_Abaqus_Extend.AllOS.3-5.tar + 'c085066ae2df68c9c61ea345808042ddb205c642d649f1ec3b7db4aaffb3d544', # 2022.AM_SIM_Abaqus_Extend.AllOS.4-5.tar + 'bfbc2c1a402881308f68f054e1e376fe153053b4287018ddbc80e76710f6969f', # 2022.AM_SIM_Abaqus_Extend.AllOS.5-5.tar + # 2022.FP.CFA.2223.Part_SIMULIA_EstPrd.Linux64.tar + 'bb05b07072ded86944eb44908875e6813c6ea18b2e6ab4dc7f8ef1ef368851e2', + # 2022.FP.CFA.2223.Part_SIMULIA_FlexNet.Linux64.tar + '32895726d409af8f7055b0f2bad53d10e7c32e36712e3eda8ff860f02622ee6f', +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022.eb index 6ce57875272..dc2c3525813 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022.eb @@ -22,6 +22,4 @@ checksums = [ 'bfbc2c1a402881308f68f054e1e376fe153053b4287018ddbc80e76710f6969f', # 2022.AM_SIM_Abaqus_Extend.AllOS.5-5.tar ] -dependencies = [('Java', '11')] - moduleclass = 'cae' From c09d5d632246167f20b07780ed9ce5c9cf607e50 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 26 Sep 2022 18:28:28 +0200 Subject: [PATCH 182/793] adding easyconfigs: LMfit-1.0.3-foss-2022a.eb, LMfit-1.0.3-intel-2022a.eb --- .../l/LMfit/LMfit-1.0.3-foss-2022a.eb | 33 +++++++++++++++++++ .../l/LMfit/LMfit-1.0.3-intel-2022a.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-foss-2022a.eb create mode 100644 easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-intel-2022a.eb diff --git a/easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-foss-2022a.eb b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-foss-2022a.eb new file mode 100644 index 00000000000..6b753c7eca3 --- /dev/null +++ b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-foss-2022a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'LMfit' +version = '1.0.3' + +homepage = 'https://lmfit.github.io/lmfit-py' +description = """Lmfit provides a high-level interface to non-linear optimization +and curve fitting problems for Python""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('asteval', '0.9.27', { + 'checksums': ['de838c33aed4c9bb25737eadbb7d1edaaf875e2bab505cc079f1a4b35de03e47'], + }), + ('uncertainties', '3.1.7', { + 'checksums': ['80111e0839f239c5b233cb4772017b483a0b7a1573a581b92ab7746a35e6faab'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['d067c3ea501f035af5d3c079e6e6e35dc3cc1ac7d439429a425b0aeb5a7858a2'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-intel-2022a.eb b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-intel-2022a.eb new file mode 100644 index 00000000000..d68900b073e --- /dev/null +++ b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-intel-2022a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'LMfit' +version = '1.0.3' + +homepage = 'https://lmfit.github.io/lmfit-py' +description = """Lmfit provides a high-level interface to non-linear optimization +and curve fitting problems for Python""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('asteval', '0.9.27', { + 'checksums': ['de838c33aed4c9bb25737eadbb7d1edaaf875e2bab505cc079f1a4b35de03e47'], + }), + ('uncertainties', '3.1.7', { + 'checksums': ['80111e0839f239c5b233cb4772017b483a0b7a1573a581b92ab7746a35e6faab'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['d067c3ea501f035af5d3c079e6e6e35dc3cc1ac7d439429a425b0aeb5a7858a2'], + }), +] + +moduleclass = 'math' From 16d944dc648b897816e1905885809e733c51ae9c Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 26 Sep 2022 14:00:54 -0700 Subject: [PATCH 183/793] one more dep --- easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb index b9b1b8b9017..c541f370006 100644 --- a/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb @@ -24,6 +24,11 @@ exts_defaultclass = 'PerlModule' exts_filter = ("perldoc -lm %(ext_name)s ", "") exts_list = [ + ('Set::Object', '1.42', { + 'source_tmpl': 'Set-Object-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN'], + 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], + }), ('File::Share', '0.27', { 'source_tmpl': 'File-Share-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], From 17c98f530c96c5c6e3ebed0715acac0fdb9de512 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 26 Sep 2022 14:34:35 -0700 Subject: [PATCH 184/793] ncbi-vdb-3.0.0 requires multidep exception for HDF5 --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 0fb05afe876..5a2a62e69c1 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -494,8 +494,8 @@ def check_dep_vars(self, gen, dep, dep_vars): # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], - # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) - 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], + # ncbi-vdb v2.x and v3.0.0 require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) + 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'ncbi-vdb-3\.0\.0', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], # VMTK 1.4.x requires ITK 4.13.x 'ITK': [(r'4\.13\.', [r'VMTK-1\.4\.'])], # Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x) From 7628a715b23afd4eb9fdaa43a0c5f851f2b51ee5 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 26 Sep 2022 15:36:55 -0700 Subject: [PATCH 185/793] missing pkg-config --- easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb index 209645c0e7c..456da718458 100644 --- a/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb @@ -21,6 +21,7 @@ checksums = ['c7935b7a29e42443f6a35d35cf20ffa7d028c399303f872cd1219598a83656ae'] builddependencies = [ ('Autotools', '20210726'), ('binutils', '2.37'), + ('pkg-config', '0.29.2'), ] dependencies = [ From 530cc4783bde6e5d31de8badea7313f85f3e43e5 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 26 Sep 2022 16:22:34 -0700 Subject: [PATCH 186/793] missing build dep pkg-config --- .../easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) mode change 100644 => 100755 easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb old mode 100644 new mode 100755 index 3f4b2a24826..751a1a06f3a --- a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb @@ -25,6 +25,7 @@ builddependencies = [ ('Autotools', '20210726'), ('binutils', '2.37'), ('M4', '1.4.19'), + ('pkg-config', '0.29.2'), ] preconfigopts = "autoreconf -vfi && " From 4ab4314ec1c8b433156adf70e4e2e60135531da8 Mon Sep 17 00:00:00 2001 From: guacke Date: Tue, 27 Sep 2022 10:21:48 +0200 Subject: [PATCH 187/793] Bugfix: use version templating. --- .../a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb b/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb index 0e2597cebb9..3dd1e871019 100644 --- a/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb @@ -14,13 +14,14 @@ description = """ toolchain = SYSTEM sources = [{ - 'source_urls': ['https://github.com/OpenChemistry/avogadroapp/releases/download/1.97.0'], - 'filename': 'avogadro2', - 'download_filename': 'Avogadro2-x86_64.AppImage' + 'source_urls': ['https://github.com/OpenChemistry/avogadroapp/releases/download/%(version)s/'], + 'filename': '%(name)s-%(version)s.bin', + 'download_filename': 'Avogadro2-x86_64.AppImage', }] - checksums = ['cc522dbdaa6e5386cb7101d382c5730f0d1ff71f2e70eb10f7e55f4ca052c89d'] +postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.bin %(installdir)s/avogadro2"] + sanity_check_paths = { 'files': ['avogadro2'], 'dirs': [], From 4770a3875fe686548fda2cc062a10dd207170515 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 27 Sep 2022 09:40:01 +0100 Subject: [PATCH 188/793] Entry for ccache corrected so GCCcore will be used --- .../easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb index 9026c3b2c20..5e41bdddcfb 100644 --- a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb @@ -38,7 +38,7 @@ builddependencies = [ ('Perl', '5.34.0', '-minimal'), ('GObject-Introspection', '1.68.0'), ('pkg-config', '0.29.2'), - ('ccache', '4.6.1', '', True), + ('ccache', '4.6.1'), ] dependencies = [ ('GLib', '2.69.1'), From a498e98277e9f648b341abe19f483f138604780f Mon Sep 17 00:00:00 2001 From: software Date: Tue, 27 Sep 2022 09:01:31 +0000 Subject: [PATCH 189/793] adding easyconfigs: paladin-1.4.6-GCCcore-10.3.0.eb, paladin-1.4.6-GCCcore-11.2.0.eb --- .../p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb | 41 +++++++++++++++++++ .../p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb | 41 +++++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..79ae059d08f --- /dev/null +++ b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb @@ -0,0 +1,41 @@ + +easyblock = 'MakeCp' + +name = 'paladin' +version = '1.4.6' + +homepage = 'https://github.com/ToniWestbrook/paladin' +description = """ +Protein ALignment And Detection INterface + +PALADIN is a protein sequence alignment tool designed for the accurate functional characterization of metagenomes. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ToniWestbrook/paladin/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fd23a8907d832cada060e112addb1b3b3751353dda515887c69c1772fd37cc4a'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +# Use EB build flags +buildopts = 'CFLAGS="$CFLAGS"' + +dependencies = [ + ('zlib', '1.2.11'), + ('cURL', '7.76.0'), + ('OpenSSL', '1.1', '', True), +] + +files_to_copy = [(['paladin'], 'bin'), 'run.py', 'sample_data', 'scripts'] + +sanity_check_paths = { + 'files': ['bin/paladin'], + 'dirs': ['sample_data'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f573e5e725d --- /dev/null +++ b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ + +easyblock = 'MakeCp' + +name = 'paladin' +version = '1.4.6' + +homepage = 'https://github.com/ToniWestbrook/paladin' +description = """ +Protein ALignment And Detection INterface + +PALADIN is a protein sequence alignment tool designed for the accurate functional characterization of metagenomes. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ToniWestbrook/paladin/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fd23a8907d832cada060e112addb1b3b3751353dda515887c69c1772fd37cc4a'] + +builddependencies = [ + ('binutils', '2.37'), +] + +# Use EB build flags +buildopts = 'CFLAGS="$CFLAGS"' + +dependencies = [ + ('zlib', '1.2.11'), + ('cURL', '7.78.0'), + ('OpenSSL', '1.1', '', True), +] + +files_to_copy = [(['paladin'], 'bin'), 'run.py', 'sample_data', 'scripts'] + +sanity_check_paths = { + 'files': ['bin/paladin'], + 'dirs': ['sample_data'], +} + +moduleclass = 'bio' From 3dad2ffddc61bcf245c847efab2c9b0414c0e5b1 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 27 Sep 2022 13:42:11 +0200 Subject: [PATCH 190/793] adding easyconfigs: FFTW-3.3.10-iimpi-2022a.eb --- .../f/FFTW/FFTW-3.3.10-iimpi-2022a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2022a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2022a.eb new file mode 100644 index 00000000000..63d8bd8e1e6 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2022a.eb @@ -0,0 +1,27 @@ +name = 'FFTW' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +# no quad precision, requires GCC v4.6 or higher +# see also +# https://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails on AMD systems when configuring with --enable-avx-128-fma, +# because Intel compilers do not support FMA4 instructions +use_fma4 = False + + +runtest = 'check' + +moduleclass = 'numlib' From 00124096c038b6a59f479a3ee4adbb580c69eb8f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 27 Sep 2022 14:07:44 +0200 Subject: [PATCH 191/793] adding easyconfigs: PostgreSQL-14.4-GCCcore-11.3.0.eb --- .../PostgreSQL-14.4-GCCcore-11.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-14.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-14.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-14.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f3972f8c07f --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-14.4-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '14.4' + +homepage = 'https://www.postgresql.org/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ebb58a3ac76b910cd7ca103636d19efdc262cab841e9be00705456813d980955'] + +builddependencies = [ + ('binutils', '2.38'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Perl', '5.34.1'), + ('Python', '3.10.4'), +] + +dependencies = [ + ('libreadline', '8.1.2'), + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', True), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' From 43718e73d4be1e733b0cff4932896bfc5713e160 Mon Sep 17 00:00:00 2001 From: kErica <31503643+kErica@users.noreply.github.com> Date: Tue, 27 Sep 2022 14:22:12 +0200 Subject: [PATCH 192/793] change tqdm version in umap-learn recipe Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb index 449a1fd265a..7a58535e76e 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb @@ -21,7 +21,7 @@ dependencies = [ ('scikit-learn', '0.24.2'), ('numba', '0.53.1'), ('LLVM', '11.1.0'), - ('tqdm', '4.61.1'), + ('tqdm', '4.61.2'), ] use_pip = True From f59935e1db759c1007e09df0fc3444d62eccf0e3 Mon Sep 17 00:00:00 2001 From: kErica <31503643+kErica@users.noreply.github.com> Date: Tue, 27 Sep 2022 14:55:37 +0200 Subject: [PATCH 193/793] Update easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb index 7a58535e76e..52a71470882 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb @@ -25,7 +25,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True exts_default_options = {'source_urls': [PYPI_SOURCE]} From 659fdacac8cdb2f1d62e0b13cbb1541ed62d215a Mon Sep 17 00:00:00 2001 From: kErica <31503643+kErica@users.noreply.github.com> Date: Tue, 27 Sep 2022 14:55:45 +0200 Subject: [PATCH 194/793] Update easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb index 52a71470882..366787e8caa 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb @@ -40,4 +40,4 @@ exts_list = [ sanity_pip_check = True -moduleclass = 'lib' +moduleclass = 'tools' From e16c6433a7b544d1194e30da7a54a84d5a0e5adf Mon Sep 17 00:00:00 2001 From: kErica <31503643+kErica@users.noreply.github.com> Date: Tue, 27 Sep 2022 14:55:51 +0200 Subject: [PATCH 195/793] Update easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb index 366787e8caa..cc3f7112b03 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb @@ -26,8 +26,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('pynndescent', '0.5.7', { 'checksums': ['ecb395255fa36a748b5870b4ba0300ea0f7da8b1964864b8edd62577a84dfd7d'], From da4055f14050df7a5a90cfc26c8e3929e7aad017 Mon Sep 17 00:00:00 2001 From: kErica <31503643+kErica@users.noreply.github.com> Date: Tue, 27 Sep 2022 14:55:59 +0200 Subject: [PATCH 196/793] Update easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../u/umap-learn/umap-learn-0.5.3-foss-2021a.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb index cc3f7112b03..8a85ad9aea3 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb @@ -8,9 +8,11 @@ name = 'umap-learn' version = '0.5.3' homepage = 'https://umap-learn.readthedocs.io/en/latest/' -description = """Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique - that can be used for visualisation similarly to t-SNE, but also for general non-linear - dimension reduction.""" +description = """ +Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique +that can be used for visualisation similarly to t-SNE, but also for general non-linear +dimension reduction. +""" toolchain = {'name': 'foss', 'version': '2021a'} From e680f4518f3beaf137e3698193269e9b675e458c Mon Sep 17 00:00:00 2001 From: kErica <31503643+kErica@users.noreply.github.com> Date: Tue, 27 Sep 2022 14:56:10 +0200 Subject: [PATCH 197/793] Update easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb index 8a85ad9aea3..914a9481bfd 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb @@ -15,8 +15,6 @@ dimension reduction. """ toolchain = {'name': 'foss', 'version': '2021a'} - - dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), From 875a454be18570e744114e1028b30f0ebd31afa6 Mon Sep 17 00:00:00 2001 From: jefscheepers <51341187+jefscheepers@users.noreply.github.com> Date: Tue, 27 Sep 2022 16:42:17 +0200 Subject: [PATCH 198/793] Delete python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb --- ...lient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100755 easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb deleted file mode 100755 index 5a022f20b13..00000000000 --- a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'python-irodsclient' -version = '1.1.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/irods/python-irodsclient' -description = "A python API for iRODS" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -dependencies = [ - ('Python', '3.9.6'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('defusedxml', '0.7.1', { - 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], - }), - ('prettytable', '3.3.0', { - 'checksums': ['118eb54fd2794049b810893653b20952349df6d3bc1764e7facd8a18064fa9b0'], - }), - (name, version, { - 'modulename': 'irods', - 'checksums': ['f427699739911042dc35a7fbd92f7ba87db9fad3977423c2fa2ab61a0ffebe43'], - }), -] - -moduleclass = 'lib' - From 1218fe448fdb6047c1c2ca877e9591a9c28582ba Mon Sep 17 00:00:00 2001 From: jefscheepers <51341187+jefscheepers@users.noreply.github.com> Date: Tue, 27 Sep 2022 16:57:49 +0200 Subject: [PATCH 199/793] Add binutils as builddependency --- .../python-irodsclient-1.1.4-GCCcore-11.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0.eb index a039002b7e6..c68d09039d3 100755 --- a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0.eb @@ -8,6 +8,8 @@ description = "A python API for iRODS" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +builddependencies = [('binutils', '2.37')] + dependencies = [ ('Python', '3.9.6'), ] @@ -29,4 +31,3 @@ exts_list = [ ] moduleclass = 'lib' - From 5ba19ccfb4b1d3db8cab2d4b4cebb2dc4d77469d Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 27 Sep 2022 18:18:12 +0200 Subject: [PATCH 200/793] Remove importlib_metadata --- .../easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb index 329c77c8106..4cf2f36f1d5 100644 --- a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb @@ -47,9 +47,6 @@ exts_list = [ 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", 'checksums': ['d4725fc9ec8e8822906ae26bb26f5546891aa7fbc3443de970cc556d43a5c99f'], }), - ('importlib_metadata', '4.12.0', { - 'checksums': ['637245b8bab2b6502fcbc752cc4b7a6f6243bb02b31c5c26156ad103d3d45670'], - }), ('Markdown', '3.4.1', { 'checksums': ['3b809086bb6efad416156e00a0da66fe47618a5d6918dd688f53f40c8e4cfeff'], }), From 66105ebfa3f0c0cdf636caf517e08b6598fd84bb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 28 Sep 2022 10:59:09 +0200 Subject: [PATCH 201/793] adding easyconfigs: PyCharm-2022.2.2.eb --- .../easyconfigs/p/PyCharm/PyCharm-2022.2.2.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyCharm/PyCharm-2022.2.2.eb diff --git a/easybuild/easyconfigs/p/PyCharm/PyCharm-2022.2.2.eb b/easybuild/easyconfigs/p/PyCharm/PyCharm-2022.2.2.eb new file mode 100644 index 00000000000..831033dc25b --- /dev/null +++ b/easybuild/easyconfigs/p/PyCharm/PyCharm-2022.2.2.eb @@ -0,0 +1,20 @@ +easyblock = 'Tarball' + +name = 'PyCharm' +version = "2022.2.2" + +homepage = 'https://www.jetbrains.com/pycharm/' +description = """PyCharm Community Edition: Python IDE for Professional Developers""" + +toolchain = SYSTEM + +source_urls = ['https://download-cf.jetbrains.com/python'] +sources = ['pycharm-community-%(version)s.tar.gz'] +checksums = ['2f361c5f59c685c9f8d1385029ed753eabe5b688a82acef6e83a50f0d2b9d7a8'] + +sanity_check_paths = { + 'files': ["bin/pycharm.sh"], + 'dirs': [], +} + +moduleclass = 'devel' From e0648f8b93c4117e97161c7bc5e5acb902c3b2c8 Mon Sep 17 00:00:00 2001 From: software Date: Wed, 28 Sep 2022 10:24:08 +0000 Subject: [PATCH 202/793] Add missing sanity check command --- easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb | 2 ++ easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb index 79ae059d08f..eec314fb855 100644 --- a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb @@ -33,6 +33,8 @@ dependencies = [ files_to_copy = [(['paladin'], 'bin'), 'run.py', 'sample_data', 'scripts'] +sanity_check_commands = ["paladin version 2>&1 | grep 'Program: PALADIN (Protein Alignment and Detection Interface)'"] + sanity_check_paths = { 'files': ['bin/paladin'], 'dirs': ['sample_data'], diff --git a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb index f573e5e725d..22b6836b5ba 100644 --- a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb @@ -33,6 +33,8 @@ dependencies = [ files_to_copy = [(['paladin'], 'bin'), 'run.py', 'sample_data', 'scripts'] +sanity_check_commands = ["paladin version 2>&1 | grep 'Program: PALADIN (Protein Alignment and Detection Interface)'"] + sanity_check_paths = { 'files': ['bin/paladin'], 'dirs': ['sample_data'], From f81983bf2f8b8c1682c42d237377f34e2392bf31 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 28 Sep 2022 11:27:48 +0100 Subject: [PATCH 203/793] Update easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb Co-authored-by: Sam Moors --- easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb index 22b6836b5ba..bc0742d120f 100644 --- a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb @@ -28,7 +28,7 @@ buildopts = 'CFLAGS="$CFLAGS"' dependencies = [ ('zlib', '1.2.11'), ('cURL', '7.78.0'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] files_to_copy = [(['paladin'], 'bin'), 'run.py', 'sample_data', 'scripts'] From a454dc465c7e09dfcdebca6274545ad9b5b2ebd7 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 28 Sep 2022 11:27:59 +0100 Subject: [PATCH 204/793] Update easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb Co-authored-by: Sam Moors --- easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb index eec314fb855..942e8e2ff5d 100644 --- a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb @@ -28,7 +28,7 @@ buildopts = 'CFLAGS="$CFLAGS"' dependencies = [ ('zlib', '1.2.11'), ('cURL', '7.76.0'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] files_to_copy = [(['paladin'], 'bin'), 'run.py', 'sample_data', 'scripts'] From 5bf85e732ec71c1e9ad92dc8da3e5f2866c88b76 Mon Sep 17 00:00:00 2001 From: robogast Date: Wed, 28 Sep 2022 13:27:06 +0200 Subject: [PATCH 205/793] adding easyconfigs: ASAP-2.1-foss-2022a.eb, DCMTK-3.6.7-GCCcore-11.3.0.eb, OpenJPEG-2.5.0-GCCcore-11.3.0.eb, OpenSlide-3.4.1-GCCcore-11.3.0-largefiles.eb, pugixml-1.12.1-GCCcore-11.3.0.eb and patches: ASAP-2.1-libjpeg.patch, ASAP-2.1-pugixml.patch, ASAP-2.1-cmath.patch --- .../easyconfigs/a/ASAP/ASAP-2.1-cmath.patch | 12 +++ .../easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb | 72 ++++++++++++++ .../easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch | 35 +++++++ .../easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch | 52 ++++++++++ .../d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb | 56 +++++++++++ .../l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb | 44 +++++++++ .../OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 94 +++++++++++++++++++ .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 36 +++++++ .../OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb | 47 ++++++++++ ...enSlide-3.4.1-GCCcore-11.3.0-largefiles.eb | 56 +++++++++++ .../pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb | 29 ++++++ 11 files changed, 533 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch create mode 100644 easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch create mode 100644 easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch create mode 100644 easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.3.0-largefiles.eb create mode 100644 easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch new file mode 100644 index 00000000000..b4ca984d421 --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch @@ -0,0 +1,12 @@ +diff --git a/annotation/ImageScopeRepository.cpp b/annotation/ImageScopeRepository.cpp +index 6916a58..c135cb3 100644 +--- a/annotation/ImageScopeRepository.cpp ++++ b/annotation/ImageScopeRepository.cpp +@@ -9,6 +9,7 @@ + #include + #include "pugixml.hpp" + #include ++#include + + ImageScopeRepository::ImageScopeRepository(const std::shared_ptr& list) : + Repository(list), diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb new file mode 100644 index 00000000000..7dd82903d65 --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb @@ -0,0 +1,72 @@ +easyblock = 'CMakeMake' + +name = 'ASAP' +version = '2.1' + +homepage = 'https://computationalpathologygroup.github.io/ASAP/' +description = """ASAP focuses on fast and fluid image viewing with an easy-to-use interface +for making annotations. It consists of two main components: an IO library for reading and writing +multi-resolution images and a viewer component for visualizing such images.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/computationalpathologygroup/%(name)s/archive'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'ASAP-2.1-libjpeg.patch', + 'ASAP-2.1-pugixml.patch', + 'ASAP-2.1-cmath.patch', +] +checksums = [ + '7ba9f39d09bada808f760c5dc9ac0cda0d221fd1393a0a3f9decfd6b5e913b3c', # ASAP-2.1.tar.gz + 'dbdf26324a7521b4beaa7ec2c0585f0816619cd73b3125efd313eb48c4813a43', # ASAP-2.1-libjpeg.patch + 'f578bb3ec4cbce573d4b9acd695eb55446592f4ac00551656a06f113ba09a9a7', # ASAP-2.1-pugixml.patch + 'e33d83853e0bd51113a886d0793504ce0abfb15fdf88410a19287d46fafd33c4', # ASAP-2.1-cmath.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] +dependencies = [ + ('Boost', '1.79.0'), + ('Python', '3.10.4'), + ('OpenCV', '4.6.0', '-contrib'), + ('Qt5', '5.15.5'), + ('LibTIFF', '4.3.0'), + ('libjpeg-turbo', '2.1.3'), + ('JasPer', '2.0.33'), + ('DCMTK', '3.6.7'), + ('SWIG', '4.0.2'), + ('OpenSlide', '3.4.1', '-largefiles'), + ('pugixml', '1.12.1'), + ('zlib', '1.2.12'), +] + +configopts = " ".join([ + "-DOPENSLIDE_INCLUDE_DIR=$EBROOTOPENSLIDE/include/openslide", + "-DPugiXML_INCLUDE_DIR=$EBROOTPUGIXML/include", + "-DDCMTKJPEG_INCLUDE_DIR=$EBROOTDCMTK/include", + "-DWRAP_MULTIRESOLUTIONIMAGEINTERFACE_PYTHON=TRUE", + "-DBUILD_ASAP=TRUE", + "-DBUILD_EXECUTABLES=TRUE", + "-DBUILD_IMAGEPROCESSING=TRUE", + "-DBUILD_MULTIRESOLUTIONIMAGEINTERFACE_VSI_SUPPORT=TRUE", + "-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig" +]) + + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s', + 'bin/multiresolutionimageinterface.py', + 'lib/libmultiresolutionimageinterface.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +sanity_check_commands = ['python -c "import multiresolutionimageinterface"'] + +# ASAP installs its python interface in bin. Ugly, but we'll need to add it to PYTHONPATH +modextrapaths = {'PYTHONPATH': ['bin']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch new file mode 100644 index 00000000000..eeab7c05144 --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch @@ -0,0 +1,35 @@ +diff --git a/multiresolutionimageinterface/VSIImage.cpp b/multiresolutionimageinterface/VSIImage.cpp +index 509bb18..1763201 100644 +--- a/multiresolutionimageinterface/VSIImage.cpp ++++ b/multiresolutionimageinterface/VSIImage.cpp +@@ -11,7 +11,7 @@ + // Include DCMTK LIBJPEG for lossy and lossless JPEG compression + extern "C" { + #define boolean ijg_boolean +-#include "dcmtk/dcmjpeg/libijg8/jpeglib8.h" ++#include "jpeglib.h" + #include "jpeg_mem_src.h" + #undef boolean + #undef const +@@ -234,7 +234,7 @@ char* VSIImage::decodeTile(int no, int row, int col) const { + jpeg_source_mgr src_mem; + jpeg_create_decompress(&cinfo); + cinfo.err = jpeg_std_error(&jerr); +- jpeg_mem_src(&cinfo, &src_mem, (void*)buf, size); ++ jpeg_mem_src_asap(&cinfo, &src_mem, (void*)buf, size); + jpeg_read_header(&cinfo, true); + if (_compressionType == 2) { + cinfo.jpeg_color_space = JCS_YCbCr; +diff --git a/multiresolutionimageinterface/jpeg_mem_src.h b/multiresolutionimageinterface/jpeg_mem_src.h +index b9b91e9..13b9040 100644 +--- a/multiresolutionimageinterface/jpeg_mem_src.h ++++ b/multiresolutionimageinterface/jpeg_mem_src.h +@@ -47,7 +47,7 @@ static void mem_skip_input_data( j_decompress_ptr cinfo, long num_bytes ) + } + } + +-static void jpeg_mem_src( j_decompress_ptr cinfo, jpeg_source_mgr * const src, void const * const buffer, long nbytes ) ++static void jpeg_mem_src_asap( j_decompress_ptr cinfo, jpeg_source_mgr * const src, void const * const buffer, long nbytes ) + { + src->init_source = mem_init_source; + src->fill_input_buffer = mem_fill_input_buffer; diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch new file mode 100644 index 00000000000..2b4a652369f --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch @@ -0,0 +1,52 @@ +diff --git a/annotation/CMakeLists.txt b/annotation/CMakeLists.txt +index 114babe..2156cd3 100644 +--- a/annotation/CMakeLists.txt ++++ b/annotation/CMakeLists.txt +@@ -25,10 +25,9 @@ set(ANNOTATION_SOURCE + ) + + add_library(annotation SHARED ${ANNOTATION_SOURCE} ${ANNOTATION_HEADERS}) +-target_compile_definitions(annotation PRIVATE "PUGIXML_HEADER_ONLY") + generate_export_header(annotation) + target_include_directories(annotation PUBLIC $ $ PRIVATE ${DIAGPathology_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR} ${Boost_INCLUDE_DIRS} ${PugiXML_INCLUDE_DIR}) +-target_link_libraries(annotation PUBLIC core PRIVATE multiresolutionimageinterface) ++target_link_libraries(annotation PUBLIC core PRIVATE multiresolutionimageinterface ${PUGIXML_LIBRARY}) + set_target_properties(annotation PROPERTIES DEBUG_POSTFIX _d) + + IF(APPLE) +diff --git a/cmakemodules/FindPugiXML.cmake b/cmakemodules/FindPugiXML.cmake +index ccffcc4..9afcfb4 100644 +--- a/cmakemodules/FindPugiXML.cmake ++++ b/cmakemodules/FindPugiXML.cmake +@@ -5,11 +5,12 @@ + # PugiXML_FOUND, If false, do not try to use PugiXML. + + find_path(PugiXML_INCLUDE_DIR pugixml.hpp) ++find_library(PUGIXML_LIBRARY NAMES pugixml) + + # handle the QUIETLY and REQUIRED arguments and set PugiXML_FOUND to TRUE if + # all listed variables are TRUE + include(${CMAKE_ROOT}/Modules/FindPackageHandleStandardArgs.cmake) + FIND_PACKAGE_HANDLE_STANDARD_ARGS(PugiXML +- REQUIRED_VARS PugiXML_INCLUDE_DIR) ++ REQUIRED_VARS PUGIXML_LIBRARY PugiXML_INCLUDE_DIR) + +-mark_as_advanced(PugiXML_INCLUDE_DIR) ++mark_as_advanced(PugiXML_INCLUDE_DIR PUGIXML_LIBRARY) +diff --git a/multiresolutionimageinterface/CMakeLists.txt b/multiresolutionimageinterface/CMakeLists.txt +index 132e6ef..8d24176 100644 +--- a/multiresolutionimageinterface/CMakeLists.txt ++++ b/multiresolutionimageinterface/CMakeLists.txt +@@ -87,11 +87,10 @@ endif(BUILD_MULTIRESOLUTIONIMAGEINTERFACE_VSI_SUPPORT) + + add_library(multiresolutionimageinterface SHARED ${MULTIRESOLUTIONIMAGEINTERFACE_SRCS} ${MULTIRESOLUTIONIMAGEINTERFACE_HS} ${VSI_SOURCE_HS} ${VSI_SOURCE_SRCS}) + target_include_directories(multiresolutionimageinterface PUBLIC $ $ $ $ PRIVATE ${PugiXML_INCLUDE_DIR} ${TIFF_INCLUDE_DIR}) +-target_link_libraries(multiresolutionimageinterface PUBLIC core PRIVATE jpeg2kcodec libtiff) ++target_link_libraries(multiresolutionimageinterface PUBLIC core PRIVATE jpeg2kcodec libtiff ${PUGIXML_LIBRARY}) + IF(NOT WIN32) + target_link_libraries(multiresolutionimageinterface PRIVATE dl) + ENDIF(NOT WIN32) +-target_compile_definitions(multiresolutionimageinterface PRIVATE PUGIXML_HEADER_ONLY) + generate_export_header(multiresolutionimageinterface) + set_target_properties(multiresolutionimageinterface PROPERTIES DEBUG_POSTFIX _d) + diff --git a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6bffa6ad7b9 --- /dev/null +++ b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakeMake' + +name = 'DCMTK' +version = '3.6.7' + +homepage = 'https://dicom.offis.de/dcmtk' +description = """DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. +It includes software for examining, constructing and converting DICOM image files, handling offline media, sending +and receiving images over a network connection, as well as demonstrative image storage and worklist servers.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +local_stripped_version = version.replace('.', '') + +source_urls = ['https://dicom.offis.de/download/%(namelower)s/dcmtk{}/'.format(local_stripped_version)] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] +dependencies = [ + ('zlib', '1.2.12'), + ('libjpeg-turbo', '2.1.3'), + ('LibTIFF', '4.3.0'), + ('libpng', '1.6.37'), + ('libxml2', '2.9.13'), + ('libiconv', '1.17'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=OFF', + '-DBUILD_SHARED_LIBS=ON' +] + + +sanity_check_paths = { + 'files': ['bin/dcmdump', 'bin/dcmj2pnm'], + 'dirs': ['lib'], +} + +sanity_check_commands = [ + 'dcmdata_tests | grep " 0 failed"', + 'dcmect_tests | grep " 0 failed"', + 'dcmfg_tests | grep " 0 failed"', + 'dcmiod_tests | grep " 0 failed"', + 'dcmnet_tests | grep " 0 failed"', + 'dcmrt_tests | grep " 0 failed"', + 'dcmseg_tests | grep " 0 failed"', + 'dcmsr_tests | grep " 0 failed"', + 'dcmtls_tests | grep " 0 failed"', + 'ofstd_tests | grep " 0 failed"', +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0c0b2fbef39 --- /dev/null +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'libwebp' +version = '1.2.4' + +homepage = 'https://developers.google.com/speed/webp/' +description = """WebP is a modern image format that provides superior +lossless and lossy compression for images on the web. Using WebP, +webmasters and web developers can create smaller, richer images that +make the web faster.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7bf5a8a28cc69bcfa8cb214f2c3095703c6b73ac5fba4d5480c205331d9494df'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('giflib', '5.2.1'), +] + +configopts = '--enable-libwebpmux' + +local_headers, local_libs = ( + ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h'], + ['webp', 'webpdemux', 'webpmux'] +) + +sanity_check_paths = { + 'files': ( + ['include/webp/%s' % h for h in local_headers] + + ['lib/lib%s.a' % s for s in local_libs] + + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + ), + 'dirs': ['lib/'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb new file mode 100644 index 00000000000..48f3aa8178e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -0,0 +1,94 @@ +name = 'OpenCV' +version = '4.6.0' +versionsuffix = '-contrib' + +# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake +local_ippicv_hash = 'a56b6ac6f030c312b2dce17430eef13aed9af274' + +homepage = 'https://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products. + Includes extra modules for OpenCV from the contrib repository.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [ + { + 'source_urls': ['https://github.com/%(namelower)s/%(namelower)s/archive/'], + 'download_filename': '%(version)s.zip', + 'filename': SOURCELOWER_ZIP + }, + { + 'source_urls': ['https://github.com/%(namelower)s/opencv_contrib/archive/'], + 'download_filename': '%(version)s.zip', + 'filename': '%(namelower)s_contrib-%(version)s.zip' + }, + { + 'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], + 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', + 'extract_cmd': 'cp %s %(builddir)s' + }, +] +checksums = [ + '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359', # opencv-4.6.0.zip + '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3', # opencv_contrib-4.6.0.zip + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz +] + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('zlib', '1.2.12'), + ('FFmpeg', '5.0.1'), + ('freetype', '2.12.1'), + ('HarfBuzz', '4.2.1'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('libwebp', '1.2.4'), + ('OpenEXR', '3.1.5'), + ('JasPer', '2.0.33'), + ('Java', '11', '', True), + ('ant', '1.10.12', '-Java-%(javaver)s', True), + ('GLib', '2.72.1'), + ('GTK4', '4.7.0'), + ('HDF5', '1.12.2'), +] + +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = " ".join([ + "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules", + "-DFREETYPE_FOUND=ON", + "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/", + "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES_XXXXX=ON", + "-DHARFBUZZ_FOUND=ON", + "-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz", + "-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON", + "-DBUILD_opencv_python2=OFF", +]) + +enhance_sanity_check = True + +local_contrib_libs = [ + 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', + 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', + 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', + 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' +] + +sanity_check_paths = { + 'files': ['lib64/libopencv_%s.%s' % (s, SHLIB_EXT) for s in local_contrib_libs], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d607a01b64d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '3.1.5' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['93925805c1fc4f8162b35f0ae109c4a75344e6decae5a240afdfce25f8a433ec'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' + +local_libs, local_bins = [ + ['Iex', 'IlmThread', 'Imath', 'OpenEXR', 'OpenEXRUtil'], + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] +] + +sanity_check_paths = { + 'files': ( + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + + ['bin/exr%s' % b for b in local_bins] + ), + 'dirs': ['include/%(name)s', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6c76dae7c5d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,47 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchenson Cancer Research Center Seattle WA +easyblock = 'CMakeMake' + +name = 'OpenJPEG' +version = '2.5.0' + +homepage = 'https://www.openjpeg.org/' +description = """OpenJPEG is an open-source JPEG 2000 codec written in + C language. It has been developed in order to promote the use of JPEG 2000, + a still-image compression standard from the Joint Photographic Experts Group + (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as + a JPEG 2000 Reference Software.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/uclouvain/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0333806d6adecc6f7a91243b2b839ff4d2053823634d4f6ed7a59bc87409122a'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] +# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), +] + +sanity_check_paths = { + 'files': [ + 'bin/opj_compress', + 'bin/opj_decompress', + 'bin/opj_dump', + 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', + 'lib/libopenjp2.%s' % SHLIB_EXT + ], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.3.0-largefiles.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.3.0-largefiles.eb new file mode 100644 index 00000000000..b39f32e43c6 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.3.0-largefiles.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'OpenSlide' +version = '3.4.1' +versionsuffix = '-largefiles' + +homepage = 'https://openslide.org/' +description = """OpenSlide is a C library that provides a simple interface to +read whole-slide images (also known as virtual slides).""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_large_file_support.patch'] +checksums = [ + # v3.4.1.tar.gz + 'a5d869916e370125421535dcce778b2ba625dc50d920aa4ca93bbaaa6a7b470c', + # %(name)s-%(version_major_minor)s.1_large_file_support.patch + 'cb618053f4ae6c3ce37d1b8b0e4ef7c55fd17378776d13be4aa4efab91706b8c', +] + +builddependencies = [ + ('Autotools', '20220317'), + ('M4', '1.4.19'), + ('pkg-config', '0.29.2'), + ('binutils', '2.38'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), + ('LibTIFF', '4.3.0'), + ('OpenJPEG', '2.5.0'), + ('libxml2', '2.9.13'), + ('SQLite', '3.38.3'), + ('cairo', '1.17.4'), + ('Gdk-Pixbuf', '2.42.8'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': [ + 'bin/openslide-quickhash1sum', + 'bin/openslide-show-properties', + 'bin/openslide-write-png', + 'lib/libopenslide.la', + 'lib/libopenslide.%s' % SHLIB_EXT + ], + 'dirs': ['include/openslide'] +} + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1e32278858c --- /dev/null +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'pugixml' +version = '1.12.1' + +homepage = 'https://pugixml.org/' +description = "pugixml is a light-weight C++ XML processing library" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/zeux/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version_major_minor)s.4_pugixml_remove_headeronly.patch'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +configopts = "-DBUILD_SHARED_AND_STATIC_LIBS=ON -DPUGIXML_HEADER_ONLY=True " + + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib'], +} + +moduleclass = 'data' From edccc61548f18e5fa1076fc6f39a62627e3150a8 Mon Sep 17 00:00:00 2001 From: robogast Date: Wed, 28 Sep 2022 13:35:17 +0200 Subject: [PATCH 206/793] deleted OpenCV ec and its deps --- .../l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb | 44 --------- .../OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 94 ------------------- .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 36 ------- 3 files changed, 174 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb delete mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb delete mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb deleted file mode 100644 index 0c0b2fbef39..00000000000 --- a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libwebp' -version = '1.2.4' - -homepage = 'https://developers.google.com/speed/webp/' -description = """WebP is a modern image format that provides superior -lossless and lossy compression for images on the web. Using WebP, -webmasters and web developers can create smaller, richer images that -make the web faster.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['7bf5a8a28cc69bcfa8cb214f2c3095703c6b73ac5fba4d5480c205331d9494df'] - -builddependencies = [ - ('binutils', '2.38'), -] -dependencies = [ - ('libjpeg-turbo', '2.1.3'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.3.0'), - ('giflib', '5.2.1'), -] - -configopts = '--enable-libwebpmux' - -local_headers, local_libs = ( - ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h'], - ['webp', 'webpdemux', 'webpmux'] -) - -sanity_check_paths = { - 'files': ( - ['include/webp/%s' % h for h in local_headers] + - ['lib/lib%s.a' % s for s in local_libs] + - ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] - ), - 'dirs': ['lib/'] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb deleted file mode 100644 index 48f3aa8178e..00000000000 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ /dev/null @@ -1,94 +0,0 @@ -name = 'OpenCV' -version = '4.6.0' -versionsuffix = '-contrib' - -# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake -local_ippicv_hash = 'a56b6ac6f030c312b2dce17430eef13aed9af274' - -homepage = 'https://opencv.org/' -description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision - and machine learning software library. OpenCV was built to provide - a common infrastructure for computer vision applications and to accelerate - the use of machine perception in the commercial products. - Includes extra modules for OpenCV from the contrib repository.""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -sources = [ - { - 'source_urls': ['https://github.com/%(namelower)s/%(namelower)s/archive/'], - 'download_filename': '%(version)s.zip', - 'filename': SOURCELOWER_ZIP - }, - { - 'source_urls': ['https://github.com/%(namelower)s/opencv_contrib/archive/'], - 'download_filename': '%(version)s.zip', - 'filename': '%(namelower)s_contrib-%(version)s.zip' - }, - { - 'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], - 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', - 'extract_cmd': 'cp %s %(builddir)s' - }, -] -checksums = [ - '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359', # opencv-4.6.0.zip - '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3', # opencv_contrib-4.6.0.zip - '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz -] - -builddependencies = [ - ('CMake', '3.23.1'), -] -dependencies = [ - ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), - ('zlib', '1.2.12'), - ('FFmpeg', '5.0.1'), - ('freetype', '2.12.1'), - ('HarfBuzz', '4.2.1'), - ('libjpeg-turbo', '2.1.3'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.3.0'), - ('libwebp', '1.2.4'), - ('OpenEXR', '3.1.5'), - ('JasPer', '2.0.33'), - ('Java', '11', '', True), - ('ant', '1.10.12', '-Java-%(javaver)s', True), - ('GLib', '2.72.1'), - ('GTK4', '4.7.0'), - ('HDF5', '1.12.2'), -] - -# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz -# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 -configopts = " ".join([ - "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules", - "-DFREETYPE_FOUND=ON", - "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/", - "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", - "-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", - "-DFREETYPE_LINK_LIBRARIES_XXXXX=ON", - "-DHARFBUZZ_FOUND=ON", - "-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz", - "-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", - "-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", - "-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON", - "-DBUILD_opencv_python2=OFF", -]) - -enhance_sanity_check = True - -local_contrib_libs = [ - 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', - 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', - 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', - 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' -] - -sanity_check_paths = { - 'files': ['lib64/libopencv_%s.%s' % (s, SHLIB_EXT) for s in local_contrib_libs], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb deleted file mode 100644 index d607a01b64d..00000000000 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'OpenEXR' -version = '3.1.5' - -homepage = 'https://www.openexr.com/' -description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic - for use in computer imaging applications""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['93925805c1fc4f8162b35f0ae109c4a75344e6decae5a240afdfce25f8a433ec'] - -builddependencies = [ - ('binutils', '2.38'), - ('CMake', '3.23.1'), -] - -configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' - -local_libs, local_bins = [ - ['Iex', 'IlmThread', 'Imath', 'OpenEXR', 'OpenEXRUtil'], - ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] -] - -sanity_check_paths = { - 'files': ( - ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + - ['bin/exr%s' % b for b in local_bins] - ), - 'dirs': ['include/%(name)s', 'share'], -} - -moduleclass = 'vis' From ce611aa982d47c19d0f078bf2a13f8ac80ddeaa7 Mon Sep 17 00:00:00 2001 From: robogast Date: Wed, 28 Sep 2022 14:41:18 +0200 Subject: [PATCH 207/793] removed pugixml header only --- .../p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb index 1e32278858c..1cf51118427 100644 --- a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb @@ -9,21 +9,24 @@ description = "pugixml is a light-weight C++ XML processing library" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://github.com/zeux/%(name)s/archive/'] +source_urls = ['https://github.com/zeux/pugixml/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version_major_minor)s.4_pugixml_remove_headeronly.patch'] +checksums = ['1e28ab24b6e04e013d96f45d25e9f2d04c921dc68c613fd010ecaaad3892c14d'] builddependencies = [ ('binutils', '2.38'), ('CMake', '3.23.1'), ] -configopts = "-DBUILD_SHARED_AND_STATIC_LIBS=ON -DPUGIXML_HEADER_ONLY=True " - +configopts = " ".join([ + "-DBUILD_SHARED_LIBS=ON", + "-DPUGIXML_BUILD_SHARED_AND_STATIC_LIBS=ON", +]) sanity_check_paths = { - 'files': [], - 'dirs': ['lib'], + 'files': ['include/pugiconfig.hpp', 'include/pugixml.hpp', 'lib/libpugixml.a', + 'lib/libpugixml.%s' % SHLIB_EXT, 'lib/pkgconfig/pugixml.pc'], + 'dirs': ['lib/cmake/pugixml'], } moduleclass = 'data' From dc6b25696beda3085bcbde7a6d7d741162ab7a3d Mon Sep 17 00:00:00 2001 From: Jef Scheepers Date: Wed, 28 Sep 2022 16:02:03 +0200 Subject: [PATCH 208/793] add new python-irodsclient easyconfig --- ...python-irodsclient-1.1.4-GCCcore-10.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100755 easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-10.3.0.eb new file mode 100755 index 00000000000..136c97d177d --- /dev/null +++ b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'python-irodsclient' +version = '1.1.4' + +homepage = 'https://github.com/irods/python-irodsclient' +description = "A python API for iRODS" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('prettytable', '3.3.0', { + 'checksums': ['118eb54fd2794049b810893653b20952349df6d3bc1764e7facd8a18064fa9b0'], + }), + (name, version, { + 'modulename': 'irods', + 'checksums': ['f427699739911042dc35a7fbd92f7ba87db9fad3977423c2fa2ab61a0ffebe43'], + }), +] + +moduleclass = 'lib' From 5b9ad1f5ecd5dae77dcbc1b351f87b3174e93b9b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 28 Sep 2022 16:30:17 +0200 Subject: [PATCH 209/793] adding easyconfigs: netCDF-4.9.0-iimpi-2022a.eb, netcdf4-python-1.6.1-foss-2022a.eb, netcdf4-python-1.6.1-intel-2022a.eb, xarray-2022.6.0-foss-2022a.eb, xarray-2022.6.0-intel-2022a.eb, ArviZ-0.12.1-foss-2022a.eb, ArviZ-0.12.1-intel-2022a.eb --- .../a/ArviZ/ArviZ-0.12.1-foss-2022a.eb | 34 +++++++++++++ .../a/ArviZ/ArviZ-0.12.1-intel-2022a.eb | 34 +++++++++++++ .../n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 50 ++++++++++++++++++ .../netcdf4-python-1.6.1-foss-2022a.eb | 51 +++++++++++++++++++ .../netcdf4-python-1.6.1-intel-2022a.eb | 51 +++++++++++++++++++ .../x/xarray/xarray-2022.6.0-foss-2022a.eb | 25 +++++++++ .../x/xarray/xarray-2022.6.0-intel-2022a.eb | 25 +++++++++ 7 files changed, 270 insertions(+) create mode 100644 easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb create mode 100644 easybuild/easyconfigs/x/xarray/xarray-2022.6.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/x/xarray/xarray-2022.6.0-intel-2022a.eb diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb new file mode 100644 index 00000000000..bc9c93cbf77 --- /dev/null +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'ArviZ' +version = '0.12.1' + +homepage = 'https://github.com/arviz-devs/arviz' +description = "Exploratory analysis of Bayesian models with Python" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # numpy, scipy, pandas + ('netcdf4-python', '1.6.1'), + ('xarray', '2022.6.0'), + ('matplotlib', '3.5.2'), +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + ('xarray-einstats', '0.3.0', { + 'checksums': ['81217c145218479327469f1669f34763b7e149ed6789fd596cc90ff2d772098e'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['57d80eacc51909f18e6ab63c96a6b02227c3b077c5ffa406d5f4dabe03b8f019'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb new file mode 100644 index 00000000000..ac8ac445dc2 --- /dev/null +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'ArviZ' +version = '0.12.1' + +homepage = 'https://github.com/arviz-devs/arviz' +description = "Exploratory analysis of Bayesian models with Python" + +toolchain = {'name': 'intel', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # numpy, scipy, pandas + ('netcdf4-python', '1.6.1'), + ('xarray', '2022.6.0'), + ('matplotlib', '3.5.2'), +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + ('xarray-einstats', '0.3.0', { + 'checksums': ['81217c145218479327469f1669f34763b7e149ed6789fd596cc90ff2d772098e'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['57d80eacc51909f18e6ab63c96a6b02227c3b077c5ffa406d5f4dabe03b8f019'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb new file mode 100644 index 00000000000..182023f4691 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -0,0 +1,50 @@ +name = 'netCDF' +version = '4.9.0' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'netCDF-%(version)s_fix-lib-name.patch', + 'netCDF-%(version)s_fix-linking-errors.patch', + 'netCDF-%(version)s_skip-nasa-test.patch', +] +checksums = [ + '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6', # v4.9.0.tar.gz + 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a', # netCDF-4.9.0_fix-lib-name.patch + '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15', # netCDF-4.9.0_fix-linking-errors.patch + '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a', # netCDF-4.9.0_skip-nasa-test.patch +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.23.1'), + ('Doxygen', '1.9.4'), +] + +dependencies = [ + ('HDF5', '1.12.2'), + ('cURL', '7.83.0'), + ('Szip', '2.1.1'), + ('zstd', '1.5.2'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", +] + +# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " + +runtest = 'test' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb new file mode 100644 index 00000000000..e4909b8b62d --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.6.1' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('netCDF', '4.9.0'), + ('cURL', '7.83.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cftime', '1.6.2', { + 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], + }), + (name, version, { + 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + 'ba8dc5d65293a99f1afb8c2acf588d903fdfdc1963a62545b677fa2734262a78', # netCDF4-1.6.1.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb new file mode 100644 index 00000000000..60eb9cd8eef --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.6.1' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('netCDF', '4.9.0'), + ('cURL', '7.83.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cftime', '1.6.2', { + 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], + }), + (name, version, { + 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + 'ba8dc5d65293a99f1afb8c2acf588d903fdfdc1963a62545b677fa2734262a78', # netCDF4-1.6.1.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-2022.6.0-foss-2022a.eb b/easybuild/easyconfigs/x/xarray/xarray-2022.6.0-foss-2022a.eb new file mode 100644 index 00000000000..6b557c9ef71 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-2022.6.0-foss-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '2022.6.0' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['1028d198493f66bb15bd35dcfdd11defd831cbee3af6589fff16f41bddd67e84'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # required for numpy, pandas +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-2022.6.0-intel-2022a.eb b/easybuild/easyconfigs/x/xarray/xarray-2022.6.0-intel-2022a.eb new file mode 100644 index 00000000000..a0756e083cc --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-2022.6.0-intel-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '2022.6.0' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['1028d198493f66bb15bd35dcfdd11defd831cbee3af6589fff16f41bddd67e84'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # required for numpy, pandas +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' From de07c62b780e3c92d11971d7c9473b743f802846 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 28 Sep 2022 16:51:44 +0200 Subject: [PATCH 210/793] ArviZ v0.12.1 - Remove download_dep_fail --- easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb | 1 - easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb index bc9c93cbf77..12bc8838f20 100644 --- a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb @@ -16,7 +16,6 @@ dependencies = [ ('matplotlib', '3.5.2'), ] -download_dep_fail = True use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb index ac8ac445dc2..365dbb5575c 100644 --- a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb @@ -16,7 +16,6 @@ dependencies = [ ('matplotlib', '3.5.2'), ] -download_dep_fail = True use_pip = True exts_list = [ From 027a0140f1294c748a86b1b8c4c2da00a4df0bf5 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 28 Sep 2022 13:30:06 -0700 Subject: [PATCH 211/793] add sanity_check_commands --- easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb index c541f370006..050b60477d2 100644 --- a/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb @@ -64,4 +64,5 @@ sanity_check_paths = { 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/%(name)s'], } +sanity_check_commands = ['agat_convert_bed2gff.pl --help'] moduleclass = 'bio' From 5a9f694e58c90ad77db9fa3e3c3c161f8194ad03 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 28 Sep 2022 13:44:10 -0700 Subject: [PATCH 212/793] fix line to long --- test/easyconfigs/easyconfigs.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 5a2a62e69c1..095300b7ae2 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -495,7 +495,10 @@ def check_dep_vars(self, gen, dep, dep_vars): 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], # ncbi-vdb v2.x and v3.0.0 require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) - 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'ncbi-vdb-3\.0\.0', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], + 'HDF5': [ + (r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'ncbi-vdb-3\.0\.0', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', + r'shovill-1\.1\.']), + ], # VMTK 1.4.x requires ITK 4.13.x 'ITK': [(r'4\.13\.', [r'VMTK-1\.4\.'])], # Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x) From 72863ee57b6b3bbacd0c63382fbec3d29afe2dc4 Mon Sep 17 00:00:00 2001 From: adam Date: Thu, 29 Sep 2022 10:55:00 +0100 Subject: [PATCH 213/793] adding easyconfigs: pairsnp-0.0.7-foss-2021a.eb --- .../p/pairsnp/pairsnp-0.0.7-foss-2021a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/pairsnp/pairsnp-0.0.7-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/pairsnp/pairsnp-0.0.7-foss-2021a.eb b/easybuild/easyconfigs/p/pairsnp/pairsnp-0.0.7-foss-2021a.eb new file mode 100644 index 00000000000..faf81064d4d --- /dev/null +++ b/easybuild/easyconfigs/p/pairsnp/pairsnp-0.0.7-foss-2021a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'pairsnp' +version = '0.0.7' + +homepage = 'https://github.com/gtonkinhill/pairsnp' +description = """ + A set of scripts for very quickly obtaining pairwise SNP distance matrices from multiple sequence alignments + using sparse matrix libraries to improve performance. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['591f395c59d91056882f0b349c201b2d708a093d6b6ffd3c2ee34aed8767ee98'] + +sanity_check_commands = ['pairsnp -h'] + +moduleclass = 'bio' From 7d10f04b86bd69104f1c8b2a7f24e7bf00974279 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Thu, 29 Sep 2022 12:39:38 +0200 Subject: [PATCH 214/793] Update GPAW to 2022a toolchains and fix incompatibilites between ASE and other packages in said tool chain. --- ....22.1-Compatibility-with-Flask-2-2-2.patch | 26 ++++++++ ...2.1-Compatibility-with-Scipy-2022-05.patch | 66 +++++++++++++++++++ ...ibility-with-pytest-from-Python-3-10.patch | 53 +++++++++++++++ ...2.1-Compatibility-with-pytest-part-2.patch | 25 +++++++ .../a/ASE/ASE-3.22.1-foss-2022a.eb | 18 ++++- .../a/ASE/ASE-3.22.1-intel-2022a.eb | 63 ++++++++++++++++++ .../g/GPAW/GPAW-22.8.0-foss-2022a.eb | 50 ++++++++++++++ .../g/GPAW/GPAW-22.8.0-intel-2022a.eb | 49 ++++++++++++++ .../l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb | 27 ++++++++ 9 files changed, 376 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-pytest-part-2.patch create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-intel-2022a.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb create mode 100644 easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch new file mode 100644 index 00000000000..003c76ba96d --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch @@ -0,0 +1,26 @@ +From b0ac97556b7f973392fd7610bf39d112093230b3 Mon Sep 17 00:00:00 2001 +From: Jakob Schiotz +Date: Mon, 26 Sep 2022 10:19:45 +0200 +Subject: [PATCH] Fix test suite to work with newer versions of Flask (2.2.2) + +--- + ase/test/db/test_db_web.py | 3 ++- + 1 file changed, 2 insertions(+), 1 deletion(-) + +diff --git a/ase/test/db/test_db_web.py b/ase/test/db/test_db_web.py +index 8cea28e..73ec70c 100644 +--- a/ase/test/db/test_db_web.py ++++ b/ase/test/db/test_db_web.py +@@ -66,7 +66,8 @@ def test_add_columns(database): + + + def test_favicon(client): +- assert client.get('/favicon.ico').status_code == 308 # redirect ++ # no content or redirect ++ assert client.get('/favicon.ico').status_code in (204, 308) + assert client.get('/favicon.ico/').status_code == 204 # no content + + +-- +1.8.3.1 + diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch new file mode 100644 index 00000000000..7abbd939ea5 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch @@ -0,0 +1,66 @@ +From ead1bd015b52e60cab729081d7c1da2951f1f95c Mon Sep 17 00:00:00 2001 +From: Ask Hjorth Larsen +Date: Sat, 16 Jul 2022 12:48:01 +0200 +Subject: [PATCH] remove test which compares our units to scipy codata. All + the surrounding modules/methods in scipy seem to be deprecated + +--- + ase/test/test_units.py | 39 +-------------------------------------- + 1 file changed, 1 insertion(+), 38 deletions(-) + +diff --git a/ase/test/test_units.py b/ase/test/test_units.py +index b8a1293..fcbe451 100644 +--- a/ase/test/test_units.py ++++ b/ase/test/test_units.py +@@ -2,47 +2,10 @@ + implementation that SciPy brings with it. + """ + +-import numpy as np + import pytest + + import ase.units +-from ase.units import CODATA, create_units +-import scipy.constants.codata +- +- +-# Scipy lacks data for some of the codata versions: +-codata_scipy_versions = set(CODATA) - {'1998', '1986'} +- +- +-@pytest.mark.parametrize('version', sorted(codata_scipy_versions)) +-def test_units(version): +- name_map = {'_c': 'speed of light in vacuum', +- '_mu0': 'mag. const.', +- '_Grav': 'Newtonian constant of gravitation', +- '_hplanck': 'Planck constant', +- '_e': 'elementary charge', +- '_me': 'electron mass', +- '_mp': 'proton mass', +- '_Nav': 'Avogadro constant', +- '_k': 'Boltzmann constant', +- '_amu': 'atomic mass unit-kilogram relationship'} +- +- scipy_CODATA = getattr(scipy.constants.codata, +- f'_physical_constants_{version}', None) +- if version == '2018' and scipy_CODATA is None: +- pytest.skip('No CODATA for 2018 with this scipy') +- +- assert scipy_CODATA is not None +- +- for asename, scipyname in name_map.items(): +- aseval = CODATA[version][asename] +- try: +- scipyval = scipy_CODATA[scipyname][0] +- except KeyError: +- # XXX Can we be more specific? +- continue # 2002 in scipy contains too little data +- +- assert np.isclose(aseval, scipyval), scipyname ++from ase.units import create_units + + + def test_create_units(): +-- +1.8.3.1 + diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch new file mode 100644 index 00000000000..c73f65f4396 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch @@ -0,0 +1,53 @@ +From c0d155a34dd4115c0aa1c16bb218d808ddfcbbeb Mon Sep 17 00:00:00 2001 +From: Ask Hjorth Larsen +Date: Fri, 4 Feb 2022 14:36:13 +0100 +Subject: [PATCH] update warning handling to appease old and new pytest + simultaneously + +--- + ase/test/test_imports.py | 26 ++++++++++++++------------ + 1 file changed, 14 insertions(+), 12 deletions(-) + +diff --git a/ase/test/test_imports.py b/ase/test/test_imports.py +index 5267a06..93c3bfa 100644 +--- a/ase/test/test_imports.py ++++ b/ase/test/test_imports.py +@@ -1,3 +1,4 @@ ++import contextlib + from pathlib import Path + from importlib import import_module + from numpy import VisibleDeprecationWarning +@@ -58,17 +59,18 @@ newpy_only_modules = { + @pytest.mark.filterwarnings('ignore:Moved to') + def test_imports(): + for module in all_modules: +- if module in deprecated_modules: +- warning = (DeprecationWarning, VisibleDeprecationWarning) +- else: +- warning = None ++ with contextlib.ExitStack() as ignored_warnings: ++ if module in deprecated_modules: ++ ignored_warnings.enter_context( ++ pytest.warns((DeprecationWarning, ++ VisibleDeprecationWarning))) + +- try: +- with pytest.warns(warning): ++ try: + import_module(module) +- except SyntaxError: +- if module not in newpy_only_modules: +- raise +- except ImportError as err: +- if err.name not in ignore_imports and 'deprecated' not in str(err): +- raise ++ except SyntaxError: ++ if module not in newpy_only_modules: ++ raise ++ except ImportError as err: ++ ok = err.name in ignore_imports or 'deprecated' in str(err) ++ if not ok: ++ raise +-- +1.8.3.1 + diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-pytest-part-2.patch b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-pytest-part-2.patch new file mode 100644 index 00000000000..0eb432bf558 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-pytest-part-2.patch @@ -0,0 +1,25 @@ +From 74dba1a8cfe4ee79c1436bdcf0195b79e7c5536e Mon Sep 17 00:00:00 2001 +From: Ask Hjorth Larsen +Date: Fri, 4 Feb 2022 14:41:38 +0100 +Subject: [PATCH] update pytest.warns() call to latest pytest + +--- + ase/test/calculator/castep/test_castep_interface.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/ase/test/calculator/castep/test_castep_interface.py b/ase/test/calculator/castep/test_castep_interface.py +index 623836b..08c72c6 100644 +--- a/ase/test/calculator/castep/test_castep_interface.py ++++ b/ase/test/calculator/castep/test_castep_interface.py +@@ -121,7 +121,7 @@ def test_fundamental_params(): + + # Test special parsers + mock_cparam.continuation = 'default' +- with pytest.warns(None): ++ with pytest.warns(UserWarning): + mock_cparam.reuse = 'default' + assert mock_cparam.reuse.value is None + +-- +1.8.3.1 + diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022a.eb index 98481085f40..c5a508e2a0d 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022a.eb @@ -29,7 +29,23 @@ exts_list = [ 'checksums': ['77f03f4554392558700295e05aed0b1096a20d4a60a4f3ddcde58b0c31c8fca2'], }), ('ase', version, { - 'checksums': ['004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432'], + 'patches': [ + 'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch', + 'ASE-3.22.1-Compatibility-with-pytest-part-2.patch', + 'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch', + 'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch', + ], + 'checksums': [ + '004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432', # ase-3.22.1.tar.gz + # ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch + '8184765ecc9e14081b183fee5c4470da716d77caa67c25164018ac1fdd225eac', + # ASE-3.22.1-Compatibility-with-pytest-part-2.patch + '3a3473912f5f96ffc625119d87227781ba4ea581de15d4af6a58ba960cdf4601', + # ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch + 'c1cb07160b063d432f098efd40dd4b3c9f015b7966572c838a908613a482e0c8', + # ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch + '2a05f98291dc970cb759904988783d1ecc3512ba6a0da852af1d3205667b398d', + ], }), ('ase-ext', '20.9.0', { 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-intel-2022a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-intel-2022a.eb new file mode 100644 index 00000000000..6862f915f93 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-intel-2022a.eb @@ -0,0 +1,63 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Flask', '2.2.2'), + ('matplotlib', '3.5.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '2.0.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.8.2', { + 'checksums': ['77f03f4554392558700295e05aed0b1096a20d4a60a4f3ddcde58b0c31c8fca2'], + }), + ('ase', version, { + 'patches': [ + 'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch', + 'ASE-3.22.1-Compatibility-with-pytest-part-2.patch', + 'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch', + 'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch', + ], + 'checksums': [ + '004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432', # ase-3.22.1.tar.gz + # ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch + '8184765ecc9e14081b183fee5c4470da716d77caa67c25164018ac1fdd225eac', + # ASE-3.22.1-Compatibility-with-pytest-part-2.patch + '3a3473912f5f96ffc625119d87227781ba4ea581de15d4af6a58ba960cdf4601', + # ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch + 'c1cb07160b063d432f098efd40dd4b3c9f015b7966572c838a908613a482e0c8', + # ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch + '2a05f98291dc970cb759904988783d1ecc3512ba6a0da852af1d3205667b398d', + ], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb new file mode 100644 index 00000000000..b400a2bd2c3 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb @@ -0,0 +1,50 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '22.8.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), + ('GPAW-22.8.0-Remove-MPI-compiler-hack.patch', 0), +] +checksums = [ + '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c', # gpaw-22.8.0.tar.gz + # GPAW-20.1.0-Add-Easybuild-configuration-files.patch + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', + '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e', # GPAW-22.8.0-Remove-MPI-compiler-hack.patch +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('ASE', '3.22.1'), + ('libxc', '5.2.3'), + ('libvdwxc', '0.4.0'), + ('PyYAML', '6.0'), + ('GPAW-setups', '0.9.20000', '', True), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb new file mode 100644 index 00000000000..58087303e00 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb @@ -0,0 +1,49 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '22.8.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), + ('GPAW-22.8.0-Remove-MPI-compiler-hack.patch', 0), +] +checksums = [ + '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c', # gpaw-22.8.0.tar.gz + # GPAW-20.1.0-Add-Easybuild-configuration-files.patch + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', + '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e', # GPAW-22.8.0-Remove-MPI-compiler-hack.patch +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('ASE', '3.22.1'), + ('libxc', '5.2.3'), + ('PyYAML', '6.0'), + ('GPAW-setups', '0.9.20000', '', True), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb new file mode 100644 index 00000000000..b1785ef119b --- /dev/null +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libvdwxc' +version = '0.4.0' + +homepage = 'https://libvdwxc.org' +description = """libvdwxc is a general library for evaluating energy and potential for +exchange-correlation (XC) functionals from the vdW-DF family that can be used with various +of density functional theory (DFT) codes.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://launchpad.net/libvdwxc/stable/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3524feb5bb2be86b4688f71653502146b181e66f3f75b8bdaf23dd1ae4a56b33'] + +preconfigopts = 'unset CC && unset FC && ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['libvdwxc_fdtest', 'libvdwxc_maintest', + 'libvdwxc_q0test', 'libvdwxc_q0test2']] + + ['lib/lib%s.%s' % (x, y) for x in ['vdwxc', 'vdwxcfort'] + for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'chem' From c216f1e617e3e1e2921c20b1ba2d38a32362d97b Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 29 Sep 2022 12:11:01 +0100 Subject: [PATCH 215/793] adding easyconfigs: TRUST4-1.0.7-GCC-11.3.0.eb --- .../t/TRUST4/TRUST4-1.0.7-GCC-11.3.0.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.7-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.7-GCC-11.3.0.eb b/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.7-GCC-11.3.0.eb new file mode 100644 index 00000000000..e0aa3914a2d --- /dev/null +++ b/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.7-GCC-11.3.0.eb @@ -0,0 +1,71 @@ +easyblock = 'MakeCp' + +name = 'TRUST4' +version = '1.0.7' + +homepage = 'https://github.com/liulab-dfci/TRUST4' +description = """Tcr Receptor Utilities for Solid Tissue (TRUST) is a +computational tool to analyze TCR and BCR sequences using unselected RNA +sequencing data, profiled from solid tissues, including tumors. TRUST4 performs +de novo assembly on V, J, C genes including the hypervariable +complementarity-determining region 3 (CDR3) and reports consensus of BCR/TCR +sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to +report the corresponding information. TRUST4 supports both single-end and +paired-end sequencing data with any read length.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'liulab-dfci' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['633cab6ef0fa082012ce6a185e818b5454ef16576e9a165f268d69335b3aef5f'] + +# TRUST4 uses an old API of SAMtools and links agains libbam.a, that has been +# removed in SAMtools 1.14 (https://github.com/liulab-dfci/TRUST4/issues/95). +# For this reason, we use the SAMtools bundled by TRUST4. +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('Python', '3.10.4'), + ('Perl', '5.34.1'), +] + +# Fix the wrong version in run-trust4 +prebuildopts = 'sed -i "s/v1.0.6/v1.0.7/" run-trust4 && ' + +local_binaries = [ + 'run-trust4', 'trust4', 'bam-extractor', 'fastq-extractor', 'annotator', + 'BuildDatabaseFa.pl', 'BuildImgtAnnot.pl', 'BuildImgtVquestAnnot.pl', + 'FilterAnnotatedAssembly.pl', 'trust-airr.pl', 'trust-barcoderep.pl', + 'trust-simplerep.pl', 'trust-smartseq.pl', +] +local_scripts = [ + 'AddSequenceToCDR3File.pl', 'barcoderep-filter.py', 'GetFullLengthAssembly.pl', + 'trust-barcoderep-to-10X.pl', 'trust-cluster.py', 'trust-stats.py' +] +files_to_copy = [ + (local_binaries, 'bin'), + (['scripts/%s' % x for x in local_scripts], 'bin'), +] + +fix_perl_shebang_for = ['bin/*.pl'] +fix_python_shebang_for = ['bin/*.py'] + +postinstallcmds = ["chmod a+x %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['bin/' + x for x in local_binaries + local_scripts], + 'dirs': [], +} + +sanity_check_commands = [ + "run-trust4 2>&1 | grep 'TRUST4 v%(version)s'", + "BuildDatabaseFa.pl 2>&1 | grep 'usage: perl BuildDatabaseFa.pl'", + "trust-cluster.py 2>&1 | grep 'usage: a.py trust_cdr3.out'", + "cd %(builddir)s/%(name)s-%(version)s && " + "run-trust4 -b example/example.bam -f hg38_bcrtcr.fa --ref human_IMGT+C.fa && " + "test -f example/TRUST_example_report.tsv" +] + +moduleclass = 'bio' From 25a2b32b7906257593ad1239ead671134dfeecae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 29 Sep 2022 12:13:00 +0000 Subject: [PATCH 216/793] adding easyconfigs: xprop-1.2.5-GCCcore-11.3.0.eb, FLTK-1.3.8-GCCcore-11.3.0.eb --- .../f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb | 43 +++++++++++++++++++ .../x/xprop/xprop-1.2.5-GCCcore-11.3.0.eb | 32 ++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..899952c376c --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.8' + +homepage = 'https://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://fltk.org/pub/%(namelower)s/%(version)s/'] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +patches = ['FLTK-1.3.6_fix-LDFLAGS.patch'] +checksums = [ + '5d2ccb7ad94e595d3d97509c7a931554e059dd970b7b29e6fd84cb70fd5491c6', # fltk-1.3.7-source.tar.gz + 'f8af2414a1ee193a186b0d98d1e3567add0ee003f44ec64dce2ce2dfd6d95ebf', # FLTK-1.3.6_fix-LDFLAGS.patch +] + +configopts = '--enable-shared --enable-threads --enable-xft' + +builddependencies = [ + ('binutils', '2.38'), + ('groff', '1.22.4'), +] + +dependencies = [ + ('Mesa', '22.0.3'), + ('libGLU', '9.0.2'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), + ('xprop', '1.2.5'), + ('zlib', '1.2.12'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2d806a829fc --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'xprop' +version = '1.2.5' + +homepage = "https://www.x.org/wiki/" +description = """The xprop utility is for displaying window and font properties in an X server. + One window or font is selected using the command line arguments or possibly + in the case of a window, by clicking on the desired window. A list of + properties is then given, possibly with formatting information.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://ftp.x.org/archive/individual/app/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b7bf6b6be6cf23e7966a153fc84d5901c14f01ee952fbd9d930aa48e2385d670'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('X11', '20220504'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' From bce9138539e26dbf0fee3675888d7d09b28352b3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 29 Sep 2022 12:16:38 +0000 Subject: [PATCH 217/793] Fix checksum --- easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb index 899952c376c..602304596e1 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb @@ -15,7 +15,7 @@ source_urls = ['https://fltk.org/pub/%(namelower)s/%(version)s/'] sources = ['%(namelower)s-%(version)s-source.tar.gz'] patches = ['FLTK-1.3.6_fix-LDFLAGS.patch'] checksums = [ - '5d2ccb7ad94e595d3d97509c7a931554e059dd970b7b29e6fd84cb70fd5491c6', # fltk-1.3.7-source.tar.gz + 'f3c1102b07eb0e7a50538f9fc9037c18387165bc70d4b626e94ab725b9d4d1bf', # fltk-1.3.8-source.tar.gz 'f8af2414a1ee193a186b0d98d1e3567add0ee003f44ec64dce2ce2dfd6d95ebf', # FLTK-1.3.6_fix-LDFLAGS.patch ] From 1f55c6c6bfa6025d6daa1ac4ce6cea53e0aee36e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 29 Sep 2022 14:28:32 +0200 Subject: [PATCH 218/793] adding easyconfigs: Score-P-7.1-gompi-2021a-CUDA-11.3.1.eb --- .../Score-P-7.1-gompi-2021a-CUDA-11.3.1.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..9fc1ae2e8bb --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2021a-CUDA-11.3.1.eb @@ -0,0 +1,62 @@ +## +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'Score-P' +version = '7.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['98dea497982001fb82da3429ca55669b2917a0858c71abe2cfe7cd113381f1f7'] + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('UCX-CUDA', '1.10.0', versionsuffix), + ('CubeLib', '4.6'), + ('CubeWriter', '4.6'), + ('libunwind', '1.4.0'), + ('OPARI2', '2.0.6'), + ('OTF2', '2.3'), + # Hardware counter support (optional): + ('PAPI', '6.0.0.1'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' From 111fe5fa6e1222ce5ffd0bac9578824c0aefaab1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 29 Sep 2022 12:45:06 +0000 Subject: [PATCH 219/793] adding easyconfigs: POV-Ray-3.7.0.10-GCC-11.3.0.eb --- .../p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb new file mode 100644 index 00000000000..04c5b90e972 --- /dev/null +++ b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb @@ -0,0 +1,63 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'POV-Ray' +version = '3.7.0.10' + +homepage = 'https://www.povray.org/' +description = """The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program + which generates images from a text-based scene description, and is available for a variety + of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning + three-dimensional graphics. The source code is available for those wanting to do their own ports.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/POV-Ray/povray/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['POV-Ray-3.7.0.7_dont-touch-home.patch'] +checksums = [ + '7bee83d9296b98b7956eb94210cf30aa5c1bbeada8ef6b93bb52228bbc83abff', # v3.7.0.10.tar.gz + '45103afca808e279dcdee80194c65e2a760c76d011d351392a46e817b0b655f7', # POV-Ray-3.7.0.7_dont-touch-home.patch +] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('Boost', '1.79.0'), + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), + ('X11', '20220504'), + ('LibTIFF', '4.3.0'), + ('SDL2', '2.0.22'), +] + +preconfigopts = "cd unix && sed -i 's/^automake/automake --add-missing; automake/g' prebuild.sh && " +preconfigopts += " ./prebuild.sh && cd .. && " +configopts = "COMPILED_BY='EasyBuild' " +configopts += "--with-boost=$EBROOTBOOST --with-zlib=$EBROOTZLIB --with-libpng=$EBROOTLIBPNG " +configopts += "--with-libtiff=$EBROOTLIBTIFF --with-libjpeg=$EBROOTLIBJPEGMINTURBO --with-libsdl=$EBROOTSDL2 " +# configopts += " --with-libmkl=DIR " ## upstream needs to fix this, still in BETA + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/povray'], + 'dirs': ['etc/povray/%(version_major_minor)s', 'share'] +} + +moduleclass = 'vis' From de74f8c244d5bd864c589857e93aee80f2293ff5 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 29 Sep 2022 14:47:44 +0200 Subject: [PATCH 220/793] adding easyconfigs: Infernal-1.1.4-foss-2021a.eb --- .../i/Infernal/Infernal-1.1.4-foss-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2021a.eb diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2021a.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2021a.eb new file mode 100644 index 00000000000..2f490f5de24 --- /dev/null +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2021a.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: BSD +# Updated:: Denis Kristak (INUITS) +# Updated:: Sebastien Moretti (SIB) +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'Infernal' +version = "1.1.4" + +homepage = 'http://eddylab.org/infernal/' +description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +source_urls = ['http://eddylab.org/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc'] + +local_bins = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'press', 'scan', 'search', 'stat'] + +sanity_check_paths = { + 'files': ['bin/cm%s' % x for x in local_bins], + 'dirs': [] +} + +sanity_check_commands = ['cm%s -h' % x for x in local_bins] + +moduleclass = 'bio' From 3e4ecf15507a771836c618b547cd43f42463f47e Mon Sep 17 00:00:00 2001 From: robogast Date: Thu, 29 Sep 2022 16:27:34 +0200 Subject: [PATCH 221/793] OpenEXR updated: Imath detached, zlib added --- .../i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb | 33 +++++++++++++++++++ .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 6 +++- 2 files changed, 38 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..b4f0f0223ca --- /dev/null +++ b/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'Imath' +version = '3.1.5' + +homepage = 'https://imath.readthedocs.io/en/latest/' +description = """ +Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +sources = [{ + 'filename': '%(name)s_v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/AcademySoftwareFoundation', + 'repo_name': '%(name)s', + 'tag': 'v%(version)s', + }, +}] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['lib/libImath.%s' % SHLIB_EXT], + 'dirs': ['include/Imath'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb index d607a01b64d..2e44695eb49 100644 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -17,11 +17,15 @@ builddependencies = [ ('binutils', '2.38'), ('CMake', '3.23.1'), ] +dependencies = [ + ('Imath', '3.1.5'), + ('zlib', '1.2.12') +] configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' local_libs, local_bins = [ - ['Iex', 'IlmThread', 'Imath', 'OpenEXR', 'OpenEXRUtil'], + ['Iex', 'IlmThread', 'OpenEXR', 'OpenEXRUtil'], ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] ] From 459784bb605832a2a69d53c4e2bf809fa8dca508 Mon Sep 17 00:00:00 2001 From: robogast Date: Thu, 29 Sep 2022 16:32:12 +0200 Subject: [PATCH 222/793] OpenEXR updated: removed stray configopt --- easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb index 2e44695eb49..d85c1503e24 100644 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -22,8 +22,6 @@ dependencies = [ ('zlib', '1.2.12') ] -configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' - local_libs, local_bins = [ ['Iex', 'IlmThread', 'OpenEXR', 'OpenEXRUtil'], ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] From 1ae7ca64ec4bf84bc8e8e914c6e91ed48b28b2b0 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 29 Sep 2022 17:15:46 +0200 Subject: [PATCH 223/793] Increase the number of allowed test failures, as with https://github.com/easybuilders/easybuild-easyblocks/pull/2794 we'll actually start counting failing tests, instead of failing test suites. Thus, much higher numbers can be expected, since many test suites have multiple failing tests --- .../p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb index 9a48694ea1f..0840f2a441b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb @@ -112,8 +112,8 @@ excluded_tests = { runtest = "cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s" # several tests are known to be flaky, and fail in some contexts (like having multiple GPUs available), -# so we allow up to 20 (out of ~90k) tests to fail before treating the installation to be faulty -max_failed_tests = 20 +# so we allow up to 400 (out of ~90k) tests to fail before treating the installation to be faulty +max_failed_tests = 400 # The readelf sanity check command can be taken out once the TestRPATH test from # https://github.com/pytorch/pytorch/pull/68912 is accepted, since it is then checked as part of the PyTorch test suite From 407fb92fc7e89c2d7daf5a42748029410ccb79fc Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 29 Sep 2022 17:17:00 +0200 Subject: [PATCH 224/793] Changed moduleclass to 'ai' --- .../p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb index 0840f2a441b..64343b457dc 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb @@ -124,4 +124,4 @@ sanity_check_commands = [ tests = ['%(name)s-check-cpp-extension.py'] -moduleclass = 'devel' +moduleclass = 'ai' From 7b72fe8a83006b85204350f18210a0212627a9b7 Mon Sep 17 00:00:00 2001 From: robogast Date: Thu, 29 Sep 2022 17:25:19 +0200 Subject: [PATCH 225/793] DCMTK added hash, pugixml fixed E121 --- .../d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb | 13 +++---------- .../p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb | 13 +++++++++---- 2 files changed, 12 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb index 6bffa6ad7b9..5d7107ed091 100644 --- a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb @@ -15,6 +15,7 @@ local_stripped_version = version.replace('.', '') source_urls = ['https://dicom.offis.de/download/%(namelower)s/dcmtk{}/'.format(local_stripped_version)] sources = [SOURCELOWER_TAR_GZ] +checksums = ['7c58298e3e8d60232ee6fc8408cfadd14463cc11a3c4ca4c59af5988c7e9710a'] builddependencies = [ ('binutils', '2.38'), @@ -40,17 +41,9 @@ sanity_check_paths = { 'dirs': ['lib'], } +local_test_modules = ['dcmdata', 'dcmect', 'dcmfg', 'dcmiod', 'dcmnet', 'dcmrt', 'dcmseg', 'dcmsr', 'dcmtls', 'ofstd'] sanity_check_commands = [ - 'dcmdata_tests | grep " 0 failed"', - 'dcmect_tests | grep " 0 failed"', - 'dcmfg_tests | grep " 0 failed"', - 'dcmiod_tests | grep " 0 failed"', - 'dcmnet_tests | grep " 0 failed"', - 'dcmrt_tests | grep " 0 failed"', - 'dcmseg_tests | grep " 0 failed"', - 'dcmsr_tests | grep " 0 failed"', - 'dcmtls_tests | grep " 0 failed"', - 'ofstd_tests | grep " 0 failed"', + '%s_tests | grep " 0 failed"' % s for s in local_test_modules ] moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb index 1cf51118427..c171baaaab1 100644 --- a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb @@ -19,13 +19,18 @@ builddependencies = [ ] configopts = " ".join([ - "-DBUILD_SHARED_LIBS=ON", - "-DPUGIXML_BUILD_SHARED_AND_STATIC_LIBS=ON", + "-DBUILD_SHARED_LIBS=ON", + "-DPUGIXML_BUILD_SHARED_AND_STATIC_LIBS=ON", ]) sanity_check_paths = { - 'files': ['include/pugiconfig.hpp', 'include/pugixml.hpp', 'lib/libpugixml.a', - 'lib/libpugixml.%s' % SHLIB_EXT, 'lib/pkgconfig/pugixml.pc'], + 'files': [ + 'include/pugiconfig.hpp', + 'include/pugixml.hpp', + 'lib/libpugixml.a', + 'lib/libpugixml.%s' % SHLIB_EXT, + 'lib/pkgconfig/pugixml.pc' + ], 'dirs': ['lib/cmake/pugixml'], } From 4caeb178a840be213ad37866ffb2c863133c5483 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 29 Sep 2022 18:15:34 +0200 Subject: [PATCH 226/793] fix exts_filter --- easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb index 050b60477d2..b269f17cc28 100644 --- a/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb @@ -21,7 +21,7 @@ dependencies = [ ] exts_defaultclass = 'PerlModule' -exts_filter = ("perldoc -lm %(ext_name)s ", "") +exts_filter = ("perl -e 'require %(ext_name)s'", '') exts_list = [ ('Set::Object', '1.42', { From 107805868dc2a91c8246eeef5b00090a9c3be914 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 29 Sep 2022 18:33:21 -0700 Subject: [PATCH 227/793] correct dep pkgconfig for Guile 3.0.7 --- easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb index 456da718458..6e956e7e513 100644 --- a/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb @@ -21,7 +21,7 @@ checksums = ['c7935b7a29e42443f6a35d35cf20ffa7d028c399303f872cd1219598a83656ae'] builddependencies = [ ('Autotools', '20210726'), ('binutils', '2.37'), - ('pkg-config', '0.29.2'), + ('pkgconfig', '0.29.2'), ] dependencies = [ From b1882d25d3f73462c6bd2b388cb2ae80c5702522 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 29 Sep 2022 16:07:48 +0200 Subject: [PATCH 228/793] adding easyconfigs: ccache-4.6.3.eb, hiredis-1.0.2-GCCcore-11.3.0.eb --- .../easyconfigs/c/ccache/ccache-4.6.3.eb | 54 +++++++ .../h/hiredis/hiredis-1.0.2-GCCcore-11.3.0.eb | 49 ++++++ ...edis-1.0.2_build-also-static-library.patch | 151 ++++++++++++++++++ ...s-1.0.2_use-same-name-for-static-lib.patch | 43 +++++ 4 files changed, 297 insertions(+) create mode 100644 easybuild/easyconfigs/c/ccache/ccache-4.6.3.eb create mode 100644 easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/h/hiredis/hiredis-1.0.2_build-also-static-library.patch create mode 100644 easybuild/easyconfigs/h/hiredis/hiredis-1.0.2_use-same-name-for-static-lib.patch diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.6.3.eb b/easybuild/easyconfigs/c/ccache/ccache-4.6.3.eb new file mode 100644 index 00000000000..68ac0da6cad --- /dev/null +++ b/easybuild/easyconfigs/c/ccache/ccache-4.6.3.eb @@ -0,0 +1,54 @@ +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL + +easyblock = 'CMakeNinja' + +name = 'ccache' +version = '4.6.3' + +homepage = 'https://ccache.dev/' +description = """Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by +caching previous compilations and detecting when the same compilation is being done again""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/ccache/ccache/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['f46ba3706ad80c30d4d5874dee2bf9227a7fcd0ccaac31b51919a3053d84bd05'] + +osdependencies = [('glibc-static', 'libc6-dev')] + +local_gccver = '11.3.0' +builddependencies = [ + ('GCC', local_gccver), + ('CMake', '3.23.1', '', ('GCCcore', local_gccver)), + ('Ninja', '1.10.2', '', ('GCCcore', local_gccver)), + ('hiredis', '1.0.2', '', ('GCCcore', local_gccver)), + ('zstd', '1.5.2', '', ('GCCcore', local_gccver)), +] + +# use BFD linker rather than default ld.gold (required on CentOS 8) +preconfigopts = 'LDFLAGS="-fuse-ld=bfd"' +configopts = ' '.join([ + '-DENABLE_DOCUMENTATION=OFF', + '-DENABLE_IPO=ON', + # Link dependencies and binary statically + '-DCMAKE_EXE_LINKER_FLAGS="-static"', + '-DZSTD_LIBRARY="$EBROOTZSTD/lib/libzstd.a"', + '-DHIREDIS_LIBRARY="$EBROOTHIREDIS/lib/libhiredis.a"', + # Disable downloading dependencies + '-DZSTD_FROM_INTERNET=OFF -DHIREDIS_FROM_INTERNET=OFF', +]) + +sanity_check_paths = { + 'files': ['bin/ccache'], + 'dirs': [] +} +sanity_check_commands = [ + 'ccache --help', + # Ensure that the binary does not depend on any shared library + 'ldd $(which ccache) | grep -q "not a dynamic executable"', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3d70862e8f0 --- /dev/null +++ b/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.3.0.eb @@ -0,0 +1,49 @@ +# Author: Alexander Grund (TU Dresden) +# Based on EC by J. Sassmannshausen (Imperial College London) + +easyblock = 'CMakeMake' + +name = 'hiredis' +version = '1.0.2' + +homepage = 'https://github.com/redis/hiredis' +description = """Hiredis is a minimalistic C client library for the Redis database. + +It is minimalistic because it just adds minimal support for the protocol, +but at the same time it uses a high level printf-alike API in order to +make it much higher level than otherwise suggested by its minimal code base +and the lack of explicit bindings for every Redis command.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'redis' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_build-also-static-library.patch', + '%(name)s-%(version)s_use-same-name-for-static-lib.patch' +] +checksums = [ + 'e0ab696e2f07deb4252dda45b703d09854e53b9703c7d52182ce5a22616c3819', # v1.0.2.tar.gz + # hiredis-1.0.2_build-also-static-library.patch + '224cb6fdbf8488cc6583323f5cde09e98d10fd201ddfd117572594ed98eb642c', + # hiredis-1.0.2_use-same-name-for-static-lib.patch + '7ef1c90331a0ed92e7ae2905827c3c8bb79e19545b0bae3b44a06a11564ec8de', +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['lib/libhiredis.a', 'lib/libhiredis.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2_build-also-static-library.patch b/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2_build-also-static-library.patch new file mode 100644 index 00000000000..85f0463b3bf --- /dev/null +++ b/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2_build-also-static-library.patch @@ -0,0 +1,151 @@ +From https://github.com/redis/hiredis/pull/851 + +From 07c3618ffe7912c2ebc589ea45501c687a19cf2c Mon Sep 17 00:00:00 2001 +From: masariello +Date: Wed, 22 Jul 2020 14:23:53 +0100 +Subject: [PATCH 1/2] Add static library target and cpack support + +--- + CMakeLists.txt | 42 +++++++++++++++++++++++++++++++++++++++--- + hiredis.targets | 11 +++++++++++ + 2 files changed, 50 insertions(+), 3 deletions(-) + create mode 100644 hiredis.targets + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 87a4ac614..55c026b8f 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -40,6 +40,7 @@ IF(WIN32) + ENDIF() + + ADD_LIBRARY(hiredis SHARED ${hiredis_sources}) ++ADD_LIBRARY(hiredis_static STATIC ${hiredis_sources}) + + SET_TARGET_PROPERTIES(hiredis + PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE +@@ -48,16 +49,47 @@ IF(WIN32 OR MINGW) + TARGET_LINK_LIBRARIES(hiredis PRIVATE ws2_32) + ENDIF() + +-TARGET_INCLUDE_DIRECTORIES(hiredis PUBLIC $ $) ++TARGET_INCLUDE_DIRECTORIES(hiredis PUBLIC $ $) ++TARGET_INCLUDE_DIRECTORIES(hiredis_static PUBLIC $ $) + + CONFIGURE_FILE(hiredis.pc.in hiredis.pc @ONLY) + +-INSTALL(TARGETS hiredis ++set(CPACK_PACKAGE_VENDOR "Redis") ++set(CPACK_PACKAGE_DESCRIPTION "\ ++Hiredis is a minimalistic C client library for the Redis database. ++ ++It is minimalistic because it just adds minimal support for the protocol, \ ++but at the same time it uses a high level printf-alike API in order to make \ ++it much higher level than otherwise suggested by its minimal code base and the \ ++lack of explicit bindings for every Redis command. ++ ++Apart from supporting sending commands and receiving replies, it comes with a \ ++reply parser that is decoupled from the I/O layer. It is a stream parser designed \ ++for easy reusability, which can for instance be used in higher level language bindings \ ++for efficient reply parsing. ++ ++Hiredis only supports the binary-safe Redis protocol, so you can use it with any Redis \ ++version >= 1.2.0. ++ ++The library comes with multiple APIs. There is the synchronous API, the asynchronous API \ ++and the reply parsing API.") ++set(CPACK_PACKAGE_HOMEPAGE_URL "https://github.com/redis/hiredis") ++set(CPACK_PACKAGE_CONTACT "michael dot grunder at gmail dot com") ++set(CPACK_DEBIAN_PACKAGE_SHLIBDEPS ON) ++set(CPACK_RPM_PACKAGE_AUTOREQPROV ON) ++ ++include(CPack) ++ ++INSTALL(TARGETS hiredis hiredis_static + EXPORT hiredis-targets + RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} + LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} + ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ++# For NuGet packages ++INSTALL(FILES hiredis.targets ++ DESTINATION build/native) ++ + INSTALL(FILES hiredis.h read.h sds.h async.h alloc.h + DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/hiredis) + +@@ -98,6 +130,8 @@ IF(ENABLE_SSL) + ssl.c) + ADD_LIBRARY(hiredis_ssl SHARED + ${hiredis_ssl_sources}) ++ ADD_LIBRARY(hiredis_ssl_static STATIC ++ ${hiredis_ssl_sources}) + + IF (APPLE) + SET_PROPERTY(TARGET hiredis_ssl PROPERTY LINK_FLAGS "-Wl,-undefined -Wl,dynamic_lookup") +@@ -109,13 +143,15 @@ IF(ENABLE_SSL) + VERSION "${HIREDIS_SONAME}") + + TARGET_INCLUDE_DIRECTORIES(hiredis_ssl PRIVATE "${OPENSSL_INCLUDE_DIR}") ++ TARGET_INCLUDE_DIRECTORIES(hiredis_ssl_static PRIVATE "${OPENSSL_INCLUDE_DIR}") ++ + TARGET_LINK_LIBRARIES(hiredis_ssl PRIVATE ${OPENSSL_LIBRARIES}) + IF (WIN32 OR MINGW) + TARGET_LINK_LIBRARIES(hiredis_ssl PRIVATE hiredis) + ENDIF() + CONFIGURE_FILE(hiredis_ssl.pc.in hiredis_ssl.pc @ONLY) + +- INSTALL(TARGETS hiredis_ssl ++ INSTALL(TARGETS hiredis_ssl hiredis_ssl_static + EXPORT hiredis_ssl-targets + RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} + LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} +diff --git a/hiredis.targets b/hiredis.targets +new file mode 100644 +index 000000000..effd8a561 +--- /dev/null ++++ b/hiredis.targets +@@ -0,0 +1,11 @@ ++ ++ ++ ++ ++ $(MSBuildThisFileDirectory)\..\..\include;%(AdditionalIncludeDirectories) ++ ++ ++ $(MSBuildThisFileDirectory)\..\..\lib;%(AdditionalLibraryDirectories) ++ ++ ++ +\ No newline at end of file + +From 1b40ec509628c73ac272c8599a3c923e34800d54 Mon Sep 17 00:00:00 2001 +From: Alessio M +Date: Fri, 4 Sep 2020 09:37:11 +0100 +Subject: [PATCH 2/2] fixed issue with unit test linking on windows with SSL + +--- + CMakeLists.txt | 4 +++- + 1 file changed, 3 insertions(+), 1 deletion(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 4bdee1864..53e9f5871 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -50,7 +50,8 @@ SET_TARGET_PROPERTIES(hiredis + PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE + VERSION "${HIREDIS_SONAME}") + IF(WIN32 OR MINGW) +- TARGET_LINK_LIBRARIES(hiredis PRIVATE ws2_32) ++ TARGET_LINK_LIBRARIES(hiredis PUBLIC ws2_32 crypt32) ++ TARGET_LINK_LIBRARIES(hiredis_static PUBLIC ws2_32 crypt32) + ENDIF() + + TARGET_INCLUDE_DIRECTORIES(hiredis PUBLIC $ $) +@@ -152,6 +153,7 @@ IF(ENABLE_SSL) + TARGET_LINK_LIBRARIES(hiredis_ssl PRIVATE ${OPENSSL_LIBRARIES}) + IF (WIN32 OR MINGW) + TARGET_LINK_LIBRARIES(hiredis_ssl PRIVATE hiredis) ++ TARGET_LINK_LIBRARIES(hiredis_ssl_static PUBLIC hiredis_static) + ENDIF() + CONFIGURE_FILE(hiredis_ssl.pc.in hiredis_ssl.pc @ONLY) + diff --git a/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2_use-same-name-for-static-lib.patch b/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2_use-same-name-for-static-lib.patch new file mode 100644 index 00000000000..4e6003d989e --- /dev/null +++ b/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2_use-same-name-for-static-lib.patch @@ -0,0 +1,43 @@ +From https://patch-diff.githubusercontent.com/raw/redis/hiredis/pull/1057 + +From dd4bf97836d07df0a4502b72f9024d0231156711 Mon Sep 17 00:00:00 2001 +From: Orgad Shaneh +Date: Tue, 29 Mar 2022 17:16:19 +0300 +Subject: [PATCH] Use the same name for static and shared libraries + +On all system except MSVC, the targets are different. + +Unix: libhiredis.so, libhiredis.a +MinGW: libhiredis.dll+libhiredis.dll.a, libhiredis.a +MSVC: hiredis.dll+hiredis.lib, hiredis_static.lib +--- + CMakeLists.txt | 9 +++++++++ + 1 file changed, 9 insertions(+) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index fe6720b28..899cd14d0 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -50,6 +50,11 @@ ADD_LIBRARY(hiredis_static STATIC ${hiredis_sources}) + ADD_LIBRARY(hiredis::hiredis ALIAS hiredis) + ADD_LIBRARY(hiredis::hiredis_static ALIAS hiredis_static) + ++IF(NOT MSVC) ++ SET_TARGET_PROPERTIES(hiredis_static ++ PROPERTIES OUTPUT_NAME hiredis) ++ENDIF() ++ + SET_TARGET_PROPERTIES(hiredis + PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE + VERSION "${HIREDIS_SONAME}") +@@ -160,6 +165,10 @@ IF(ENABLE_SSL) + ${hiredis_ssl_sources}) + ADD_LIBRARY(hiredis_ssl_static STATIC + ${hiredis_ssl_sources}) ++ IF(NOT MSVC) ++ SET_TARGET_PROPERTIES(hiredis_ssl_static ++ PROPERTIES OUTPUT_NAME hiredis_ssl) ++ ENDIF() + + IF (APPLE) + SET_PROPERTY(TARGET hiredis_ssl PROPERTY LINK_FLAGS "-Wl,-undefined -Wl,dynamic_lookup") From ea4782886948036ce8d97ed746ff151e80d406df Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 29 Sep 2022 16:44:02 +0200 Subject: [PATCH 229/793] Fix PyTorch 1.11 on POWER --- .../PyTorch-1.10.0_fix-XNNPACK-tests.patch | 236 ++++++++++++++++++ .../PyTorch-1.10.0_fix-kineto-crash.patch | 24 ++ ...orch-1.10.0_fix-vsx-vector-functions.patch | 39 +++ ...10.0_skip-nnapi-test-without-qnnpack.patch | 30 +++ .../PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 69 ++--- ...1.11.0_fix-attention_cpp-compilation.patch | 61 +++++ .../PyTorch-1.11.0_fix-test_utils.patch | 20 ++ ...h-1.11.0_increase-tolerance-test_ops.patch | 22 ++ ...Torch-1.11.0_install-vsx-vec-headers.patch | 30 +++ 9 files changed, 503 insertions(+), 28 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-XNNPACK-tests.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-kineto-crash.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-vsx-vector-functions.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-attention_cpp-compilation.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-test_utils.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase-tolerance-test_ops.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_install-vsx-vec-headers.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-XNNPACK-tests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-XNNPACK-tests.patch new file mode 100644 index 00000000000..c9a82a56164 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-XNNPACK-tests.patch @@ -0,0 +1,236 @@ +When XNNPACK is disabled tests run into assertion failures. +Fix by using (most of) https://github.com/pytorch/pytorch/pull/72642 + +Author: Digant Desai + +Backported by Alexander Grund (TU Dresden) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 0c11507838..5b74b7f63c 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -275,7 +275,14 @@ option(USE_LITE_INTERPRETER_PROFILER "Enable " ON) + option(USE_VULKAN_FP16_INFERENCE "Vulkan - Use fp16 inference" OFF) + option(USE_VULKAN_RELAXED_PRECISION "Vulkan - Use relaxed precision math in the kernels (mediump)" OFF) + option(USE_VULKAN_SHADERC_RUNTIME "Vulkan - Use runtime shader compilation as opposed to build-time (needs libshaderc)" OFF) +-option(USE_XNNPACK "Use XNNPACK" ON) ++# option USE_XNNPACK: try to enable xnnpack by default. ++set(XNNPACK_MIN_CMAKE_VER 3.12) ++cmake_dependent_option( ++ USE_XNNPACK "Use XNNPACK. Requires cmake >= ${XNNPACK_MIN_CMAKE_VER}." ON ++ "CMAKE_VERSION VERSION_GREATER_EQUAL ${XNNPACK_MIN_CMAKE_VER}" OFF) ++if(NOT USE_XNNPACK AND CMAKE_VERSION VERSION_LESS ${XNNPACK_MIN_CMAKE_VER}) ++ message(WARNING "USE_XNNPACK is set to OFF. XNNPACK requires CMake version ${XNNPACK_MIN_CMAKE_VER} or greater.") ++endif() + option(USE_ZMQ "Use ZMQ" OFF) + option(USE_ZSTD "Use ZSTD" OFF) + # Ensure that an MKLDNN build is the default for x86 CPUs +diff --git a/cmake/Summary.cmake b/cmake/Summary.cmake +index 6d021536c1..7c1ac64539 100644 +--- a/cmake/Summary.cmake ++++ b/cmake/Summary.cmake +@@ -165,6 +165,7 @@ function(caffe2_print_configuration_summary) + message(STATUS " USE_PROF : ${USE_PROF}") + message(STATUS " USE_QNNPACK : ${USE_QNNPACK}") + message(STATUS " USE_PYTORCH_QNNPACK : ${USE_PYTORCH_QNNPACK}") ++ message(STATUS " USE_XNNPACK : ${USE_XNNPACK}") + message(STATUS " USE_REDIS : ${USE_REDIS}") + message(STATUS " USE_ROCKSDB : ${USE_ROCKSDB}") + message(STATUS " USE_ZMQ : ${USE_ZMQ}") +diff --git a/test/jit/test_optimize_for_mobile_preserve_debug_info.py b/test/jit/test_optimize_for_mobile_preserve_debug_info.py +index c08f3b5838..1b93f54c15 100644 +--- a/test/jit/test_optimize_for_mobile_preserve_debug_info.py ++++ b/test/jit/test_optimize_for_mobile_preserve_debug_info.py +@@ -1,8 +1,8 @@ + import torch + import torch._C +-import torch.backends.xnnpack + import torch.nn.functional as F + from torch.testing._internal.jit_utils import JitTestCase ++from torch.testing._internal.common_utils import skipIfNoXNNPACK + + class TestOptimizeForMobilePreserveDebugInfo(JitTestCase): + def check_replacement( +@@ -34,6 +34,7 @@ class TestOptimizeForMobilePreserveDebugInfo(JitTestCase): + original_source_ranges[replacements[node.kind()]], + ) + ++ @skipIfNoXNNPACK + def test_replace_conv1d_with_conv2d(self): + class TestConv1d(torch.nn.Module): + def __init__(self, weight, bias): +@@ -61,6 +62,7 @@ class TestOptimizeForMobilePreserveDebugInfo(JitTestCase): + jit_pass=torch._C._jit_pass_transform_conv1d_to_conv2d, + ) + ++ @skipIfNoXNNPACK + def test_insert_pre_packed_linear_before_inline_and_conv_2d_op(self): + class TestPrepackedLinearBeforeInlineAndConv2dOp(torch.nn.Module): + def __init__( +@@ -137,6 +139,7 @@ class TestOptimizeForMobilePreserveDebugInfo(JitTestCase): + jit_pass=torch._C._jit_pass_insert_prepacked_ops, + ) + ++ @skipIfNoXNNPACK + def test_insert_pre_packed_linear_op(self): + self.check_replacement( + model=torch.jit.trace(torch.nn.Linear(5, 4), torch.rand(3, 2, 5)), +@@ -228,6 +231,7 @@ class TestOptimizeForMobilePreserveDebugInfo(JitTestCase): + jit_pass=torch._C._jit_pass_fuse_clamp_w_prepacked_linear_conv, + ) + ++ @skipIfNoXNNPACK + def test_fuse_activation_with_pack_ops_linear_conv2d_1(self): + self.run_test_fuse_activation_with_pack_ops_linear_conv2d( + linear_activation=F.hardtanh, +@@ -236,6 +240,7 @@ class TestOptimizeForMobilePreserveDebugInfo(JitTestCase): + conv2d_activation_kind="aten::hardtanh_" + ) + ++ @skipIfNoXNNPACK + def test_fuse_activation_with_pack_ops_linear_conv2d_2(self): + self.run_test_fuse_activation_with_pack_ops_linear_conv2d( + linear_activation=F.hardtanh_, +@@ -244,6 +249,7 @@ class TestOptimizeForMobilePreserveDebugInfo(JitTestCase): + conv2d_activation_kind="aten::hardtanh" + ) + ++ @skipIfNoXNNPACK + def test_fuse_activation_with_pack_ops_linear_conv2d_3(self): + self.run_test_fuse_activation_with_pack_ops_linear_conv2d( + linear_activation=F.relu, +@@ -252,6 +258,7 @@ class TestOptimizeForMobilePreserveDebugInfo(JitTestCase): + conv2d_activation_kind="aten::relu_" + ) + ++ @skipIfNoXNNPACK + def test_fuse_activation_with_pack_ops_linear_conv2d_4(self): + self.run_test_fuse_activation_with_pack_ops_linear_conv2d( + linear_activation=F.relu_, +diff --git a/test/test_mobile_optimizer.py b/test/test_mobile_optimizer.py +index 19f07e2454..21ae5d3ee9 100644 +--- a/test/test_mobile_optimizer.py ++++ b/test/test_mobile_optimizer.py +@@ -1,9 +1,8 @@ + import unittest + import torch + import torch.nn as nn +-import torch.backends.xnnpack + import torch.utils.bundled_inputs +-from torch.testing._internal.common_utils import TestCase, run_tests ++from torch.testing._internal.common_utils import TestCase, run_tests, skipIfNoXNNPACK + from torch.testing._internal.jit_utils import get_forward, get_forward_graph + from torch.utils.mobile_optimizer import (LintCode, + generate_mobile_module_lints, +@@ -22,9 +21,7 @@ FileCheck = torch._C.FileCheck + + class TestOptimizer(TestCase): + +- @unittest.skipUnless(torch.backends.xnnpack.enabled, +- " XNNPACK must be enabled for these tests." +- " Please build with USE_XNNPACK=1.") ++ @skipIfNoXNNPACK + def test_optimize_for_mobile(self): + batch_size = 2 + input_channels_per_group = 6 +@@ -263,9 +260,7 @@ class TestOptimizer(TestCase): + rtol=1e-2, + atol=1e-3) + +- @unittest.skipUnless(torch.backends.xnnpack.enabled, +- " XNNPACK must be enabled for these tests." +- " Please build with USE_XNNPACK=1.") ++ @skipIfNoXNNPACK + def test_quantized_conv_no_asan_failures(self): + # There were ASAN failures when fold_conv_bn was run on + # already quantized conv modules. Verifying that this does +@@ -359,6 +354,7 @@ class TestOptimizer(TestCase): + bi_module_lint_list = generate_mobile_module_lints(bi_module) + self.assertEqual(len(bi_module_lint_list), 0) + ++ @skipIfNoXNNPACK + def test_preserve_bundled_inputs_methods(self): + class MyBundledInputModule(torch.nn.Module): + def __init__(self): +@@ -413,9 +409,7 @@ class TestOptimizer(TestCase): + incomplete_bi_module_optim = optimize_for_mobile(incomplete_bi_module, preserved_methods=['get_all_bundled_inputs']) + self.assertTrue(hasattr(incomplete_bi_module_optim, 'get_all_bundled_inputs')) + +- @unittest.skipUnless(torch.backends.xnnpack.enabled, +- " XNNPACK must be enabled for these tests." +- " Please build with USE_XNNPACK=1.") ++ @skipIfNoXNNPACK + def test_hoist_conv_packed_params(self): + + if 'qnnpack' not in torch.backends.quantized.supported_engines: +@@ -509,6 +503,7 @@ class TestOptimizer(TestCase): + m_optim_res = m_optim(data) + torch.testing.assert_close(m_res, m_optim_res, rtol=1e-2, atol=1e-3) + ++ @skipIfNoXNNPACK + @unittest.skipUnless(HAS_TORCHVISION, "Needs torchvision") + def test_mobilenet_optimize_for_mobile(self): + m = torchvision.models.mobilenet_v3_small() +diff --git a/test/test_model_dump.py b/test/test_model_dump.py +index 417bb2a91a..e4a9ffa1bd 100644 +--- a/test/test_model_dump.py ++++ b/test/test_model_dump.py +@@ -8,9 +8,10 @@ import urllib + import unittest + + import torch ++import torch.backends.xnnpack + import torch.utils.model_dump + import torch.utils.mobile_optimizer +-from torch.testing._internal.common_utils import TestCase, run_tests, IS_WINDOWS ++from torch.testing._internal.common_utils import TestCase, run_tests, IS_WINDOWS, skipIfNoXNNPACK + from torch.testing._internal.common_quantized import supported_qengines + + +@@ -170,6 +171,7 @@ class TestModelDump(TestCase): + qmodel = self.get_quant_model() + self.do_dump_model(torch.jit.script(qmodel)) + ++ @skipIfNoXNNPACK + @unittest.skipUnless("qnnpack" in supported_qengines, "QNNPACK not available") + def test_optimized_quantized_model(self): + qmodel = self.get_quant_model() +diff --git a/test/test_xnnpack_integration.py b/test/test_xnnpack_integration.py +index a0f8328ec6..a737ed4b8b 100644 +--- a/test/test_xnnpack_integration.py ++++ b/test/test_xnnpack_integration.py +@@ -51,7 +51,6 @@ class TestXNNPACKOps(TestCase): + output_linearprepacked = torch.ops.prepacked.linear_clamp_run(input_data, packed_weight_bias) + torch.testing.assert_close(ref_result, output_linearprepacked, rtol=1e-2, atol=1e-3) + +- + @given(batch_size=st.integers(0, 3), + input_channels_per_group=st.integers(1, 32), + height=st.integers(5, 64), +diff --git a/torch/testing/_internal/common_utils.py b/torch/testing/_internal/common_utils.py +index b4ef79620d..18d8925d6a 100644 +--- a/torch/testing/_internal/common_utils.py ++++ b/torch/testing/_internal/common_utils.py +@@ -56,6 +56,7 @@ from torch._six import string_classes + from torch import Tensor + import torch.backends.cudnn + import torch.backends.mkl ++import torch.backends.xnnpack + from enum import Enum + + torch.backends.disable_global_flags() +@@ -908,6 +909,14 @@ def _test_function(fn, device): + return fn(self, device) + return run_test_function + ++def skipIfNoXNNPACK(fn): ++ @wraps(fn) ++ def wrapper(*args, **kwargs): ++ if not torch.backends.xnnpack.enabled: ++ raise unittest.SkipTest('XNNPACK must be enabled for these tests. Please build with USE_XNNPACK=1.') ++ else: ++ fn(*args, **kwargs) ++ return wrapper + + def skipIfNoLapack(fn): + @wraps(fn) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-kineto-crash.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-kineto-crash.patch new file mode 100644 index 00000000000..7858aa1f8cf --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-kineto-crash.patch @@ -0,0 +1,24 @@ +Fix a crash during application shutdown visible in test_profiler on some machines. +See https://github.com/pytorch/kineto/pull/642 + +Author: Alexander Grund (TU Dresden) + +diff -aur a/third_party/kineto/libkineto/src/EventProfilerController.cpp b/third_party/kineto/libkineto/src/EventProfilerController.cpp +--- a/third_party/kineto/libkineto/src/EventProfilerController.cpp 2022-08-05 13:10:46.175716618 +0200 ++++ b/third_party/kineto/libkineto/src/EventProfilerController.cpp 2022-08-05 13:16:00.654118490 +0200 +@@ -233,9 +233,14 @@ EventProfilerController::~EventProfilerController() { + + // Must be called under lock + void EventProfilerController::start(CUcontext ctx, ConfigLoader& configLoader) { +- profilerMap()[ctx] = unique_ptr( ++ // Avoid static initialization order fiasco: ++ // We need the profilerMap and with it all controllers to be destroyed ++ // before everything the controller accesses gets destroyed. ++ // Hence access the profilerMap after initialization of the controller. ++ auto controller = unique_ptr( + new EventProfilerController( + ctx, configLoader, detail::HeartbeatMonitor::instance())); ++ profilerMap()[ctx] = std::move(controller); + } + + // Must be called under lock diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-vsx-vector-functions.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-vsx-vector-functions.patch new file mode 100644 index 00000000000..7d35ac8d134 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-vsx-vector-functions.patch @@ -0,0 +1,39 @@ +This fixes the remaining bug introduced by the VSX optimized code in https://github.com/pytorch/pytorch/pull/41541 + +See https://github.com/pytorch/pytorch/pull/59382 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +index 2427276bce..2b46e0a662 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +@@ -558,27 +558,7 @@ class Vectorized { + } + + Vectorized C10_ALWAYS_INLINE pow(const Vectorized& exp) const { +- auto x = *this; +- auto sign_bit = (*this) & sign_mask; +- // |b| +- auto exp_abs = exp.abs(); +- auto exp_trunc = exp.trunc(); +- Vectorized odd_mask; +- odd_mask._vecb0 = (vec_signed(exp._vec0) & vi_1) != vi_0; +- odd_mask._vecb1 = (vec_signed(exp._vec1) & vi_1) != vi_0; +- // using ln fuction +- auto temp = (abs().log() * exp).exp(); +- +- // is odd or even check from Sleef +- auto is_int = (exp == exp_trunc) | (exp_abs >= vcheck); +- auto is_odd = odd_mask & is_int & (exp_abs < vcheck); +- // if even then then pow result should be absolute +- auto temp_sign = temp | sign_bit; // copy_sign +- auto out = blendv(temp, temp_sign, is_odd); +- // x<0 and y != N, then NAN +- auto out1 = blendv(out, v_nan, ((exp.floor() != exp) & (x < zero))); +- // y = 0 then 1 +- return blendv(out1, one, (exp_abs == zero)); ++ return {Sleef_powf4_u10vsx(_vec0, exp._vec0), Sleef_powf4_u10vsx(_vec1, exp._vec1)}; + } + + Vectorized fmod(const Vectorized& b) const { diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch new file mode 100644 index 00000000000..ce5acf4a884 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch @@ -0,0 +1,30 @@ +When QNNPACK is not available the test will fail trying to use it. +Skip them conditionally. +See https://github.com/pytorch/pytorch/pull/82882 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_nnapi.py b/test/test_nnapi.py +index f8db7e1a3d..1d4fd52e28 100644 +--- a/test/test_nnapi.py ++++ b/test/test_nnapi.py +@@ -2,8 +2,10 @@ + import os + import ctypes + import torch ++import unittest + from typing import Tuple + from torch.backends._nnapi.prepare import convert_model_to_nnapi ++from torch.testing._internal.common_quantized import supported_qengines + from torch.testing._internal.common_utils import TestCase, run_tests + + +@@ -18,6 +20,8 @@ def nhwc(t): + return t + + ++@unittest.skipUnless('qnnpack' in supported_qengines, ++ "This Pytorch Build has not been built with or does not support QNNPACK") + class TestNNAPI(TestCase): + + def setUp(self): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 5aba12b3957..75c7d8f133b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -8,51 +8,64 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'foss', 'version': '2021a'} -sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/pytorch', - 'repo_name': 'pytorch', - 'tag': 'v%(version)s', - 'recursive': True, - }, -}] +source_urls = ['https://github.com/%(github_account)s/%(namelower)s/releases/download/v%(version)s'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', - 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_fix-XNNPACK-tests.patch', 'PyTorch-1.10.0_skip_cmake_rpath.patch', - 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', - 'PyTorch-1.11.0_skip_failing_ops_tests.patch', - 'PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch', + 'PyTorch-1.11.0_fix-attention_cpp-compilation.patch', 'PyTorch-1.11.0_fix_sharded_imports.patch', - 'PyTorch-1.11.0_increase_test_tolerances_TF32.patch', + 'PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', - 'PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_increase_test_tolerances_TF32.patch', + 'PyTorch-1.11.0_increase-tolerance-test_ops.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.11.0_skip_failing_ops_tests.patch', ] checksums = [ - None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + 'dc0c2b8d13c112a2b9ea8757a475b0ce2ca97cd19c50a8b70b8c286676616f1d', # pytorch-v1.11.0.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch - # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch - 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_fix-XNNPACK-tests.patch + 'd3e749a2a42efce463e3b8a1aebb21f0edf2256682c4417297d9a44a6210e5f8', 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', # PyTorch-1.10.0_skip_cmake_rpath.patch + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + # PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch + 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', + # PyTorch-1.11.0_fix-attention_cpp-compilation.patch + '84214fcc7e30cf70659a7c3bd70bf11e73d58fd4f7fff2c233e3225619b0e42c', + '9a04f4285b800dad8a00c3014af0a9713d40d5dd35d10931c7c0da4e89c558e9', # PyTorch-1.11.0_fix_sharded_imports.patch + '21fc678febcdfbb9dabd72235be23cd392044e9a954f6580d15b530e1f69dcc1', # PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch + '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', # PyTorch-1.11.0_increase-distributed-test-timeout.patch '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', - '8eaca92d64fcadb0552d28e9c7ea5c4bc669d2fe33004e45a3519ce8d0d136a2', # PyTorch-1.11.0_skip_failing_ops_tests.patch - '21fc678febcdfbb9dabd72235be23cd392044e9a954f6580d15b530e1f69dcc1', # PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch - '9a04f4285b800dad8a00c3014af0a9713d40d5dd35d10931c7c0da4e89c558e9', # PyTorch-1.11.0_fix_sharded_imports.patch # PyTorch-1.11.0_increase_test_tolerances_TF32.patch '26e179a4f6f57e49209092612ae5f5cd8c03fd2ca84566ba0244eabefc3736ba', - # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch - '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', - # PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch - 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', + # PyTorch-1.11.0_increase-tolerance-test_ops.patch + 'ceec745c68a405bba79efb4dc61c662ca84eb950cd0163c7104330f4bf614cf5', + 'f765093765c07ae488e15b33184709bd1e9c799f6640695be71dca3df02f83c3', # PyTorch-1.11.0_install-vsx-vec-headers.patch + '8eaca92d64fcadb0552d28e9c7ea5c4bc669d2fe33004e45a3519ce8d0d136a2', # PyTorch-1.11.0_skip_failing_ops_tests.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] @@ -112,10 +125,10 @@ excluded_tests = { runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' # several tests are known to be flaky, and fail in some contexts (like having multiple GPUs available), -# so we allow up to 10 (out of ~90k) tests to fail before treating the installation to be faulty -max_failed_tests = 10 +# so we allow some (out of ~90k) tests to fail before treating the installation to be faulty +max_failed_tests = 1 -# The readelf sanity check command can be taken out once the TestRPATH test from +# The readelf sanity check command can be taken out once the TestRPATH test from # https://github.com/pytorch/pytorch/pull/68912 is accepted, since it is then checked as part of the PyTorch test suite local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT sanity_check_commands = [ diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-attention_cpp-compilation.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-attention_cpp-compilation.patch new file mode 100644 index 00000000000..751e954f75f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-attention_cpp-compilation.patch @@ -0,0 +1,61 @@ +Fix failure to compile attention.cpp on some platforms, e.g. POWER. +I.e. those 3 errors: + +../aten/src/ATen/native/attention.cpp:145:46: error: call to deleted function 'double& at::vec::CPU_CAPABILITY::Vectorized::operator[](int)' + 145 | hmax = std::max(max_input[i], hmax); +[snip] +../aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h:190:11: note: declared here + 190 | double& operator[](int idx) = delete; + +../aten/src/ATen/native/attention.cpp:152:66: error: call to deleted function 'double& at::vec::CPU_CAPABILITY::Vectorized::operator[](int)' + 152 | hsum += std::exp(static_cast(v[i]) - hmax); + +../aten/src/ATen/native/attention.cpp:168:100: error: call to deleted function 'double& at::vec::CPU_CAPABILITY::Vectorized::operator[](int)' + 168 | input_data[t + i] = static_cast(std::exp(static_cast(v[i]) - hmax) * inv_denominator); + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/attention.cpp b/aten/src/ATen/native/attention.cpp +index 188de5e2cd..7f3e8e5af2 100644 +--- a/aten/src/ATen/native/attention.cpp ++++ b/aten/src/ATen/native/attention.cpp +@@ -140,22 +140,18 @@ void masked_softmax_dropout( + max_input = vec::maximum(max_input, v); + } + ++ __at_align__ scalar_t arr_max_input[V]; ++ max_input.store(arr_max_input); + auto hmax = std::numeric_limits::lowest(); + for (auto i = 0; i < V; ++i) { +- hmax = std::max(max_input[i], hmax); ++ hmax = std::max(arr_max_input[i], hmax); + } + accscalar_t hsum = 0; +- for (auto t = 0; t < T; t += V) { +- auto v = Vec::loadu(&input_data[t]); +- // TODO: vectorize in accscalar_t? +- for (auto i = 0; i < V; ++i) { +- hsum += std::exp(static_cast(v[i]) - hmax); +- } ++ for (auto t = 0; t < T; ++t) { ++ hsum += std::exp(static_cast(input_data[t]) - hmax); + } + auto inv_denominator = 1.0 / hsum; +- for (auto t = 0; t < T; t += V) { +- Vec v = Vec::loadu(&input_data[t]); +- ++ for (auto t = 0; t < T; ++t) { + // TODO: vectorize in accscalar_t? + // TODO this faster solution does not work on Android build + /* +@@ -164,9 +160,7 @@ void masked_softmax_dropout( + } + v.store(&input_data[t]); + */ +- for (auto i = 0; i < V; ++i) { +- input_data[t + i] = static_cast(std::exp(static_cast(v[i]) - hmax) * inv_denominator); +- } ++ input_data[t] = static_cast(std::exp(static_cast(input_data[t]) - hmax) * inv_denominator); + } + } + }); diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-test_utils.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-test_utils.patch new file mode 100644 index 00000000000..a42166c927c --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-test_utils.patch @@ -0,0 +1,20 @@ +The function tested is dependent on the current locale and may fail on non-English systems. +See https://github.com/pytorch/pytorch/pull/85891 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/utils/cpp_extension.py b/torch/utils/cpp_extension.py +index 9c6635f111..d99aae1ca2 100644 +--- a/torch/utils/cpp_extension.py ++++ b/torch/utils/cpp_extension.py +@@ -292,7 +292,9 @@ def check_compiler_ok_for_platform(compiler: str) -> bool: + if any(name in compiler_path for name in _accepted_compilers_for_platform()): + return True + # If compiler wrapper is used try to infer the actual compiler by invoking it with -v flag +- version_string = subprocess.check_output([compiler, '-v'], stderr=subprocess.STDOUT).decode(*SUBPROCESS_DECODE_ARGS) ++ env = os.environ.copy() ++ env['LC_ALL'] = 'C' # Don't localize output ++ version_string = subprocess.check_output([compiler, '-v'], stderr=subprocess.STDOUT, env=env).decode(*SUBPROCESS_DECODE_ARGS) + if IS_LINUX: + # Check for 'gcc' or 'g++' for sccache warpper + pattern = re.compile("^COLLECT_GCC=(.*)$", re.MULTILINE) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase-tolerance-test_ops.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase-tolerance-test_ops.patch new file mode 100644 index 00000000000..69d58f7a334 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase-tolerance-test_ops.patch @@ -0,0 +1,22 @@ +`test_out` may fail due to slightly different values caused by different order of matrizes in SGEMM: + +> Mismatched elements: 1 / 50 (2.0%) +> Greatest absolute difference: 1.430511474609375e-05 at index (4, 5) (up to 1e-05 allowed) +> Greatest relative difference: 4.65393206065873e-06 at index (4, 5) (up to 1.3e-06 allowed) + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_ops.py b/test/test_ops.py +index 291361d53d..2e0597376d 100644 +--- a/test/test_ops.py ++++ b/test/test_ops.py +@@ -418,6 +418,9 @@ class TestCommon(TestCase): + self.skipTest("Skipped! Op has not supported dtypes on this device.") + dtype = torch.float32 if torch.float32 in supported_dtypes else list(supported_dtypes)[0] + ++ if dtype is torch.float32: ++ self.precision, self.rel_tol = (1.5e-05, 1e-05) ++ + # NOTE: only tests on first sample + samples = op.sample_inputs(device, dtype) + sample = first_sample(self, samples) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_install-vsx-vec-headers.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_install-vsx-vec-headers.patch new file mode 100644 index 00000000000..a3da950d7d9 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_install-vsx-vec-headers.patch @@ -0,0 +1,30 @@ +Add missing headers to the installation which fixes e.g. test_cpp_extensions_aot_ninja +See https://github.com/pytorch/pytorch/pull/85547 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/CMakeLists.txt b/aten/src/ATen/CMakeLists.txt +index 5710eca27c..0cd15c2ad2 100644 +--- a/aten/src/ATen/CMakeLists.txt ++++ b/aten/src/ATen/CMakeLists.txt +@@ -56,7 +56,7 @@ if(NOT BUILD_CAFFE2 AND NOT BUILD_LITE_INTERPRETER) + EXCLUDE(ATen_CORE_TEST_SRCS "${ATen_CORE_TEST_SRCS}" ${ATen_CORE_EXCLUDED_TEST_SRCS}) + endif() + +-file(GLOB base_h "*.h" "detail/*.h" "cpu/*.h" "cpu/vec/vec512/*.h" "cpu/vec/vec256/*.h" "cpu/vec/*.h" "quantized/*.h") ++file(GLOB base_h "*.h" "detail/*.h" "cpu/*.h" "cpu/vec/vec512/*.h" "cpu/vec/vec256/*.h" "cpu/vec/vec256/vsx/*.h" "cpu/vec/*.h" "quantized/*.h") + file(GLOB base_cpp "*.cpp" "detail/*.cpp" "cpu/*.cpp") + file(GLOB cuda_h "cuda/*.h" "cuda/detail/*.h" "cuda/*.cuh" "cuda/detail/*.cuh") + file(GLOB cuda_cpp "cuda/*.cpp" "cuda/detail/*.cpp") +diff --git a/setup.py b/setup.py +index f1ebab7391..c73b6df665 100644 +--- a/setup.py ++++ b/setup.py +@@ -942,6 +942,7 @@ if __name__ == '__main__': + 'include/ATen/*.h', + 'include/ATen/cpu/*.h', + 'include/ATen/cpu/vec/vec256/*.h', ++ 'include/ATen/cpu/vec/vec256/vsx/*.h', + 'include/ATen/cpu/vec/vec512/*.h', + 'include/ATen/cpu/vec/*.h', + 'include/ATen/core/*.h', From 15c9ee3d42dcab34e47e9eb02c3e24fd4589352f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 29 Sep 2022 17:05:33 +0200 Subject: [PATCH 230/793] Add patch for test_fsdp_pure_fp16 --- .../PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 2 ++ .../PyTorch-1.11.0_fix-fsdp-fp16-test.patch | 21 +++++++++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 75c7d8f133b..dfd9742736f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -23,6 +23,7 @@ patches = [ 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', 'PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch', 'PyTorch-1.11.0_fix-attention_cpp-compilation.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', 'PyTorch-1.11.0_fix_sharded_imports.patch', 'PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch', 'PyTorch-1.11.0_fix-test_utils.patch', @@ -53,6 +54,7 @@ checksums = [ 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', # PyTorch-1.11.0_fix-attention_cpp-compilation.patch '84214fcc7e30cf70659a7c3bd70bf11e73d58fd4f7fff2c233e3225619b0e42c', + '69546ab7371667370eb52b8e46fee7f39deff493fc12cfdcc6f49dde69848f8d', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch '9a04f4285b800dad8a00c3014af0a9713d40d5dd35d10931c7c0da4e89c558e9', # PyTorch-1.11.0_fix_sharded_imports.patch '21fc678febcdfbb9dabd72235be23cd392044e9a954f6580d15b530e1f69dcc1', # PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch new file mode 100644 index 00000000000..bd860be61f7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch @@ -0,0 +1,21 @@ +The test fails on a node with more than 5 GPUs. +Hence limit the world_size to 5 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributed/fsdp/test_fsdp_pure_fp16.py b/test/distributed/fsdp/test_fsdp_pure_fp16.py +index eea03bea3d..d3a4bb8257 100644 +--- a/test/distributed/fsdp/test_fsdp_pure_fp16.py ++++ b/test/distributed/fsdp/test_fsdp_pure_fp16.py +@@ -32,6 +32,11 @@ if TEST_WITH_DEV_DBG_ASAN: + + class TestPureFP16(FSDPTest): + ++ @property ++ def world_size(self): ++ # Test fails due to inaccuracies when using more than 5 GPUs ++ return min(5, super().world_size) ++ + @skip_if_lt_x_gpu(2) + @parametrize( + "cpu_offload", From 8a5ffb8dbdcf07d8283f4a77e3886e41e7acd3ae Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 30 Sep 2022 11:32:37 +0200 Subject: [PATCH 231/793] adding easyconfigs: htop-3.2.1.eb --- easybuild/easyconfigs/h/htop/htop-3.2.1.eb | 28 ++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/h/htop/htop-3.2.1.eb diff --git a/easybuild/easyconfigs/h/htop/htop-3.2.1.eb b/easybuild/easyconfigs/h/htop/htop-3.2.1.eb new file mode 100644 index 00000000000..c1cdf13a220 --- /dev/null +++ b/easybuild/easyconfigs/h/htop/htop-3.2.1.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'htop' +version = "3.2.1" + +homepage = 'https://htop.dev' + +description = """An interactive process viewer for Unix""" + +toolchain = SYSTEM + +github_account = 'htop-dev' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['b5ffac1949a8daaabcffa659c0964360b5008782aae4dfa7702d2323cfb4f438'] + +dependencies = [ + ('ncurses', '6.2'), +] + +preconfigopts = 'LIBS="$LIBS -ltinfo" && ./autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/htop'], + 'dirs': ['share'], +} + +moduleclass = 'tools' From 08d45b3280c471b9881c6661eab445a7abbff9a3 Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 30 Sep 2022 12:20:30 +0200 Subject: [PATCH 232/793] As discussed in the conf call of https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20220928 we'll stick to 4.4.2 for 2022a --- .../p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb index 64343b457dc..cf6a5d92445 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb @@ -62,7 +62,7 @@ dependencies = [ ('MPFR', '4.1.0'), ('GMP', '6.2.1'), ('numactl', '2.0.14'), - ('FFmpeg', '5.0.1'), + ('FFmpeg', '4.4.2'), ('Pillow', '9.1.1'), ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', True), ('magma', '2.6.2', '-CUDA-%(cudaver)s'), From 1657192c75113b43f86a1440de39258a09505186 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 30 Sep 2022 13:57:08 +0200 Subject: [PATCH 233/793] adding easyconfigs: CWIPI-0.12.0-gompi-2021a.eb --- .../c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb diff --git a/easybuild/easyconfigs/c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb b/easybuild/easyconfigs/c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb new file mode 100644 index 00000000000..f22001bd4fc --- /dev/null +++ b/easybuild/easyconfigs/c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'CWIPI' +version = '0.12.0' + +homepage = 'https://w3.onera.fr/cwipi/' +description = """CWIPI (Coupling With Interpolation Parallel Interface) library helps in +chaining and coupling codes. Provides exchanges of interpolated fields through +a non-compliant geometric interface and allows control of the coupling +algorithm using control parameters. CWIPI takes advantage of the distribution +of the definition of the coupling algorithm in the different codes. +""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://w3.onera.fr/cwipi/sites/w3.onera.fr.cwipi/files/u4'] +sources = [SOURCELOWER_TGZ] +checksums = ['775dedd6afd5e148f008fc19b98ad0879a0091880af682cbed89c4978bef5575'] + +builddependencies = [('CMake', '3.20.1')] + +configopts = "-DCWP_ENABLE_Fortran=ON" + +_cwipi_bin = ['c_linear_coupling', 'c_surf_coupling_P1P0_P0P1', 'c_surf_coupling_P1P1', + 'c_surf_coupling_simple_location', 'c_surf_coupling_vector_exchange', 'c_surf_location_triaP2', + 'c_surf_sequential_coupling', 'c_vol_coupling_P1P1', 'c_vol_coupling_polyhedra_P1P1', + 'fortran_plane_PiQj', 'fortran_surf_P1P1', 'fortran_surf_PiQj'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _cwipi_bin] + + ['lib/libcwp.a', 'lib/libcwp.%s' % SHLIB_EXT, 'lib/libcwpf.a', 'lib/libcwpf.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' From b7dab3b09a4204c22c4821d16cdc6972a36bb6ad Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 30 Sep 2022 15:16:37 +0200 Subject: [PATCH 234/793] homogenize easyconfigs of Mmg v5.6.0 --- .../easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb | 12 ++++-------- .../easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021b.eb | 13 ++++++------- 2 files changed, 10 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb index 80a0bcb4e5e..eb07a34b0a1 100644 --- a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb @@ -6,11 +6,11 @@ version = '5.6.0' homepage = 'https://www.mmgtools.org/' description = """ Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries: -the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional +the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation and generation of a triangulation from a set of points or from given boundary edges the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation -and isovalue discretization the mmg3d application and the libmmg3d library: adaptation and optimization -of a tetrahedral mesh and implicit domain meshing the libmmg library gathering the libmmg2d, +and isovalue discretization the mmg3d application and the libmmg3d library: adaptation and optimization +of a tetrahedral mesh and implicit domain meshing the libmmg library gathering the libmmg2d, libmmgs and libmmg3d libraries.""" toolchain = {'name': 'gompi', 'version': '2021a'} @@ -25,14 +25,10 @@ checksums = [ ] -builddependencies = [ - ('CMake', '3.20.1'), -] +builddependencies = [('CMake', '3.20.1')] dependencies = [('SCOTCH', '6.1.0')] -separate_build_dir = True - # CI tests require downloading of data that might not be available in the future. # Sticking to tests included in the source with help of patch configopts = '-DUSE_SCOTCH=ON -DBUILD_TESTING=ON -DONLY_VERY_SHORT_TESTS=ON ' diff --git a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021b.eb b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021b.eb index a27faef39a9..517ba6a3440 100644 --- a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021b.eb @@ -6,14 +6,12 @@ version = '5.6.0' homepage = 'https://www.mmgtools.org/' description = """ Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries: -the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation -and generation of a triangulation from a set of points or from given boundary edges +the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional +triangulation and generation of a triangulation from a set of points or from given boundary edges the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation -and isovalue discretization -the mmg3d application and the libmmg3d library: adaptation and optimization of a tetrahedral mesh -and implicit domain meshing -the libmmg library gathering the libmmg2d, libmmgs and libmmg3d libraries -""" +and isovalue discretization the mmg3d application and the libmmg3d library: adaptation and optimization +of a tetrahedral mesh and implicit domain meshing the libmmg library gathering the libmmg2d, +libmmgs and libmmg3d libraries.""" toolchain = {'name': 'gompi', 'version': '2021b'} @@ -35,6 +33,7 @@ configopts = '-DUSE_SCOTCH=ON -DBUILD_TESTING=ON -DONLY_VERY_SHORT_TESTS=ON ' configopts += '-DTEST_LIBMMG2D=ON -DTEST_LIBMMG3D=ON -DTEST_LIBMMGS=ON ' configopts += '-DLIBMMG2D_SHARED=ON -DLIBMMG3D_SHARED=ON -DLIBMMGS_SHARED=ON -DLIBMMG_SHARED=ON ' +pretestopts = 'export CTEST_PARALLEL_LEVEL=%(parallel)s &&' runtest = 'test' sanity_check_paths = { From ed7ec796589c4becabfff0d0bf97e08b36067421 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 30 Sep 2022 16:00:33 +0200 Subject: [PATCH 235/793] add patches for ambertools to work with new easyblock --- .../Amber-20.11-foss-2020b-AmberTools-21.3.eb | 38 ++++++++++++++++--- 1 file changed, 33 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb index ee8d80b6270..1f0d542911d 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb @@ -15,21 +15,49 @@ toolchainopts = {'usempi': True, 'openmp': True} sources = [ '%%(name)s%s.tar.bz2' % local_amber_ver, - 'AmberTools%s.tar.bz2' % local_ambertools_ver, + {'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, 'alt_location': 'AmberTools'} ] patches = [ - 'AmberTools-20_cmake-locate-netcdf.patch', - 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', - 'AmberTools-20_fix_xblas_missing_make_dependency.patch', + {'name': 'AmberTools-20_cmake-locate-netcdf.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-20_fix_xblas_missing_make_dependency.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_CMake-FlexiBLAS.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_DGESVD_workspace_query.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_incorrect_dvout_call.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_incorrect_mexit_calls.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_more_blas_argument_problems.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_multiple_definition.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_potential_use_before_init.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_rism_argument_mismatch.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-22_fix_test_missing_cuda_dir.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_dont_include_config.h_in_top_Makefile.patch', 'alt_location': 'AmberTools'}, ] checksums = [ 'a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75', # Amber20.tar.bz2 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', # AmberTools21.tar.bz2 '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch - '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', + '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', # AmberTools-20_fix_xblas_missing_make_dependency.patch 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', + '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch + # AmberTools-21_fix_DGESVD_workspace_query.patch + '560c73e9d8bd159c609098c63a0256cdee78f49e524d06ea94d16d3146f69bcd', + '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b', # AmberTools-21_fix_incorrect_dvout_call.patch + 'd1de8c596119dcedbb809515816f0c98762306c469e9caf2c0b878d9b0a1095f', # AmberTools-21_fix_incorrect_mexit_calls.patch + # AmberTools-21_fix_more_blas_argument_problems.patch + 'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c', + 'ce30eeaba9feea53aa115e4b0dcc5be943b8a55abe322480c807ca7ea963d83b', # AmberTools-21_fix_multiple_definition.patch + # AmberTools-21_fix_potential_use_before_init.patch + '377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139', + # AmberTools-21_fix_rism_argument_mismatch.patch + '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1', + # AmberTools-21_fix_xray_fftpack_arg_mismatch.patch + '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f', + 'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737', # AmberTools-22_fix_test_missing_cuda_dir.patch + # AmberTools-21_dont_include_config.h_in_top_Makefile.patch + 'b5a20a63904344fc3d1469841f0ea7d5ddaaa01462742bab958c3bba4a9b7ad9', ] builddependencies = [ From 1804e66d1d3462f82a6dbd48465d2c9b66803bcc Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Fri, 30 Sep 2022 16:04:38 +0200 Subject: [PATCH 236/793] add recipe for torchdata 0.3.0 --- .../t/torchdata-0.3.0-PyTorch-1.11.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb diff --git a/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb b/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb new file mode 100644 index 00000000000..6f5908e93ce --- /dev/null +++ b/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'torchdata' +version = '0.3.0' +local_python_version = '3.9.5' +local_pytorch_version = '1.11.0' +versionsuffix = '-PyTorch-%s' % local_pytorch_version +local_pytorch_versionsuffix = '-foss-2021a-CUDA-11.3.1' + +homepage = 'https://github.com/pytorch/data' +description = "TorchData is a prototype library of common modular data loading primitives for easily constructing flexible and performant data pipelines." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', local_python_version), + ('PyTorch', local_pytorch_version, local_pytorch_versionsuffix), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pytorch/data/archive'], + }), +] + +moduleclass = 'lib' From 52a610d9d41431a6bbc928fcc146b61da429c613 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 30 Sep 2022 17:08:42 +0200 Subject: [PATCH 237/793] adding easyconfigs: f90wrap-0.2.8-foss-2021a.eb --- .../f/f90wrap/f90wrap-0.2.8-foss-2021a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb diff --git a/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb b/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb new file mode 100644 index 00000000000..87eab2439f1 --- /dev/null +++ b/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'f90wrap' +version = '0.2.8' + +homepage = 'https://github.com/jameskermode/f90wrap' +description = """f90wrap is a tool to automatically generate Python extension modules which +interface to Fortran code that makes use of derived types. It builds on the +capabilities of the popular f2py utility by generating a simpler Fortran 90 +interface to the original Fortran code which is then suitable for wrapping with +f2py, together with a higher-level Pythonic wrapper that makes the existance of +an additional layer transparent to the final user.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['23524b66ffb71365d93a701065cefb33bc3ba869bed18d0884d08fac05f097f2'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/f2py-f90wrap', 'bin/f90doc', 'bin/f90wrap'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'devel' From 36607a9ddb89c2a619d23a06a46dd7080772513c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 1 Oct 2022 01:46:02 +0200 Subject: [PATCH 238/793] remove default source URLs from f90wrap --- easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb b/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb index 87eab2439f1..55a22a746dc 100644 --- a/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb +++ b/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb @@ -13,7 +13,6 @@ an additional layer transparent to the final user.""" toolchain = {'name': 'foss', 'version': '2021a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['23524b66ffb71365d93a701065cefb33bc3ba869bed18d0884d08fac05f097f2'] From 33b2c8c2b7396932722d01703084bb53d53aa5d6 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 1 Oct 2022 08:48:04 +0200 Subject: [PATCH 239/793] use pkgconf rather than pkg-config --- easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb index 6e956e7e513..a5cf58c0819 100644 --- a/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb @@ -21,7 +21,7 @@ checksums = ['c7935b7a29e42443f6a35d35cf20ffa7d028c399303f872cd1219598a83656ae'] builddependencies = [ ('Autotools', '20210726'), ('binutils', '2.37'), - ('pkgconfig', '0.29.2'), + ('pkgconf', '1.8.0'), ] dependencies = [ From 6767e6b2937634ac43833193fe6a1a1ee4275dca Mon Sep 17 00:00:00 2001 From: Lars Hellemo Date: Sat, 1 Oct 2022 10:49:27 +0200 Subject: [PATCH 240/793] Add Julia v1.8.2 --- .../j/Julia/Julia-1.8.2-linux-x86_64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb new file mode 100644 index 00000000000..dcca93e7871 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.8.2' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['671cf3a450b63a717e1eedd7f69087e3856f015b2e146cb54928f19a3c05e796'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' From 03d8f61650cb93c669251892bc1af1c60aa1f40e Mon Sep 17 00:00:00 2001 From: Lars Hellemo Date: Sat, 1 Oct 2022 10:51:30 +0200 Subject: [PATCH 241/793] Add LTS julia 1.6.7 --- .../j/Julia/Julia-1.6.7-linux-x86_64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb new file mode 100644 index 00000000000..65d335bfb8c --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.6.7' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['6c4522d595e4cbcd00157ac458a72f8aec01757053d2073f99daa39e442b2a36'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' From d9be0b9a851fddce631ece65c318c3a41cb9d2b1 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Sat, 1 Oct 2022 12:38:06 +0200 Subject: [PATCH 242/793] Delete easyconfigs.py --- test/easyconfigs/easyconfigs.py | 1512 ------------------------------- 1 file changed, 1512 deletions(-) delete mode 100644 test/easyconfigs/easyconfigs.py diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py deleted file mode 100644 index da15318ca58..00000000000 --- a/test/easyconfigs/easyconfigs.py +++ /dev/null @@ -1,1512 +0,0 @@ -## -# Copyright 2013-2022 Ghent University -# -# This file is part of EasyBuild, -# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), -# with support of Ghent University (http://ugent.be/hpc), -# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), -# Flemish Research Foundation (FWO) (http://www.fwo.be/en) -# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). -# -# https://github.com/easybuilders/easybuild -# -# EasyBuild is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation v2. -# -# EasyBuild is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with EasyBuild. If not, see . -## -""" -Unit tests for easyconfig files. - -@author: Kenneth Hoste (Ghent University) -""" -import glob -import os -import re -import shutil -import sys -import tempfile -from distutils.version import LooseVersion -from unittest import TestCase, TestLoader, main, skip - -import easybuild.main as eb_main -import easybuild.tools.options as eboptions -from easybuild.base import fancylogger -from easybuild.easyblocks.generic.configuremake import ConfigureMake -from easybuild.easyblocks.generic.pythonpackage import PythonPackage -from easybuild.framework.easyblock import EasyBlock -from easybuild.framework.easyconfig.constants import EASYCONFIG_CONSTANTS -from easybuild.framework.easyconfig.default import DEFAULT_CONFIG -from easybuild.framework.easyconfig.format.format import DEPENDENCY_PARAMETERS -from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, letter_dir_for -from easybuild.framework.easyconfig.easyconfig import resolve_template -from easybuild.framework.easyconfig.parser import EasyConfigParser, fetch_parameters_from_easyconfig -from easybuild.framework.easyconfig.tools import check_sha256_checksums, dep_graph, get_paths_for, process_easyconfig -from easybuild.tools import config -from easybuild.tools.build_log import EasyBuildError -from easybuild.tools.config import GENERAL_CLASS, build_option -from easybuild.tools.filetools import change_dir, is_generic_easyblock, read_file, remove_file -from easybuild.tools.filetools import verify_checksum, which, write_file -from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version -from easybuild.tools.modules import modules_tool -from easybuild.tools.py2vs3 import string_type, urlopen -from easybuild.tools.robot import check_conflicts, resolve_dependencies -from easybuild.tools.run import run_cmd -from easybuild.tools.options import set_tmpdir -from easybuild.tools.utilities import nub - - -# indicates whether all the single tests are OK, -# and that bigger tests (building dep graph, testing for conflicts, ...) can be run as well -# other than optimizing for time, this also helps to get around problems like http://bugs.python.org/issue10949 -single_tests_ok = True - - -def is_pr(): - """Return true if run in a pull request CI""" - # $TRAVIS_PULL_REQUEST should be a PR number, otherwise we're not running tests for a PR - travis_pr_test = re.match('^[0-9]+$', os.environ.get('TRAVIS_PULL_REQUEST', '')) - - # when testing a PR in GitHub Actions, $GITHUB_EVENT_NAME will be set to 'pull_request' - github_pr_test = os.environ.get('GITHUB_EVENT_NAME') == 'pull_request' - return travis_pr_test or github_pr_test - - -def get_target_branch(): - """Return the target branch of a pull request""" - # target branch should be anything other than 'master'; - # usually is 'develop', but could also be a release branch like '3.7.x' - target_branch = os.environ.get('GITHUB_BASE_REF', None) - if not target_branch: - target_branch = os.environ.get('TRAVIS_BRANCH', None) - if not target_branch: - raise RuntimeError("Did not find a target branch") - return target_branch - - -def skip_if_not_pr_to_non_main_branch(): - if not is_pr(): - return skip("Only run for pull requests") - if get_target_branch() == "main": - return skip("Not run for pull requests against main") - return lambda func: func - - -def get_files_from_diff(diff_filter, ext, basename=True): - """Return the files changed on HEAD relative to the current target branch""" - target_branch = get_target_branch() - - # relocate to top-level directory of repository to run 'git diff' command - top_dir = os.path.dirname(os.path.dirname(get_paths_for('easyconfigs')[0])) - cwd = change_dir(top_dir) - - # first determine the 'merge base' between target branch and PR branch - # cfr. https://git-scm.com/docs/git-merge-base - cmd = "git merge-base %s HEAD" % target_branch - out, ec = run_cmd(cmd, simple=False, log_ok=False) - if ec == 0: - merge_base = out.strip() - print("Merge base for %s and HEAD: %s" % (target_branch, merge_base)) - else: - msg = "Failed to determine merge base (ec: %s, output: '%s'), " - msg += "falling back to specifying target branch %s" - print(msg % (ec, out, target_branch)) - merge_base = target_branch - - # determine list of changed files using 'git diff' and merge base determined above - cmd = "git diff --name-only --diff-filter=%s %s..HEAD --" % (diff_filter, merge_base) - out, _ = run_cmd(cmd, simple=False) - if basename: - files = [os.path.basename(f) for f in out.strip().split('\n') if f.endswith(ext)] - else: - files = [f for f in out.strip().split('\n') if f.endswith(ext)] - - change_dir(cwd) - return files - - -def get_eb_files_from_diff(diff_filter): - """Return the easyconfig files changed on HEAD relative to the current target branch""" - return get_files_from_diff(diff_filter, '.eb') - - -class EasyConfigTest(TestCase): - """Baseclass for easyconfig testcases.""" - - @classmethod - def setUpClass(cls): - """Setup environment for all tests. Called once!""" - # make sure that the EasyBuild installation is still known even if we purge an EB module - if os.getenv('EB_SCRIPT_PATH') is None: - eb_path = which('eb') - if eb_path is not None: - os.environ['EB_SCRIPT_PATH'] = eb_path - - # initialize configuration (required for e.g. default modules_tool setting) - eb_go = eboptions.parse_options(args=[]) # Ignore cmdline args as those are meant for the unittest framework - config.init(eb_go.options, eb_go.get_options_by_section('config')) - build_options = { - 'check_osdeps': False, - 'external_modules_metadata': {}, - 'force': True, - 'local_var_naming_check': 'error', - 'optarch': 'test', - 'robot_path': get_paths_for("easyconfigs")[0], - 'silent': True, - 'suffix_modules_path': GENERAL_CLASS, - 'valid_module_classes': config.module_classes(), - 'valid_stops': [x[0] for x in EasyBlock.get_steps()], - } - config.init_build_options(build_options=build_options) - set_tmpdir() - - # put dummy 'craype-test' module in place, which is required for parsing easyconfigs using Cray* toolchains - cls.TMPDIR = tempfile.mkdtemp() - os.environ['MODULEPATH'] = cls.TMPDIR - write_file(os.path.join(cls.TMPDIR, 'craype-test'), '#%Module\n') - - log = fancylogger.getLogger("EasyConfigTest", fname=False) - - # make sure a logger is present for main - eb_main._log = log - - cls._ordered_specs = None - cls._parsed_easyconfigs = [] - cls._parsed_all_easyconfigs = False - cls._changed_ecs = None # easyconfigs changed in a PR - cls._changed_patches = None # patches changed in a PR - - @classmethod - def tearDownClass(cls): - """Cleanup after running all tests""" - shutil.rmtree(cls.TMPDIR) - - @classmethod - def parse_all_easyconfigs(cls): - """Parse all easyconfigs.""" - if cls._parsed_all_easyconfigs: - return - # all available easyconfig files - easyconfigs_path = get_paths_for("easyconfigs")[0] - specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path) - parsed_specs = set(ec['spec'] for ec in cls._parsed_easyconfigs) - for spec in specs: - if spec not in parsed_specs: - cls._parsed_easyconfigs.extend(process_easyconfig(spec)) - cls._parsed_all_easyconfigs = True - - @classmethod - def resolve_all_dependencies(cls): - """Resolve dependencies between easyconfigs""" - # Parse all easyconfigs if not done yet - cls.parse_all_easyconfigs() - # filter out external modules - for ec in cls._parsed_easyconfigs: - for dep in ec['dependencies'][:]: - if dep.get('external_module', False): - ec['dependencies'].remove(dep) - cls._ordered_specs = resolve_dependencies( - cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True) - - def _get_changed_easyconfigs(self): - """Gather all added or modified easyconfigs""" - # get list of changed easyconfigs - changed_ecs_filenames = get_eb_files_from_diff(diff_filter='M') - added_ecs_filenames = get_eb_files_from_diff(diff_filter='A') - if changed_ecs_filenames: - print("\nList of changed easyconfig files in this PR:\n\t%s" % '\n\t'.join(changed_ecs_filenames)) - if added_ecs_filenames: - print("\nList of added easyconfig files in this PR:\n\t%s" % '\n\t'.join(added_ecs_filenames)) - EasyConfigTest._changed_ecs_filenames = changed_ecs_filenames - EasyConfigTest._added_ecs_filenames = added_ecs_filenames - - # grab parsed easyconfigs for changed easyconfig files - changed_ecs = [] - for ec_fn in changed_ecs_filenames + added_ecs_filenames: - match = None - for ec in self.parsed_easyconfigs: - if os.path.basename(ec['spec']) == ec_fn: - match = ec['ec'] - break - - if match: - changed_ecs.append(match) - else: - # if no easyconfig is found, it's possible some archived easyconfigs were touched in the PR... - # so as a last resort, try to find the easyconfig file in __archive__ - easyconfigs_path = get_paths_for("easyconfigs")[0] - specs = glob.glob('%s/__archive__/*/*/%s' % (easyconfigs_path, ec_fn)) - if len(specs) == 1: - ec = process_easyconfig(specs[0])[0] - changed_ecs.append(ec['ec']) - else: - raise RuntimeError("Failed to find parsed easyconfig for %s" - " (and could not isolate it in easyconfigs archive either)" % ec_fn) - EasyConfigTest._changed_ecs = changed_ecs - - def _get_changed_patches(self): - """Gather all added or modified patches""" - - # get list of changed/added patch files - changed_patches_filenames = get_files_from_diff(diff_filter='M', ext='.patch', basename=False) - added_patches_filenames = get_files_from_diff(diff_filter='A', ext='.patch', basename=False) - - if changed_patches_filenames: - print("\nList of changed patch files in this PR:\n\t%s" % '\n\t'.join(changed_patches_filenames)) - if added_patches_filenames: - print("\nList of added patch files in this PR:\n\t%s" % '\n\t'.join(added_patches_filenames)) - - EasyConfigTest._changed_patches = changed_patches_filenames + added_patches_filenames - - @property - def parsed_easyconfigs(self): - # parse all easyconfigs if they haven't been already - EasyConfigTest.parse_all_easyconfigs() - return EasyConfigTest._parsed_easyconfigs - - @property - def ordered_specs(self): - # Resolve dependencies if not done - if EasyConfigTest._ordered_specs is None: - EasyConfigTest.resolve_all_dependencies() - return EasyConfigTest._ordered_specs - - @property - def changed_ecs_filenames(self): - if EasyConfigTest._changed_ecs is None: - self._get_changed_easyconfigs() - return EasyConfigTest._changed_ecs_filenames - - @property - def added_ecs_filenames(self): - if EasyConfigTest._changed_ecs is None: - self._get_changed_easyconfigs() - return EasyConfigTest._added_ecs_filenames - - @property - def changed_ecs(self): - if EasyConfigTest._changed_ecs is None: - self._get_changed_easyconfigs() - return EasyConfigTest._changed_ecs - - @property - def changed_patches(self): - if EasyConfigTest._changed_patches is None: - self._get_changed_patches() - return EasyConfigTest._changed_patches - - def test_dep_graph(self): - """Unit test that builds a full dependency graph.""" - # pygraph dependencies required for constructing dependency graph are not available prior to Python 2.6 - if LooseVersion(sys.version) >= LooseVersion('2.6') and single_tests_ok: - # temporary file for dep graph - (hn, fn) = tempfile.mkstemp(suffix='.dot') - os.close(hn) - - dep_graph(fn, self.ordered_specs) - - remove_file(fn) - else: - print("(skipped dep graph test)") - - def test_conflicts(self): - """Check whether any conflicts occur in software dependency graphs.""" - - if not single_tests_ok: - print("(skipped conflicts test)") - return - - self.assertFalse(check_conflicts(self.ordered_specs, modules_tool(), check_inter_ec_conflicts=False), - "No conflicts detected") - - def test_deps(self): - """Perform checks on dependencies in easyconfig files""" - - fails = [] - - for ec in self.parsed_easyconfigs: - # make sure that no odd versions (like 1.13) of HDF5 are used as a dependency, - # since those are released candidates - only even versions (like 1.12) are stable releases; - # see https://docs.hdfgroup.org/archive/support/HDF5/doc/TechNotes/Version.html - for dep in ec['ec'].dependencies(): - if dep['name'] == 'HDF5': - ver = dep['version'] - if int(ver.split('.')[1]) % 2 == 1: - fail = "Odd minor versions of HDF5 should not be used as a dependency: " - fail += "found HDF5 v%s as dependency in %s" % (ver, os.path.basename(ec['spec'])) - fails.append(fail) - - self.assertFalse(len(fails), '\n'.join(sorted(fails))) - - def check_dep_vars(self, gen, dep, dep_vars): - """Check whether available variants of a particular dependency are acceptable or not.""" - - # 'guilty' until proven 'innocent' - res = False - - # filter out wrapped Java versions - # i.e. if the version of one is a prefix of the version of the other one (e.g. 1.8 & 1.8.0_181) - if dep == 'Java': - dep_vars_to_check = sorted(dep_vars.keys()) - - retained_dep_vars = [] - - while dep_vars_to_check: - dep_var = dep_vars_to_check.pop() - dep_var_version = dep_var.split(';')[0] - - # remove dep vars wrapped by current dep var - dep_vars_to_check = [x for x in dep_vars_to_check if not x.startswith(dep_var_version + '.')] - - retained_dep_vars = [x for x in retained_dep_vars if not x.startswith(dep_var_version + '.')] - - retained_dep_vars.append(dep_var) - - for key in list(dep_vars.keys()): - if key not in retained_dep_vars: - del dep_vars[key] - - version_regex = re.compile('^version: (?P[^;]+);') - - # filter out binutils with empty versionsuffix which is used to build toolchain compiler - if dep == 'binutils' and len(dep_vars) > 1: - empty_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: ')] - if len(empty_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != empty_vsuff_vars[0]) - - # multiple variants of HTSlib is OK as long as they are deps for a matching version of BCFtools; - # same goes for WRF and WPS; Gurobi and Rgurobi - for dep_name, parent_name in [('HTSlib', 'BCFtools'), ('WRF', 'WPS'), ('Gurobi', 'Rgurobi')]: - if dep == dep_name and len(dep_vars) > 1: - for key in list(dep_vars): - ecs = dep_vars[key] - # filter out dep variants that are only used as dependency for parent with same version - dep_ver = version_regex.search(key).group('version') - if all(ec.startswith('%s-%s-' % (parent_name, dep_ver)) for ec in ecs) and len(dep_vars) > 1: - dep_vars.pop(key) - - # multiple versions of Boost is OK as long as they are deps for a matching Boost.Python - if dep == 'Boost' and len(dep_vars) > 1: - for key in list(dep_vars): - ecs = dep_vars[key] - # filter out Boost variants that are only used as dependency for Boost.Python with same version - boost_ver = version_regex.search(key).group('version') - if all(ec.startswith('Boost.Python-%s-' % boost_ver) for ec in ecs): - dep_vars.pop(key) - - # filter out Perl with -minimal versionsuffix which are only used in makeinfo-minimal - if dep == 'Perl': - minimal_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -minimal')] - if len(minimal_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != minimal_vsuff_vars[0]) - - # filter out FFTW and imkl with -serial versionsuffix which are used in non-MPI subtoolchains - if dep in ['FFTW', 'imkl']: - serial_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -serial')] - if len(serial_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != serial_vsuff_vars[0]) - - # filter out BLIS and libFLAME with -amd versionsuffix - # (AMD forks, used in gobff/*-amd toolchains) - if dep in ['BLIS', 'libFLAME']: - amd_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -amd')] - if len(amd_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != amd_vsuff_vars[0]) - - # filter out ScaLAPACK with -BLIS-* versionsuffix, used in goblf toolchain - if dep == 'ScaLAPACK': - blis_vsuff_vars = [v for v in dep_vars.keys() if '; versionsuffix: -BLIS-' in v] - if len(blis_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != blis_vsuff_vars[0]) - - if dep == 'ScaLAPACK': - # filter out ScaLAPACK with -bf versionsuffix, used in gobff toolchain - bf_vsuff_vars = [v for v in dep_vars.keys() if '; versionsuffix: -bf' in v] - if len(bf_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != bf_vsuff_vars[0]) - # filter out ScaLAPACK with -bl versionsuffix, used in goblf toolchain - bl_vsuff_vars = [v for v in dep_vars.keys() if '; versionsuffix: -bl' in v] - if len(bl_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != bl_vsuff_vars[0]) - - # filter out HDF5 with -serial versionsuffix which is used in HDF5 for Python (h5py) - if dep in ['HDF5']: - serial_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -serial')] - if len(serial_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != serial_vsuff_vars[0]) - - # for some dependencies, we allow exceptions for software that depends on a particular version, - # as long as that's indicated by the versionsuffix - versionsuffix_deps = ['ASE', 'Boost', 'CUDAcore', 'Java', 'Lua', - 'PLUMED', 'PyTorch', 'R', 'TensorFlow'] - if dep in versionsuffix_deps and len(dep_vars) > 1: - - # check for '-CUDA-*' versionsuffix for CUDAcore dependency - if dep == 'CUDAcore': - dep = 'CUDA' - - for key in list(dep_vars): - dep_ver = version_regex.search(key).group('version') - # use version of Java wrapper rather than full Java version - if dep == 'Java': - dep_ver = '.'.join(dep_ver.split('.')[:2]) - # filter out dep version if all easyconfig filenames using it include specific dep version - if all(re.search('-%s-%s' % (dep, dep_ver), v) for v in dep_vars[key]): - dep_vars.pop(key) - # always retain at least one dep variant - if len(dep_vars) == 1: - break - - # filter R dep for a specific version of Python 2.x - if dep == 'R' and len(dep_vars) > 1: - for key in list(dep_vars): - if '; versionsuffix: -Python-2' in key: - dep_vars.pop(key) - # always retain at least one variant - if len(dep_vars) == 1: - break - - # filter out variants that are specific to a particular version of CUDA - cuda_dep_vars = [v for v in dep_vars.keys() if '-CUDA' in v] - if len(dep_vars) >= len(cuda_dep_vars) and len(dep_vars) > 1: - for key in list(dep_vars): - if re.search('; versionsuffix: .*-CUDA-[0-9.]+', key): - dep_vars.pop(key) - # always retain at least one dep variant - if len(dep_vars) == 1: - break - - # some software packages require a specific (older/newer) version of a particular dependency - alt_dep_versions = { - 'jax': [(r'0\.3\.9', [r'AlphaFold-2\.2\.2-'])], - # arrow-R 6.0.0.2 is used for two R/R-bundle-Bioconductor sets (4.1.2/3.14 and 4.2.0/3.15) - 'arrow-R': [('6.0.0.2', [r'R-bundle-Bioconductor-'])], - # EMAN2 2.3 requires Boost(.Python) 1.64.0 - 'Boost': [('1.64.0;', [r'Boost.Python-1\.64\.0-', r'EMAN2-2\.3-'])], - 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], - # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x - 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], - # ParaView 5.10.x requires FFmpeg 4.x - 'FFmpeg': [(r'4\.4\.', [r'ParaView-5\.10\.', 'OpenFOAM-v2206'])], - 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], - # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) - 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], - # VMTK 1.4.x requires ITK 4.13.x - 'ITK': [(r'4\.13\.', [r'VMTK-1\.4\.'])], - # Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x) - 'Jellyfish': [(r'1\.', [r'Kraken-1\.', r'Roary-3\.12\.0', r'metaWRAP-1\.2'])], - # Libint 1.1.6 is required by older CP2K versions - 'Libint': [(r'1\.1\.6', [r'CP2K-[3-6]'])], - # libxc 2.x or 3.x is required by ABINIT, AtomPAW, CP2K, GPAW, horton, PySCF, WIEN2k - # libxc 4.x is required by libGridXC - # (Qiskit depends on PySCF), Elk 7.x requires libxc >= 5 - 'libxc': [ - (r'[23]\.', [r'ABINIT-', r'AtomPAW-', r'CP2K-', r'GPAW-', r'horton-', - r'PySCF-', r'Qiskit-', r'WIEN2k-']), - (r'4\.', [r'libGridXC-']), - (r'5\.', [r'Elk-']), - ], - # some software depends on numba, which typically requires an older LLVM; - # this includes BirdNET, cell2location, cryoDRGN, librosa, PyOD, Python-Geometric, scVelo, scanpy - 'LLVM': [ - # numba 0.47.x requires LLVM 7.x or 8.x (see https://github.com/numba/llvmlite#compatibility) - (r'8\.', [r'numba-0\.47\.0-', r'librosa-0\.7\.2-', r'BirdNET-20201214-', - r'scVelo-0\.1\.24-', r'PyTorch-Geometric-1\.[346]\.[23]']), - (r'10\.0\.1', [r'cell2location-0\.05-alpha-', r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-', - r'numba-0\.52\.0-', r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', - r'scanpy-1\.7\.2-', r'umap-learn-0\.4\.6-']), - ], - 'Lua': [ - # SimpleITK 2.1.0 requires Lua 5.3.x, MedPy and nnU-Net depend on SimpleITK - (r'5\.3\.5', [r'nnU-Net-1\.7\.0-', r'MedPy-0\.4\.0-', r'SimpleITK-2\.1\.0-']), - ], - # TensorFlow 2.5+ requires a more recent NCCL than version 2.4.8 used in 2019b generation; - # Horovod depends on TensorFlow, so same exception required there - 'NCCL': [(r'2\.11\.4', [r'TensorFlow-2\.[5-9]\.', r'Horovod-0\.2[2-9]'])], - # rampart requires nodejs > 10, artic-ncov2019 requires rampart - 'nodejs': [('12.16.1', ['rampart-1.2.0rc3-', 'artic-ncov2019-2020.04.13'])], - # some software depends on an older numba; - # this includes BirdNET, cell2location, cryoDRGN, librosa, PyOD, Python-Geometric, scVelo, scanpy - 'numba': [ - (r'0\.52\.0', [r'cell2location-0\.05-alpha-', r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-', - r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', r'scanpy-1\.7\.2-', - r'umap-learn-0\.4\.6-']), - ], - # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, - # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; - # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 - # WhatsHap 1.4 + medaka 1.6.0 require Pysam >= 0.18.0 (NGSpeciesID depends on medaka) - 'Pysam': [ - ('0.16.0.1;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'medaka-1.4.3-', 'decona-0.1.2-', - 'NGSpeciesID-0.1.1.1-']), - ('0.18.0;', ['medaka-1.6.0-', 'NGSpeciesID-0.1.2.1-', 'WhatsHap-1.4-']), - ], - # OPERA requires SAMtools 0.x - 'SAMtools': [(r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', - r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1'])], - # NanoPlot, NanoComp use an older version of Seaborn - 'Seaborn': [(r'0\.10\.1', [r'NanoComp-1\.13\.1-', r'NanoPlot-1\.33\.0-'])], - # Shasta requires spoa 3.x - 'spoa': [(r'3\.4\.0', [r'Shasta-0\.8\.0-'])], - # UShER requires tbb-2020.3 as newer versions will not build - 'tbb': [('2020.3', ['UShER-0.5.0-'])], - 'TensorFlow': [ - # medaka 0.11.4/0.12.0 requires recent TensorFlow <= 1.14 (and Python 3.6), - # artic-ncov2019 requires medaka - ('1.13.1;', ['medaka-0.11.4-', 'medaka-0.12.0-', 'artic-ncov2019-2020.04.13']), - # medaka 1.1.* and 1.2.* requires TensorFlow 2.2.0 - # (while other 2019b easyconfigs use TensorFlow 2.1.0 as dep); - # TensorFlow 2.2.0 is also used as a dep for Horovod 0.19.5; - # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 - ('2.2.0;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'Horovod-0.19.5-', 'decona-0.1.2-', - 'NGSpeciesID-0.1.1.1-']), - # medaka 1.4.3 (foss/2019b) depends on TensorFlow 2.2.2 - ('2.2.2;', ['medaka-1.4.3-']), - # medaka 1.4.3 (foss/2020b) depends on TensorFlow 2.2.3; longread_umi and artic depend on medaka - ('2.2.3;', ['medaka-1.4.3-', 'artic-ncov2019-2021.06.24-', 'longread_umi-0.3.2-']), - # AlphaFold 2.1.2 (foss/2020b) depends on TensorFlow 2.5.0 - ('2.5.0;', ['AlphaFold-2.1.2-']), - # medaka 1.5.0 (foss/2021a) depends on TensorFlow >=2.5.2, <2.6.0 - ('2.5.3;', ['medaka-1.5.0-']), - ], - # smooth-topk uses a newer version of torchvision - 'torchvision': [('0.11.3;', ['smooth-topk-1.0-20210817-'])], - # for the sake of backwards compatibility, keep UCX-CUDA v1.11.0 which depends on UCX v1.11.0 - # (for 2021b, UCX was updated to v1.11.2) - 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])], - # WPS 3.9.1 requires WRF 3.9.1.1 - 'WRF': [(r'3\.9\.1\.1', [r'WPS-3\.9\.1'])], - } - if dep in alt_dep_versions and len(dep_vars) > 1: - for key in list(dep_vars): - for version_pattern, parents in alt_dep_versions[dep]: - # filter out known alternative dependency versions - if re.search('^version: %s' % version_pattern, key): - # only filter if the easyconfig using this dep variants is known - if all(any(re.search(p, x) for p in parents) for x in dep_vars[key]): - dep_vars.pop(key) - - # filter out ELSI variants with -PEXSI suffix - if dep == 'ELSI' and len(dep_vars) > 1: - pexsi_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -PEXSI')] - if len(pexsi_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != pexsi_vsuff_vars[0]) - - # only single variant is always OK - if len(dep_vars) == 1: - res = True - - elif len(dep_vars) == 2 and dep in ['Python', 'Tkinter']: - # for Python & Tkinter, it's OK to have on 2.x and one 3.x version - v2_dep_vars = [x for x in dep_vars.keys() if x.startswith('version: 2.')] - v3_dep_vars = [x for x in dep_vars.keys() if x.startswith('version: 3.')] - if len(v2_dep_vars) == 1 and len(v3_dep_vars) == 1: - res = True - - # two variants is OK if one is for Python 2.x and the other is for Python 3.x (based on versionsuffix) - elif len(dep_vars) == 2: - py2_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-2.' in x] - py3_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-3.' in x] - if len(py2_dep_vars) == 1 and len(py3_dep_vars) == 1: - res = True - - # for recent generations, there's no versionsuffix anymore for Python 3, - # but we still allow variants depending on Python 2.x + 3.x - is_recent_gen = False - full_toolchain_regex = re.compile(r'^20[1-9][0-9][ab]$') - gcc_toolchain_regex = re.compile(r'^GCC(core)?-[0-9]?[0-9]\.[0-9]$') - if full_toolchain_regex.match(gen): - is_recent_gen = LooseVersion(gen) >= LooseVersion('2020b') - elif gcc_toolchain_regex.match(gen): - genver = gen.split('-', 1)[1] - is_recent_gen = LooseVersion(genver) >= LooseVersion('10.2') - else: - raise EasyBuildError("Unkown type of toolchain generation: %s" % gen) - - if is_recent_gen: - py2_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-2.' in x] - py3_dep_vars = [x for x in dep_vars.keys() if x.strip().endswith('; versionsuffix:')] - if len(py2_dep_vars) == 1 and len(py3_dep_vars) == 1: - res = True - - return res - - def test_check_dep_vars(self): - """Test check_dep_vars utility method.""" - - # one single dep version: OK - self.assertTrue(self.check_dep_vars('2019b', 'testdep', { - 'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb', 'bar-4.5.6.eb'], - })) - self.assertTrue(self.check_dep_vars('2019b', 'testdep', { - 'version: 1.2.3; versionsuffix: -test': ['foo-1.2.3.eb', 'bar-4.5.6.eb'], - })) - - # two or more dep versions (no special case: not OK) - self.assertFalse(self.check_dep_vars('2019b', 'testdep', { - 'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 4.5.6; versionsuffix:': ['bar-4.5.6.eb'], - })) - self.assertFalse(self.check_dep_vars('2019b', 'testdep', { - 'version: 0.0; versionsuffix:': ['foobar-0.0.eb'], - 'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 4.5.6; versionsuffix:': ['bar-4.5.6.eb'], - })) - - # Java is a special case, with wrapped Java versions - self.assertTrue(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - })) - # two Java wrappers is not OK - self.assertFalse(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11.0.2; versionsuffix:': ['bar-4.5.6.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6.eb'], - })) - # OK to have two or more wrappers if versionsuffix is used to indicate exception - self.assertTrue(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - })) - # versionsuffix must be there for all easyconfigs to indicate exception - self.assertFalse(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb', 'bar-4.5.6.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb', 'bar-4.5.6.eb'], - })) - self.assertTrue(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - 'version: 12.1.6; versionsuffix:': ['foobar-0.0-Java-12.eb'], - 'version: 12; versionsuffix:': ['foobar-0.0-Java-12.eb'], - })) - - # strange situation: odd number of Java versions - # not OK: two Java wrappers (and no versionsuffix to indicate exception) - self.assertFalse(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6.eb'], - })) - # OK because of -Java-11 versionsuffix - self.assertTrue(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - })) - # not OK: two Java wrappers (and no versionsuffix to indicate exception) - self.assertFalse(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11.0.2; versionsuffix:': ['bar-4.5.6.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6.eb'], - })) - # OK because of -Java-11 versionsuffix - self.assertTrue(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - })) - - # two different versions of Boost is not OK - self.assertFalse(self.check_dep_vars('2019b', 'Boost', { - 'version: 1.64.0; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], - })) - - # a different Boost version that is only used as dependency for a matching Boost.Python is fine - self.assertTrue(self.check_dep_vars('2019a', 'Boost', { - 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'], - 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], - })) - self.assertTrue(self.check_dep_vars('2019a', 'Boost', { - 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'], - 'version: 1.66.0; versionsuffix:': ['Boost.Python-1.66.0-gompi-2019a.eb'], - 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], - })) - self.assertFalse(self.check_dep_vars('2019a', 'Boost', { - 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'], - 'version: 1.66.0; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], - })) - - self.assertTrue(self.check_dep_vars('2018a', 'Boost', { - 'version: 1.63.0; versionsuffix: -Python-2.7.14': ['EMAN2-2.21a-foss-2018a-Python-2.7.14-Boost-1.63.0.eb'], - 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2018a.eb'], - 'version: 1.66.0; versionsuffix:': ['BLAST+-2.7.1-foss-2018a.eb'], - })) - - self.assertTrue(self.check_dep_vars('2019a', 'Boost', { - 'version: 1.64.0; versionsuffix:': [ - 'Boost.Python-1.64.0-gompi-2019a.eb', - 'EMAN2-2.3-foss-2019a-Python-2.7.15.eb', - ], - 'version: 1.70.0; versionsuffix:': [ - 'BLAST+-2.9.0-gompi-2019a.eb', - 'Boost.Python-1.70.0-gompi-2019a.eb', - ], - })) - - # two variants is OK, if they're for Python 2.x and 3.x - self.assertTrue(self.check_dep_vars('2020a', 'Python', { - 'version: 2.7.18; versionsuffix:': ['SciPy-bundle-2020.03-foss-2020a-Python-2.7.18.eb'], - 'version: 3.8.2; versionsuffix:': ['SciPy-bundle-2020.03-foss-2020a-Python-3.8.2.eb'], - })) - - self.assertTrue(self.check_dep_vars('2020a', 'SciPy-bundle', { - 'version: 2020.03; versionsuffix: -Python-2.7.18': ['matplotlib-3.2.1-foss-2020a-Python-2.7.18.eb'], - 'version: 2020.03; versionsuffix: -Python-3.8.2': ['matplotlib-3.2.1-foss-2020a-Python-3.8.2.eb'], - })) - - # for recent easyconfig generations, there's no versionsuffix anymore for Python 3 - self.assertTrue(self.check_dep_vars('2020b', 'Python', { - 'version: 2.7.18; versionsuffix:': ['SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb'], - 'version: 3.8.6; versionsuffix:': ['SciPy-bundle-2020.11-foss-2020b.eb'], - })) - - self.assertTrue(self.check_dep_vars('GCCcore-10.2', 'PyYAML', { - 'version: 5.3.1; versionsuffix:': ['IPython-7.18.1-GCCcore-10.2.0.eb'], - 'version: 5.3.1; versionsuffix: -Python-2.7.18': ['IPython-7.18.1-GCCcore-10.2.0-Python-2.7.18.eb'], - })) - - self.assertTrue(self.check_dep_vars('2020b', 'SciPy-bundle', { - 'version: 2020.11; versionsuffix: -Python-2.7.18': ['matplotlib-3.3.3-foss-2020b-Python-2.7.18.eb'], - 'version: 2020.11; versionsuffix:': ['matplotlib-3.3.3-foss-2020b.eb'], - })) - - # not allowed for older generations (foss/intel 2020a or older, GCC(core) 10.1.0 or older) - self.assertFalse(self.check_dep_vars('2020a', 'SciPy-bundle', { - 'version: 2020.03; versionsuffix: -Python-2.7.18': ['matplotlib-3.2.1-foss-2020a-Python-2.7.18.eb'], - 'version: 2020.03; versionsuffix:': ['matplotlib-3.2.1-foss-2020a.eb'], - })) - - def test_dep_versions_per_toolchain_generation(self): - """ - Check whether there's only one dependency version per toolchain generation actively used. - This is enforced to try and limit the chance of running into conflicts when multiple modules built with - the same toolchain are loaded together. - """ - ecs_by_full_mod_name = dict((ec['full_mod_name'], ec) for ec in self.parsed_easyconfigs) - if len(ecs_by_full_mod_name) != len(self.parsed_easyconfigs): - self.fail('Easyconfigs with duplicate full_mod_name found') - - # Cache already determined dependencies - ec_to_deps = dict() - - def get_deps_for(ec): - """Get list of (direct) dependencies for specified easyconfig.""" - ec_mod_name = ec['full_mod_name'] - deps = ec_to_deps.get(ec_mod_name) - if deps is None: - deps = [] - for dep in ec['ec']['dependencies']: - dep_mod_name = dep['full_mod_name'] - deps.append((dep['name'], dep['version'], dep['versionsuffix'], dep_mod_name)) - # Note: Raises KeyError if dep not found - res = ecs_by_full_mod_name[dep_mod_name] - deps.extend(get_deps_for(res)) - ec_to_deps[ec_mod_name] = deps - - return deps - - # some software also follows {a,b} versioning scheme, - # which throws off the pattern matching done below for toolchain versions - false_positives_regex = re.compile('^MATLAB-Engine-20[0-9][0-9][ab]') - - # restrict to checking dependencies of easyconfigs using common toolchains (start with 2018a) - # and GCCcore subtoolchain for common toolchains, starting with GCCcore 7.x - for pattern in ['20(1[89]|[2-9][0-9])[ab]', r'GCCcore-([7-9]|[1-9][0-9])\.[0-9]']: - all_deps = {} - regex = re.compile(r'^.*-(?P%s).*\.eb$' % pattern) - - # collect variants for all dependencies of easyconfigs that use a toolchain that matches - for ec in self.ordered_specs: - ec_file = os.path.basename(ec['spec']) - - # take into account software which also follows a {a,b} versioning scheme - ec_file = false_positives_regex.sub('', ec_file) - - res = regex.match(ec_file) - if res: - tc_gen = res.group('tc_gen') - all_deps_tc_gen = all_deps.setdefault(tc_gen, {}) - for dep_name, dep_ver, dep_versuff, dep_mod_name in get_deps_for(ec): - dep_variants = all_deps_tc_gen.setdefault(dep_name, {}) - # a variant is defined by version + versionsuffix - variant = "version: %s; versionsuffix: %s" % (dep_ver, dep_versuff) - # keep track of which easyconfig this is a dependency - dep_variants.setdefault(variant, set()).add(ec_file) - - # check which dependencies have more than 1 variant - multi_dep_vars, multi_dep_vars_msg = [], '' - for tc_gen in sorted(all_deps.keys()): - for dep in sorted(all_deps[tc_gen].keys()): - dep_vars = all_deps[tc_gen][dep] - if not self.check_dep_vars(tc_gen, dep, dep_vars): - multi_dep_vars.append(dep) - multi_dep_vars_msg += "\nfound %s variants of '%s' dependency " % (len(dep_vars), dep) - multi_dep_vars_msg += "in easyconfigs using '%s' toolchain generation\n* " % tc_gen - multi_dep_vars_msg += '\n* '.join("%s as dep for %s" % v for v in sorted(dep_vars.items())) - multi_dep_vars_msg += '\n' - - error_msg = "No multi-variant deps found for '%s' easyconfigs:\n%s" % (regex.pattern, multi_dep_vars_msg) - self.assertFalse(multi_dep_vars, error_msg) - - def test_sanity_check_paths(self): - """Make sure specified sanity check paths adher to the requirements.""" - - for ec in self.parsed_easyconfigs: - ec_scp = ec['ec']['sanity_check_paths'] - if ec_scp != {}: - # if sanity_check_paths is specified (i.e., non-default), it must adher to the requirements - # both 'files' and 'dirs' keys, both with list values and with at least one a non-empty list - error_msg = "sanity_check_paths for %s does not meet requirements: %s" % (ec['spec'], ec_scp) - self.assertEqual(sorted(ec_scp.keys()), ['dirs', 'files'], error_msg) - self.assertTrue(isinstance(ec_scp['dirs'], list), error_msg) - self.assertTrue(isinstance(ec_scp['files'], list), error_msg) - self.assertTrue(ec_scp['dirs'] or ec_scp['files'], error_msg) - - def test_r_libs_site_env_var(self): - """Make sure $R_LIBS_SITE is being updated, rather than $R_LIBS.""" - # cfr. https://github.com/easybuilders/easybuild-easyblocks/pull/2326 - - r_libs_ecs = [] - for ec in self.parsed_easyconfigs: - for key in ('modextrapaths', 'modextravars'): - if 'R_LIBS' in ec['ec'][key]: - r_libs_ecs.append(ec['spec']) - - error_msg = "%d easyconfigs found which set $R_LIBS, should be $R_LIBS_SITE: %s" - self.assertEqual(r_libs_ecs, [], error_msg % (len(r_libs_ecs), ', '.join(r_libs_ecs))) - - def test_easyconfig_locations(self): - """Make sure all easyconfigs files are in the right location.""" - easyconfig_dirs_regex = re.compile(r'/easybuild/easyconfigs/[0a-z]/[^/]+$') - topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__))) - for (dirpath, _, filenames) in os.walk(topdir): - # ignore git/svn dirs & archived easyconfigs - if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath: - continue - # check whether list of .eb files is non-empty - easyconfig_files = [fn for fn in filenames if fn.endswith('eb')] - if easyconfig_files: - # check whether path matches required pattern - if not easyconfig_dirs_regex.search(dirpath): - # only exception: TEMPLATE.eb - if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']): - self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) - - @skip_if_not_pr_to_non_main_branch() - def test_pr_sha256_checksums(self): - """Make sure changed easyconfigs have SHA256 checksums in place.""" - - # list of software for which checksums can not be required, - # e.g. because 'source' files need to be constructed manually - whitelist = [ - 'Kent_tools-*', - 'MATLAB-*', - 'OCaml-*', - 'OpenFOAM-Extend-4.1-*', - # sources for old versions of Bioconductor packages are no longer available, - # so not worth adding checksums for at this point - 'R-bundle-Bioconductor-3.[2-5]', - ] - - # the check_sha256_checksums function (again) creates an EasyBlock instance - # for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter - # is updated in place (sources for components are added to the 'parent' sources) in Bundle's __init__; - # therefore, we need to reset 'sources' to an empty list here if Bundle is used... - # likewise for 'patches' and 'checksums' - for ec in self.changed_ecs: - if ec['easyblock'] in ['Bundle', 'PythonBundle', 'EB_OpenSSL_wrapper'] or ec['name'] in ['Clang-AOMP']: - ec['sources'] = [] - ec['patches'] = [] - ec['checksums'] = [] - - # filter out deprecated easyconfigs - retained_changed_ecs = [] - for ec in self.changed_ecs: - if not ec['deprecated']: - retained_changed_ecs.append(ec) - - checksum_issues = check_sha256_checksums(retained_changed_ecs, whitelist=whitelist) - self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues)) - - @skip_if_not_pr_to_non_main_branch() - def test_pr_python_packages(self): - """Several checks for easyconfigs that install (bundles of) Python packages.""" - - # These packages do not support installation with 'pip' - whitelist_pip = [ - r'ESMPy-.*', - r'MATLAB-Engine-.*', - r'Meld-.*', - r'PyTorch-.*', - ] - - whitelist_pip_check = [ - r'Mako-1.0.4.*Python-2.7.12.*', - # no pip 9.x or newer for configparser easyconfigs using a 2016a or 2016b toolchain - r'configparser-3.5.0.*-2016[ab].*', - # mympirun is installed with system Python, pip may not be installed for system Python - r'vsc-mympirun.*', - ] - - failing_checks = [] - - python_default_urls = PythonPackage.extra_options()['source_urls'][0] - - for ec in self.changed_ecs: - - with ec.disable_templating(): - ec_fn = os.path.basename(ec.path) - easyblock = ec.get('easyblock') - exts_defaultclass = ec.get('exts_defaultclass') - exts_default_options = ec.get('exts_default_options', {}) - - download_dep_fail = ec.get('download_dep_fail') - exts_download_dep_fail = ec.get('exts_download_dep_fail') - use_pip = ec.get('use_pip') - if use_pip is None: - use_pip = exts_default_options.get('use_pip') - - # only easyconfig parameters as they are defined in the easyconfig file, - # does *not* include other easyconfig parameters with their default value! - pure_ec = ec.parser.get_config_dict() - - # download_dep_fail should be set when using PythonPackage - if easyblock == 'PythonPackage': - if download_dep_fail is None: - failing_checks.append("'download_dep_fail' should be set in %s" % ec_fn) - - if pure_ec.get('source_urls') == python_default_urls: - failing_checks.append("'source_urls' should not be defined when using the default value " - "in %s" % ec_fn) - - # use_pip should be set when using PythonPackage or PythonBundle (except for whitelisted easyconfigs) - if easyblock in ['PythonBundle', 'PythonPackage']: - if use_pip is None and not any(re.match(regex, ec_fn) for regex in whitelist_pip): - failing_checks.append("'use_pip' should be set in %s" % ec_fn) - - # download_dep_fail is enabled automatically in PythonBundle easyblock, so shouldn't be set - if easyblock == 'PythonBundle': - if download_dep_fail or exts_download_dep_fail: - fail = "'*download_dep_fail' should not be set in %s since PythonBundle easyblock is used" % ec_fn - failing_checks.append(fail) - if pure_ec.get('exts_default_options', {}).get('source_urls') == python_default_urls: - failing_checks.append("'source_urls' should not be defined in exts_default_options when using " - "the default value in %s" % ec_fn) - - elif exts_defaultclass == 'PythonPackage': - # bundle of Python packages should use PythonBundle - if easyblock == 'Bundle': - fail = "'PythonBundle' easyblock should be used for bundle of Python packages in %s" % ec_fn - failing_checks.append(fail) - else: - # both download_dep_fail and use_pip should be set via exts_default_options - # when installing Python packages as extensions - for key in ['download_dep_fail', 'use_pip']: - if exts_default_options.get(key) is None: - failing_checks.append("'%s' should be set in exts_default_options in %s" % (key, ec_fn)) - - # if Python is a dependency, that should be reflected in the versionsuffix - # Tkinter is an exception, since its version always matches the Python version anyway - # Python 3.8.6 and later are also excluded, as we consider python 3 the default python - # Also whitelist some updated versions of Amber - whitelist_python_suffix = [ - 'Amber-16-*-2018b-AmberTools-17-patchlevel-10-15.eb', - 'Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb', - 'R-keras-2.1.6-foss-2018a-R-3.4.4.eb', - ] - whitelisted = any(re.match(regex, ec_fn) for regex in whitelist_python_suffix) - has_python_dep = any(LooseVersion(dep['version']) < LooseVersion('3.8.6') - for dep in ec['dependencies'] if dep['name'] == 'Python') - if has_python_dep and ec.name != 'Tkinter' and not whitelisted: - if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): - msg = "'-Python-%%(pyver)s' should be included in versionsuffix in %s" % ec_fn - # This is only a failure for newly added ECs, not for existing ECS - # As that would probably break many ECs - if ec_fn in self.added_ecs_filenames: - failing_checks.append(msg) - else: - print('\nNote: Failed non-critical check: ' + msg) - else: - has_recent_python3_dep = any(LooseVersion(dep['version']) >= LooseVersion('3.8.6') - for dep in ec['dependencies'] if dep['name'] == 'Python') - if has_recent_python3_dep and re.search(r'-Python-3\.[0-9]+\.[0-9]+', ec['versionsuffix']): - msg = "'-Python-%%(pyver)s' should no longer be included in versionsuffix in %s" % ec_fn - failing_checks.append(msg) - - # require that running of "pip check" during sanity check is enabled via sanity_pip_check - if easyblock in ['PythonBundle', 'PythonPackage']: - sanity_pip_check = ec.get('sanity_pip_check') or exts_default_options.get('sanity_pip_check') - if not sanity_pip_check and not any(re.match(regex, ec_fn) for regex in whitelist_pip_check): - failing_checks.append("sanity_pip_check should be enabled in %s" % ec_fn) - - if failing_checks: - self.fail('\n'.join(failing_checks)) - - @skip_if_not_pr_to_non_main_branch() - def test_pr_R_packages(self): - """Several checks for easyconfigs that install (bundles of) R packages.""" - failing_checks = [] - - for ec in self.changed_ecs: - ec_fn = os.path.basename(ec.path) - exts_defaultclass = ec.get('exts_defaultclass') - if exts_defaultclass == 'RPackage' or ec.name == 'R': - seen_exts = set() - for ext in ec['exts_list']: - if isinstance(ext, (tuple, list)): - ext_name = ext[0] - else: - ext_name = ext - if ext_name in seen_exts: - failing_checks.append('%s was added multiple times to exts_list in %s' % (ext_name, ec_fn)) - else: - seen_exts.add(ext_name) - self.assertFalse(failing_checks, '\n'.join(failing_checks)) - - @skip_if_not_pr_to_non_main_branch() - def test_pr_sanity_check_paths(self): - """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" - - # some generic easyblocks already have a decent customised sanity_check_paths, - # including CMakePythonPackage, GoPackage, PythonBundle & PythonPackage; - # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check. - whitelist = ['BuildEnv', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage', 'ModuleRC', - 'PythonBundle', 'PythonPackage', 'Toolchain'] - # Bundles of dependencies without files of their own - # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, - # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co - bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle', 'ROCm'] - - failing_checks = [] - - for ec in self.changed_ecs: - easyblock = ec.get('easyblock') - if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'): - - sanity_check_ok = False - - if easyblock in whitelist or (easyblock == 'Bundle' and ec['name'] in bundles_whitelist): - sanity_check_ok = True - - # also allow bundles that enable per-component sanity checks - elif easyblock == 'Bundle': - if ec['sanity_check_components'] or ec['sanity_check_all_components']: - sanity_check_ok = True - - if not sanity_check_ok: - ec_fn = os.path.basename(ec.path) - failing_checks.append("No custom sanity_check_paths found in %s" % ec_fn) - - self.assertFalse(failing_checks, '\n'.join(failing_checks)) - - @skip_if_not_pr_to_non_main_branch() - def test_pr_https(self): - """Make sure https:// URL is used (if it exists) for homepage/source_urls (rather than http://).""" - - whitelist = [ - 'Kaiju', # invalid certificate at https://kaiju.binf.ku.dk - 'libxml2', # https://xmlsoft.org works, but invalid certificate - 'p4vasp', # https://www.p4vasp.at doesn't work - 'ITSTool', # https://itstool.org/ doesn't work - 'UCX-', # bad certificate for https://www.openucx.org - 'MUMPS', # https://mumps.enseeiht.fr doesn't work - 'PyFR', # https://www.pyfr.org doesn't work - 'PycURL', # bad certificate for https://pycurl.io/ - ] - url_whitelist = [ - # https:// doesn't work, results in index page being downloaded instead - # (see https://github.com/easybuilders/easybuild-easyconfigs/issues/9692) - 'http://isl.gforge.inria.fr', - # https:// leads to File Not Found - 'http://tau.uoregon.edu/', - # https:// has outdated SSL configurations - 'http://faculty.scs.illinois.edu', - ] - # Cache: Mapping of already checked HTTP urls to whether the HTTPS variant works - checked_urls = dict() - - def check_https_url(http_url): - """Check if the https url works""" - http_url = http_url.rstrip('/') # Remove trailing slashes - https_url_works = checked_urls.get(http_url) - if https_url_works is None: - https_url = http_url.replace('http://', 'https://') - try: - https_url_works = bool(urlopen(https_url, timeout=5)) - except Exception: - https_url_works = False - checked_urls[http_url] = https_url_works - - http_regex = re.compile('http://[^"\'\n]+', re.M) - - failing_checks = [] - for ec in self.changed_ecs: - ec_fn = os.path.basename(ec.path) - - # skip whitelisted easyconfigs - if any(ec_fn.startswith(x) for x in whitelist): - continue - - # ignore commented out lines in easyconfig files when checking for http:// URLs - ec_txt = '\n'.join(line for line in ec.rawtxt.split('\n') if not line.startswith('#')) - - for http_url in http_regex.findall(ec_txt): - - # skip whitelisted http:// URLs - if any(http_url.startswith(x) for x in url_whitelist): - continue - - if check_https_url(http_url): - failing_checks.append("Found http:// URL in %s, should be https:// : %s" % (ec_fn, http_url)) - if failing_checks: - self.fail('\n'.join(failing_checks)) - - @skip_if_not_pr_to_non_main_branch() - def test_pr_patch_descr(self): - """ - Check whether all patch files touched in PR have a description on top. - """ - no_descr_patches = [] - for patch in self.changed_patches: - patch_txt = read_file(patch) - if patch_txt.startswith('--- '): - no_descr_patches.append(patch) - - self.assertFalse(no_descr_patches, "No description found in patches: %s" % ', '.join(no_descr_patches)) - - -def template_easyconfig_test(self, spec): - """Tests for an individual easyconfig: parsing, instantiating easyblock, check patches, ...""" - - # set to False, so it's False in case of this test failing - global single_tests_ok - prev_single_tests_ok = single_tests_ok - single_tests_ok = False - - # parse easyconfig - ecs = process_easyconfig(spec) - if len(ecs) == 1: - ec = ecs[0]['ec'] - - # cache the parsed easyconfig, to avoid that it is parsed again - EasyConfigTest._parsed_easyconfigs.append(ecs[0]) - else: - self.assertTrue(False, "easyconfig %s does not contain blocks, yields only one parsed easyconfig" % spec) - - # check easyconfig file name - expected_fn = '%s-%s.eb' % (ec['name'], det_full_ec_version(ec)) - msg = "Filename '%s' of parsed easyconfig matches expected filename '%s'" % (spec, expected_fn) - self.assertEqual(os.path.basename(spec), expected_fn, msg) - - name, easyblock = fetch_parameters_from_easyconfig(ec.rawtxt, ['name', 'easyblock']) - - # make sure easyconfig file is in expected location - expected_subdir = os.path.join('easybuild', 'easyconfigs', letter_dir_for(name), name) - subdir = os.path.join(*spec.split(os.path.sep)[-5:-1]) - fail_msg = "Easyconfig file %s not in expected subdirectory %s" % (spec, expected_subdir) - self.assertEqual(expected_subdir, subdir, fail_msg) - - # sanity check for software name, moduleclass - self.assertEqual(ec['name'], name) - self.assertTrue(ec['moduleclass'] in build_option('valid_module_classes')) - - # instantiate easyblock with easyconfig file - app_class = get_easyblock_class(easyblock, name=name) - - # check that automagic fallback to ConfigureMake isn't done (deprecated behaviour) - fn = os.path.basename(spec) - error_msg = "%s relies on automagic fallback to ConfigureMake, should use easyblock = 'ConfigureMake' instead" % fn - self.assertTrue(easyblock or app_class is not ConfigureMake, error_msg) - - # dump the easyconfig file; - # this should be done before creating the easyblock instance (done below via app_class), - # because some easyblocks (like PythonBundle) modify easyconfig parameters at initialisation - handle, test_ecfile = tempfile.mkstemp() - os.close(handle) - - ec.dump(test_ecfile) - dumped_ec = EasyConfigParser(test_ecfile).get_config_dict() - os.remove(test_ecfile) - - app = app_class(ec) - - # more sanity checks - self.assertTrue(name, app.name) - self.assertTrue(ec['version'], app.version) - - # make sure that deprecated 'dummy' toolchain is no longer used, should use 'system' toolchain instead - ec_fn = os.path.basename(spec) - error_msg_tmpl = "%s should use 'system' toolchain rather than deprecated 'dummy' toolchain" - self.assertFalse(ec['toolchain']['name'] == 'dummy', error_msg_tmpl % os.path.basename(spec)) - - # make sure that $root is not used, since it is not compatible with module files in Lua syntax - res = re.findall(r'.*\$root.*', ec.rawtxt, re.M) - error_msg = "Found use of '$root', not compatible with modules in Lua syntax, use '%%(installdir)s' instead: %s" - self.assertFalse(res, error_msg % res) - - # check for redefined easyconfig parameters, there should be none... - param_def_regex = re.compile(r'^(?P\w+)\s*=', re.M) - keys = param_def_regex.findall(ec.rawtxt) - redefined_keys = [] - for key in sorted(nub(keys)): - cnt = keys.count(key) - if cnt > 1: - redefined_keys.append((key, cnt)) - - redefined_keys_error_msg = "There should be no redefined easyconfig parameters, found %d: " % len(redefined_keys) - redefined_keys_error_msg += ', '.join('%s (%d)' % x for x in redefined_keys) - - self.assertFalse(redefined_keys, redefined_keys_error_msg) - - # make sure old GitHub urls for EasyBuild that include 'hpcugent' are no longer used - old_urls = [ - 'github.com/hpcugent/easybuild', - 'hpcugent.github.com/easybuild', - 'hpcugent.github.io/easybuild', - ] - for old_url in old_urls: - self.assertFalse(old_url in ec.rawtxt, "Old URL '%s' not found in %s" % (old_url, spec)) - - # make sure binutils is included as a (build) dep if toolchain is GCCcore - if ec['toolchain']['name'] == 'GCCcore': - # easyblocks without a build step - non_build_blocks = ['Binary', 'JAR', 'PackedBinary', 'Tarball'] - # some software packages do not have a build step - non_build_soft = ['ANIcalculator', 'Eigen'] - - requires_binutils = ec['easyblock'] not in non_build_blocks and ec['name'] not in non_build_soft - - # let's also exclude the very special case where the system GCC is used as GCCcore, and only apply this - # exception to the dependencies of binutils (since we should eventually build a new binutils with GCCcore) - if ec['toolchain']['version'] == 'system': - binutils_complete_dependencies = ['M4', 'Bison', 'flex', 'help2man', 'zlib', 'binutils'] - requires_binutils &= bool(ec['name'] not in binutils_complete_dependencies) - - # if no sources/extensions/components are specified, it's just a bundle (nothing is being compiled) - requires_binutils &= bool(ec['sources'] or ec['exts_list'] or ec.get('components')) - - if requires_binutils: - # dependencies() returns both build and runtime dependencies - # in some cases, binutils can also be a runtime dep (e.g. for Clang) - # Also using GCC directly as a build dep is also allowed (it includes the correct binutils) - dep_names = [d['name'] for d in ec.dependencies()] - self.assertTrue('binutils' in dep_names or 'GCC' in dep_names, - "binutils or GCC is a build dep in %s: %s" % (spec, dep_names)) - - # make sure that OpenSSL wrapper is used rather than OS dependency, - # for easyconfigs using a 2021a (sub)toolchain or more recent common toolchain version - osdeps = ec['osdependencies'] - if osdeps: - # check whether any entry in osdependencies related to OpenSSL - openssl_osdep = False - for osdep in osdeps: - if isinstance(osdep, string_type): - osdep = [osdep] - if any('libssl' in x for x in osdep) or any('openssl' in x for x in osdep): - openssl_osdep = True - - if openssl_osdep: - tcname = ec['toolchain']['name'] - tcver = LooseVersion(ec['toolchain']['version']) - - gcc_subtc_2021a = tcname in ('GCCcore', 'GCC') and tcver > LooseVersion('10.3') - if gcc_subtc_2021a or (tcname in ('foss', 'gompi', 'iimpi', 'intel') and tcver >= LooseVersion('2021')): - self.assertFalse(openssl_osdep, "OpenSSL should not be listed as OS dependency in %s" % spec) - - src_cnt = len(ec['sources']) - patch_checksums = ec['checksums'][src_cnt:] - - # make sure all patch files are available - specdir = os.path.dirname(spec) - specfn = os.path.basename(spec) - for idx, patch in enumerate(ec['patches']): - if isinstance(patch, (tuple, list)): - patch = patch[0] - - # only check actual patch files, not other files being copied via the patch functionality - patch_full = os.path.join(specdir, patch) - if patch.endswith('.patch'): - msg = "Patch file %s is available for %s" % (patch_full, specfn) - self.assertTrue(os.path.isfile(patch_full), msg) - - # verify checksum for each patch file - if idx < len(patch_checksums) and (os.path.exists(patch_full) or patch.endswith('.patch')): - checksum = patch_checksums[idx] - error_msg = "Invalid checksum for patch file %s in %s: %s" % (patch, ec_fn, checksum) - res = verify_checksum(patch_full, checksum) - self.assertTrue(res, error_msg) - - # make sure 'source' step is not being skipped, - # since that implies not verifying the checksum - error_msg = "'source' step should not be skipped in %s, since that implies not verifying checksums" % ec_fn - self.assertFalse(ec['checksums'] and ('source' in ec['skipsteps']), error_msg) - - for ext in ec.get_ref('exts_list'): - if isinstance(ext, (tuple, list)) and len(ext) == 3: - ext_name = ext[0] - self.assertTrue(isinstance(ext[2], dict), - "3rd element of extension spec for %s must be a dictionary" % ext_name) - - # After the sanity check above, use collect_exts_file_info to resolve templates etc. correctly - for ext in app.collect_exts_file_info(fetch_files=False, verify_checksums=False): - try: - ext_options = ext['options'] - except KeyError: - # No options --> Only have a name which is valid, so nothing to check - continue - - checksums = ext_options.get('checksums', []) - src_cnt = len(ext_options.get('sources', [])) or 1 - patch_checksums = checksums[src_cnt:] - - for idx, ext_patch in enumerate(ext.get('patches', [])): - if isinstance(ext_patch, (tuple, list)): - ext_patch = ext_patch[0] - - # only check actual patch files, not other files being copied via the patch functionality - ext_patch_full = os.path.join(specdir, ext_patch['name']) - if ext_patch_full.endswith('.patch'): - msg = "Patch file %s is available for %s" % (ext_patch_full, specfn) - self.assertTrue(os.path.isfile(ext_patch_full), msg) - - # verify checksum for each patch file - if idx < len(patch_checksums) and (os.path.exists(ext_patch_full) or ext_patch.endswith('.patch')): - checksum = patch_checksums[idx] - error_msg = "Invalid checksum for patch %s for %s extension in %s: %s" - res = verify_checksum(ext_patch_full, checksum) - self.assertTrue(res, error_msg % (ext_patch, ext_name, ec_fn, checksum)) - - # check whether all extra_options defined for used easyblock are defined - extra_opts = app.extra_options() - for key in extra_opts: - self.assertTrue(key in app.cfg) - - app.close_log() - os.remove(app.logfile) - - # inject dummy values for templates that are only known at a later stage - dummy_template_values = { - 'builddir': '/dummy/builddir', - 'installdir': '/dummy/installdir', - 'parallel': '2', - } - ec.template_values.update(dummy_template_values) - - ec_dict = ec.parser.get_config_dict() - orig_toolchain = ec_dict['toolchain'] - for key in ec_dict: - # skip parameters for which value is equal to default value - orig_val = ec_dict[key] - if key in DEFAULT_CONFIG and orig_val == DEFAULT_CONFIG[key][0]: - continue - if key in extra_opts and orig_val == extra_opts[key][0]: - continue - if key not in DEFAULT_CONFIG and key not in extra_opts: - continue - - orig_val = resolve_template(ec_dict[key], ec.template_values) - dumped_val = resolve_template(dumped_ec[key], ec.template_values) - - # take into account that dumped value for *dependencies may include hard-coded subtoolchains - # if no easyconfig was found for the dependency with the 'parent' toolchain, - # if may get resolved using a subtoolchain, which is then hardcoded in the dumped easyconfig - if key in DEPENDENCY_PARAMETERS: - # number of dependencies should remain the same - self.assertEqual(len(orig_val), len(dumped_val)) - for orig_dep, dumped_dep in zip(orig_val, dumped_val): - # name should always match - self.assertEqual(orig_dep[0], dumped_dep[0]) - - # version should always match, or be a possibility from the version dict - if isinstance(orig_dep[1], dict): - self.assertTrue(dumped_dep[1] in orig_dep[1].values()) - else: - self.assertEqual(orig_dep[1], dumped_dep[1]) - - # 3rd value is versionsuffix; - if len(dumped_dep) >= 3: - # if no versionsuffix was specified in original dep spec, then dumped value should be empty string - if len(orig_dep) >= 3: - self.assertEqual(dumped_dep[2], orig_dep[2]) - else: - self.assertEqual(dumped_dep[2], '') - - # 4th value is toolchain spec - if len(dumped_dep) >= 4: - if len(orig_dep) >= 4: - # if True was used to indicate that dependency should use system toolchain, - # then we need to compare the value for the dumped easyconfig more carefully; - # see also https://github.com/easybuilders/easybuild-framework/pull/4069 - if orig_dep[3] is True: - self.assertEqual(dumped_dep[3], EASYCONFIG_CONSTANTS['SYSTEM'][0]) - else: - self.assertEqual(dumped_dep[3], orig_dep[3]) - else: - # if a subtoolchain is specifed (only) in the dumped easyconfig, - # it should *not* be the same as the parent toolchain - self.assertNotEqual(dumped_dep[3], (orig_toolchain['name'], orig_toolchain['version'])) - - # take into account that for some string-valued easyconfig parameters (configopts & co), - # the easyblock may have injected additional values, which affects the dumped easyconfig file - elif isinstance(orig_val, string_type): - error_msg = "%s value '%s' should start with '%s'" % (key, dumped_val, orig_val) - self.assertTrue(dumped_val.startswith(orig_val), error_msg) - else: - error_msg = "%s value should be equal in original and dumped easyconfig: '%s' vs '%s'" - self.assertEqual(orig_val, dumped_val, error_msg % (key, orig_val, dumped_val)) - - # test passed, so set back to True - single_tests_ok = True and prev_single_tests_ok - - -def suite(loader=None): - """Return all easyblock initialisation tests.""" - def make_inner_test(spec_path): - def innertest(self): - template_easyconfig_test(self, spec_path) - return innertest - - # dynamically generate a separate test for each of the available easyconfigs - # define new inner functions that can be added as class methods to InitTest - easyconfigs_path = get_paths_for('easyconfigs')[0] - cnt = 0 - for (subpath, dirs, specs) in os.walk(easyconfigs_path, topdown=True): - - # ignore archived easyconfigs - if '__archive__' in dirs: - dirs.remove('__archive__') - - for spec in specs: - if spec.endswith('.eb') and spec != 'TEMPLATE.eb': - cnt += 1 - innertest = make_inner_test(os.path.join(subpath, spec)) - innertest.__doc__ = "Test for easyconfig %s" % spec - # double underscore so parsing tests are run first - innertest.__name__ = "test__parse_easyconfig_%s" % spec - setattr(EasyConfigTest, innertest.__name__, innertest) - - print("Found %s easyconfigs..." % cnt) - if not loader: - loader = TestLoader() - return loader.loadTestsFromTestCase(EasyConfigTest) - - -if __name__ == '__main__': - main() From e3096767a8806ccd2bd2b595c934b4e94e699754 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 1 Oct 2022 12:44:25 +0200 Subject: [PATCH 243/793] re-add accidentally deleted test/easyconfigs/easyconfigs.py --- test/easyconfigs/easyconfigs.py | 1510 +++++++++++++++++++++++++++++++ 1 file changed, 1510 insertions(+) create mode 100644 test/easyconfigs/easyconfigs.py diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py new file mode 100644 index 00000000000..0fb05afe876 --- /dev/null +++ b/test/easyconfigs/easyconfigs.py @@ -0,0 +1,1510 @@ +## +# Copyright 2013-2022 Ghent University +# +# This file is part of EasyBuild, +# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), +# with support of Ghent University (http://ugent.be/hpc), +# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), +# Flemish Research Foundation (FWO) (http://www.fwo.be/en) +# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). +# +# https://github.com/easybuilders/easybuild +# +# EasyBuild is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation v2. +# +# EasyBuild is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with EasyBuild. If not, see . +## +""" +Unit tests for easyconfig files. + +@author: Kenneth Hoste (Ghent University) +""" +import glob +import os +import re +import shutil +import sys +import tempfile +from distutils.version import LooseVersion +from unittest import TestCase, TestLoader, main, skip + +import easybuild.main as eb_main +import easybuild.tools.options as eboptions +from easybuild.base import fancylogger +from easybuild.easyblocks.generic.configuremake import ConfigureMake +from easybuild.easyblocks.generic.pythonpackage import PythonPackage +from easybuild.framework.easyblock import EasyBlock +from easybuild.framework.easyconfig.constants import EASYCONFIG_CONSTANTS +from easybuild.framework.easyconfig.default import DEFAULT_CONFIG +from easybuild.framework.easyconfig.format.format import DEPENDENCY_PARAMETERS +from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, letter_dir_for +from easybuild.framework.easyconfig.easyconfig import resolve_template +from easybuild.framework.easyconfig.parser import EasyConfigParser, fetch_parameters_from_easyconfig +from easybuild.framework.easyconfig.tools import check_sha256_checksums, dep_graph, get_paths_for, process_easyconfig +from easybuild.tools import config +from easybuild.tools.build_log import EasyBuildError +from easybuild.tools.config import GENERAL_CLASS, build_option +from easybuild.tools.filetools import change_dir, is_generic_easyblock, read_file, remove_file +from easybuild.tools.filetools import verify_checksum, which, write_file +from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version +from easybuild.tools.modules import modules_tool +from easybuild.tools.py2vs3 import string_type, urlopen +from easybuild.tools.robot import check_conflicts, resolve_dependencies +from easybuild.tools.run import run_cmd +from easybuild.tools.options import set_tmpdir +from easybuild.tools.utilities import nub + + +# indicates whether all the single tests are OK, +# and that bigger tests (building dep graph, testing for conflicts, ...) can be run as well +# other than optimizing for time, this also helps to get around problems like http://bugs.python.org/issue10949 +single_tests_ok = True + + +def is_pr(): + """Return true if run in a pull request CI""" + # $TRAVIS_PULL_REQUEST should be a PR number, otherwise we're not running tests for a PR + travis_pr_test = re.match('^[0-9]+$', os.environ.get('TRAVIS_PULL_REQUEST', '')) + + # when testing a PR in GitHub Actions, $GITHUB_EVENT_NAME will be set to 'pull_request' + github_pr_test = os.environ.get('GITHUB_EVENT_NAME') == 'pull_request' + return travis_pr_test or github_pr_test + + +def get_target_branch(): + """Return the target branch of a pull request""" + # target branch should be anything other than 'master'; + # usually is 'develop', but could also be a release branch like '3.7.x' + target_branch = os.environ.get('GITHUB_BASE_REF', None) + if not target_branch: + target_branch = os.environ.get('TRAVIS_BRANCH', None) + if not target_branch: + raise RuntimeError("Did not find a target branch") + return target_branch + + +def skip_if_not_pr_to_non_main_branch(): + if not is_pr(): + return skip("Only run for pull requests") + if get_target_branch() == "main": + return skip("Not run for pull requests against main") + return lambda func: func + + +def get_files_from_diff(diff_filter, ext, basename=True): + """Return the files changed on HEAD relative to the current target branch""" + target_branch = get_target_branch() + + # relocate to top-level directory of repository to run 'git diff' command + top_dir = os.path.dirname(os.path.dirname(get_paths_for('easyconfigs')[0])) + cwd = change_dir(top_dir) + + # first determine the 'merge base' between target branch and PR branch + # cfr. https://git-scm.com/docs/git-merge-base + cmd = "git merge-base %s HEAD" % target_branch + out, ec = run_cmd(cmd, simple=False, log_ok=False) + if ec == 0: + merge_base = out.strip() + print("Merge base for %s and HEAD: %s" % (target_branch, merge_base)) + else: + msg = "Failed to determine merge base (ec: %s, output: '%s'), " + msg += "falling back to specifying target branch %s" + print(msg % (ec, out, target_branch)) + merge_base = target_branch + + # determine list of changed files using 'git diff' and merge base determined above + cmd = "git diff --name-only --diff-filter=%s %s..HEAD --" % (diff_filter, merge_base) + out, _ = run_cmd(cmd, simple=False) + if basename: + files = [os.path.basename(f) for f in out.strip().split('\n') if f.endswith(ext)] + else: + files = [f for f in out.strip().split('\n') if f.endswith(ext)] + + change_dir(cwd) + return files + + +def get_eb_files_from_diff(diff_filter): + """Return the easyconfig files changed on HEAD relative to the current target branch""" + return get_files_from_diff(diff_filter, '.eb') + + +class EasyConfigTest(TestCase): + """Baseclass for easyconfig testcases.""" + + @classmethod + def setUpClass(cls): + """Setup environment for all tests. Called once!""" + # make sure that the EasyBuild installation is still known even if we purge an EB module + if os.getenv('EB_SCRIPT_PATH') is None: + eb_path = which('eb') + if eb_path is not None: + os.environ['EB_SCRIPT_PATH'] = eb_path + + # initialize configuration (required for e.g. default modules_tool setting) + eb_go = eboptions.parse_options(args=[]) # Ignore cmdline args as those are meant for the unittest framework + config.init(eb_go.options, eb_go.get_options_by_section('config')) + build_options = { + 'check_osdeps': False, + 'external_modules_metadata': {}, + 'force': True, + 'local_var_naming_check': 'error', + 'optarch': 'test', + 'robot_path': get_paths_for("easyconfigs")[0], + 'silent': True, + 'suffix_modules_path': GENERAL_CLASS, + 'valid_module_classes': config.module_classes(), + 'valid_stops': [x[0] for x in EasyBlock.get_steps()], + } + config.init_build_options(build_options=build_options) + set_tmpdir() + + # put dummy 'craype-test' module in place, which is required for parsing easyconfigs using Cray* toolchains + cls.TMPDIR = tempfile.mkdtemp() + os.environ['MODULEPATH'] = cls.TMPDIR + write_file(os.path.join(cls.TMPDIR, 'craype-test'), '#%Module\n') + + log = fancylogger.getLogger("EasyConfigTest", fname=False) + + # make sure a logger is present for main + eb_main._log = log + + cls._ordered_specs = None + cls._parsed_easyconfigs = [] + cls._parsed_all_easyconfigs = False + cls._changed_ecs = None # easyconfigs changed in a PR + cls._changed_patches = None # patches changed in a PR + + @classmethod + def tearDownClass(cls): + """Cleanup after running all tests""" + shutil.rmtree(cls.TMPDIR) + + @classmethod + def parse_all_easyconfigs(cls): + """Parse all easyconfigs.""" + if cls._parsed_all_easyconfigs: + return + # all available easyconfig files + easyconfigs_path = get_paths_for("easyconfigs")[0] + specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path) + parsed_specs = set(ec['spec'] for ec in cls._parsed_easyconfigs) + for spec in specs: + if spec not in parsed_specs: + cls._parsed_easyconfigs.extend(process_easyconfig(spec)) + cls._parsed_all_easyconfigs = True + + @classmethod + def resolve_all_dependencies(cls): + """Resolve dependencies between easyconfigs""" + # Parse all easyconfigs if not done yet + cls.parse_all_easyconfigs() + # filter out external modules + for ec in cls._parsed_easyconfigs: + for dep in ec['dependencies'][:]: + if dep.get('external_module', False): + ec['dependencies'].remove(dep) + cls._ordered_specs = resolve_dependencies( + cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True) + + def _get_changed_easyconfigs(self): + """Gather all added or modified easyconfigs""" + # get list of changed easyconfigs + changed_ecs_filenames = get_eb_files_from_diff(diff_filter='M') + added_ecs_filenames = get_eb_files_from_diff(diff_filter='A') + if changed_ecs_filenames: + print("\nList of changed easyconfig files in this PR:\n\t%s" % '\n\t'.join(changed_ecs_filenames)) + if added_ecs_filenames: + print("\nList of added easyconfig files in this PR:\n\t%s" % '\n\t'.join(added_ecs_filenames)) + EasyConfigTest._changed_ecs_filenames = changed_ecs_filenames + EasyConfigTest._added_ecs_filenames = added_ecs_filenames + + # grab parsed easyconfigs for changed easyconfig files + changed_ecs = [] + for ec_fn in changed_ecs_filenames + added_ecs_filenames: + match = None + for ec in self.parsed_easyconfigs: + if os.path.basename(ec['spec']) == ec_fn: + match = ec['ec'] + break + + if match: + changed_ecs.append(match) + else: + # if no easyconfig is found, it's possible some archived easyconfigs were touched in the PR... + # so as a last resort, try to find the easyconfig file in __archive__ + easyconfigs_path = get_paths_for("easyconfigs")[0] + specs = glob.glob('%s/__archive__/*/*/%s' % (easyconfigs_path, ec_fn)) + if len(specs) == 1: + ec = process_easyconfig(specs[0])[0] + changed_ecs.append(ec['ec']) + else: + raise RuntimeError("Failed to find parsed easyconfig for %s" + " (and could not isolate it in easyconfigs archive either)" % ec_fn) + EasyConfigTest._changed_ecs = changed_ecs + + def _get_changed_patches(self): + """Gather all added or modified patches""" + + # get list of changed/added patch files + changed_patches_filenames = get_files_from_diff(diff_filter='M', ext='.patch', basename=False) + added_patches_filenames = get_files_from_diff(diff_filter='A', ext='.patch', basename=False) + + if changed_patches_filenames: + print("\nList of changed patch files in this PR:\n\t%s" % '\n\t'.join(changed_patches_filenames)) + if added_patches_filenames: + print("\nList of added patch files in this PR:\n\t%s" % '\n\t'.join(added_patches_filenames)) + + EasyConfigTest._changed_patches = changed_patches_filenames + added_patches_filenames + + @property + def parsed_easyconfigs(self): + # parse all easyconfigs if they haven't been already + EasyConfigTest.parse_all_easyconfigs() + return EasyConfigTest._parsed_easyconfigs + + @property + def ordered_specs(self): + # Resolve dependencies if not done + if EasyConfigTest._ordered_specs is None: + EasyConfigTest.resolve_all_dependencies() + return EasyConfigTest._ordered_specs + + @property + def changed_ecs_filenames(self): + if EasyConfigTest._changed_ecs is None: + self._get_changed_easyconfigs() + return EasyConfigTest._changed_ecs_filenames + + @property + def added_ecs_filenames(self): + if EasyConfigTest._changed_ecs is None: + self._get_changed_easyconfigs() + return EasyConfigTest._added_ecs_filenames + + @property + def changed_ecs(self): + if EasyConfigTest._changed_ecs is None: + self._get_changed_easyconfigs() + return EasyConfigTest._changed_ecs + + @property + def changed_patches(self): + if EasyConfigTest._changed_patches is None: + self._get_changed_patches() + return EasyConfigTest._changed_patches + + def test_dep_graph(self): + """Unit test that builds a full dependency graph.""" + # pygraph dependencies required for constructing dependency graph are not available prior to Python 2.6 + if LooseVersion(sys.version) >= LooseVersion('2.6') and single_tests_ok: + # temporary file for dep graph + (hn, fn) = tempfile.mkstemp(suffix='.dot') + os.close(hn) + + dep_graph(fn, self.ordered_specs) + + remove_file(fn) + else: + print("(skipped dep graph test)") + + def test_conflicts(self): + """Check whether any conflicts occur in software dependency graphs.""" + + if not single_tests_ok: + print("(skipped conflicts test)") + return + + self.assertFalse(check_conflicts(self.ordered_specs, modules_tool(), check_inter_ec_conflicts=False), + "No conflicts detected") + + def test_deps(self): + """Perform checks on dependencies in easyconfig files""" + + fails = [] + + for ec in self.parsed_easyconfigs: + # make sure that no odd versions (like 1.13) of HDF5 are used as a dependency, + # since those are released candidates - only even versions (like 1.12) are stable releases; + # see https://docs.hdfgroup.org/archive/support/HDF5/doc/TechNotes/Version.html + for dep in ec['ec'].dependencies(): + if dep['name'] == 'HDF5': + ver = dep['version'] + if int(ver.split('.')[1]) % 2 == 1: + fail = "Odd minor versions of HDF5 should not be used as a dependency: " + fail += "found HDF5 v%s as dependency in %s" % (ver, os.path.basename(ec['spec'])) + fails.append(fail) + + self.assertFalse(len(fails), '\n'.join(sorted(fails))) + + def check_dep_vars(self, gen, dep, dep_vars): + """Check whether available variants of a particular dependency are acceptable or not.""" + + # 'guilty' until proven 'innocent' + res = False + + # filter out wrapped Java versions + # i.e. if the version of one is a prefix of the version of the other one (e.g. 1.8 & 1.8.0_181) + if dep == 'Java': + dep_vars_to_check = sorted(dep_vars.keys()) + + retained_dep_vars = [] + + while dep_vars_to_check: + dep_var = dep_vars_to_check.pop() + dep_var_version = dep_var.split(';')[0] + + # remove dep vars wrapped by current dep var + dep_vars_to_check = [x for x in dep_vars_to_check if not x.startswith(dep_var_version + '.')] + + retained_dep_vars = [x for x in retained_dep_vars if not x.startswith(dep_var_version + '.')] + + retained_dep_vars.append(dep_var) + + for key in list(dep_vars.keys()): + if key not in retained_dep_vars: + del dep_vars[key] + + version_regex = re.compile('^version: (?P[^;]+);') + + # filter out binutils with empty versionsuffix which is used to build toolchain compiler + if dep == 'binutils' and len(dep_vars) > 1: + empty_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: ')] + if len(empty_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != empty_vsuff_vars[0]) + + # multiple variants of HTSlib is OK as long as they are deps for a matching version of BCFtools; + # same goes for WRF and WPS; Gurobi and Rgurobi + for dep_name, parent_name in [('HTSlib', 'BCFtools'), ('WRF', 'WPS'), ('Gurobi', 'Rgurobi')]: + if dep == dep_name and len(dep_vars) > 1: + for key in list(dep_vars): + ecs = dep_vars[key] + # filter out dep variants that are only used as dependency for parent with same version + dep_ver = version_regex.search(key).group('version') + if all(ec.startswith('%s-%s-' % (parent_name, dep_ver)) for ec in ecs) and len(dep_vars) > 1: + dep_vars.pop(key) + + # multiple versions of Boost is OK as long as they are deps for a matching Boost.Python + if dep == 'Boost' and len(dep_vars) > 1: + for key in list(dep_vars): + ecs = dep_vars[key] + # filter out Boost variants that are only used as dependency for Boost.Python with same version + boost_ver = version_regex.search(key).group('version') + if all(ec.startswith('Boost.Python-%s-' % boost_ver) for ec in ecs): + dep_vars.pop(key) + + # filter out Perl with -minimal versionsuffix which are only used in makeinfo-minimal + if dep == 'Perl': + minimal_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -minimal')] + if len(minimal_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != minimal_vsuff_vars[0]) + + # filter out FFTW and imkl with -serial versionsuffix which are used in non-MPI subtoolchains + if dep in ['FFTW', 'imkl']: + serial_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -serial')] + if len(serial_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != serial_vsuff_vars[0]) + + # filter out BLIS and libFLAME with -amd versionsuffix + # (AMD forks, used in gobff/*-amd toolchains) + if dep in ['BLIS', 'libFLAME']: + amd_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -amd')] + if len(amd_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != amd_vsuff_vars[0]) + + # filter out ScaLAPACK with -BLIS-* versionsuffix, used in goblf toolchain + if dep == 'ScaLAPACK': + blis_vsuff_vars = [v for v in dep_vars.keys() if '; versionsuffix: -BLIS-' in v] + if len(blis_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != blis_vsuff_vars[0]) + + if dep == 'ScaLAPACK': + # filter out ScaLAPACK with -bf versionsuffix, used in gobff toolchain + bf_vsuff_vars = [v for v in dep_vars.keys() if '; versionsuffix: -bf' in v] + if len(bf_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != bf_vsuff_vars[0]) + # filter out ScaLAPACK with -bl versionsuffix, used in goblf toolchain + bl_vsuff_vars = [v for v in dep_vars.keys() if '; versionsuffix: -bl' in v] + if len(bl_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != bl_vsuff_vars[0]) + + # filter out HDF5 with -serial versionsuffix which is used in HDF5 for Python (h5py) + if dep in ['HDF5']: + serial_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -serial')] + if len(serial_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != serial_vsuff_vars[0]) + + # for some dependencies, we allow exceptions for software that depends on a particular version, + # as long as that's indicated by the versionsuffix + versionsuffix_deps = ['ASE', 'Boost', 'CUDAcore', 'Java', 'Lua', + 'PLUMED', 'PyTorch', 'R', 'TensorFlow'] + if dep in versionsuffix_deps and len(dep_vars) > 1: + + # check for '-CUDA-*' versionsuffix for CUDAcore dependency + if dep == 'CUDAcore': + dep = 'CUDA' + + for key in list(dep_vars): + dep_ver = version_regex.search(key).group('version') + # use version of Java wrapper rather than full Java version + if dep == 'Java': + dep_ver = '.'.join(dep_ver.split('.')[:2]) + # filter out dep version if all easyconfig filenames using it include specific dep version + if all(re.search('-%s-%s' % (dep, dep_ver), v) for v in dep_vars[key]): + dep_vars.pop(key) + # always retain at least one dep variant + if len(dep_vars) == 1: + break + + # filter R dep for a specific version of Python 2.x + if dep == 'R' and len(dep_vars) > 1: + for key in list(dep_vars): + if '; versionsuffix: -Python-2' in key: + dep_vars.pop(key) + # always retain at least one variant + if len(dep_vars) == 1: + break + + # filter out variants that are specific to a particular version of CUDA + cuda_dep_vars = [v for v in dep_vars.keys() if '-CUDA' in v] + if len(dep_vars) >= len(cuda_dep_vars) and len(dep_vars) > 1: + for key in list(dep_vars): + if re.search('; versionsuffix: .*-CUDA-[0-9.]+', key): + dep_vars.pop(key) + # always retain at least one dep variant + if len(dep_vars) == 1: + break + + # some software packages require a specific (older/newer) version of a particular dependency + alt_dep_versions = { + 'jax': [(r'0\.3\.9', [r'AlphaFold-2\.2\.2-'])], + # arrow-R 6.0.0.2 is used for two R/R-bundle-Bioconductor sets (4.1.2/3.14 and 4.2.0/3.15) + 'arrow-R': [('6.0.0.2', [r'R-bundle-Bioconductor-'])], + # EMAN2 2.3 requires Boost(.Python) 1.64.0 + 'Boost': [('1.64.0;', [r'Boost.Python-1\.64\.0-', r'EMAN2-2\.3-'])], + 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], + # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x + 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], + 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], + # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) + 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], + # VMTK 1.4.x requires ITK 4.13.x + 'ITK': [(r'4\.13\.', [r'VMTK-1\.4\.'])], + # Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x) + 'Jellyfish': [(r'1\.', [r'Kraken-1\.', r'Roary-3\.12\.0', r'metaWRAP-1\.2'])], + # Libint 1.1.6 is required by older CP2K versions + 'Libint': [(r'1\.1\.6', [r'CP2K-[3-6]'])], + # libxc 2.x or 3.x is required by ABINIT, AtomPAW, CP2K, GPAW, horton, PySCF, WIEN2k + # libxc 4.x is required by libGridXC + # (Qiskit depends on PySCF), Elk 7.x requires libxc >= 5 + 'libxc': [ + (r'[23]\.', [r'ABINIT-', r'AtomPAW-', r'CP2K-', r'GPAW-', r'horton-', + r'PySCF-', r'Qiskit-', r'WIEN2k-']), + (r'4\.', [r'libGridXC-']), + (r'5\.', [r'Elk-']), + ], + # some software depends on numba, which typically requires an older LLVM; + # this includes BirdNET, cell2location, cryoDRGN, librosa, PyOD, Python-Geometric, scVelo, scanpy + 'LLVM': [ + # numba 0.47.x requires LLVM 7.x or 8.x (see https://github.com/numba/llvmlite#compatibility) + (r'8\.', [r'numba-0\.47\.0-', r'librosa-0\.7\.2-', r'BirdNET-20201214-', + r'scVelo-0\.1\.24-', r'PyTorch-Geometric-1\.[346]\.[23]']), + (r'10\.0\.1', [r'cell2location-0\.05-alpha-', r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-', + r'numba-0\.52\.0-', r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', + r'scanpy-1\.7\.2-', r'umap-learn-0\.4\.6-']), + ], + 'Lua': [ + # SimpleITK 2.1.0 requires Lua 5.3.x, MedPy and nnU-Net depend on SimpleITK + (r'5\.3\.5', [r'nnU-Net-1\.7\.0-', r'MedPy-0\.4\.0-', r'SimpleITK-2\.1\.0-']), + ], + # TensorFlow 2.5+ requires a more recent NCCL than version 2.4.8 used in 2019b generation; + # Horovod depends on TensorFlow, so same exception required there + 'NCCL': [(r'2\.11\.4', [r'TensorFlow-2\.[5-9]\.', r'Horovod-0\.2[2-9]'])], + # rampart requires nodejs > 10, artic-ncov2019 requires rampart + 'nodejs': [('12.16.1', ['rampart-1.2.0rc3-', 'artic-ncov2019-2020.04.13'])], + # some software depends on an older numba; + # this includes BirdNET, cell2location, cryoDRGN, librosa, PyOD, Python-Geometric, scVelo, scanpy + 'numba': [ + (r'0\.52\.0', [r'cell2location-0\.05-alpha-', r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-', + r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', r'scanpy-1\.7\.2-', + r'umap-learn-0\.4\.6-']), + ], + # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, + # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; + # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 + # WhatsHap 1.4 + medaka 1.6.0 require Pysam >= 0.18.0 (NGSpeciesID depends on medaka) + 'Pysam': [ + ('0.16.0.1;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'medaka-1.4.3-', 'decona-0.1.2-', + 'NGSpeciesID-0.1.1.1-']), + ('0.18.0;', ['medaka-1.6.0-', 'NGSpeciesID-0.1.2.1-', 'WhatsHap-1.4-']), + ], + # OPERA requires SAMtools 0.x + 'SAMtools': [(r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', + r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1'])], + # NanoPlot, NanoComp use an older version of Seaborn + 'Seaborn': [(r'0\.10\.1', [r'NanoComp-1\.13\.1-', r'NanoPlot-1\.33\.0-'])], + # Shasta requires spoa 3.x + 'spoa': [(r'3\.4\.0', [r'Shasta-0\.8\.0-'])], + # UShER requires tbb-2020.3 as newer versions will not build + 'tbb': [('2020.3', ['UShER-0.5.0-'])], + 'TensorFlow': [ + # medaka 0.11.4/0.12.0 requires recent TensorFlow <= 1.14 (and Python 3.6), + # artic-ncov2019 requires medaka + ('1.13.1;', ['medaka-0.11.4-', 'medaka-0.12.0-', 'artic-ncov2019-2020.04.13']), + # medaka 1.1.* and 1.2.* requires TensorFlow 2.2.0 + # (while other 2019b easyconfigs use TensorFlow 2.1.0 as dep); + # TensorFlow 2.2.0 is also used as a dep for Horovod 0.19.5; + # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 + ('2.2.0;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'Horovod-0.19.5-', 'decona-0.1.2-', + 'NGSpeciesID-0.1.1.1-']), + # medaka 1.4.3 (foss/2019b) depends on TensorFlow 2.2.2 + ('2.2.2;', ['medaka-1.4.3-']), + # medaka 1.4.3 (foss/2020b) depends on TensorFlow 2.2.3; longread_umi and artic depend on medaka + ('2.2.3;', ['medaka-1.4.3-', 'artic-ncov2019-2021.06.24-', 'longread_umi-0.3.2-']), + # AlphaFold 2.1.2 (foss/2020b) depends on TensorFlow 2.5.0 + ('2.5.0;', ['AlphaFold-2.1.2-']), + # medaka 1.5.0 (foss/2021a) depends on TensorFlow >=2.5.2, <2.6.0 + ('2.5.3;', ['medaka-1.5.0-']), + ], + # smooth-topk uses a newer version of torchvision + 'torchvision': [('0.11.3;', ['smooth-topk-1.0-20210817-'])], + # for the sake of backwards compatibility, keep UCX-CUDA v1.11.0 which depends on UCX v1.11.0 + # (for 2021b, UCX was updated to v1.11.2) + 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])], + # WPS 3.9.1 requires WRF 3.9.1.1 + 'WRF': [(r'3\.9\.1\.1', [r'WPS-3\.9\.1'])], + } + if dep in alt_dep_versions and len(dep_vars) > 1: + for key in list(dep_vars): + for version_pattern, parents in alt_dep_versions[dep]: + # filter out known alternative dependency versions + if re.search('^version: %s' % version_pattern, key): + # only filter if the easyconfig using this dep variants is known + if all(any(re.search(p, x) for p in parents) for x in dep_vars[key]): + dep_vars.pop(key) + + # filter out ELSI variants with -PEXSI suffix + if dep == 'ELSI' and len(dep_vars) > 1: + pexsi_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -PEXSI')] + if len(pexsi_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != pexsi_vsuff_vars[0]) + + # only single variant is always OK + if len(dep_vars) == 1: + res = True + + elif len(dep_vars) == 2 and dep in ['Python', 'Tkinter']: + # for Python & Tkinter, it's OK to have on 2.x and one 3.x version + v2_dep_vars = [x for x in dep_vars.keys() if x.startswith('version: 2.')] + v3_dep_vars = [x for x in dep_vars.keys() if x.startswith('version: 3.')] + if len(v2_dep_vars) == 1 and len(v3_dep_vars) == 1: + res = True + + # two variants is OK if one is for Python 2.x and the other is for Python 3.x (based on versionsuffix) + elif len(dep_vars) == 2: + py2_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-2.' in x] + py3_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-3.' in x] + if len(py2_dep_vars) == 1 and len(py3_dep_vars) == 1: + res = True + + # for recent generations, there's no versionsuffix anymore for Python 3, + # but we still allow variants depending on Python 2.x + 3.x + is_recent_gen = False + full_toolchain_regex = re.compile(r'^20[1-9][0-9][ab]$') + gcc_toolchain_regex = re.compile(r'^GCC(core)?-[0-9]?[0-9]\.[0-9]$') + if full_toolchain_regex.match(gen): + is_recent_gen = LooseVersion(gen) >= LooseVersion('2020b') + elif gcc_toolchain_regex.match(gen): + genver = gen.split('-', 1)[1] + is_recent_gen = LooseVersion(genver) >= LooseVersion('10.2') + else: + raise EasyBuildError("Unkown type of toolchain generation: %s" % gen) + + if is_recent_gen: + py2_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-2.' in x] + py3_dep_vars = [x for x in dep_vars.keys() if x.strip().endswith('; versionsuffix:')] + if len(py2_dep_vars) == 1 and len(py3_dep_vars) == 1: + res = True + + return res + + def test_check_dep_vars(self): + """Test check_dep_vars utility method.""" + + # one single dep version: OK + self.assertTrue(self.check_dep_vars('2019b', 'testdep', { + 'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb', 'bar-4.5.6.eb'], + })) + self.assertTrue(self.check_dep_vars('2019b', 'testdep', { + 'version: 1.2.3; versionsuffix: -test': ['foo-1.2.3.eb', 'bar-4.5.6.eb'], + })) + + # two or more dep versions (no special case: not OK) + self.assertFalse(self.check_dep_vars('2019b', 'testdep', { + 'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 4.5.6; versionsuffix:': ['bar-4.5.6.eb'], + })) + self.assertFalse(self.check_dep_vars('2019b', 'testdep', { + 'version: 0.0; versionsuffix:': ['foobar-0.0.eb'], + 'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 4.5.6; versionsuffix:': ['bar-4.5.6.eb'], + })) + + # Java is a special case, with wrapped Java versions + self.assertTrue(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + })) + # two Java wrappers is not OK + self.assertFalse(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11.0.2; versionsuffix:': ['bar-4.5.6.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6.eb'], + })) + # OK to have two or more wrappers if versionsuffix is used to indicate exception + self.assertTrue(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + })) + # versionsuffix must be there for all easyconfigs to indicate exception + self.assertFalse(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb', 'bar-4.5.6.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb', 'bar-4.5.6.eb'], + })) + self.assertTrue(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + 'version: 12.1.6; versionsuffix:': ['foobar-0.0-Java-12.eb'], + 'version: 12; versionsuffix:': ['foobar-0.0-Java-12.eb'], + })) + + # strange situation: odd number of Java versions + # not OK: two Java wrappers (and no versionsuffix to indicate exception) + self.assertFalse(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6.eb'], + })) + # OK because of -Java-11 versionsuffix + self.assertTrue(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + })) + # not OK: two Java wrappers (and no versionsuffix to indicate exception) + self.assertFalse(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11.0.2; versionsuffix:': ['bar-4.5.6.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6.eb'], + })) + # OK because of -Java-11 versionsuffix + self.assertTrue(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + })) + + # two different versions of Boost is not OK + self.assertFalse(self.check_dep_vars('2019b', 'Boost', { + 'version: 1.64.0; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], + })) + + # a different Boost version that is only used as dependency for a matching Boost.Python is fine + self.assertTrue(self.check_dep_vars('2019a', 'Boost', { + 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'], + 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], + })) + self.assertTrue(self.check_dep_vars('2019a', 'Boost', { + 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'], + 'version: 1.66.0; versionsuffix:': ['Boost.Python-1.66.0-gompi-2019a.eb'], + 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], + })) + self.assertFalse(self.check_dep_vars('2019a', 'Boost', { + 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'], + 'version: 1.66.0; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], + })) + + self.assertTrue(self.check_dep_vars('2018a', 'Boost', { + 'version: 1.63.0; versionsuffix: -Python-2.7.14': ['EMAN2-2.21a-foss-2018a-Python-2.7.14-Boost-1.63.0.eb'], + 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2018a.eb'], + 'version: 1.66.0; versionsuffix:': ['BLAST+-2.7.1-foss-2018a.eb'], + })) + + self.assertTrue(self.check_dep_vars('2019a', 'Boost', { + 'version: 1.64.0; versionsuffix:': [ + 'Boost.Python-1.64.0-gompi-2019a.eb', + 'EMAN2-2.3-foss-2019a-Python-2.7.15.eb', + ], + 'version: 1.70.0; versionsuffix:': [ + 'BLAST+-2.9.0-gompi-2019a.eb', + 'Boost.Python-1.70.0-gompi-2019a.eb', + ], + })) + + # two variants is OK, if they're for Python 2.x and 3.x + self.assertTrue(self.check_dep_vars('2020a', 'Python', { + 'version: 2.7.18; versionsuffix:': ['SciPy-bundle-2020.03-foss-2020a-Python-2.7.18.eb'], + 'version: 3.8.2; versionsuffix:': ['SciPy-bundle-2020.03-foss-2020a-Python-3.8.2.eb'], + })) + + self.assertTrue(self.check_dep_vars('2020a', 'SciPy-bundle', { + 'version: 2020.03; versionsuffix: -Python-2.7.18': ['matplotlib-3.2.1-foss-2020a-Python-2.7.18.eb'], + 'version: 2020.03; versionsuffix: -Python-3.8.2': ['matplotlib-3.2.1-foss-2020a-Python-3.8.2.eb'], + })) + + # for recent easyconfig generations, there's no versionsuffix anymore for Python 3 + self.assertTrue(self.check_dep_vars('2020b', 'Python', { + 'version: 2.7.18; versionsuffix:': ['SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb'], + 'version: 3.8.6; versionsuffix:': ['SciPy-bundle-2020.11-foss-2020b.eb'], + })) + + self.assertTrue(self.check_dep_vars('GCCcore-10.2', 'PyYAML', { + 'version: 5.3.1; versionsuffix:': ['IPython-7.18.1-GCCcore-10.2.0.eb'], + 'version: 5.3.1; versionsuffix: -Python-2.7.18': ['IPython-7.18.1-GCCcore-10.2.0-Python-2.7.18.eb'], + })) + + self.assertTrue(self.check_dep_vars('2020b', 'SciPy-bundle', { + 'version: 2020.11; versionsuffix: -Python-2.7.18': ['matplotlib-3.3.3-foss-2020b-Python-2.7.18.eb'], + 'version: 2020.11; versionsuffix:': ['matplotlib-3.3.3-foss-2020b.eb'], + })) + + # not allowed for older generations (foss/intel 2020a or older, GCC(core) 10.1.0 or older) + self.assertFalse(self.check_dep_vars('2020a', 'SciPy-bundle', { + 'version: 2020.03; versionsuffix: -Python-2.7.18': ['matplotlib-3.2.1-foss-2020a-Python-2.7.18.eb'], + 'version: 2020.03; versionsuffix:': ['matplotlib-3.2.1-foss-2020a.eb'], + })) + + def test_dep_versions_per_toolchain_generation(self): + """ + Check whether there's only one dependency version per toolchain generation actively used. + This is enforced to try and limit the chance of running into conflicts when multiple modules built with + the same toolchain are loaded together. + """ + ecs_by_full_mod_name = dict((ec['full_mod_name'], ec) for ec in self.parsed_easyconfigs) + if len(ecs_by_full_mod_name) != len(self.parsed_easyconfigs): + self.fail('Easyconfigs with duplicate full_mod_name found') + + # Cache already determined dependencies + ec_to_deps = dict() + + def get_deps_for(ec): + """Get list of (direct) dependencies for specified easyconfig.""" + ec_mod_name = ec['full_mod_name'] + deps = ec_to_deps.get(ec_mod_name) + if deps is None: + deps = [] + for dep in ec['ec']['dependencies']: + dep_mod_name = dep['full_mod_name'] + deps.append((dep['name'], dep['version'], dep['versionsuffix'], dep_mod_name)) + # Note: Raises KeyError if dep not found + res = ecs_by_full_mod_name[dep_mod_name] + deps.extend(get_deps_for(res)) + ec_to_deps[ec_mod_name] = deps + + return deps + + # some software also follows {a,b} versioning scheme, + # which throws off the pattern matching done below for toolchain versions + false_positives_regex = re.compile('^MATLAB-Engine-20[0-9][0-9][ab]') + + # restrict to checking dependencies of easyconfigs using common toolchains (start with 2018a) + # and GCCcore subtoolchain for common toolchains, starting with GCCcore 7.x + for pattern in ['20(1[89]|[2-9][0-9])[ab]', r'GCCcore-([7-9]|[1-9][0-9])\.[0-9]']: + all_deps = {} + regex = re.compile(r'^.*-(?P%s).*\.eb$' % pattern) + + # collect variants for all dependencies of easyconfigs that use a toolchain that matches + for ec in self.ordered_specs: + ec_file = os.path.basename(ec['spec']) + + # take into account software which also follows a {a,b} versioning scheme + ec_file = false_positives_regex.sub('', ec_file) + + res = regex.match(ec_file) + if res: + tc_gen = res.group('tc_gen') + all_deps_tc_gen = all_deps.setdefault(tc_gen, {}) + for dep_name, dep_ver, dep_versuff, dep_mod_name in get_deps_for(ec): + dep_variants = all_deps_tc_gen.setdefault(dep_name, {}) + # a variant is defined by version + versionsuffix + variant = "version: %s; versionsuffix: %s" % (dep_ver, dep_versuff) + # keep track of which easyconfig this is a dependency + dep_variants.setdefault(variant, set()).add(ec_file) + + # check which dependencies have more than 1 variant + multi_dep_vars, multi_dep_vars_msg = [], '' + for tc_gen in sorted(all_deps.keys()): + for dep in sorted(all_deps[tc_gen].keys()): + dep_vars = all_deps[tc_gen][dep] + if not self.check_dep_vars(tc_gen, dep, dep_vars): + multi_dep_vars.append(dep) + multi_dep_vars_msg += "\nfound %s variants of '%s' dependency " % (len(dep_vars), dep) + multi_dep_vars_msg += "in easyconfigs using '%s' toolchain generation\n* " % tc_gen + multi_dep_vars_msg += '\n* '.join("%s as dep for %s" % v for v in sorted(dep_vars.items())) + multi_dep_vars_msg += '\n' + + error_msg = "No multi-variant deps found for '%s' easyconfigs:\n%s" % (regex.pattern, multi_dep_vars_msg) + self.assertFalse(multi_dep_vars, error_msg) + + def test_sanity_check_paths(self): + """Make sure specified sanity check paths adher to the requirements.""" + + for ec in self.parsed_easyconfigs: + ec_scp = ec['ec']['sanity_check_paths'] + if ec_scp != {}: + # if sanity_check_paths is specified (i.e., non-default), it must adher to the requirements + # both 'files' and 'dirs' keys, both with list values and with at least one a non-empty list + error_msg = "sanity_check_paths for %s does not meet requirements: %s" % (ec['spec'], ec_scp) + self.assertEqual(sorted(ec_scp.keys()), ['dirs', 'files'], error_msg) + self.assertTrue(isinstance(ec_scp['dirs'], list), error_msg) + self.assertTrue(isinstance(ec_scp['files'], list), error_msg) + self.assertTrue(ec_scp['dirs'] or ec_scp['files'], error_msg) + + def test_r_libs_site_env_var(self): + """Make sure $R_LIBS_SITE is being updated, rather than $R_LIBS.""" + # cfr. https://github.com/easybuilders/easybuild-easyblocks/pull/2326 + + r_libs_ecs = [] + for ec in self.parsed_easyconfigs: + for key in ('modextrapaths', 'modextravars'): + if 'R_LIBS' in ec['ec'][key]: + r_libs_ecs.append(ec['spec']) + + error_msg = "%d easyconfigs found which set $R_LIBS, should be $R_LIBS_SITE: %s" + self.assertEqual(r_libs_ecs, [], error_msg % (len(r_libs_ecs), ', '.join(r_libs_ecs))) + + def test_easyconfig_locations(self): + """Make sure all easyconfigs files are in the right location.""" + easyconfig_dirs_regex = re.compile(r'/easybuild/easyconfigs/[0a-z]/[^/]+$') + topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__))) + for (dirpath, _, filenames) in os.walk(topdir): + # ignore git/svn dirs & archived easyconfigs + if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath: + continue + # check whether list of .eb files is non-empty + easyconfig_files = [fn for fn in filenames if fn.endswith('eb')] + if easyconfig_files: + # check whether path matches required pattern + if not easyconfig_dirs_regex.search(dirpath): + # only exception: TEMPLATE.eb + if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']): + self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) + + @skip_if_not_pr_to_non_main_branch() + def test_pr_sha256_checksums(self): + """Make sure changed easyconfigs have SHA256 checksums in place.""" + + # list of software for which checksums can not be required, + # e.g. because 'source' files need to be constructed manually + whitelist = [ + 'Kent_tools-*', + 'MATLAB-*', + 'OCaml-*', + 'OpenFOAM-Extend-4.1-*', + # sources for old versions of Bioconductor packages are no longer available, + # so not worth adding checksums for at this point + 'R-bundle-Bioconductor-3.[2-5]', + ] + + # the check_sha256_checksums function (again) creates an EasyBlock instance + # for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter + # is updated in place (sources for components are added to the 'parent' sources) in Bundle's __init__; + # therefore, we need to reset 'sources' to an empty list here if Bundle is used... + # likewise for 'patches' and 'checksums' + for ec in self.changed_ecs: + if ec['easyblock'] in ['Bundle', 'PythonBundle', 'EB_OpenSSL_wrapper'] or ec['name'] in ['Clang-AOMP']: + ec['sources'] = [] + ec['patches'] = [] + ec['checksums'] = [] + + # filter out deprecated easyconfigs + retained_changed_ecs = [] + for ec in self.changed_ecs: + if not ec['deprecated']: + retained_changed_ecs.append(ec) + + checksum_issues = check_sha256_checksums(retained_changed_ecs, whitelist=whitelist) + self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues)) + + @skip_if_not_pr_to_non_main_branch() + def test_pr_python_packages(self): + """Several checks for easyconfigs that install (bundles of) Python packages.""" + + # These packages do not support installation with 'pip' + whitelist_pip = [ + r'ESMPy-.*', + r'MATLAB-Engine-.*', + r'Meld-.*', + r'PyTorch-.*', + ] + + whitelist_pip_check = [ + r'Mako-1.0.4.*Python-2.7.12.*', + # no pip 9.x or newer for configparser easyconfigs using a 2016a or 2016b toolchain + r'configparser-3.5.0.*-2016[ab].*', + # mympirun is installed with system Python, pip may not be installed for system Python + r'vsc-mympirun.*', + ] + + failing_checks = [] + + python_default_urls = PythonPackage.extra_options()['source_urls'][0] + + for ec in self.changed_ecs: + + with ec.disable_templating(): + ec_fn = os.path.basename(ec.path) + easyblock = ec.get('easyblock') + exts_defaultclass = ec.get('exts_defaultclass') + exts_default_options = ec.get('exts_default_options', {}) + + download_dep_fail = ec.get('download_dep_fail') + exts_download_dep_fail = ec.get('exts_download_dep_fail') + use_pip = ec.get('use_pip') + if use_pip is None: + use_pip = exts_default_options.get('use_pip') + + # only easyconfig parameters as they are defined in the easyconfig file, + # does *not* include other easyconfig parameters with their default value! + pure_ec = ec.parser.get_config_dict() + + # download_dep_fail should be set when using PythonPackage + if easyblock == 'PythonPackage': + if download_dep_fail is None: + failing_checks.append("'download_dep_fail' should be set in %s" % ec_fn) + + if pure_ec.get('source_urls') == python_default_urls: + failing_checks.append("'source_urls' should not be defined when using the default value " + "in %s" % ec_fn) + + # use_pip should be set when using PythonPackage or PythonBundle (except for whitelisted easyconfigs) + if easyblock in ['PythonBundle', 'PythonPackage']: + if use_pip is None and not any(re.match(regex, ec_fn) for regex in whitelist_pip): + failing_checks.append("'use_pip' should be set in %s" % ec_fn) + + # download_dep_fail is enabled automatically in PythonBundle easyblock, so shouldn't be set + if easyblock == 'PythonBundle': + if download_dep_fail or exts_download_dep_fail: + fail = "'*download_dep_fail' should not be set in %s since PythonBundle easyblock is used" % ec_fn + failing_checks.append(fail) + if pure_ec.get('exts_default_options', {}).get('source_urls') == python_default_urls: + failing_checks.append("'source_urls' should not be defined in exts_default_options when using " + "the default value in %s" % ec_fn) + + elif exts_defaultclass == 'PythonPackage': + # bundle of Python packages should use PythonBundle + if easyblock == 'Bundle': + fail = "'PythonBundle' easyblock should be used for bundle of Python packages in %s" % ec_fn + failing_checks.append(fail) + else: + # both download_dep_fail and use_pip should be set via exts_default_options + # when installing Python packages as extensions + for key in ['download_dep_fail', 'use_pip']: + if exts_default_options.get(key) is None: + failing_checks.append("'%s' should be set in exts_default_options in %s" % (key, ec_fn)) + + # if Python is a dependency, that should be reflected in the versionsuffix + # Tkinter is an exception, since its version always matches the Python version anyway + # Python 3.8.6 and later are also excluded, as we consider python 3 the default python + # Also whitelist some updated versions of Amber + whitelist_python_suffix = [ + 'Amber-16-*-2018b-AmberTools-17-patchlevel-10-15.eb', + 'Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb', + 'R-keras-2.1.6-foss-2018a-R-3.4.4.eb', + ] + whitelisted = any(re.match(regex, ec_fn) for regex in whitelist_python_suffix) + has_python_dep = any(LooseVersion(dep['version']) < LooseVersion('3.8.6') + for dep in ec['dependencies'] if dep['name'] == 'Python') + if has_python_dep and ec.name != 'Tkinter' and not whitelisted: + if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): + msg = "'-Python-%%(pyver)s' should be included in versionsuffix in %s" % ec_fn + # This is only a failure for newly added ECs, not for existing ECS + # As that would probably break many ECs + if ec_fn in self.added_ecs_filenames: + failing_checks.append(msg) + else: + print('\nNote: Failed non-critical check: ' + msg) + else: + has_recent_python3_dep = any(LooseVersion(dep['version']) >= LooseVersion('3.8.6') + for dep in ec['dependencies'] if dep['name'] == 'Python') + if has_recent_python3_dep and re.search(r'-Python-3\.[0-9]+\.[0-9]+', ec['versionsuffix']): + msg = "'-Python-%%(pyver)s' should no longer be included in versionsuffix in %s" % ec_fn + failing_checks.append(msg) + + # require that running of "pip check" during sanity check is enabled via sanity_pip_check + if easyblock in ['PythonBundle', 'PythonPackage']: + sanity_pip_check = ec.get('sanity_pip_check') or exts_default_options.get('sanity_pip_check') + if not sanity_pip_check and not any(re.match(regex, ec_fn) for regex in whitelist_pip_check): + failing_checks.append("sanity_pip_check should be enabled in %s" % ec_fn) + + if failing_checks: + self.fail('\n'.join(failing_checks)) + + @skip_if_not_pr_to_non_main_branch() + def test_pr_R_packages(self): + """Several checks for easyconfigs that install (bundles of) R packages.""" + failing_checks = [] + + for ec in self.changed_ecs: + ec_fn = os.path.basename(ec.path) + exts_defaultclass = ec.get('exts_defaultclass') + if exts_defaultclass == 'RPackage' or ec.name == 'R': + seen_exts = set() + for ext in ec['exts_list']: + if isinstance(ext, (tuple, list)): + ext_name = ext[0] + else: + ext_name = ext + if ext_name in seen_exts: + failing_checks.append('%s was added multiple times to exts_list in %s' % (ext_name, ec_fn)) + else: + seen_exts.add(ext_name) + self.assertFalse(failing_checks, '\n'.join(failing_checks)) + + @skip_if_not_pr_to_non_main_branch() + def test_pr_sanity_check_paths(self): + """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" + + # some generic easyblocks already have a decent customised sanity_check_paths, + # including CMakePythonPackage, GoPackage, PythonBundle & PythonPackage; + # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check. + whitelist = ['BuildEnv', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage', 'ModuleRC', + 'PythonBundle', 'PythonPackage', 'Toolchain'] + # Bundles of dependencies without files of their own + # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, + # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co + bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle', 'ROCm'] + + failing_checks = [] + + for ec in self.changed_ecs: + easyblock = ec.get('easyblock') + if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'): + + sanity_check_ok = False + + if easyblock in whitelist or (easyblock == 'Bundle' and ec['name'] in bundles_whitelist): + sanity_check_ok = True + + # also allow bundles that enable per-component sanity checks + elif easyblock == 'Bundle': + if ec['sanity_check_components'] or ec['sanity_check_all_components']: + sanity_check_ok = True + + if not sanity_check_ok: + ec_fn = os.path.basename(ec.path) + failing_checks.append("No custom sanity_check_paths found in %s" % ec_fn) + + self.assertFalse(failing_checks, '\n'.join(failing_checks)) + + @skip_if_not_pr_to_non_main_branch() + def test_pr_https(self): + """Make sure https:// URL is used (if it exists) for homepage/source_urls (rather than http://).""" + + whitelist = [ + 'Kaiju', # invalid certificate at https://kaiju.binf.ku.dk + 'libxml2', # https://xmlsoft.org works, but invalid certificate + 'p4vasp', # https://www.p4vasp.at doesn't work + 'ITSTool', # https://itstool.org/ doesn't work + 'UCX-', # bad certificate for https://www.openucx.org + 'MUMPS', # https://mumps.enseeiht.fr doesn't work + 'PyFR', # https://www.pyfr.org doesn't work + 'PycURL', # bad certificate for https://pycurl.io/ + ] + url_whitelist = [ + # https:// doesn't work, results in index page being downloaded instead + # (see https://github.com/easybuilders/easybuild-easyconfigs/issues/9692) + 'http://isl.gforge.inria.fr', + # https:// leads to File Not Found + 'http://tau.uoregon.edu/', + # https:// has outdated SSL configurations + 'http://faculty.scs.illinois.edu', + ] + # Cache: Mapping of already checked HTTP urls to whether the HTTPS variant works + checked_urls = dict() + + def check_https_url(http_url): + """Check if the https url works""" + http_url = http_url.rstrip('/') # Remove trailing slashes + https_url_works = checked_urls.get(http_url) + if https_url_works is None: + https_url = http_url.replace('http://', 'https://') + try: + https_url_works = bool(urlopen(https_url, timeout=5)) + except Exception: + https_url_works = False + checked_urls[http_url] = https_url_works + + http_regex = re.compile('http://[^"\'\n]+', re.M) + + failing_checks = [] + for ec in self.changed_ecs: + ec_fn = os.path.basename(ec.path) + + # skip whitelisted easyconfigs + if any(ec_fn.startswith(x) for x in whitelist): + continue + + # ignore commented out lines in easyconfig files when checking for http:// URLs + ec_txt = '\n'.join(line for line in ec.rawtxt.split('\n') if not line.startswith('#')) + + for http_url in http_regex.findall(ec_txt): + + # skip whitelisted http:// URLs + if any(http_url.startswith(x) for x in url_whitelist): + continue + + if check_https_url(http_url): + failing_checks.append("Found http:// URL in %s, should be https:// : %s" % (ec_fn, http_url)) + if failing_checks: + self.fail('\n'.join(failing_checks)) + + @skip_if_not_pr_to_non_main_branch() + def test_pr_patch_descr(self): + """ + Check whether all patch files touched in PR have a description on top. + """ + no_descr_patches = [] + for patch in self.changed_patches: + patch_txt = read_file(patch) + if patch_txt.startswith('--- '): + no_descr_patches.append(patch) + + self.assertFalse(no_descr_patches, "No description found in patches: %s" % ', '.join(no_descr_patches)) + + +def template_easyconfig_test(self, spec): + """Tests for an individual easyconfig: parsing, instantiating easyblock, check patches, ...""" + + # set to False, so it's False in case of this test failing + global single_tests_ok + prev_single_tests_ok = single_tests_ok + single_tests_ok = False + + # parse easyconfig + ecs = process_easyconfig(spec) + if len(ecs) == 1: + ec = ecs[0]['ec'] + + # cache the parsed easyconfig, to avoid that it is parsed again + EasyConfigTest._parsed_easyconfigs.append(ecs[0]) + else: + self.assertTrue(False, "easyconfig %s does not contain blocks, yields only one parsed easyconfig" % spec) + + # check easyconfig file name + expected_fn = '%s-%s.eb' % (ec['name'], det_full_ec_version(ec)) + msg = "Filename '%s' of parsed easyconfig matches expected filename '%s'" % (spec, expected_fn) + self.assertEqual(os.path.basename(spec), expected_fn, msg) + + name, easyblock = fetch_parameters_from_easyconfig(ec.rawtxt, ['name', 'easyblock']) + + # make sure easyconfig file is in expected location + expected_subdir = os.path.join('easybuild', 'easyconfigs', letter_dir_for(name), name) + subdir = os.path.join(*spec.split(os.path.sep)[-5:-1]) + fail_msg = "Easyconfig file %s not in expected subdirectory %s" % (spec, expected_subdir) + self.assertEqual(expected_subdir, subdir, fail_msg) + + # sanity check for software name, moduleclass + self.assertEqual(ec['name'], name) + self.assertTrue(ec['moduleclass'] in build_option('valid_module_classes')) + + # instantiate easyblock with easyconfig file + app_class = get_easyblock_class(easyblock, name=name) + + # check that automagic fallback to ConfigureMake isn't done (deprecated behaviour) + fn = os.path.basename(spec) + error_msg = "%s relies on automagic fallback to ConfigureMake, should use easyblock = 'ConfigureMake' instead" % fn + self.assertTrue(easyblock or app_class is not ConfigureMake, error_msg) + + # dump the easyconfig file; + # this should be done before creating the easyblock instance (done below via app_class), + # because some easyblocks (like PythonBundle) modify easyconfig parameters at initialisation + handle, test_ecfile = tempfile.mkstemp() + os.close(handle) + + ec.dump(test_ecfile) + dumped_ec = EasyConfigParser(test_ecfile).get_config_dict() + os.remove(test_ecfile) + + app = app_class(ec) + + # more sanity checks + self.assertTrue(name, app.name) + self.assertTrue(ec['version'], app.version) + + # make sure that deprecated 'dummy' toolchain is no longer used, should use 'system' toolchain instead + ec_fn = os.path.basename(spec) + error_msg_tmpl = "%s should use 'system' toolchain rather than deprecated 'dummy' toolchain" + self.assertFalse(ec['toolchain']['name'] == 'dummy', error_msg_tmpl % os.path.basename(spec)) + + # make sure that $root is not used, since it is not compatible with module files in Lua syntax + res = re.findall(r'.*\$root.*', ec.rawtxt, re.M) + error_msg = "Found use of '$root', not compatible with modules in Lua syntax, use '%%(installdir)s' instead: %s" + self.assertFalse(res, error_msg % res) + + # check for redefined easyconfig parameters, there should be none... + param_def_regex = re.compile(r'^(?P\w+)\s*=', re.M) + keys = param_def_regex.findall(ec.rawtxt) + redefined_keys = [] + for key in sorted(nub(keys)): + cnt = keys.count(key) + if cnt > 1: + redefined_keys.append((key, cnt)) + + redefined_keys_error_msg = "There should be no redefined easyconfig parameters, found %d: " % len(redefined_keys) + redefined_keys_error_msg += ', '.join('%s (%d)' % x for x in redefined_keys) + + self.assertFalse(redefined_keys, redefined_keys_error_msg) + + # make sure old GitHub urls for EasyBuild that include 'hpcugent' are no longer used + old_urls = [ + 'github.com/hpcugent/easybuild', + 'hpcugent.github.com/easybuild', + 'hpcugent.github.io/easybuild', + ] + for old_url in old_urls: + self.assertFalse(old_url in ec.rawtxt, "Old URL '%s' not found in %s" % (old_url, spec)) + + # make sure binutils is included as a (build) dep if toolchain is GCCcore + if ec['toolchain']['name'] == 'GCCcore': + # easyblocks without a build step + non_build_blocks = ['Binary', 'JAR', 'PackedBinary', 'Tarball'] + # some software packages do not have a build step + non_build_soft = ['ANIcalculator', 'Eigen'] + + requires_binutils = ec['easyblock'] not in non_build_blocks and ec['name'] not in non_build_soft + + # let's also exclude the very special case where the system GCC is used as GCCcore, and only apply this + # exception to the dependencies of binutils (since we should eventually build a new binutils with GCCcore) + if ec['toolchain']['version'] == 'system': + binutils_complete_dependencies = ['M4', 'Bison', 'flex', 'help2man', 'zlib', 'binutils'] + requires_binutils &= bool(ec['name'] not in binutils_complete_dependencies) + + # if no sources/extensions/components are specified, it's just a bundle (nothing is being compiled) + requires_binutils &= bool(ec['sources'] or ec['exts_list'] or ec.get('components')) + + if requires_binutils: + # dependencies() returns both build and runtime dependencies + # in some cases, binutils can also be a runtime dep (e.g. for Clang) + # Also using GCC directly as a build dep is also allowed (it includes the correct binutils) + dep_names = [d['name'] for d in ec.dependencies()] + self.assertTrue('binutils' in dep_names or 'GCC' in dep_names, + "binutils or GCC is a build dep in %s: %s" % (spec, dep_names)) + + # make sure that OpenSSL wrapper is used rather than OS dependency, + # for easyconfigs using a 2021a (sub)toolchain or more recent common toolchain version + osdeps = ec['osdependencies'] + if osdeps: + # check whether any entry in osdependencies related to OpenSSL + openssl_osdep = False + for osdep in osdeps: + if isinstance(osdep, string_type): + osdep = [osdep] + if any('libssl' in x for x in osdep) or any('openssl' in x for x in osdep): + openssl_osdep = True + + if openssl_osdep: + tcname = ec['toolchain']['name'] + tcver = LooseVersion(ec['toolchain']['version']) + + gcc_subtc_2021a = tcname in ('GCCcore', 'GCC') and tcver > LooseVersion('10.3') + if gcc_subtc_2021a or (tcname in ('foss', 'gompi', 'iimpi', 'intel') and tcver >= LooseVersion('2021')): + self.assertFalse(openssl_osdep, "OpenSSL should not be listed as OS dependency in %s" % spec) + + src_cnt = len(ec['sources']) + patch_checksums = ec['checksums'][src_cnt:] + + # make sure all patch files are available + specdir = os.path.dirname(spec) + specfn = os.path.basename(spec) + for idx, patch in enumerate(ec['patches']): + if isinstance(patch, (tuple, list)): + patch = patch[0] + + # only check actual patch files, not other files being copied via the patch functionality + patch_full = os.path.join(specdir, patch) + if patch.endswith('.patch'): + msg = "Patch file %s is available for %s" % (patch_full, specfn) + self.assertTrue(os.path.isfile(patch_full), msg) + + # verify checksum for each patch file + if idx < len(patch_checksums) and (os.path.exists(patch_full) or patch.endswith('.patch')): + checksum = patch_checksums[idx] + error_msg = "Invalid checksum for patch file %s in %s: %s" % (patch, ec_fn, checksum) + res = verify_checksum(patch_full, checksum) + self.assertTrue(res, error_msg) + + # make sure 'source' step is not being skipped, + # since that implies not verifying the checksum + error_msg = "'source' step should not be skipped in %s, since that implies not verifying checksums" % ec_fn + self.assertFalse(ec['checksums'] and ('source' in ec['skipsteps']), error_msg) + + for ext in ec.get_ref('exts_list'): + if isinstance(ext, (tuple, list)) and len(ext) == 3: + ext_name = ext[0] + self.assertTrue(isinstance(ext[2], dict), + "3rd element of extension spec for %s must be a dictionary" % ext_name) + + # After the sanity check above, use collect_exts_file_info to resolve templates etc. correctly + for ext in app.collect_exts_file_info(fetch_files=False, verify_checksums=False): + try: + ext_options = ext['options'] + except KeyError: + # No options --> Only have a name which is valid, so nothing to check + continue + + checksums = ext_options.get('checksums', []) + src_cnt = len(ext_options.get('sources', [])) or 1 + patch_checksums = checksums[src_cnt:] + + for idx, ext_patch in enumerate(ext.get('patches', [])): + if isinstance(ext_patch, (tuple, list)): + ext_patch = ext_patch[0] + + # only check actual patch files, not other files being copied via the patch functionality + ext_patch_full = os.path.join(specdir, ext_patch['name']) + if ext_patch_full.endswith('.patch'): + msg = "Patch file %s is available for %s" % (ext_patch_full, specfn) + self.assertTrue(os.path.isfile(ext_patch_full), msg) + + # verify checksum for each patch file + if idx < len(patch_checksums) and (os.path.exists(ext_patch_full) or ext_patch.endswith('.patch')): + checksum = patch_checksums[idx] + error_msg = "Invalid checksum for patch %s for %s extension in %s: %s" + res = verify_checksum(ext_patch_full, checksum) + self.assertTrue(res, error_msg % (ext_patch, ext_name, ec_fn, checksum)) + + # check whether all extra_options defined for used easyblock are defined + extra_opts = app.extra_options() + for key in extra_opts: + self.assertTrue(key in app.cfg) + + app.close_log() + os.remove(app.logfile) + + # inject dummy values for templates that are only known at a later stage + dummy_template_values = { + 'builddir': '/dummy/builddir', + 'installdir': '/dummy/installdir', + 'parallel': '2', + } + ec.template_values.update(dummy_template_values) + + ec_dict = ec.parser.get_config_dict() + orig_toolchain = ec_dict['toolchain'] + for key in ec_dict: + # skip parameters for which value is equal to default value + orig_val = ec_dict[key] + if key in DEFAULT_CONFIG and orig_val == DEFAULT_CONFIG[key][0]: + continue + if key in extra_opts and orig_val == extra_opts[key][0]: + continue + if key not in DEFAULT_CONFIG and key not in extra_opts: + continue + + orig_val = resolve_template(ec_dict[key], ec.template_values) + dumped_val = resolve_template(dumped_ec[key], ec.template_values) + + # take into account that dumped value for *dependencies may include hard-coded subtoolchains + # if no easyconfig was found for the dependency with the 'parent' toolchain, + # if may get resolved using a subtoolchain, which is then hardcoded in the dumped easyconfig + if key in DEPENDENCY_PARAMETERS: + # number of dependencies should remain the same + self.assertEqual(len(orig_val), len(dumped_val)) + for orig_dep, dumped_dep in zip(orig_val, dumped_val): + # name should always match + self.assertEqual(orig_dep[0], dumped_dep[0]) + + # version should always match, or be a possibility from the version dict + if isinstance(orig_dep[1], dict): + self.assertTrue(dumped_dep[1] in orig_dep[1].values()) + else: + self.assertEqual(orig_dep[1], dumped_dep[1]) + + # 3rd value is versionsuffix; + if len(dumped_dep) >= 3: + # if no versionsuffix was specified in original dep spec, then dumped value should be empty string + if len(orig_dep) >= 3: + self.assertEqual(dumped_dep[2], orig_dep[2]) + else: + self.assertEqual(dumped_dep[2], '') + + # 4th value is toolchain spec + if len(dumped_dep) >= 4: + if len(orig_dep) >= 4: + # if True was used to indicate that dependency should use system toolchain, + # then we need to compare the value for the dumped easyconfig more carefully; + # see also https://github.com/easybuilders/easybuild-framework/pull/4069 + if orig_dep[3] is True: + self.assertEqual(dumped_dep[3], EASYCONFIG_CONSTANTS['SYSTEM'][0]) + else: + self.assertEqual(dumped_dep[3], orig_dep[3]) + else: + # if a subtoolchain is specifed (only) in the dumped easyconfig, + # it should *not* be the same as the parent toolchain + self.assertNotEqual(dumped_dep[3], (orig_toolchain['name'], orig_toolchain['version'])) + + # take into account that for some string-valued easyconfig parameters (configopts & co), + # the easyblock may have injected additional values, which affects the dumped easyconfig file + elif isinstance(orig_val, string_type): + error_msg = "%s value '%s' should start with '%s'" % (key, dumped_val, orig_val) + self.assertTrue(dumped_val.startswith(orig_val), error_msg) + else: + error_msg = "%s value should be equal in original and dumped easyconfig: '%s' vs '%s'" + self.assertEqual(orig_val, dumped_val, error_msg % (key, orig_val, dumped_val)) + + # test passed, so set back to True + single_tests_ok = True and prev_single_tests_ok + + +def suite(loader=None): + """Return all easyblock initialisation tests.""" + def make_inner_test(spec_path): + def innertest(self): + template_easyconfig_test(self, spec_path) + return innertest + + # dynamically generate a separate test for each of the available easyconfigs + # define new inner functions that can be added as class methods to InitTest + easyconfigs_path = get_paths_for('easyconfigs')[0] + cnt = 0 + for (subpath, dirs, specs) in os.walk(easyconfigs_path, topdown=True): + + # ignore archived easyconfigs + if '__archive__' in dirs: + dirs.remove('__archive__') + + for spec in specs: + if spec.endswith('.eb') and spec != 'TEMPLATE.eb': + cnt += 1 + innertest = make_inner_test(os.path.join(subpath, spec)) + innertest.__doc__ = "Test for easyconfig %s" % spec + # double underscore so parsing tests are run first + innertest.__name__ = "test__parse_easyconfig_%s" % spec + setattr(EasyConfigTest, innertest.__name__, innertest) + + print("Found %s easyconfigs..." % cnt) + if not loader: + loader = TestLoader() + return loader.loadTestsFromTestCase(EasyConfigTest) + + +if __name__ == '__main__': + main() From e18aa2a792eec59ec08c8ecc75084e7a49d72c20 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 3 Oct 2022 09:26:33 +0200 Subject: [PATCH 244/793] Revert "Remove AmberTools-20 patch file from Amber, it's now located in AmberTools only." This reverts commit ed3095735a1eaff3e992f9d0c19f0a57da170ace. Must leave this patch in the Amber directory until all older Amber easyconfigs have been changed to use alt_location. --- ...ols-20_fix_missing_MPI_LIBRARY_error.patch | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch diff --git a/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch b/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch new file mode 100644 index 00000000000..8d96ce176c0 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch @@ -0,0 +1,21 @@ +When using "usempi" there will be no MPI_xxx_LIBRARIES set and that causes +import_libraries to error out. We know it is correct so comment out that +FATAL_ERROR. + +Åke Sandgren, 2021-06-16 +diff -ru amber20_src.orig/cmake/LibraryTracking.cmake amber20_src/cmake/LibraryTracking.cmake +--- amber20_src.orig/cmake/LibraryTracking.cmake 2021-04-25 02:51:44.000000000 +0200 ++++ amber20_src/cmake/LibraryTracking.cmake 2021-06-16 13:30:26.568317368 +0200 +@@ -170,9 +170,9 @@ + + cmake_parse_arguments(IMP_LIBS "" "" "LIBRARIES;INCLUDES" ${ARGN}) + +- if("${IMP_LIBS_LIBRARIES}" STREQUAL "") +- message(FATAL_ERROR "Incorrect usage. At least one LIBRARY should be provided.") +- endif() ++ #if("${IMP_LIBS_LIBRARIES}" STREQUAL "") ++ # message(FATAL_ERROR "Incorrect usage. At least one LIBRARY should be provided.") ++ #endif() + + if(NOT "${IMP_LIBS_UNPARSED_ARGUMENTS}" STREQUAL "") + message(FATAL_ERROR "Incorrect usage. Extra arguments provided.") From 5a6407ebe03f4435c7cd6d394b5df896918dc477 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Mon, 3 Oct 2022 11:57:56 +0200 Subject: [PATCH 245/793] Update easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb b/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb index 6f5908e93ce..4619097f434 100644 --- a/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb +++ b/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb @@ -2,10 +2,8 @@ easyblock = 'PythonBundle' name = 'torchdata' version = '0.3.0' -local_python_version = '3.9.5' local_pytorch_version = '1.11.0' -versionsuffix = '-PyTorch-%s' % local_pytorch_version -local_pytorch_versionsuffix = '-foss-2021a-CUDA-11.3.1' +versionsuffix = '-PyTorch-%s-CUDA-%(cudaver)s' % local_pytorch_version homepage = 'https://github.com/pytorch/data' description = "TorchData is a prototype library of common modular data loading primitives for easily constructing flexible and performant data pipelines." From e04259dadf79a42c8eb92e006130a636c36a9d7d Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 3 Oct 2022 12:12:26 +0200 Subject: [PATCH 246/793] Add back the authors info --- easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb index caccb37e498..1a8eb57f361 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb @@ -1,3 +1,8 @@ +# updated to version 2.0.6, based on the previous 2.0.5 version +# J. Sassmannshausen (Imperial College London, UK) +# Alex Domingo (Vrije Universiteit Brussel, BE) +# Maxim Masterov (SURF, NL) + easyblock = 'ConfigureMake' name = 'CDO' From 37208d40c446fcbf1c2ebfd20b278d2b14b12c06 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 3 Oct 2022 12:13:41 +0200 Subject: [PATCH 247/793] Update easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb index 9c572a880b6..62a2ee5fb72 100644 --- a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('X11', '20220504'), ('pixman', '0.40.0'), ('libjpeg-turbo', '2.1.3'), From b6b443d22427f2003ad51dede120246c3576e6a8 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 3 Oct 2022 12:13:57 +0200 Subject: [PATCH 248/793] Update easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb index 62a2ee5fb72..1a7ea3b2793 100644 --- a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb @@ -30,7 +30,7 @@ dependencies = [ ('Mesa', '22.0.3'), ('libGLU', '9.0.2'), ('libglvnd', '1.4.0'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] osdependencies = [ From 6db598d1c0501c60521e744950da1343cd4154f4 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 3 Oct 2022 12:29:13 +0200 Subject: [PATCH 249/793] Remove duplicate config option --- .../easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb index 9c572a880b6..101ddc3ec47 100644 --- a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb @@ -43,7 +43,6 @@ configopts += "-DX11_Xau_LIB=$EBROOTX11/lib/libXau.%s " % SHLIB_EXT configopts += "-DX11_SM_LIB=$EBROOTX11/lib/libSM.%s " % SHLIB_EXT configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libICE.%s " % SHLIB_EXT configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libXext.%s " % SHLIB_EXT -configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libICE.%s " % SHLIB_EXT configopts += "-DX11_Pixman_LIB=$EBROOTPIXMAN/lib/libpixman-1.%s.0 " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_egl_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s " % SHLIB_EXT From ce120776e83ff72e910fe540daa623fb18724fdd Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 3 Oct 2022 12:46:17 +0200 Subject: [PATCH 250/793] Restore sanity check command --- easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb index 1a8eb57f361..8c3b14ced52 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb @@ -48,4 +48,6 @@ sanity_check_paths = { 'dirs': ['include'], } +sanity_check_commands = ["cdo --version 2>&1 | grep 'CDI library version : 2.0.6'"] + moduleclass = 'data' From dafb1e51c4a19b002095a72e5d064316e21e0966 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 3 Oct 2022 13:37:01 +0200 Subject: [PATCH 251/793] Update easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb Co-authored-by: Sam Moors --- easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb index 8c3b14ced52..2cca13754df 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb @@ -48,6 +48,6 @@ sanity_check_paths = { 'dirs': ['include'], } -sanity_check_commands = ["cdo --version 2>&1 | grep 'CDI library version : 2.0.6'"] +sanity_check_commands = ["cdo --version 2>&1 | grep 'CDI library version : %(version)s'"] moduleclass = 'data' From ec5d169c2af2ecd61ba695a7b70ad28785964213 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 3 Oct 2022 13:54:56 +0200 Subject: [PATCH 252/793] Remove duplicate in configopts --- .../easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb index b0e26d19a7b..2301a297350 100644 --- a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb @@ -42,7 +42,6 @@ configopts += "-DX11_X11_LIB=$EBROOTX11/lib/libX11.%s " % SHLIB_EXT configopts += "-DX11_Xau_LIB=$EBROOTX11/lib/libXau.%s " % SHLIB_EXT configopts += "-DX11_SM_LIB=$EBROOTX11/lib/libSM.%s " % SHLIB_EXT configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libICE.%s " % SHLIB_EXT -configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libXext.%s " % SHLIB_EXT configopts += "-DX11_Pixman_LIB=$EBROOTPIXMAN/lib/libpixman-1.%s.0 " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_egl_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s " % SHLIB_EXT From 4356dc7b95e3473949f09e4ff7ce4df472f6a203 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Oct 2022 14:02:15 +0200 Subject: [PATCH 253/793] adding easyconfigs: bcl-convert-4.0.3-2el7.x86_64.eb --- .../bcl-convert-4.0.3-2el7.x86_64.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.0.3-2el7.x86_64.eb diff --git a/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.0.3-2el7.x86_64.eb b/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.0.3-2el7.x86_64.eb new file mode 100644 index 00000000000..e06bf2fdde6 --- /dev/null +++ b/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.0.3-2el7.x86_64.eb @@ -0,0 +1,24 @@ +easyblock = 'Rpm' + +name = 'bcl-convert' +version = '4.0.3-2' +versionsuffix = 'el7.x86_64' + +homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html' +description = """The Illumina BCL Convert v4.0 is a standalone local software app that converts the + Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files.""" + +toolchain = SYSTEM + +source_urls = ['https://webdata.illumina.com/downloads/software/bcl-convert/'] +sources = ['bcl-convert-%(version)s.%(versionsuffix)s.rpm'] +checksums = ['be4f3d1d31cb36618f909cdbc0ed0fe70ef57a645e46b421b6e1a7f90c6c9430'] + +sanity_check_paths = { + 'files': ['usr/bin/bcl-convert'], + 'dirs': [], +} + +sanity_check_commands = ["bcl-convert --help"] + +moduleclass = 'bio' From 62cd95bc3503fb591710a07b60bffa8574639794 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 3 Oct 2022 14:19:21 +0200 Subject: [PATCH 254/793] Update easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb index 0feea67dfc8..6a2591a4271 100644 --- a/easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb @@ -21,6 +21,7 @@ checksums = ['f25ae0c26e911af1b5005292d4f56621879f74d6958b30741cf67d8b6feb2016'] builddependencies = [ ('Autotools', '20220317'), ('binutils', '2.38'), + ('pkgconf', '1.8.0'), ] dependencies = [ From 22db793612fc2dd55a90e968f595b868fcb94423 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 3 Oct 2022 15:34:46 +0200 Subject: [PATCH 255/793] add sanity check commands for f90wrap --- easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb b/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb index 55a22a746dc..d4004ab3cc4 100644 --- a/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb +++ b/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb @@ -30,4 +30,8 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], } +sanity_check_commands = [ + ('f90wrap', '--help'), +] + moduleclass = 'devel' From da7aea23602285dec3a6c89d165c569ea138e78f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 3 Oct 2022 15:39:45 +0200 Subject: [PATCH 256/793] CWIPI tools need at least 2 processes to run --- easybuild/easyconfigs/c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb b/easybuild/easyconfigs/c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb index f22001bd4fc..cdd531cbacf 100644 --- a/easybuild/easyconfigs/c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb @@ -26,6 +26,7 @@ _cwipi_bin = ['c_linear_coupling', 'c_surf_coupling_P1P0_P0P1', 'c_surf_coupling 'c_surf_sequential_coupling', 'c_vol_coupling_P1P1', 'c_vol_coupling_polyhedra_P1P1', 'fortran_plane_PiQj', 'fortran_surf_P1P1', 'fortran_surf_PiQj'] +# Only sanity check installation files as the tools of CWIPI need at least 2 MPI processes to run sanity_check_paths = { 'files': ['bin/%s' % x for x in _cwipi_bin] + ['lib/libcwp.a', 'lib/libcwp.%s' % SHLIB_EXT, 'lib/libcwpf.a', 'lib/libcwpf.%s' % SHLIB_EXT], From b0544535e41fc941a6399e244680c6c0c1ed65cb Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 3 Oct 2022 15:53:32 +0200 Subject: [PATCH 257/793] Add libaec as a dependency --- easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb index 742bdb55b84..1f313a6f013 100644 --- a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb @@ -23,6 +23,7 @@ dependencies = [ ('libjpeg-turbo', '2.1.3'), ('libpng', '1.6.37'), ('zlib', '1.2.12'), + ('libaec', '1.0.6'), ] # Python bindings are provided by a separate package 'eccodes-python' From 79a42c0fb12c286248df89dd35515191d7a5b35e Mon Sep 17 00:00:00 2001 From: rocky_build Date: Mon, 3 Oct 2022 14:13:13 -0400 Subject: [PATCH 258/793] adding easyconfigs: SRA-Toolkit-3.0.0-centos_linux64.eb --- .../SRA-Toolkit-3.0.0-centos_linux64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-centos_linux64.eb diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-centos_linux64.eb new file mode 100644 index 00000000000..fe5cd26a6c5 --- /dev/null +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-centos_linux64.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# @author: Adam Huffman - The Francis Crick Institute +# Based on work by npklein +# +# updated to version 3.0.0 by +# @author: Graham Derryberry + +easyblock = 'PackedBinary' + +name = 'SRA-Toolkit' +version = '3.0.0' +versionsuffix = '-centos_linux64' + +homepage = 'https://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software' +description = """The SRA Toolkit, and the source-code SRA System Development + Kit (SDK), will allow you to programmatically access data housed within SRA + and convert it from the SRA format""" + +toolchain = SYSTEM + +source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] +sources = ['sratoolkit.%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['89d11fc284e32d38b6639c551df6d658075cd268913f8ba2af65026e4a161dfe'] + +sanity_check_paths = { + 'files': ['bin/abi-load', 'bin/fastq-dump', 'bin/sff-load', 'bin/vdb-dump'], + 'dirs': [] +} + +moduleclass = 'bio' From dc46f4af3c1296788d00a5e4335e661be65dbc2a Mon Sep 17 00:00:00 2001 From: rocky_build Date: Mon, 3 Oct 2022 14:15:37 -0400 Subject: [PATCH 259/793] adding easyconfigs: file-5.41-GCCcore-11.3.0.eb --- .../f/file/file-5.41-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f65e804f400 --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.41' + +homepage = 'https://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] +checksums = ['13e532c7b364f7d57e23dfeea3147103150cb90593a57af86c10e4f6e411603f'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' From 48ef1a4fa69c9642aa2731cab32b689699f9cb66 Mon Sep 17 00:00:00 2001 From: robogast Date: Tue, 4 Oct 2022 10:50:18 +0200 Subject: [PATCH 260/793] Revert "Added exception for FFmpeg versions for Paraview and OpenFOAM" This reverts commit 2f0c9a08a15784d70cb130b7443805338b2eca1e. --- test/easyconfigs/easyconfigs.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index da15318ca58..0fb05afe876 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -493,8 +493,6 @@ def check_dep_vars(self, gen, dep, dep_vars): 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], - # ParaView 5.10.x requires FFmpeg 4.x - 'FFmpeg': [(r'4\.4\.', [r'ParaView-5\.10\.', 'OpenFOAM-v2206'])], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], From 9063cfbcf942d2e374bbf63f0a4d19ca2e1062da Mon Sep 17 00:00:00 2001 From: robogast Date: Tue, 4 Oct 2022 11:55:15 +0200 Subject: [PATCH 261/793] OpenCV FFMpeg back to 4.4.2 --- .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index 48f3aa8178e..25b509d1e9b 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -44,7 +44,7 @@ dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('zlib', '1.2.12'), - ('FFmpeg', '5.0.1'), + ('FFmpeg', '4.4.2'), ('freetype', '2.12.1'), ('HarfBuzz', '4.2.1'), ('libjpeg-turbo', '2.1.3'), From bf8be24d19496c1f0fcc0765ea4c78c400748ae2 Mon Sep 17 00:00:00 2001 From: satishk Date: Tue, 4 Oct 2022 12:43:48 +0200 Subject: [PATCH 262/793] adding easyconfigs: PETSc-3.17.4-foss-2022a.eb --- .../p/PETSc/PETSc-3.17.4-foss-2022a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb new file mode 100644 index 00000000000..058019a15f9 --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb @@ -0,0 +1,51 @@ +## +# Author: Robert Mijakovic +# Author: Jasper Grimm (UoY) +## +name = 'PETSc' +version = '3.17.4' + +homepage = 'https://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = [ + 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', + 'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'PETSc_ranlib-fix.patch', +] +checksums = [ + '99c127486722a3ffd95a268b4ceb0976cbf217926c681a9631bd7246eab8cb2a', # petsc-3.17.4.tar.gz + '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297', # PETSc_ranlib-fix.patch +] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost', '1.79.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.1'), + ('MUMPS', '5.5.1', '-metis'), + ('SuiteSparse', '5.13.0', '-METIS-5.1.0'), + ('Hypre', '2.25.0'), +] + +# enabling --with-mpi4py seems to be totally broken, leads to make errors like: +# No rule to make target 'mpi4py-build' +configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0 ' + +shared_libs = 1 + +# only required when building PETSc in a SLURM job environment +# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' +# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " + +moduleclass = 'numlib' From 5fecef6ec8b47119b9a3301e459955413184696a Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Tue, 4 Oct 2022 14:28:24 +0200 Subject: [PATCH 263/793] Specify CUDA version explicitly --- easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb b/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb index 4619097f434..29b133bc3d0 100644 --- a/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb +++ b/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb @@ -11,8 +11,9 @@ description = "TorchData is a prototype library of common modular data loading p toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('Python', local_python_version), - ('PyTorch', local_pytorch_version, local_pytorch_versionsuffix), + ('CUDA', '11.3.1', '', True) + ('Python', '3.9.5'), + ('PyTorch', local_pytorch_version, '-CUDA-%(cudaver)s'), ] sanity_pip_check = True From 4e9dc088db249774b60b4a26bebeba190e3a0565 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Tue, 4 Oct 2022 14:38:26 +0200 Subject: [PATCH 264/793] Update torchdata filename --- .../torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb} | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/t/{torchdata-0.3.0-PyTorch-1.11.0.eb => torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb} (70%) diff --git a/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb similarity index 70% rename from easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb rename to easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb index 29b133bc3d0..6f5908e93ce 100644 --- a/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb +++ b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb @@ -2,8 +2,10 @@ easyblock = 'PythonBundle' name = 'torchdata' version = '0.3.0' +local_python_version = '3.9.5' local_pytorch_version = '1.11.0' -versionsuffix = '-PyTorch-%s-CUDA-%(cudaver)s' % local_pytorch_version +versionsuffix = '-PyTorch-%s' % local_pytorch_version +local_pytorch_versionsuffix = '-foss-2021a-CUDA-11.3.1' homepage = 'https://github.com/pytorch/data' description = "TorchData is a prototype library of common modular data loading primitives for easily constructing flexible and performant data pipelines." @@ -11,9 +13,8 @@ description = "TorchData is a prototype library of common modular data loading p toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True) - ('Python', '3.9.5'), - ('PyTorch', local_pytorch_version, '-CUDA-%(cudaver)s'), + ('Python', local_python_version), + ('PyTorch', local_pytorch_version, local_pytorch_versionsuffix), ] sanity_pip_check = True From 6d9ccdf10ecae21a4d75091149ca48a83ef901e9 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Tue, 4 Oct 2022 16:50:26 +0200 Subject: [PATCH 265/793] Revert changes that slipped with rename --- ...0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb new file mode 100644 index 00000000000..ec87e0cccd0 --- /dev/null +++ b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'torchdata' +version = '0.3.0' +local_pytorch_version = '1.11.0' +versionsuffix = '-PyTorch-' + local_pytorch_version + '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/pytorch/data' +description = "TorchData is a prototype library of common modular data loading primitives for easily constructing flexible and performant data pipelines." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('PyTorch', local_pytorch_version, '-CUDA-%(cudaver)s'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pytorch/data/archive'], + }), +] + +moduleclass = 'lib' From 6158fc35374138734d455fc8fa35203962a7b9ac Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Tue, 4 Oct 2022 16:52:34 +0200 Subject: [PATCH 266/793] Delete torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb --- ...rchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb | 30 ------------------- 1 file changed, 30 deletions(-) delete mode 100644 easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb diff --git a/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb deleted file mode 100644 index 6f5908e93ce..00000000000 --- a/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'torchdata' -version = '0.3.0' -local_python_version = '3.9.5' -local_pytorch_version = '1.11.0' -versionsuffix = '-PyTorch-%s' % local_pytorch_version -local_pytorch_versionsuffix = '-foss-2021a-CUDA-11.3.1' - -homepage = 'https://github.com/pytorch/data' -description = "TorchData is a prototype library of common modular data loading primitives for easily constructing flexible and performant data pipelines." - -toolchain = {'name': 'foss', 'version': '2021a'} - -dependencies = [ - ('Python', local_python_version), - ('PyTorch', local_pytorch_version, local_pytorch_versionsuffix), -] - -sanity_pip_check = True -use_pip = True - -exts_list = [ - (name, version, { - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/pytorch/data/archive'], - }), -] - -moduleclass = 'lib' From 288ddd3205bc8191aef50afea11eb77c4831eb9d Mon Sep 17 00:00:00 2001 From: rocky_build Date: Tue, 4 Oct 2022 16:21:45 -0400 Subject: [PATCH 267/793] Updated for file version 5.43 as requested --- .../f/file/file-5.43-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1128c37d6ac --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.43' + +homepage = 'https://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] +checksums = ['8c8015e91ae0e8d0321d94c78239892ef9dbc70c4ade0008c0e95894abfb1991'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' From d208e43d9c247055273d3f46d3a6aa49c4d1cf23 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 5 Oct 2022 08:53:03 +0200 Subject: [PATCH 268/793] adding easyconfigs: AMS-2022.102-iimpi-2021b-intelmpi.eb --- .../AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb diff --git a/easybuild/easyconfigs/a/AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb b/easybuild/easyconfigs/a/AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb new file mode 100644 index 00000000000..466df5f61ac --- /dev/null +++ b/easybuild/easyconfigs/a/AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb @@ -0,0 +1,41 @@ +easyblock = 'Tarball' + +name = 'AMS' +version = '2022.102' +versionsuffix = '-intelmpi' + +homepage = 'https://www.scm.com/amsterdam-modeling-suite/' +description = """ +The Amsterdam Modeling Suite (AMS) provides a comprehensive set of modules for computational chemistry and materials +science, from quantum mechanics to fluid thermodynamics. +""" + +toolchain = {'name': 'iimpi', 'version': '2021b'} + +sources = ['ams%(version)s.pc64_linux.intelmpi.bin.tgz'] +checksums = ['a1791e0ea17426199a8c82668858a509debd3a6b99adc107e452084095d72344'] + +dependencies = [('libGLU', '9.0.2')] + +keepsymlinks = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['atomicdata', 'bin', 'examples'], +} + +# check if license file is installed +# sanity_check_commands = ['dirac check'] + +modextrapaths = { + 'AMSHOME': '', + 'AMSBIN': 'bin', + 'AMSRESOURCES': 'atomicdata', +} + +modloadmsg = """These environment variables need to be defined before using AMS: + * $SCMLICENSE: path to AMS license file + * $SCM_TMPDIR: path to user scratch directory +""" + +moduleclass = 'chem' From 4ceed01f1b3f80c735890e720da178292d253ae0 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 5 Oct 2022 12:23:52 +0200 Subject: [PATCH 269/793] Fix test_model_dump and test_cpp_extensions_aot* --- .../PyTorch-1.10.0_fix-test-model_dump.patch | 36 +++++++++++++++++++ .../PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 13 +++---- ...Torch-1.11.0_install-vsx-vec-headers.patch | 10 +++++- 3 files changed, 49 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-model_dump.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-model_dump.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-model_dump.patch new file mode 100644 index 00000000000..1891c93e93f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-model_dump.patch @@ -0,0 +1,36 @@ +From https://github.com/pytorch/pytorch/pull/84744 + +Author: Alexander Grund (TU Dresden) + +From 4d99f72dcf71bffa7ff4275750cb86d872ac653f Mon Sep 17 00:00:00 2001 +From: Alexander Grund +Date: Fri, 9 Sep 2022 11:10:05 +0200 +Subject: [PATCH] Fix failing test_model_dump due to empty file + +The `torch.jit.save` call on a file object may not actually write the +data to disk due to buffering. The call to `model_dump.main` on that +file will when fail with an error like + +> zipfile.BadZipFile: File is not a zip file + +Inspecting the file confirms that it is either empty (usually) or +incomplete (possible). + +Fix this by flushing the file after saving the model. +--- + test/test_model_dump.py | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/test/test_model_dump.py b/test/test_model_dump.py +index a8add0e2cd923..3c682b6ce6805 100644 +--- a/test/test_model_dump.py ++++ b/test/test_model_dump.py +@@ -131,6 +131,8 @@ def test_main(self): + + with tempfile.NamedTemporaryFile() as tf: + torch.jit.save(torch.jit.script(SimpleModel()), tf) ++ # Actually write contents to disk so we can read it below ++ tf.flush() + + stdout = io.StringIO() + torch.utils.model_dump.main( diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index dfd9742736f..2192c824b84 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -17,6 +17,7 @@ patches = [ 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', 'PyTorch-1.10.0_fix-XNNPACK-tests.patch', 'PyTorch-1.10.0_skip_cmake_rpath.patch', @@ -43,6 +44,8 @@ checksums = [ 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', # PyTorch-1.10.0_fix-vsx-vector-functions.patch '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', # PyTorch-1.10.0_fix-XNNPACK-tests.patch @@ -66,7 +69,7 @@ checksums = [ '26e179a4f6f57e49209092612ae5f5cd8c03fd2ca84566ba0244eabefc3736ba', # PyTorch-1.11.0_increase-tolerance-test_ops.patch 'ceec745c68a405bba79efb4dc61c662ca84eb950cd0163c7104330f4bf614cf5', - 'f765093765c07ae488e15b33184709bd1e9c799f6640695be71dca3df02f83c3', # PyTorch-1.11.0_install-vsx-vec-headers.patch + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch '8eaca92d64fcadb0552d28e9c7ea5c4bc669d2fe33004e45a3519ce8d0d136a2', # PyTorch-1.11.0_skip_failing_ops_tests.patch ] @@ -108,16 +111,8 @@ excluded_tests = { # Bad tests: https://github.com/pytorch/pytorch/issues/60260 'distributed/elastic/utils/distributed_test', 'distributed/elastic/multiprocessing/api_test', - # These tests fail on A10s at the very least, they time out forever no matter how long the timeout is. - # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html - # 'distributed/test_distributed_fork', - 'distributed/test_distributed_spawn', # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 'test_optim', - # Test from this suite timeout often. The process group backend is deprecated anyway - # 'distributed/rpc/test_process_group_agent', - # This test fails constently when run as part of the test suite, but succeeds when run interactively - 'test_model_dump', # These tests appear flaky, possibly related to number of GPUs that are used 'distributed/fsdp/test_fsdp_memory', 'distributed/fsdp/test_fsdp_overlap', diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_install-vsx-vec-headers.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_install-vsx-vec-headers.patch index a3da950d7d9..628a59ec0a2 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_install-vsx-vec-headers.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_install-vsx-vec-headers.patch @@ -17,7 +17,7 @@ index 5710eca27c..0cd15c2ad2 100644 file(GLOB cuda_h "cuda/*.h" "cuda/detail/*.h" "cuda/*.cuh" "cuda/detail/*.cuh") file(GLOB cuda_cpp "cuda/*.cpp" "cuda/detail/*.cpp") diff --git a/setup.py b/setup.py -index f1ebab7391..c73b6df665 100644 +index f1ebab7391..92de0367ac 100644 --- a/setup.py +++ b/setup.py @@ -942,6 +942,7 @@ if __name__ == '__main__': @@ -28,3 +28,11 @@ index f1ebab7391..c73b6df665 100644 'include/ATen/cpu/vec/vec512/*.h', 'include/ATen/cpu/vec/*.h', 'include/ATen/core/*.h', +@@ -1043,6 +1044,7 @@ if __name__ == '__main__': + 'include/THH/*.cuh', + 'include/THH/*.h*', + 'include/THH/generic/*.h', ++ 'include/sleef.h', + 'share/cmake/ATen/*.cmake', + 'share/cmake/Caffe2/*.cmake', + 'share/cmake/Caffe2/public/*.cmake', From 5419c788c5bac42bb934104a9c716a6f7e1351b3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 5 Oct 2022 13:04:27 +0200 Subject: [PATCH 270/793] Reduce max GPUs to 4 for fsdp test --- .../p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch | 9 +++++---- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 2192c824b84..32f4323e49d 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -57,7 +57,7 @@ checksums = [ 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', # PyTorch-1.11.0_fix-attention_cpp-compilation.patch '84214fcc7e30cf70659a7c3bd70bf11e73d58fd4f7fff2c233e3225619b0e42c', - '69546ab7371667370eb52b8e46fee7f39deff493fc12cfdcc6f49dde69848f8d', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + 'ca48576014bceb8c6c0d06cbab666be96cb44804e0215f5c025397a75a675bab', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch '9a04f4285b800dad8a00c3014af0a9713d40d5dd35d10931c7c0da4e89c558e9', # PyTorch-1.11.0_fix_sharded_imports.patch '21fc678febcdfbb9dabd72235be23cd392044e9a954f6580d15b530e1f69dcc1', # PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch index bd860be61f7..401d0865d49 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch @@ -1,5 +1,6 @@ -The test fails on a node with more than 5 GPUs. -Hence limit the world_size to 5 +The test fails on a node with more than 5 V100 GPUs or more than 4 A100 GPUs. +Hence limit the world_size to 4 +See https://github.com/pytorch/pytorch/issues/78975 Author: Alexander Grund (TU Dresden) @@ -13,8 +14,8 @@ index eea03bea3d..d3a4bb8257 100644 + @property + def world_size(self): -+ # Test fails due to inaccuracies when using more than 5 GPUs -+ return min(5, super().world_size) ++ # Test fails due to inaccuracies when using more than 4 GPUs ++ return min(4, super().world_size) + @skip_if_lt_x_gpu(2) @parametrize( From 57a9f46f2b343c94660c0f149cb22266b4bd6767 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Oct 2022 14:42:43 +0200 Subject: [PATCH 271/793] adding easyconfigs: biogeme-3.2.10-foss-2022a.eb --- .../b/biogeme/biogeme-3.2.10-foss-2022a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/b/biogeme/biogeme-3.2.10-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/biogeme/biogeme-3.2.10-foss-2022a.eb b/easybuild/easyconfigs/b/biogeme/biogeme-3.2.10-foss-2022a.eb new file mode 100644 index 00000000000..efe335afb48 --- /dev/null +++ b/easybuild/easyconfigs/b/biogeme/biogeme-3.2.10-foss-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'biogeme' +version = '3.2.10' + +homepage = 'https://pypi.python.org/pypi/biogeme' +description = """Biogeme is a open source Python package designed for +the maximum likelihood estimation of parametric models in general, +with a special emphasis on discrete choice models.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('Unidecode', '1.3.6', { + 'checksums': ['fed09cf0be8cf415b391642c2a5addfc72194407caee4f98719e40ec2a72b830'], + }), + (name, version, { + 'checksums': ['60b865e54f4c5ed22eb4a13dc277b72a2fec13e22d243a6f97d05fe7df984d63'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From 7a17935b7e9cade82bbb4f820e87cc62297e897b Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Wed, 5 Oct 2022 14:14:45 +0100 Subject: [PATCH 272/793] Update easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb Co-authored-by: Sam Moors --- easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb index 5598e22e1d9..2d7a7d90220 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb @@ -18,7 +18,9 @@ dependencies = [ ] osdependencies = [ - 'perl-Thread-Queue', + # Thread::Queue is already available by default in Ubuntu + # providing a package that is automatically installed as workaround + ('perl-Thread-Queue', 'debianutils'), ] preconfigopts = "export PERL='/usr/bin/env perl' && " From d877bb14838740f7a6be1a636077463a8d5f2a34 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Oct 2022 17:09:00 +0200 Subject: [PATCH 273/793] adding easyconfigs: openpyxl-3.0.10-GCCcore-11.3.0.eb --- .../openpyxl-3.0.10-GCCcore-11.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.10-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.10-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..bc8a63f9df3 --- /dev/null +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.10-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'openpyxl' +version = '3.0.10' + +homepage = 'https://openpyxl.readthedocs.io' +description = "A Python library to read/write Excel 2010 xlsx/xlsm files" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('lxml', '4.9.1'), + ('Pillow', '9.1.1'), +] + +use_pip = True + +exts_list = [ + ('et_xmlfile', '1.1.0', { + 'checksums': ['8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c'], + }), + ('jdcal', '1.4.1', { + 'checksums': ['472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8'], + }), + (name, version, { + 'checksums': ['e47805627aebcf860edb4edf7987b1309c1b3632f3750538ed962bbcc3bd7449'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' From 9ed5dc61975ade0e7786f7b7faa6b3412cb544e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Oct 2022 20:08:26 +0200 Subject: [PATCH 274/793] adding easyconfigs: sympy-1.11.1-foss-2022a.eb --- .../s/sympy/sympy-1.11.1-foss-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb new file mode 100644 index 00000000000..50b43150f3e --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.11.1' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e32380dce63cb7c0108ed525570092fd45168bdae2faa17e528221ef72e88658'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('gmpy2', '2.1.2'), +] + +download_dep_fail = True +use_pip = True + +# fix broken test, sympy doesn't actually use gmpy2's Decimal anywhere; +# see https://github.com/sympy/sympy/issues/23061#issuecomment-1052424896 +#pretestopts = """sed -i "s@Decimal('0.6')@'0.6'@g" sympy/external/tests/test_pythonmpq.py && """ +runtest = 'python setup.py test' + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/isympy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], +} + +sanity_check_commands = ["isympy --help"] + +moduleclass = 'math' From 32e6ae03357bbfd0ab6922c3efffd6a127e6bfbf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Oct 2022 08:51:58 +0200 Subject: [PATCH 275/793] remove commented out pretestopts in sympy 1.11.1 easyconfig --- easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb index 50b43150f3e..9e54ecf5751 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb @@ -23,9 +23,6 @@ dependencies = [ download_dep_fail = True use_pip = True -# fix broken test, sympy doesn't actually use gmpy2's Decimal anywhere; -# see https://github.com/sympy/sympy/issues/23061#issuecomment-1052424896 -#pretestopts = """sed -i "s@Decimal('0.6')@'0.6'@g" sympy/external/tests/test_pythonmpq.py && """ runtest = 'python setup.py test' sanity_pip_check = True From a9652df05c1ab4fb4447a2e772535549df04b842 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Oct 2022 09:59:17 +0200 Subject: [PATCH 276/793] adding easyconfigs: OpenMM-7.7.0-foss-2021a.eb --- .../o/OpenMM/OpenMM-7.7.0-foss-2021a.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb new file mode 100644 index 00000000000..400ea7aa3b7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb @@ -0,0 +1,57 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.7.0' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['51970779b8dc639ea192e9c61c67f70189aa294575acb915e14be1670a586c25'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('SWIG', '4.0.2'), +] + +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/__init__.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m openmm.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From 0bb76f4d3675b03ef7163499aa027dec449ced36 Mon Sep 17 00:00:00 2001 From: robogast Date: Thu, 6 Oct 2022 10:09:28 +0200 Subject: [PATCH 277/793] Added Imath checksum --- easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb index b4f0f0223ca..a85a08e980d 100644 --- a/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb @@ -19,6 +19,7 @@ sources = [{ 'tag': 'v%(version)s', }, }] +checksums = ['5167b1441e4eaeb0f238faaac02c52ecd89940e7c77a3ed0c7356fb8934db570'] builddependencies = [ ('binutils', '2.38'), From 27eabe4cbea5923f42c791790b705589a363b548 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Oct 2022 10:57:40 +0200 Subject: [PATCH 278/793] adding easyconfigs: MDTraj-1.9.7-intel-2022a.eb --- .../m/MDTraj/MDTraj-1.9.7-intel-2022a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-intel-2022a.eb diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-intel-2022a.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-intel-2022a.eb new file mode 100644 index 00000000000..d94d68ccbdc --- /dev/null +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-intel-2022a.eb @@ -0,0 +1,45 @@ +# Updated: Pavel Grochal (INUITS) + +easyblock = 'PythonBundle' + +name = 'MDTraj' +version = '1.9.7' + +homepage = 'https://mdtraj.org' +description = "Read, write and analyze MD trajectories with only a few lines of Python code." + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('zlib', '1.2.12'), +] + +use_pip = True +exts_list = [ + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('pymbar', '3.1', { + # pymbar 3.1 is not available via PyPI, see https://github.com/choderalab/pymbar/issues/475 + 'source_urls': ['https://github.com/choderalab/pymbar/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['7a996e5d3fd8143378f9e18662483446a4a2fe7e57917511e96beb6b07fd6232'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('mdtraj', version, { + 'checksums': ['8a3309d2ef6ddb1023dcf48300d5df9b190469b63f69af9d55490bc4799d3757'], + }), +] + +# The unit tests of MDTraj are a pain to get to work: they require +# a massive number of extra dependencies. See +# https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml + +sanity_pip_check = True + +moduleclass = 'chem' From 632caa0e3ddfdfeebafa7c3d1e5ad84a434c6c70 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Oct 2022 10:57:52 +0200 Subject: [PATCH 279/793] adding easyconfigs: OpenMM-7.7.0-foss-2022a.eb --- .../o/OpenMM/OpenMM-7.7.0-foss-2022a.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2022a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2022a.eb new file mode 100644 index 00000000000..7dbd4dd5249 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2022a.eb @@ -0,0 +1,60 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.7.0' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['51970779b8dc639ea192e9c61c67f70189aa294575acb915e14be1670a586c25'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Doxygen', '1.9.4'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('SWIG', '4.0.2'), +] + +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + "python -c 'import simtk.openmm'", + "python -m openmm.testInstallation", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From 3a1ffc81f8e300d858c00b996f1e473ac8d5828b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Oct 2022 11:14:18 +0200 Subject: [PATCH 280/793] adding easyconfigs: MMseqs2-13-45111-gompi-2021a.eb --- .../m/MMseqs2/MMseqs2-13-45111-gompi-2021a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2021a.eb diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2021a.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2021a.eb new file mode 100644 index 00000000000..79c3a69f62c --- /dev/null +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2021a.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'MMseqs2' +version = '13-45111' + +homepage = 'https://mmseqs.com' +description = "MMseqs2: ultra fast and sensitive search and clustering suite" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +github_account = 'soedinglab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['6444bb682ebf5ced54b2eda7a301fa3e933c2a28b7661f96ef5bdab1d53695a2'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [('bzip2', '1.0.8')] + +sanity_check_paths = { + 'files': ['bin/mmseqs'], + 'dirs': [], +} + +sanity_check_commands = ["mmseqs --help"] + +moduleclass = 'bio' From 3becb6b4c1dde38a1adc73727e21fcb23a09a882 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 6 Oct 2022 11:20:33 +0200 Subject: [PATCH 281/793] use Intel MPI from EasyBuild toolchain in AMS (#16363) --- .../easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb | 5 +++++ .../easyconfigs/a/AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb b/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb index 0e032547e34..0d9ba4e2d49 100644 --- a/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb +++ b/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb @@ -30,6 +30,11 @@ modextrapaths = { 'AMSRESOURCES': 'atomicdata', } +modextravars = { + # use Intel MPI from EasyBuild + 'SCM_USE_LOCAL_IMPI': '1', +} + modloadmsg = """These environment variables need to be defined before using AMS: * $SCMLICENSE: path to AMS license file * $SCM_TMPDIR: path to user scratch directory diff --git a/easybuild/easyconfigs/a/AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb b/easybuild/easyconfigs/a/AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb index 466df5f61ac..fade2732728 100644 --- a/easybuild/easyconfigs/a/AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb +++ b/easybuild/easyconfigs/a/AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb @@ -33,6 +33,11 @@ modextrapaths = { 'AMSRESOURCES': 'atomicdata', } +modextravars = { + # use Intel MPI from EasyBuild + 'SCM_USE_LOCAL_IMPI': '1', +} + modloadmsg = """These environment variables need to be defined before using AMS: * $SCMLICENSE: path to AMS license file * $SCM_TMPDIR: path to user scratch directory From 5b9dae8afecda66984041eaccb942c7c594a3fd3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Oct 2022 11:25:50 +0200 Subject: [PATCH 282/793] adding easyconfigs: MDTraj-1.9.7-foss-2022a.eb --- .../m/MDTraj/MDTraj-1.9.7-foss-2022a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2022a.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2022a.eb new file mode 100644 index 00000000000..f6dd1f827d5 --- /dev/null +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2022a.eb @@ -0,0 +1,45 @@ +# Updated: Pavel Grochal (INUITS) + +easyblock = 'PythonBundle' + +name = 'MDTraj' +version = '1.9.7' + +homepage = 'https://mdtraj.org' +description = "Read, write and analyze MD trajectories with only a few lines of Python code." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('zlib', '1.2.12'), +] + +use_pip = True +exts_list = [ + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('pymbar', '3.1', { + # pymbar 3.1 is not available via PyPI, see https://github.com/choderalab/pymbar/issues/475 + 'source_urls': ['https://github.com/choderalab/pymbar/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['7a996e5d3fd8143378f9e18662483446a4a2fe7e57917511e96beb6b07fd6232'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('mdtraj', version, { + 'checksums': ['8a3309d2ef6ddb1023dcf48300d5df9b190469b63f69af9d55490bc4799d3757'], + }), +] + +# The unit tests of MDTraj are a pain to get to work: they require +# a massive number of extra dependencies. See +# https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml + +sanity_pip_check = True + +moduleclass = 'chem' From 494d36e8566d6d2e70835a73994d4f7bcebe023c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Oct 2022 11:26:31 +0200 Subject: [PATCH 283/793] adding easyconfigs: MDTraj-1.9.7-foss-2021a.eb --- .../m/MDTraj/MDTraj-1.9.7-foss-2021a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2021a.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2021a.eb new file mode 100644 index 00000000000..acc6867ceed --- /dev/null +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2021a.eb @@ -0,0 +1,45 @@ +# Updated: Pavel Grochal (INUITS) + +easyblock = 'PythonBundle' + +name = 'MDTraj' +version = '1.9.7' + +homepage = 'https://mdtraj.org' +description = "Read, write and analyze MD trajectories with only a few lines of Python code." + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('zlib', '1.2.11'), +] + +use_pip = True +exts_list = [ + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('pymbar', '3.1', { + # pymbar 3.1 is not available via PyPI, see https://github.com/choderalab/pymbar/issues/475 + 'source_urls': ['https://github.com/choderalab/pymbar/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['7a996e5d3fd8143378f9e18662483446a4a2fe7e57917511e96beb6b07fd6232'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('mdtraj', version, { + 'checksums': ['8a3309d2ef6ddb1023dcf48300d5df9b190469b63f69af9d55490bc4799d3757'], + }), +] + +# The unit tests of MDTraj are a pain to get to work: they require +# a massive number of extra dependencies. See +# https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml + +sanity_pip_check = True + +moduleclass = 'chem' From 921406cbde39c082cd922df644fe4c09b7578b21 Mon Sep 17 00:00:00 2001 From: scimerman <80223690+scimerman@users.noreply.github.com> Date: Thu, 6 Oct 2022 14:40:47 +0200 Subject: [PATCH 284/793] Create OpenSSL-1.1.1q-GCCcore-10.3.0.eb A latest version of OpenSSL with GCC 10.3.0 --- .../OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..25d87d8dddb --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb @@ -0,0 +1,25 @@ +name = 'OpenSSL' +version = '1.1.1q' + +homepage = 'https://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.openssl.org/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d7939ce614029cdff0b6c20f0e2e5703158a489a72b2507b8bd51bf8c8fd10ca'] + +dependencies = [('zlib', '1.2.11')] + +builddependencies = [ + ('Perl', '5.32.1'), + ('binutils', '2.36.1'), +] + +runtest = 'test' + +moduleclass = 'system' From 3f672f474e9b751042cba9b859280d1050a66f33 Mon Sep 17 00:00:00 2001 From: rocky_build Date: Thu, 6 Oct 2022 09:44:42 -0400 Subject: [PATCH 285/793] Drop old 5.41 version --- .../f/file/file-5.41-GCCcore-11.3.0.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.3.0.eb deleted file mode 100644 index f65e804f400..00000000000 --- a/easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'file' -version = '5.41' - -homepage = 'https://www.darwinsys.com/file/' -description = """The file command is 'a file type guesser', that is, a command-line tool - that tells you in words what kind of data a file contains.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['ftp://ftp.astron.com/pub/file/'] -sources = [SOURCE_TAR_GZ] -checksums = ['13e532c7b364f7d57e23dfeea3147103150cb90593a57af86c10e4f6e411603f'] - -builddependencies = [ - ('Autotools', '20220317'), - ('binutils', '2.38'), -] - -preconfigopts = "autoreconf -f -i && " - -sanity_check_paths = { - 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], - 'dirs': ['share'] -} - -moduleclass = 'system' From e6c111837b8212654199b0162d1f24821de92c0e Mon Sep 17 00:00:00 2001 From: robogast Date: Thu, 6 Oct 2022 15:56:00 +0200 Subject: [PATCH 286/793] Added OpenJPEG dep to OpenCV --- .../OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6c76dae7c5d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,47 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchenson Cancer Research Center Seattle WA +easyblock = 'CMakeMake' + +name = 'OpenJPEG' +version = '2.5.0' + +homepage = 'https://www.openjpeg.org/' +description = """OpenJPEG is an open-source JPEG 2000 codec written in + C language. It has been developed in order to promote the use of JPEG 2000, + a still-image compression standard from the Joint Photographic Experts Group + (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as + a JPEG 2000 Reference Software.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/uclouvain/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0333806d6adecc6f7a91243b2b839ff4d2053823634d4f6ed7a59bc87409122a'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] +# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), +] + +sanity_check_paths = { + 'files': [ + 'bin/opj_compress', + 'bin/opj_decompress', + 'bin/opj_dump', + 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', + 'lib/libopenjp2.%s' % SHLIB_EXT + ], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' From f5cd89f0bfe6fab34a0b2d954e3b0337319d6a04 Mon Sep 17 00:00:00 2001 From: robogast Date: Thu, 6 Oct 2022 16:07:32 +0200 Subject: [PATCH 287/793] Actually added OpenJPEG dep to OpenCV --- .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index 25b509d1e9b..3676ebf7da8 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -48,6 +48,7 @@ dependencies = [ ('freetype', '2.12.1'), ('HarfBuzz', '4.2.1'), ('libjpeg-turbo', '2.1.3'), + ('OpenJPEG', '2.5.0'), ('libpng', '1.6.37'), ('LibTIFF', '4.3.0'), ('libwebp', '1.2.4'), From e85a350aeb28ba6501b4f5674430b996de6120e7 Mon Sep 17 00:00:00 2001 From: robogast Date: Thu, 6 Oct 2022 16:09:16 +0200 Subject: [PATCH 288/793] moved OpenJPEG dep to PR #16276 --- .../OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb | 47 ------------------- 1 file changed, 47 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb deleted file mode 100644 index 6c76dae7c5d..00000000000 --- a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb +++ /dev/null @@ -1,47 +0,0 @@ -# easybuild easyconfig -# -# John Dey jfdey@fredhutch.org -# -# Fred Hutchenson Cancer Research Center Seattle WA -easyblock = 'CMakeMake' - -name = 'OpenJPEG' -version = '2.5.0' - -homepage = 'https://www.openjpeg.org/' -description = """OpenJPEG is an open-source JPEG 2000 codec written in - C language. It has been developed in order to promote the use of JPEG 2000, - a still-image compression standard from the Joint Photographic Experts Group - (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as - a JPEG 2000 Reference Software.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/uclouvain/%(namelower)s/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['0333806d6adecc6f7a91243b2b839ff4d2053823634d4f6ed7a59bc87409122a'] - -builddependencies = [ - ('binutils', '2.38'), - ('CMake', '3.23.1'), -] -# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. -dependencies = [ - ('zlib', '1.2.12'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.3.0'), -] - -sanity_check_paths = { - 'files': [ - 'bin/opj_compress', - 'bin/opj_decompress', - 'bin/opj_dump', - 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', - 'lib/libopenjp2.%s' % SHLIB_EXT - ], - 'dirs': ['bin', 'include', 'lib'], -} - -moduleclass = 'lib' From 986e4079fd1502bcb7046ab1ff587994c216063c Mon Sep 17 00:00:00 2001 From: robogast Date: Thu, 6 Oct 2022 16:15:26 +0200 Subject: [PATCH 289/793] Removed OpenJPEG header comment --- .../easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb index 6c76dae7c5d..a3ccd969fc7 100644 --- a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb @@ -1,8 +1,3 @@ -# easybuild easyconfig -# -# John Dey jfdey@fredhutch.org -# -# Fred Hutchenson Cancer Research Center Seattle WA easyblock = 'CMakeMake' name = 'OpenJPEG' From a1e42d736151b3e26075a70aeeca85905aa29661 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Thu, 6 Oct 2022 16:36:23 +0200 Subject: [PATCH 290/793] Inject checksum --- .../torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb index ec87e0cccd0..9c2141e4169 100644 --- a/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb @@ -23,6 +23,7 @@ exts_list = [ (name, version, { 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/pytorch/data/archive'], + 'checksums': ['ac36188bf133cf5f1041a28ccb3ee82ba52d4b5d99617be37d64d740acd6cfd4'], }), ] From b92974d8bff1ac48ee3e79a45392479c50b3d07a Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Thu, 6 Oct 2022 16:58:34 +0200 Subject: [PATCH 291/793] Adapt .eb from torchvision 0.11 --- ...0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb new file mode 100644 index 00000000000..ca3b8eac2e9 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb @@ -0,0 +1,24 @@ +name = 'torchvision' +version = '0.12.0' +local_pytorch_version = '1.11.0' +versionsuffix = '-PyTorch-' + local_pytorch_version + '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['99e6d3d304184895ff4f6152e2d2ec1cbec89b3e057d9c940ae0125546b04e91'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('Pillow-SIMD', '8.2.0'), + ('PyTorch', local_pytorch_version, '-CUDA-%(cudaver)s'), +] + +moduleclass = 'vis' From eb1691f0f7f4abe3d751888cae1a9e09bb1dc953 Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Thu, 24 Mar 2022 14:46:35 -0400 Subject: [PATCH 292/793] Update triqs and application packages to version 3.1.0 --- .../TRIQS-cthyb-3.1.0-foss-2021b.eb | 69 ++++++++++++++++++ .../TRIQS-dft_tools-3.1.0-foss-2021b.eb | 70 +++++++++++++++++++ .../TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb | 70 +++++++++++++++++++ .../t/TRIQS/TRIQS-3.1.0-foss-2021b.eb | 70 +++++++++++++++++++ 4 files changed, 279 insertions(+) create mode 100644 easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb new file mode 100644 index 00000000000..19e698e99bd --- /dev/null +++ b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb @@ -0,0 +1,69 @@ +easyblock = 'CMakeMake' + +name = 'TRIQS-cthyb' +version = '3.1.0' + +homepage = 'https://triqs.github.io/cthyb/' +description = """ + TRIQS (Toolbox for Research on Interacting Quantum Systems) is a + scientific project providing a set of C++ and Python libraries to + develop new tools for the study of interacting quantum systems. + + cthyb = continuous-time hybridisation-expansion quantum Monte Carlo + + The TRIQS-based hybridization-expansion solver allows to solve the + generic problem of a quantum impurity embedded in a conduction bath + for an arbitrary local interaction vertex. The “impurity” can be any + set of orbitals, on one or several atoms. +""" + +docurls = ['https://triqs.github.io/cthyb/%(version_major_minor)s.x/'] +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/TRIQS/cthyb/releases/download/%(version)s/'] +sources = ['cthyb-%(version)s.tar.gz'] +checksums = ['8d6d2c4d5b3928d062b72fad4ea9df9aae198e39dd9c1fd3cc5dc34a5019acc0'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Boost', '1.77.0'), + ('Clang', '13.0.1'), + ('Clang-Python-bindings', '13.0.1'), + ('GMP', '6.2.1'), + ('HDF5', '1.10.7'), + ('Mako', '1.1.4'), + ('TRIQS', '3.1.0'), + ('NFFT', '3.5.2') +] + +builddependencies = [ + ('CMake', '3.22.1') +] + +separate_build_dir = True + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libtriqs_cthyb_c.a'], + 'dirs': ['include', 'include/triqs_cthyb', 'lib', + 'lib/python%(pyshortver)s/site-packages', 'share'], +} + +sanity_check_commands = ["python -c 'import triqs_cthyb'"] + +modextrapaths = { + 'CPLUS_INCLUDE_PATH': 'include', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CMAKE_PREFIX_PATH': 'lib/cmake/triqs_cthyb', +} +modextravars = { + 'TRIQS_CTHYB_ROOT': '%(installdir)s', + 'TRIQS_CTHYB_VERSION': '%(version)s', +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb new file mode 100644 index 00000000000..abb330f2b46 --- /dev/null +++ b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb @@ -0,0 +1,70 @@ +easyblock = 'CMakeMake' + +name = 'TRIQS-dft_tools' +version = '3.1.0' + +homepage = 'https://triqs.github.io/dft_tools/' +description = """ + TRIQS (Toolbox for Research on Interacting Quantum Systems) is a + scientific project providing a set of C++ and Python libraries to + develop new tools for the study of interacting quantum systems. + + This TRIQS-based-based application is aimed at ab-initio calculations + for correlated materials, combining realistic DFT band-structure calculation + with the dynamical mean-field theory. Together with the necessary tools to + perform the DMFT self-consistency loop for realistic multi-band problems, + the package provides a full-fledged charge self-consistent interface to the + Wien2K package. In addition, if Wien2k is not available, it provides a generic + interface for one-shot DFT+DMFT calculations, where only the single-particle + Hamiltonian in orbital space has to be provided. +""" + +docurls = ['https://triqs.github.io/dft_tools/%(version_major_minor)s.x/'] +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/TRIQS/dft_tools/releases/download/%(version)s/'] +sources = ['dft_tools-%(version)s.tar.gz'] +checksums = ['57b7d0fe5a96c5a42bb684c60ca8e136a33e1385bf6cd7e9d1371fa507dc2ec4'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Boost', '1.77.0'), + ('Clang', '13.0.1'), + ('Clang-Python-bindings', '13.0.1'), + ('GMP', '6.2.1'), + ('HDF5', '1.10.7'), + ('Mako', '1.1.4'), + ('TRIQS', '3.1.0'), +] + +builddependencies = [ + ('CMake', '3.22.1') +] + +separate_build_dir = True + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/dmftproj', 'lib/libtriqs_dft_tools_c.a'], + 'dirs': ['include/triqs_dft_tools', 'bin', 'lib', 'share', + 'lib/python%(pyshortver)s/site-packages/triqs_dft_tools'], +} + +sanity_check_commands = ["python -c 'import triqs_dft_tools'"] + +modextrapaths = { + 'CPLUS_INCLUDE_PATH': 'include', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CMAKE_PREFIX_PATH': 'lib/cmake/triqs_dft_tools', +} +modextravars = { + 'TRIQS_DFT_TOOLS_ROOT': '%(installdir)s', + 'TRIQS_DFT_TOOLS_VERSION': '%(version)s', +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb new file mode 100644 index 00000000000..d79e17f9ac6 --- /dev/null +++ b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb @@ -0,0 +1,70 @@ +easyblock = 'CMakeMake' + +name = 'TRIQS-tprf' +version = '3.1.0' + +homepage = 'https://triqs.github.io/tprf' +description = """ + TRIQS (Toolbox for Research on Interacting Quantum Systems) is a + scientific project providing a set of C++ and Python libraries to + develop new tools for the study of interacting quantum systems. + + TPRF is a TRIQS-based two-particle response function tool box that + implements basic operations for higher order response functions such + as inversion, products, the random phase approximation, the bethe + salpeter equation (in the local vertex approximation), etc.. + + The aim is to provide efficient (C++/OpenMP/MPI) implementations of + the basic operations needed to compute the two-particle response in + the different two-particle channels (particle-hole, particle-particle). +""" + +docurls = ['https://triqs.github.io/tprf/%(version_major_minor)s.x/'] +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/TRIQS/tprf/releases/download/%(version)s/'] +sources = ['tprf-%(version)s.tar.gz'] +checksums = ['75f6e79d891342951652353ea4d9914074d9947c67cad60844ebaa3f82bd17b5'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Boost', '1.77.0'), + ('Clang', '13.0.1'), + ('Clang-Python-bindings', '13.0.1'), + ('GMP', '6.2.1'), + ('HDF5', '1.10.7'), + ('Mako', '1.1.4'), + ('TRIQS', '3.1.0'), +] + +builddependencies = [ + ('CMake', '3.22.1') +] + +separate_build_dir = True + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libtriqs_tprf_c.a'], + 'dirs': ['include/triqs_tprf', 'lib', 'share', + 'lib/python%(pyshortver)s/site-packages/triqs_tprf'], +} + +sanity_check_commands = ["python -c 'import triqs_tprf'"] + +modextrapaths = { + 'CPLUS_INCLUDE_PATH': 'include', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CMAKE_PREFIX_PATH': 'lib/cmake/triqs_tprf', +} +modextravars = { + 'TRIQS_TPRF_ROOT': '%(installdir)s', + 'TRIQS_TPRF_VERSION': '%(version)s' +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb new file mode 100644 index 00000000000..b4176524bb5 --- /dev/null +++ b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb @@ -0,0 +1,70 @@ +easyblock = 'CMakeMake' + +name = 'TRIQS' +version = '3.1.0' + +homepage = 'https://triqs.github.io/triqs' +description = """ + TRIQS (Toolbox for Research on Interacting Quantum Systems) is a + scientific project providing a set of C++ and Python libraries to + develop new tools for the study of interacting quantum systems. +""" + +docurls = ['https://triqs.github.io/triqs/%(version_major_minor)s.x/'] +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/TRIQS/triqs/releases/download/%(version)s/'] +sources = ['triqs-%(version)s.tar.gz'] +checksums = ['f1f358ec73498bc7ac3ed9665829d8605908f7f7fc876a5c2a01efe37d368f0e'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Boost', '1.77.0'), + ('Clang', '13.0.1'), + ('Clang-Python-bindings', '13.0.1'), + ('GMP', '6.2.1'), + ('HDF5', '1.10.7'), + ('Mako', '1.1.4') +] + +builddependencies = [ + ('CMake', '3.22.1') +] + +separate_build_dir = True + +# Remove installation directory before building. This fixes problems with +# failing builds in the presence of preexisting installation. +preconfigopts = "rm -rf %(installdir)s && " + +configopts = "" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libtriqs.%s' % SHLIB_EXT], + 'dirs': ['include/triqs', 'include/itertools', 'include/mpi', 'include/cpp2py', + 'lib/python%(pyshortver)s/site-packages', 'share'], +} + +sanity_check_commands = [ + "triqs++ --help", + "c++2py --help", + "python -c 'import triqs'" +] + +modextrapaths = { + 'CPLUS_INCLUDE_PATH': 'include', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CMAKE_PREFIX_PATH': ['lib/cmake/triqs', 'lib/cmake/cpp2py'] +} +modextravars = { + 'TRIQS_ROOT': '%(installdir)s', + 'TRIQS_VERSION': '%(version)s' +} + +moduleclass = 'phys' From 8b3550f9c227343868da1612c17f8d9b6389ddcb Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Thu, 24 Mar 2022 18:26:34 -0400 Subject: [PATCH 293/793] Bump hdf5 version to 1.12.1 --- .../easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb | 2 +- .../t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb | 2 +- .../easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb | 2 +- easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb index 19e698e99bd..73c6a1b8c97 100644 --- a/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb @@ -34,7 +34,7 @@ dependencies = [ ('Clang', '13.0.1'), ('Clang-Python-bindings', '13.0.1'), ('GMP', '6.2.1'), - ('HDF5', '1.10.7'), + ('HDF5', '1.12.1'), ('Mako', '1.1.4'), ('TRIQS', '3.1.0'), ('NFFT', '3.5.2') diff --git a/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb index abb330f2b46..3f219978bb8 100644 --- a/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb @@ -36,7 +36,7 @@ dependencies = [ ('Clang', '13.0.1'), ('Clang-Python-bindings', '13.0.1'), ('GMP', '6.2.1'), - ('HDF5', '1.10.7'), + ('HDF5', '1.12.1'), ('Mako', '1.1.4'), ('TRIQS', '3.1.0'), ] diff --git a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb index d79e17f9ac6..c4595b68429 100644 --- a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb @@ -36,7 +36,7 @@ dependencies = [ ('Clang', '13.0.1'), ('Clang-Python-bindings', '13.0.1'), ('GMP', '6.2.1'), - ('HDF5', '1.10.7'), + ('HDF5', '1.12.1'), ('Mako', '1.1.4'), ('TRIQS', '3.1.0'), ] diff --git a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb index b4176524bb5..b0b03529c2c 100644 --- a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb @@ -27,7 +27,7 @@ dependencies = [ ('Clang', '13.0.1'), ('Clang-Python-bindings', '13.0.1'), ('GMP', '6.2.1'), - ('HDF5', '1.10.7'), + ('HDF5', '1.12.1'), ('Mako', '1.1.4') ] From 49f9ac7876c2f340fe5c9f815fa2f01d9627be83 Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Fri, 25 Mar 2022 09:49:59 -0400 Subject: [PATCH 294/793] Bump python-igraph clang dep to 13.0.1 --- .../p/python-igraph/python-igraph-0.9.8-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb index f16f7fbcc66..d810a435204 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb @@ -17,7 +17,7 @@ dependencies = [ ('Python', '3.9.6'), ('igraph', '0.9.5'), ('PyCairo', '1.20.1'), - ('Clang', '12.0.1'), + ('Clang', '13.0.1'), ('libxml2', '2.9.10'), ('zlib', '1.2.11'), ] From 48f056d380db8a5b554a791380326832639a61cf Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Tue, 29 Mar 2022 10:31:13 -0400 Subject: [PATCH 295/793] No need to set configopts to empty string --- easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb index b0b03529c2c..71cf1646135 100644 --- a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb @@ -41,8 +41,6 @@ separate_build_dir = True # failing builds in the presence of preexisting installation. preconfigopts = "rm -rf %(installdir)s && " -configopts = "" - runtest = 'test' sanity_check_paths = { From 738be44783df1a0c9822dc767a4a68475b75f15b Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Wed, 29 Jun 2022 11:19:44 -0400 Subject: [PATCH 296/793] Update clang version for pocl-1.8 to 13 --- easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb index 0c7f9416308..3ae0aa3485d 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('Clang', '12.0.1'), + ('Clang', '13.0.1'), ('hwloc', '2.5.0'), ('libtool', '2.4.6'), ('libxml2', '2.9.10'), From e2d3b4371cbff53a4a35b70bfcc083be4863f0eb Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Wed, 29 Jun 2022 11:20:56 -0400 Subject: [PATCH 297/793] Update triqs to version from 3.1.0 to patch release 3.1.1 --- .../easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb | 2 +- .../t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb | 2 +- .../easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb | 2 +- .../{TRIQS-3.1.0-foss-2021b.eb => TRIQS-3.1.1-foss-2021b.eb} | 4 ++-- 4 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/t/TRIQS/{TRIQS-3.1.0-foss-2021b.eb => TRIQS-3.1.1-foss-2021b.eb} (94%) diff --git a/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb index 73c6a1b8c97..e81b7e7e49b 100644 --- a/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb @@ -36,7 +36,7 @@ dependencies = [ ('GMP', '6.2.1'), ('HDF5', '1.12.1'), ('Mako', '1.1.4'), - ('TRIQS', '3.1.0'), + ('TRIQS', '3.1.1'), ('NFFT', '3.5.2') ] diff --git a/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb index 3f219978bb8..dd112010867 100644 --- a/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb @@ -38,7 +38,7 @@ dependencies = [ ('GMP', '6.2.1'), ('HDF5', '1.12.1'), ('Mako', '1.1.4'), - ('TRIQS', '3.1.0'), + ('TRIQS', '3.1.1'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb index c4595b68429..b66a8fcd147 100644 --- a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb @@ -38,7 +38,7 @@ dependencies = [ ('GMP', '6.2.1'), ('HDF5', '1.12.1'), ('Mako', '1.1.4'), - ('TRIQS', '3.1.0'), + ('TRIQS', '3.1.1'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.1-foss-2021b.eb similarity index 94% rename from easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb rename to easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.1-foss-2021b.eb index 71cf1646135..8800fcb529b 100644 --- a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.1-foss-2021b.eb @@ -1,7 +1,7 @@ easyblock = 'CMakeMake' name = 'TRIQS' -version = '3.1.0' +version = '3.1.1' homepage = 'https://triqs.github.io/triqs' description = """ @@ -18,7 +18,7 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/TRIQS/triqs/releases/download/%(version)s/'] sources = ['triqs-%(version)s.tar.gz'] -checksums = ['f1f358ec73498bc7ac3ed9665829d8605908f7f7fc876a5c2a01efe37d368f0e'] +checksums = ['cf4f6064ea962fc088e0c2833bf7c4e52f4c827ea331bf3c57d1c9303649042b'] dependencies = [ ('Python', '3.9.6'), From 832b8d6905f2c9d27378e839473c560dc06d567b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 6 Oct 2022 18:35:38 +0200 Subject: [PATCH 298/793] Update patches to fix remaining failures --- .../PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 8 +++++- .../PyTorch-1.11.0_fix-fsdp-fp16-test.patch | 13 ++++++++++ ...1.1_skip-test_init_from_local_shards.patch | 25 +++++++++++++++++++ ...orch-1.11.1_skip-test_sibling_fusion.patch | 17 +++++++++++++ 4 files changed, 62 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.1_skip-test_init_from_local_shards.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.1_skip-test_sibling_fusion.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 32f4323e49d..8385d91b7f0 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -34,6 +34,8 @@ patches = [ 'PyTorch-1.11.0_increase-tolerance-test_ops.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.0_skip_failing_ops_tests.patch', + 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.11.1_skip-test_sibling_fusion.patch', ] checksums = [ 'dc0c2b8d13c112a2b9ea8757a475b0ce2ca97cd19c50a8b70b8c286676616f1d', # pytorch-v1.11.0.tar.gz @@ -57,7 +59,7 @@ checksums = [ 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', # PyTorch-1.11.0_fix-attention_cpp-compilation.patch '84214fcc7e30cf70659a7c3bd70bf11e73d58fd4f7fff2c233e3225619b0e42c', - 'ca48576014bceb8c6c0d06cbab666be96cb44804e0215f5c025397a75a675bab', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch '9a04f4285b800dad8a00c3014af0a9713d40d5dd35d10931c7c0da4e89c558e9', # PyTorch-1.11.0_fix_sharded_imports.patch '21fc678febcdfbb9dabd72235be23cd392044e9a954f6580d15b530e1f69dcc1', # PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch @@ -71,6 +73,10 @@ checksums = [ 'ceec745c68a405bba79efb4dc61c662ca84eb950cd0163c7104330f4bf614cf5', 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch '8eaca92d64fcadb0552d28e9c7ea5c4bc669d2fe33004e45a3519ce8d0d136a2', # PyTorch-1.11.0_skip_failing_ops_tests.patch + # PyTorch-1.11.1_skip-test_init_from_local_shards.patch + '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', + # PyTorch-1.11.1_skip-test_sibling_fusion.patch + '3d6f6395d98e8e4ad76b0b63c625fddf082cf7f066eb97d4d82401f96dab2555', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch index 401d0865d49..dc9159e5cf9 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch @@ -4,6 +4,19 @@ See https://github.com/pytorch/pytorch/issues/78975 Author: Alexander Grund (TU Dresden) +diff --git a/torch/testing/_internal/common_fsdp.py b/torch/testing/_internal/common_fsdp.py +index ff0fbb69e3..6bf3e71fde 100644 +--- a/torch/testing/_internal/common_fsdp.py ++++ b/torch/testing/_internal/common_fsdp.py +@@ -324,7 +324,7 @@ class FSDPTest(MultiProcessTestCase): + + @property + def world_size(self): +- return torch.cuda.device_count() if torch.cuda.is_available() else 4 ++ return min(4, torch.cuda.device_count()) if torch.cuda.is_available() else 4 + + @property + def init_method(self): diff --git a/test/distributed/fsdp/test_fsdp_pure_fp16.py b/test/distributed/fsdp/test_fsdp_pure_fp16.py index eea03bea3d..d3a4bb8257 100644 --- a/test/distributed/fsdp/test_fsdp_pure_fp16.py diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.1_skip-test_init_from_local_shards.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.1_skip-test_init_from_local_shards.patch new file mode 100644 index 00000000000..c63d7193b7e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.1_skip-test_init_from_local_shards.patch @@ -0,0 +1,25 @@ +The test often times out and seems to be considered flaky by PyTorch: +https://github.com/pytorch/pytorch/issues/78068 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributed/_shard/sharded_tensor/test_sharded_tensor.py b/test/distributed/_shard/sharded_tensor/test_sharded_tensor.py +index cbad9458ae..72a36e0e9a 100644 +--- a/test/distributed/_shard/sharded_tensor/test_sharded_tensor.py ++++ b/test/distributed/_shard/sharded_tensor/test_sharded_tensor.py +@@ -6,6 +6,7 @@ import io + import itertools + import pickle + import sys ++from unittest import skip + import torch + import torch.distributed as dist + from torch.distributed import rpc +@@ -1817,6 +1818,7 @@ class TestShardedTensorFromLocalShards(ShardedTensorTestBase): + @with_comms + @skip_if_lt_x_gpu(4) + @requires_nccl() ++ @skip("Times out often") + def test_init_from_local_shards(self): + local_shard_metadata = ShardMetadata( + shard_offsets=[(self.rank // 2) * 5, (self.rank % 2) * 5], diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.1_skip-test_sibling_fusion.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.1_skip-test_sibling_fusion.patch new file mode 100644 index 00000000000..6845706f484 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.1_skip-test_sibling_fusion.patch @@ -0,0 +1,17 @@ +The test fails on pre-volta devices as fusing the at::sum/at::add +is skipped if the device is not of compute capability >= 7 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_jit_cuda_fuser.py b/test/test_jit_cuda_fuser.py +index c03ff0b311..feb6e281f9 100644 +--- a/test/test_jit_cuda_fuser.py ++++ b/test/test_jit_cuda_fuser.py +@@ -3053,6 +3054,7 @@ class TestCudaFuser(JitTestCase): + self.assertGraphContainsExactly(graph, op, 0) + + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_sibling_fusion(self): From 903cb2de9cc708dac83ba7a5cfc85726d10660a9 Mon Sep 17 00:00:00 2001 From: rocky_build Date: Thu, 6 Oct 2022 14:51:34 -0400 Subject: [PATCH 299/793] adding easyconfigs: ncbi-vdb-3.0.0-gompi-2022a.eb --- .../f/file/file-5.43-GCCcore-11.3.0.eb | 28 +++++++++ .../h/HDF5/HDF5-1.10.8-gompi-2022a.eb | 28 +++++++++ .../n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb | 58 +++++++++++++++++++ 3 files changed, 114 insertions(+) create mode 100644 easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1128c37d6ac --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.43' + +homepage = 'https://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] +checksums = ['8c8015e91ae0e8d0321d94c78239892ef9dbc70c4ade0008c0e95894abfb1991'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2022a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2022a.eb new file mode 100644 index 00000000000..3091b947d74 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2022a.eb @@ -0,0 +1,28 @@ +# Updated to version 1.10.8, needed for HISAT2-2.2.1 +# J. Sassmannshausen + +name = 'HDF5' +version = '1.10.8' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['66ec544b195a4cb9f6ffed034fd82e52429d6112747c2996ab69853f606e546b'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Szip', '2.1.1'), +] + +# needed to build HL-tools: gif2h5 gif2h5 and h5watch +# beware that gif tools are affected by multiple CVEs: CVE-2018-17433, CVE-2018-17436, CVE-2020-10809 +# configopts = "--enable-hltools" + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb new file mode 100644 index 00000000000..b02b422d181 --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb @@ -0,0 +1,58 @@ +easyblock = 'CMakeMake' + +name = 'ncbi-vdb' +version = '3.0.0' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +github_account = 'ncbi' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = [ + 'ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch', + 'ncbi-vdb-cstdlib.patch', +] +checksums = [ + '154317ef265104861fe8d3d2e439939ae98f33b1e28da3c45f32ae8534dbfad7', # ncbi-vdb-3.0.0.tar.gz + 'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133', # ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch + 'db3d563262ca9b14e7b9a94a0be6683a9eef41a498c9c064aa05c2a6785f1655', # ncbi-vdb-cstdlib.patch +] + +builddependencies = [ + ('Perl', '5.34.1', '-minimal'), + ('Python', '3.10.4', '-bare'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('file', '5.43'), # provides libmagic + ('HDF5', '1.10.8'), # version 1.12.x has changes to API and is not compatible + ('libxml2', '2.9.13'), + ('bzip2', '1.0.8'), +] + +# add addtional libraries needed to statically link HDF5 from EB +preconfigopts = "sed -i 's/-lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz/'" +preconfigopts += " %(builddir)s/%(namelower)s-%(version)s/setup/konfigure.perl &&" + +configopts = '' +configopts += ' -DHDF5_LIBDIR=$EBROOTHDF5/lib -DXML2_LIBDIR=$EBROOTLIBXML2/lib' +configopts += ' -DHDF5_INCDIR=$EBROOTHDF5/include -DXML2_INCDIR=$EBROOTLIBXML2/include' + + +# replace hardcoded optimization flags with EB settings +prebuildopts = "find %(builddir)s/%(namelower)s-%(version)s/build/ -name \"Makefile*\" " +prebuildopts += "-exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && EBFLAGS=\"$CFLAGS\" " +preinstallopts = 'EBFLAGS="$CFLAGS" ' + +sanity_check_paths = { + 'files': [('lib/libncbi-%s.%s' % (k, e), 'lib64/libncbi-%s.%s' % (k, e)) + for k in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'bio' From a8daaba18b9522f284babf79aa7d3d2a3e909856 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Fri, 7 Oct 2022 08:34:47 +0200 Subject: [PATCH 300/793] Conform to style guide --- .../torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb index 9c2141e4169..b6e1c9385c7 100644 --- a/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb @@ -6,7 +6,10 @@ local_pytorch_version = '1.11.0' versionsuffix = '-PyTorch-' + local_pytorch_version + '-CUDA-%(cudaver)s' homepage = 'https://github.com/pytorch/data' -description = "TorchData is a prototype library of common modular data loading primitives for easily constructing flexible and performant data pipelines." +description = """ +TorchData is a prototype library of common modular data loading primitives for +easily constructing flexible and performant data pipelines." +""" toolchain = {'name': 'foss', 'version': '2021a'} From 45b9d5f351439197ec11442bda41cfec91a16475 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Oct 2022 16:05:29 +0200 Subject: [PATCH 301/793] {tools}[GCCcore/11.3.0] onedrive v2.4.21, LDC v1.30.0 --- .../easyconfigs/l/LDC/LDC-1.24.0-x86_64.eb | 25 +++++++++++ .../l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb | 39 +++++++++++++++++ .../onedrive-2.4.21-GCCcore-11.3.0.eb | 42 +++++++++++++++++++ 3 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/l/LDC/LDC-1.24.0-x86_64.eb create mode 100644 easybuild/easyconfigs/l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/onedrive/onedrive-2.4.21-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/LDC/LDC-1.24.0-x86_64.eb b/easybuild/easyconfigs/l/LDC/LDC-1.24.0-x86_64.eb new file mode 100644 index 00000000000..7b726673f51 --- /dev/null +++ b/easybuild/easyconfigs/l/LDC/LDC-1.24.0-x86_64.eb @@ -0,0 +1,25 @@ +easyblock = 'Tarball' + +name = 'LDC' +version = '1.24.0' +versionsuffix = '-x86_64' + +homepage = 'https://wiki.dlang.org/LDC' +description = "The LLVM-based D Compiler" + +toolchain = SYSTEM + +source_urls = ['https://github.com/ldc-developers/ldc/releases/download/v%(version)s/'] +sources = ['ldc2-%(version)s-linux%(versionsuffix)s.tar.xz'] +checksums = ['868e070fe90b06549f5fb19882a58a920c0052fad29b764eee9f409f08892ba3'] + +unpack_options = '--strip-components=1' + +sanity_check_paths = { + 'files': ['bin/dub', 'bin/ldc2', 'bin/ldmd2', 'lib/libdruntime-ldc.a'], + 'dirs': [], +} + +sanity_check_commands = ["ldc2 --help"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..9e9a544e9f6 --- /dev/null +++ b/easybuild/easyconfigs/l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeNinja' + +name = 'LDC' +version = '1.30.0' + +homepage = 'https://wiki.dlang.org/LDC' +description = "The LLVM-based D Compiler" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/ldc-developers/ldc/releases/download/v%(version)s'] +sources = ['ldc-%(version)s-src.tar.gz'] +checksums = ['fdbb376f08242d917922a6a22a773980217fafa310046fc5d6459490af23dacd'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), + # building LDC from source requires LDC + ('LDC', '1.24.0', '-%(arch)s', True), +] + +dependencies = [ + ('LLVM', '14.0.3'), +] + +configopts = "-DLLVM_ROOT_DIR=$EBROOTLLVM" + +sanity_check_paths = { + 'files': ['bin/ldc2', 'bin/ldmd2'], + 'dirs': ['include/d', 'lib'], +} + +sanity_check_commands = [ + "ldc2 --help", + "ldmd2 --help", +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/o/onedrive/onedrive-2.4.21-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/onedrive/onedrive-2.4.21-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..b75326b187d --- /dev/null +++ b/easybuild/easyconfigs/o/onedrive/onedrive-2.4.21-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'onedrive' +version = '2.4.21' + +homepage = 'https://abraunegg.github.io/' +description = """ +A free Microsoft OneDrive Client which supports OneDrive Personal, OneDrive for Business, +OneDrive for Office365 and SharePoint.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/abraunegg/onedrive/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c9991970cbb108368d16a4e6aefe66f0d61d66791ab3bbc526bff2237b926c51'] + +builddependencies = [ + ('binutils', '2.38'), + ('LDC', '1.30.0'), +] + +dependencies = [ + ('cURL', '7.83.0'), + ('SQLite', '3.38.3'), +] + +_compldir = '%(installdir)s/share/tab_completion' +configopts = 'DC="$EBROOTLDC"/bin/ldc2 --with-systemdsystemunitdir=no ' +configopts += '--enable-completions --with-bash-completion-dir=%s ' % _compldir +configopts += '--with-zsh-completion-dir=%s --with-fish-completion-dir=%s ' % (_compldir, _compldir) + +sanity_check_paths = { + 'files': ['bin/onedrive'], + 'dirs': ['etc', 'share'], +} + +sanity_check_commands = ['onedrive -h'] + +# optionally enable tab completion for bash (zsh: '_onedrive', fish: 'onedrive.fish') +modluafooter = 'execute {cmd="source $EBROOTONEDRIVE/share/tab_completion/onedrive",modeA={"load"}}' + +moduleclass = 'tools' From 26bf4b354a1859dfeec24be5d2a968a51088c83b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 7 Oct 2022 15:56:31 +0100 Subject: [PATCH 302/793] adding easyconfigs: libconfig-1.7.3-GCCcore-10.3.0.eb --- .../libconfig-1.7.3-GCCcore-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..6210df9240e --- /dev/null +++ b/easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libconfig' +version = '1.7.3' + +homepage = 'https://hyperrealm.github.io/libconfig' +description = "Libconfig is a simple library for processing structured configuration files" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://hyperrealm.github.io/libconfig/dist/'] +sources = [SOURCE_TAR_GZ] +checksums = ['545166d6cac037744381d1e9cc5a5405094e7bfad16a411699bcff40bbb31ee7'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] + +sanity_check_paths = { + 'files': ['include/libconfig.h', 'include/libconfig.h++', 'lib/libconfig.a', 'lib/libconfig++.a', + 'lib/libconfig.%s' % SHLIB_EXT, 'lib/libconfig++.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' From c2e45e758cdd8b1cde51040b04ed6b3b2f587c0d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 10 Oct 2022 11:48:17 +0200 Subject: [PATCH 303/793] Update easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb --- .../torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb index b6e1c9385c7..5995d9c3e6f 100644 --- a/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb @@ -14,7 +14,7 @@ easily constructing flexible and performant data pipelines." toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('PyTorch', local_pytorch_version, '-CUDA-%(cudaver)s'), ] From 6e75480914e06d5e61bbbc851ec60d3bb7bbda52 Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Thu, 6 Oct 2022 12:53:36 -0400 Subject: [PATCH 304/793] Move TRIQS packages to 2022a toolchain, add NFFT-3.5.3-foss-2022a -Add easyconfig Clang-Python-bindings-13.0.1-GCCcore-11.3.0 --- ...g-Python-bindings-13.0.1-GCCcore-11.3.0.eb | 31 +++++++++++++++++++ .../n/NFFT/NFFT-3.5.3-foss-2022a.eb | 31 +++++++++++++++++++ .../easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb | 2 +- .../python-igraph-0.9.8-foss-2021b.eb | 2 +- ...21b.eb => TRIQS-cthyb-3.1.0-foss-2022a.eb} | 16 +++++----- ...eb => TRIQS-dft_tools-3.1.0-foss-2022a.eb} | 14 ++++----- ...021b.eb => TRIQS-tprf-3.1.1-foss-2022a.eb} | 18 +++++------ ...oss-2021b.eb => TRIQS-3.1.1-foss-2022a.eb} | 14 ++++----- 8 files changed, 95 insertions(+), 33 deletions(-) create mode 100644 easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-13.0.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2022a.eb rename easybuild/easyconfigs/t/TRIQS-cthyb/{TRIQS-cthyb-3.1.0-foss-2021b.eb => TRIQS-cthyb-3.1.0-foss-2022a.eb} (88%) rename easybuild/easyconfigs/t/TRIQS-dft_tools/{TRIQS-dft_tools-3.1.0-foss-2021b.eb => TRIQS-dft_tools-3.1.0-foss-2022a.eb} (91%) rename easybuild/easyconfigs/t/TRIQS-tprf/{TRIQS-tprf-3.1.0-foss-2021b.eb => TRIQS-tprf-3.1.1-foss-2022a.eb} (85%) rename easybuild/easyconfigs/t/TRIQS/{TRIQS-3.1.1-foss-2021b.eb => TRIQS-3.1.1-foss-2022a.eb} (89%) diff --git a/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-13.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-13.0.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..fcbc32b1b75 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-13.0.1-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'Clang-Python-bindings' +version = '13.0.1' + +homepage = 'https://clang.llvm.org' +description = """Python bindings for libclang""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/"] +sources = ['clang-%(version)s.src.tar.xz'] +checksums = ['787a9e2d99f5c8720aa1773e4be009461cd30d3bd40fdd24591e473467c917c9'] + +dependencies = [ + ('Clang', version), + ('Python', '3.10.4') +] + +start_dir = 'bindings/python' + +sanity_check_paths = { + 'files': ['clang/cindex.py'], + 'dirs': ['clang'] +} + +sanity_check_commands = ["python -c 'import clang'"] + +modextrapaths = {'PYTHONPATH': ''} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2022a.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2022a.eb new file mode 100644 index 00000000000..5787c0ee569 --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'NFFT' +version = '3.5.3' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine + library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more + dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/NFFT/nfft/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['caf1b3b3e5bf8c33a6bfd7eca811d954efce896605ecfd0144d47d0bebdf4371'] + +dependencies = [('FFTW', '3.3.10')] + +builddependencies = [('Autotools', '20220317')] + +configure_cmd_prefix = './bootstrap.sh ; ' + +configopts = '--enable-openmp' + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3_threads.a', 'lib/libnfft3.a', + 'lib/libnfft3_threads.%s' % SHLIB_EXT, 'lib/libnfft3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb index 3ae0aa3485d..0c7f9416308 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('Clang', '13.0.1'), + ('Clang', '12.0.1'), ('hwloc', '2.5.0'), ('libtool', '2.4.6'), ('libxml2', '2.9.10'), diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb index d810a435204..f16f7fbcc66 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb @@ -17,7 +17,7 @@ dependencies = [ ('Python', '3.9.6'), ('igraph', '0.9.5'), ('PyCairo', '1.20.1'), - ('Clang', '13.0.1'), + ('Clang', '12.0.1'), ('libxml2', '2.9.10'), ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2022a.eb similarity index 88% rename from easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb rename to easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2022a.eb index e81b7e7e49b..84ff74d8ecc 100644 --- a/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2022a.eb @@ -20,7 +20,7 @@ description = """ docurls = ['https://triqs.github.io/cthyb/%(version_major_minor)s.x/'] software_license = 'LicenseGPLv3' -toolchain = {'name': 'foss', 'version': '2021b'} +toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/TRIQS/cthyb/releases/download/%(version)s/'] @@ -28,20 +28,20 @@ sources = ['cthyb-%(version)s.tar.gz'] checksums = ['8d6d2c4d5b3928d062b72fad4ea9df9aae198e39dd9c1fd3cc5dc34a5019acc0'] dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('Boost', '1.77.0'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost', '1.79.0'), ('Clang', '13.0.1'), ('Clang-Python-bindings', '13.0.1'), ('GMP', '6.2.1'), - ('HDF5', '1.12.1'), - ('Mako', '1.1.4'), + ('HDF5', '1.12.2'), + ('Mako', '1.2.0'), ('TRIQS', '3.1.1'), - ('NFFT', '3.5.2') + ('NFFT', '3.5.3') ] builddependencies = [ - ('CMake', '3.22.1') + ('CMake', '3.23.1') ] separate_build_dir = True diff --git a/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2022a.eb similarity index 91% rename from easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb rename to easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2022a.eb index dd112010867..78221bf72e6 100644 --- a/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2022a.eb @@ -22,7 +22,7 @@ description = """ docurls = ['https://triqs.github.io/dft_tools/%(version_major_minor)s.x/'] software_license = 'LicenseGPLv3' -toolchain = {'name': 'foss', 'version': '2021b'} +toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/TRIQS/dft_tools/releases/download/%(version)s/'] @@ -30,19 +30,19 @@ sources = ['dft_tools-%(version)s.tar.gz'] checksums = ['57b7d0fe5a96c5a42bb684c60ca8e136a33e1385bf6cd7e9d1371fa507dc2ec4'] dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('Boost', '1.77.0'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost', '1.79.0'), ('Clang', '13.0.1'), ('Clang-Python-bindings', '13.0.1'), ('GMP', '6.2.1'), - ('HDF5', '1.12.1'), - ('Mako', '1.1.4'), + ('HDF5', '1.12.2'), + ('Mako', '1.2.0'), ('TRIQS', '3.1.1'), ] builddependencies = [ - ('CMake', '3.22.1') + ('CMake', '3.23.1') ] separate_build_dir = True diff --git a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.1-foss-2022a.eb similarity index 85% rename from easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb rename to easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.1-foss-2022a.eb index b66a8fcd147..6ba4a624278 100644 --- a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.1-foss-2022a.eb @@ -1,7 +1,7 @@ easyblock = 'CMakeMake' name = 'TRIQS-tprf' -version = '3.1.0' +version = '3.1.1' homepage = 'https://triqs.github.io/tprf' description = """ @@ -22,27 +22,27 @@ description = """ docurls = ['https://triqs.github.io/tprf/%(version_major_minor)s.x/'] software_license = 'LicenseGPLv3' -toolchain = {'name': 'foss', 'version': '2021b'} +toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/TRIQS/tprf/releases/download/%(version)s/'] sources = ['tprf-%(version)s.tar.gz'] -checksums = ['75f6e79d891342951652353ea4d9914074d9947c67cad60844ebaa3f82bd17b5'] +checksums = ['63d4de9cfc3daf0d74db45cfa7445b817fd22a38a8485db3ce9a81febe263b50'] dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('Boost', '1.77.0'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost', '1.79.0'), ('Clang', '13.0.1'), ('Clang-Python-bindings', '13.0.1'), ('GMP', '6.2.1'), - ('HDF5', '1.12.1'), - ('Mako', '1.1.4'), + ('HDF5', '1.12.2'), + ('Mako', '1.2.0'), ('TRIQS', '3.1.1'), ] builddependencies = [ - ('CMake', '3.22.1') + ('CMake', '3.23.1') ] separate_build_dir = True diff --git a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.1-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.1-foss-2022a.eb similarity index 89% rename from easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.1-foss-2021b.eb rename to easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.1-foss-2022a.eb index 8800fcb529b..ca1bf2e6a62 100644 --- a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.1-foss-2022a.eb @@ -13,7 +13,7 @@ description = """ docurls = ['https://triqs.github.io/triqs/%(version_major_minor)s.x/'] software_license = 'LicenseGPLv3' -toolchain = {'name': 'foss', 'version': '2021b'} +toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/TRIQS/triqs/releases/download/%(version)s/'] @@ -21,18 +21,18 @@ sources = ['triqs-%(version)s.tar.gz'] checksums = ['cf4f6064ea962fc088e0c2833bf7c4e52f4c827ea331bf3c57d1c9303649042b'] dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('Boost', '1.77.0'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost', '1.79.0'), ('Clang', '13.0.1'), ('Clang-Python-bindings', '13.0.1'), ('GMP', '6.2.1'), - ('HDF5', '1.12.1'), - ('Mako', '1.1.4') + ('HDF5', '1.12.2'), + ('Mako', '1.2.0') ] builddependencies = [ - ('CMake', '3.22.1') + ('CMake', '3.23.1') ] separate_build_dir = True From 737d5eedb5a9cb75def0295a421c141a8bd5cc32 Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Mon, 10 Oct 2022 13:02:30 -0400 Subject: [PATCH 305/793] Fix sha256 for NFFT 3.5.3 tarball --- easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2022a.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2022a.eb index 5787c0ee569..36911997f51 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2022a.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2022a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} source_urls = ['https://github.com/NFFT/nfft/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['caf1b3b3e5bf8c33a6bfd7eca811d954efce896605ecfd0144d47d0bebdf4371'] +checksums = ['ccef7a8e97e40e5f962df94626ade5adc7db1fb7948e3c75aa70393468e2e8fb'] dependencies = [('FFTW', '3.3.10')] From 5c0b21b325e9ef49307de47d176c926be7c2a327 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 10 Oct 2022 23:40:06 +0000 Subject: [PATCH 306/793] adding easyconfigs: ACTC-1.1-GCCcore-11.3.0.eb, VMD-1.9.4a57-foss-2022a.eb and patches: VMD-1.9.4a57_configure.patch --- .../a/ACTC/ACTC-1.1-GCCcore-11.3.0.eb | 35 ++++ .../v/VMD/VMD-1.9.4a57-foss-2022a.eb | 46 +++++ .../v/VMD/VMD-1.9.4a57_configure.patch | 172 ++++++++++++++++++ 3 files changed, 253 insertions(+) create mode 100644 easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb create mode 100644 easybuild/easyconfigs/v/VMD/VMD-1.9.4a57_configure.patch diff --git a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..12bca02e2a6 --- /dev/null +++ b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'ACTC' +version = '1.1' + +homepage = 'https://sourceforge.net/projects/actc' +description = "ACTC converts independent triangles into triangle strips or fans." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3a1303291629b9de6008c3c9d7b020a4b854802408fb3f8222ec492808c8b44d'] + +builddependencies = [('binutils', '2.38')] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +files_to_copy = [ + (['tcsample', 'tctest', 'tctest2'], 'bin'), + (['tc.h'], 'include/ac'), + (['libactc.a'], 'lib'), + 'COPYRIGHT', 'manual.html', 'prims.gif', 'README', +] + +sanity_check_paths = { + 'files': ['bin/tctest', 'bin/tctest2', 'bin/tcsample', 'include/ac/tc.h', 'lib/libactc.a', + 'COPYRIGHT', 'manual.html', 'prims.gif', 'README'], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/ac'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb new file mode 100644 index 00000000000..c79d12f48f5 --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb @@ -0,0 +1,46 @@ +name = 'VMD' +version = '1.9.4a57' + +homepage = 'https://www.ks.uiuc.edu/Research/vmd' +description = """VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular + systems using 3-D graphics and built-in scripting.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + 'https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.4/files/alpha/', + 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', + 'https://webclu.bio.wzw.tum.de/stride/' +] +sources = [ + 'vmd-%(version)s.src.tar.gz', + {'filename': 'stride.tar.gz', 'extract_cmd': "tar -C vmd-%(version)s/lib/stride -xf %s"}, +] +patches = [ + ('VMD-1.9.3_plugins.patch'), + ('VMD-1.9.3_surf_Makefile.patch', 'vmd-%(version)s'), + ('VMD-1.9.3_surf_bad_printfs.patch', 'vmd-%(version)s'), + ('VMD-1.9.3_stride_Makefile.patch', 'vmd-%(version)s'), + ('VMD-1.9.3_stride_MAX_AT_IN_RES.patch', 'vmd-%(version)s'), + ('VMD-%(version)s_configure.patch', 'vmd-%(version)s'), + ('VMD-1.9.4a51_extra_colors.patch', 'vmd-%(version)s'), +] + +dependencies = [ + ('Tcl', '8.6.12'), + ('Tk', '8.6.12'), + ('FLTK', '1.3.8'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Tkinter', '%(pyver)s'), + ('Mesa', '22.0.3'), + ('netCDF', '4.9.0'), + ('FFmpeg', '4.4.2'), + ('ImageMagick', '7.1.0-37'), + ('ACTC', '1.1'), + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), + ('POV-Ray', '3.7.0.10'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57_configure.patch b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57_configure.patch new file mode 100644 index 00000000000..63b8e014f84 --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57_configure.patch @@ -0,0 +1,172 @@ +--- configure.orig 2022-10-03 21:19:36.313951477 +0000 ++++ configure 2022-10-03 21:44:36.664710705 +0000 +@@ -498,17 +498,17 @@ + + $arch_cc = "cc"; + $arch_ccpp = "CC"; +-$arch_nvcc = "/usr/local/cuda-10.2/bin/nvcc"; ++$arch_nvcc = "nvcc"; + $arch_nvccflags = "-lineinfo --ptxas-options=-v " . +- "-gencode arch=compute_30,code=compute_30 " . +- "-gencode arch=compute_30,code=sm_35 " . +- "-gencode arch=compute_30,code=sm_37 " . + "-gencode arch=compute_50,code=compute_50 " . + "-gencode arch=compute_50,code=sm_50 " . + "-gencode arch=compute_60,code=compute_60 " . + "-gencode arch=compute_60,code=sm_60 " . + "-gencode arch=compute_70,code=compute_70 " . + "-gencode arch=compute_70,code=sm_70 " . ++ "-gencode arch=compute_75,code=sm_75 " . ++ "-gencode arch=compute_80,code=sm_80 " . ++ "-gencode arch=compute_86,code=sm_86 " . + "--ftz=true "; + # "-gencode arch=compute_75,code=sm_75 " . + $arch_gcc = "gcc"; +@@ -634,17 +634,17 @@ + # location of Mesa library and include files; basically does the same + # as OpenGL. This is based on the default instructions from the Mesa + # README; the include files should by default be in /usr/local/include/GL. +-$mesa_dir = "$vmd_library_dir/Mesa"; ++$mesa_dir = "$ENV{'EBROOTMESA'}"; + $mesa_include = "-I$mesa_dir/include"; + $mesa_library = "-L$mesa_dir/lib_$config_arch"; + #$mesa_libs = "-lMesaGL -lMesaGLU"; +-$mesa_libs = "-lMesaGL"; ++$mesa_libs = "-lGL -lGLU"; + $mesa_defines = "-DUSELINEAXES -DVMDMESA -DVMDOPENGL"; + @mesa_cc = (); + @mesa_cu = (); +-@mesa_ccpp = @opengl_ccpp; +-@mesa_h = @opengl_h; +-@mesa_extra = @opengl_extra; ++@mesa_ccpp = (); ++@mesa_h = (); ++@mesa_extra = (); + + + # +@@ -720,10 +720,10 @@ + + ################ FLTK GUI + $fltk_defines = "-DVMDGUI -DVMDFLTK"; +-$fltk_dir = "$vmd_library_dir/fltk"; ++$fltk_dir = "$ENV{'EBROOTFLTK'}"; + $fltk_include = "-I$fltk_dir/include"; + $fltk_library = "-L$fltk_dir/$config_arch"; +-$fltk_libs = "-lfltk -lX11"; ++$fltk_libs = "-lfltk -lX11 -lXfixes -lXcursor -lXinerama"; + #@fltk_cc = ('forms_ui.c'); + @fltk_cu = (); + @fltk_ccpp = ( 'ColorFltkMenu.C', +@@ -783,8 +783,8 @@ + if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; } + $tcl_library = "-L$stock_tcl_library_dir"; + if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; } +-$tcl_libs = "-ltcl8.5"; +-if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; } ++$tcl_libs = "-ltcl8.6"; ++if ($config_tk) { $tcl_libs = "-ltk8.6 -lX11 " . $tcl_libs; } + + @tcl_cc = (); + @tcl_cu = (); +@@ -1006,7 +1006,7 @@ + # This option enables the use of CUDA GPU acceleration functions. + ####################### + $cuda_defines = "-DVMDCUDA -DMSMPOT_CUDA"; +-$cuda_dir = "/usr/local/cuda-10.2"; ++$cuda_dir = "$ENV{'CUDA_HOME'}"; + $cuda_include = ""; + $cuda_library = ""; + $cuda_libs = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart_static -lrt"; +@@ -1215,7 +1215,7 @@ + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-5.0.1-linux64"; + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-5.1.0-linux64"; + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-6.0.0-linux64"; +-$liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-6.5.0-linux64"; ++$liboptix_dir = "$ENV{'EBROOTOPTIX'}"; + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-7.0.0-linux64"; + + # NCSA Blue Waters +@@ -1370,7 +1370,7 @@ + die "LIBPNG option requires ZLIB!"; + } + $libpng_defines = "-DVMDLIBPNG"; +-$libpng_dir = "/Projects/vmd/vmd/lib/libpng"; ++$libpng_dir = "$ENV{'EBROOTLIBPNG'}"; + $libpng_include = "-I$libpng_dir/include"; + $libpng_library = "-L$libpng_dir/lib_$config_arch"; + $libpng_libs = "-lpng16"; +@@ -1398,7 +1398,7 @@ + # OPTIONAL COMPONENT: Data compresssion library + # This may be commented out if not required. + $zlib_defines = "-DVMDZLIB"; +-$zlib_dir = "/Projects/vmd/vmd/lib/zlib"; ++$zlib_dir = "$ENV{'EBROOTZLIB'}"; + $zlib_include = "-I$zlib_dir/include"; + $zlib_library = "-L$zlib_dir/lib_$config_arch"; + $zlib_libs = "-lz"; +@@ -1589,7 +1589,7 @@ + # primitives. + ####################### + $actc_defines = "-DVMDACTC"; +-$actc_dir = "$vmd_library_dir/actc"; ++$actc_dir = "$ENV{'EBROOTACTC'}"; + $actc_include = "-I$actc_dir/include"; + $actc_library = "-L$actc_dir/lib_$config_arch"; + $actc_libs = "-lactc"; +@@ -1604,7 +1604,7 @@ + # OPTIONAL COMPONENT: NetCDF I/O Library (Used by cdfplugin) + ####################### + $netcdf_defines = ""; +-$netcdf_dir = "$vmd_library_dir/netcdf"; ++$netcdf_dir = "$ENV{'EBROOTNETCDF'}"; + $netcdf_include = "-I$netcdf_dir/include"; + $netcdf_library = "-L$netcdf_dir/lib_$config_arch"; + $netcdf_libs = "-lnetcdf"; +@@ -1662,7 +1662,7 @@ + $stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "$conda_root/lib/python3.7/config-3.7m-x86_64-linux-gnu"; + $stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "$conda_root/lib/python3.7/site-packages/numpy/core/include/numpy"; + $stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "$conda_root/lib/python-3.7/site-packages/numpy/core/include"; +- $python_libs = "-fno-lto -lpython3.7m -lpthread"; ++ $python_libs = "$ENV{'PYTHON_LIBRARIES'}" || "-fno-lto -lpython3.7m -lpthread"; + } else { + # $stock_python_include_dir=$ENV{"PYTHON_INCLUDE_DIR"} || "/usr/local/include"; + # $stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "/usr/local/lib"; +@@ -1673,7 +1673,7 @@ + # $stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "/usr/local/lib"; + $stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "$vmd_library_dir/numpy/lib_$config_arch/include"; + $stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/site-packages/numpy/core/include"; +- $python_libs = "-lpython2.5 -lpthread"; ++ $python_libs = "$ENV{'PYTHON_LIBRARIES'}" || "-lpython2.5 -lpthread"; + } + + $python_defines = "-DVMDPYTHON"; +@@ -2593,7 +2593,7 @@ + + if ($config_cuda) { + $arch_nvccflags .= " --machine 64 -O3 $cuda_include"; +- $cuda_library = "-L/usr/local/cuda-10.2/lib64"; ++ $cuda_library = "-L$ENV{'EBROOTCUDA'}/lib64"; + } + + $arch_lex = "flex"; # has problems with vendor lex +@@ -2602,8 +2602,8 @@ + # override code probably date back to RHEL4.x or earlier, and + # they likely serve no useful purpose going forward. + if (!$config_opengl_dispatch) { +- $opengl_dep_libs = "-L/usr/X11R6/lib64 -lGL -lX11"; +- $mesa_libs = "-lMesaGL -L/usr/X11R6/lib64 -lXext -lX11"; ++ $opengl_dep_libs = " -lGL -lX11"; ++ $mesa_libs = "-lGL -lGLU -lXext -lX11"; + } + + # this is to make tcl happy +@@ -3789,7 +3789,7 @@ + + .cu.ptx: + \$(ECHO) "Compiling " \$< " --> " \$*.ptx " ..."; \\ +- \$(NVCC) \$(DEFINES) --use_fast_math $liboptix_include -gencode arch=compute_50,code=compute_50 -ptx \$< $arch_coptout$vmd_arch_dir/\$\@ ++ \$(NVCC) \$(DEFINES) --use_fast_math $liboptix_include -gencode arch=compute_80,code=compute_80 -ptx \$< $arch_coptout$vmd_arch_dir/\$\@ + + .y.o: + From 9bca3ca354b09bbc79e0691125fce4a96102d918 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Oct 2022 09:54:53 +0200 Subject: [PATCH 307/793] fix execution permissions for bin/ngm* for NextGenMap v0.5.5 --- .../n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb b/easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb index 0a2f01375e9..a7e7ef4fe7c 100644 --- a/easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb @@ -34,8 +34,12 @@ preconfigopts += "sed -i 's/zlibstatic/z/g' ../NextGenMap-%(version)s/{src,utils buildopts = ' && cp -r ../%(name)s-%(version)s/bin/ngm-%(version)s/. %(installdir)s/bin/' -# avoid hard overwriting of $LD_LIBRARY_PATH in ngm wrapper script -postinstallcmds = [r"sed -i 's/\(LD_LIBRARY_PATH=[^ ]*\)\"/\1:$LD_LIBRARY_PATH\"/g' %(installdir)s/bin/ngm"] +postinstallcmds = [ + # avoid hard overwriting of $LD_LIBRARY_PATH in ngm wrapper script + r"sed -i 's/\(LD_LIBRARY_PATH=[^ ]*\)\"/\1:$LD_LIBRARY_PATH\"/g' %(installdir)s/bin/ngm", + # fix execution permissions for ngm* binaries/scripts + "chmod a+x %(installdir)s/bin/ngm*", +] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['ngm', 'ngm-core', 'ngm-log', 'ngm-utils', 'oclTool']], From a6fe5e929c7e40029a5996954525b9de5c081b8a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 11 Oct 2022 09:56:55 +0100 Subject: [PATCH 308/793] deprecate use of True to indicate system-toolchain dependency in favour of the more intuitive SYSTEM template --- test/easyconfigs/easyconfigs.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 0fb05afe876..21c4692ec27 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1449,11 +1449,11 @@ def template_easyconfig_test(self, spec): # 4th value is toolchain spec if len(dumped_dep) >= 4: if len(orig_dep) >= 4: - # if True was used to indicate that dependency should use system toolchain, - # then we need to compare the value for the dumped easyconfig more carefully; - # see also https://github.com/easybuilders/easybuild-framework/pull/4069 + # use of `True` is deprecated in favour of the more intuitive `SYSTEM` template if orig_dep[3] is True: - self.assertEqual(dumped_dep[3], EASYCONFIG_CONSTANTS['SYSTEM'][0]) + error_msg = "use of `True` to indicate the system toolchain for dependency " + error_msg += "%s is deprecated, use the `SYSTEM` template instead" % dumped_dep[0] + self.fail(error_msg) else: self.assertEqual(dumped_dep[3], orig_dep[3]) else: From b3f9824e19daf673e9e9fac9740525f34371eb6a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 11 Oct 2022 11:04:26 +0100 Subject: [PATCH 309/793] update easyconfigs to use SYSTEM instead of True in dependencies --- .../__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb | 2 +- .../__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb | 2 +- .../easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb | 2 +- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb | 2 +- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb | 2 +- .../b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb | 4 ++-- .../b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb | 2 +- .../b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb | 2 +- .../b/beagle-lib/beagle-lib-20141202-intel-2015a.eb | 2 +- .../b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb | 2 +- .../b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb | 2 +- .../__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb | 2 +- .../d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb | 2 +- .../__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb | 2 +- .../__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb | 2 +- .../__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb | 2 +- .../__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb | 2 +- .../__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb | 2 +- .../__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb | 2 +- .../__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb | 2 +- .../Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb | 2 +- .../HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb | 4 ++-- .../HPCBIOS_Profilers-20130829-goolf-1.4.10.eb | 6 +++--- .../hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb | 4 ++-- .../hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb | 4 ++-- .../hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb | 4 ++-- .../hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb | 4 ++-- .../hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb | 2 +- .../hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb | 2 +- .../hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb | 2 +- .../hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb | 2 +- .../hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb | 2 +- .../i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb | 2 +- .../i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb | 2 +- ...ModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb | 2 +- .../__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb | 4 ++-- ...plus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb | 2 +- .../MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb | 2 +- .../__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb | 4 ++-- .../__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb | 4 ++-- .../__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb | 2 +- .../__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb | 2 +- .../__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb | 2 +- .../__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb | 2 +- .../__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb | 2 +- .../__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb | 2 +- .../p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 2 +- .../p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb | 2 +- .../p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb | 2 +- .../p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb | 2 +- .../__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb | 2 +- .../__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb | 2 +- .../easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb | 2 +- .../__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb | 2 +- .../__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb | 2 +- .../__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb | 2 +- .../__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb | 2 +- .../__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb | 2 +- .../__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb | 2 +- .../__archive__/r/R/R-3.1.2-intel-2015a-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb | 2 +- .../__archive__/r/R/R-3.2.0-foss-2015a-bare.eb | 2 +- .../__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb | 2 +- .../__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb | 2 +- .../__archive__/r/R/R-3.2.0-intel-2015a-bare.eb | 2 +- .../__archive__/r/R/R-3.2.1-foss-2015b-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb | 2 +- .../__archive__/r/R/R-3.2.1-intel-2015b-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb | 2 +- .../s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb | 2 +- .../Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb | 2 +- .../Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb | 2 +- .../s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb | 2 +- .../s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb | 2 +- .../t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb | 2 +- .../__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb | 4 ++-- .../__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb | 4 ++-- .../__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb | 2 +- .../t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb | 2 +- .../t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb | 2 +- .../t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb | 2 +- .../vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb | 4 ++-- .../vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb | 4 ++-- .../vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb | 4 ++-- .../easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb | 2 +- .../easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb | 2 +- .../x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb | 2 +- .../x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb | 2 +- .../x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb | 2 +- .../easyconfigs/a/ABRA2/ABRA2-2.22-iccifort-2019.5.281.eb | 4 ++-- easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb | 4 ++-- easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb | 4 ++-- ...AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-GCCcore-10.3.0-Java-11.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-GCCcore-11.2.0-Java-11.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-GCCcore-11.3.0-Java-11.eb | 2 +- .../easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-7.3.0.eb | 2 +- .../easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.2.0.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-GCCcore-8.3.0-Java-11.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-GCCcore-9.3.0-Java-11.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2017b.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-foss-2018a-Python-2.7.14.eb | 2 +- easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b.eb | 2 +- easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2019a.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-intel-2017b-Python-2.7.14.eb | 2 +- easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-intel-2018a-Python-3.6.4.eb | 2 +- .../easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../easyconfigs/a/ASTRID/ASTRID-2.2.1-gompi-2019a.eb | 2 +- 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.../easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.2.eb | 2 +- .../easyconfigs/a/Automake/Automake-1.15-GCCcore-5.3.0.eb | 2 +- .../easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/a/Automake/Automake-1.15-GCCcore-6.1.0.eb | 2 +- .../easyconfigs/a/Automake/Automake-1.15-GCCcore-6.2.0.eb | 2 +- .../easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.eb | 2 +- .../a/arcasHLA/arcasHLA-0.2.0-foss-2019b-Python-3.7.4.eb | 2 +- .../easyconfigs/a/aria2/aria2-1.35.0-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/a/aria2/aria2-1.36.0-GCCcore-11.3.0.eb | 2 +- .../easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019a.eb | 2 +- .../easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019b.eb | 2 +- .../a/arpack-ng/arpack-ng-3.7.0-intel-2019b.eb | 2 +- .../artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb | 6 +++--- .../artic-ncov2019-2021.06.24-foss-2020b.eb | 4 ++-- .../b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb | 2 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.../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.3.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.4.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.5.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.3.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-8.1.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.5-GCCcore-5.5.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.4.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.3.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.1.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.2.2-GCCcore-7.4.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.3.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.4.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.5.3-GCCcore-9.3.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.6.1-GCCcore-10.1.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.7.6-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.1.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.7.6-GCCcore-9.4.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.3.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.1.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.8.2-GCCcore-9.5.0.eb | 2 +- .../Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb | 2 +- .../easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb | 2 +- .../b/bcgTree/bcgTree-1.0.10-intel-2018a-Perl-5.26.1.eb | 2 +- .../b/bcgTree/bcgTree-1.1.0-intel-2018b-Perl-5.28.0.eb | 2 +- .../b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb | 2 +- .../b/beagle-lib/beagle-lib-2.1.2-foss-2017a.eb | 2 +- .../b/beagle-lib/beagle-lib-3.0.1-foss-2018a.eb | 2 +- .../b/beagle-lib/beagle-lib-3.0.1-intel-2018a.eb | 2 +- .../beagle-lib/beagle-lib-3.0.2-foss-2018b-CUDA-9.2.88.eb | 4 ++-- .../b/beagle-lib/beagle-lib-3.0.2-foss-2018b.eb | 2 +- .../b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb | 2 +- .../b/beagle-lib/beagle-lib-3.1.2-GCC-8.2.0-2.31.1.eb | 2 +- .../b/beagle-lib/beagle-lib-3.1.2-GCC-9.3.0.eb | 2 +- .../b/beagle-lib/beagle-lib-3.1.2-gcccuda-2019b.eb | 2 +- ...agle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 2 +- .../b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.26-GCCcore-5.5.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb | 2 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.../b/binutils/binutils-2.36.1-GCCcore-10.3.0.eb | 2 +- .../b/binutils/binutils-2.36.1-GCCcore-11.1.0.eb | 2 +- .../b/binutils/binutils-2.36.1-GCCcore-8.4.0.eb | 2 +- .../b/binutils/binutils-2.36.1-GCCcore-9.4.0.eb | 2 +- .../b/binutils/binutils-2.37-GCCcore-11.2.0.eb | 2 +- .../b/binutils/binutils-2.38-GCCcore-11.3.0.eb | 2 +- .../b/binutils/binutils-2.38-GCCcore-12.1.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.38-GCCcore-9.5.0.eb | 2 +- .../b/binutils/binutils-2.39-GCCcore-12.2.0.eb | 2 +- .../b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb | 2 +- .../b/buildenv/buildenv-default-foss-2021a-CUDA-11.3.1.eb | 2 +- .../b/buildenv/buildenv-default-foss-2021b-CUDA-11.4.1.eb | 2 +- .../b/buildenv/buildenv-default-foss-2022a-CUDA-11.7.0.eb | 2 +- .../easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/c/CESM-deps/CESM-deps-2-foss-2021b.eb | 2 +- .../c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb | 2 +- .../c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb | 2 +- .../c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb | 2 +- .../c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb | 2 +- .../c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb | 2 +- .../c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb | 2 +- .../c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb | 2 +- .../c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb | 2 +- .../c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb | 2 +- .../c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb | 2 +- .../c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb | 2 +- .../c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb | 2 +- .../c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb | 2 +- .../c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb | 2 +- .../CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb | 2 +- .../CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.21.1-GCCcore-11.2.0.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.23.1-GCCcore-11.3.0.eb | 2 +- .../c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb | 2 +- .../c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb | 2 +- .../c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb | 2 +- .../c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb | 2 +- .../c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb | 2 +- .../c/CPLEX/CPLEX-12.10-GCCcore-8.3.0-Python-3.7.4.eb | 2 +- easybuild/easyconfigs/c/CPLEX/CPLEX-12.9-GCCcore-8.2.0.eb | 2 +- .../CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb | 4 ++-- .../c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb | 4 ++-- easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-GCC-9.3.0.eb | 2 +- .../easyconfigs/c/CUDA/CUDA-11.0.2-iccifort-2020.1.217.eb | 2 +- easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb | 2 +- .../easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb | 2 +- .../Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb | 4 ++-- .../c/Cantera/Cantera-2.3.0-foss-2017b-Python-2.7.14.eb | 2 +- .../c/Cantera/Cantera-2.3.0-intel-2017a-Python-2.7.13.eb | 2 +- .../c/Cantera/Cantera-2.3.0-intel-2017b-Python-2.7.14.eb | 2 +- .../c/Cantera/Cantera-2.3.0-intel-2018a-Python-2.7.14.eb | 2 +- .../c/Cantera/Cantera-2.4.0-intel-2018a-Python-2.7.14.eb | 2 +- .../c/CheckM/CheckM-1.0.13-foss-2017b-Python-2.7.14.eb | 2 +- .../c/CheckM/CheckM-1.0.13-foss-2017b-Python-3.6.3.eb | 2 +- .../c/CheckM/CheckM-1.0.13-foss-2018b-Python-2.7.15.eb | 2 +- .../c/CheckM/CheckM-1.0.13-intel-2017b-Python-2.7.14.eb | 2 +- .../c/CheckM/CheckM-1.0.13-intel-2017b-Python-3.6.3.eb | 2 +- .../c/CheckM/CheckM-1.0.18-foss-2019a-Python-2.7.15.eb | 2 +- .../c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb | 2 +- .../c/CheckM/CheckM-1.1.2-foss-2019b-Python-3.7.4.eb | 2 +- .../c/CheckM/CheckM-1.1.2-intel-2019b-Python-3.7.4.eb | 2 +- easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021a.eb | 2 +- easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb | 2 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.../easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb | 2 +- easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb | 2 +- .../c/canu/canu-1.8-GCCcore-8.2.0-Perl-5.28.1.eb | 2 +- .../easyconfigs/c/canu/canu-1.8-foss-2017b-Perl-5.26.0.eb | 2 +- .../easyconfigs/c/canu/canu-1.8-foss-2018b-Perl-5.28.0.eb | 2 +- .../c/canu/canu-1.8-intel-2017b-Perl-5.26.0.eb | 2 +- .../easyconfigs/c/canu/canu-1.9-GCCcore-8.3.0-Java-11.eb | 2 +- easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb | 2 +- .../c/canu/canu-2.1.1-GCCcore-9.3.0-Java-11.eb | 2 +- .../easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0-Java-11.eb | 2 +- easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.2.0.eb | 2 +- .../cell2location-0.05-alpha-fosscuda-2020b.eb | 2 +- .../colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb | 2 +- .../c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/d/DB/DB-18.1.40-FCC-4.5.0.eb | 2 +- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.1.0.eb | 2 +- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.3.0.eb | 2 +- .../easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb | 2 +- .../easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb | 2 +- .../easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb | 2 +- .../DOLFIN-2018.1.0.post1-foss-2018a-Python-3.6.4.eb | 2 +- .../DOLFIN-2019.1.0.post0-foss-2019b-Python-3.7.4.eb | 2 +- .../easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb | 4 ++-- .../easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb | 4 ++-- .../easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb | 4 ++-- .../d/Detectron2/Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb | 2 +- .../d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb | 2 +- .../easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb | 2 +- .../DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb | 2 +- .../d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb | 2 +- .../d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb | 2 +- .../e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb | 2 +- .../easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.2.0-2.31.1.eb | 2 +- .../e/EMBOSS/EMBOSS-6.6.0-GCC-8.3.0-Java-11.eb | 2 +- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb | 2 +- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb | 2 +- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb | 2 +- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021b.eb | 2 +- .../EMBOSS-6.6.0-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 2 +- .../e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb | 2 +- .../easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb | 2 +- .../easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2018b.eb | 2 +- .../Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 2 +- .../easyconfigs/e/expat/expat-2.2.0-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/e/expat/expat-2.2.0-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb | 2 +- .../f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb | 4 ++-- .../f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb | 4 ++-- .../FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb | 2 +- .../FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-1.8.eb | 2 +- easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-11.eb | 2 +- easybuild/easyconfigs/f/FastQC/FastQC-0.11.9-Java-11.eb | 2 +- .../FastViromeExplorer-20180422-foss-2019b.eb | 2 +- easybuild/easyconfigs/f/Ferret/Ferret-7.3-intel-2017b.eb | 2 +- easybuild/easyconfigs/f/Ferret/Ferret-7.5.0-foss-2019b.eb | 2 +- easybuild/easyconfigs/f/Fiji/Fiji-20170530.eb | 2 +- easybuild/easyconfigs/f/Fiji/Fiji-20191119-2057.eb | 2 +- easybuild/easyconfigs/f/Fiji/Fiji-20201104-1356.eb | 2 +- .../easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb | 2 +- .../easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb | 2 +- .../FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb | 4 ++-- .../FusionCatcher-1.30-foss-2019b-Python-2.7.16.eb | 4 ++-- .../f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb | 2 +- .../f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb | 2 +- .../f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.1.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.1.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.1.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.2.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-5.5.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.2.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.1.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.1.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.2.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.5.0.eb | 2 +- .../f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb | 2 +- .../fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb | 2 +- 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.../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb | 6 +++--- .../l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb | 2 +- .../easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb | 2 +- .../easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb | 2 +- .../easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb | 2 +- .../l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb | 2 +- .../l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb | 2 +- .../easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/l/libxml2/libxml2-2.9.5-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb | 2 +- .../easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb | 2 +- .../easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.1.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.2.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.4.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.5.0.eb | 2 +- .../MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb | 2 +- .../MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb | 2 +- .../MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb | 2 +- .../MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb | 2 +- .../m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb | 2 +- .../m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb | 2 +- .../m/MATSim/MATSim-14.0-GCCcore-11.2.0-Java-11.eb | 2 +- .../MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb | 2 +- ...Splus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 2 +- .../MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb | 2 +- .../MRtrix-3.0-rc-20191217-foss-2019b-Python-2.7.16.eb | 2 +- .../MRtrix-3.0-rc-20191217-foss-2019b-Python-3.7.4.eb | 2 +- .../m/MRtrix/MRtrix-3.0_RC2-foss-2017a-Python-2.7.13.eb | 2 +- .../m/MRtrix/MRtrix-3.0_RC3-intel-2018a-Python-2.7.14.eb | 2 +- .../easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb | 2 +- .../easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb | 2 +- .../m/Megalodon/Megalodon-2.5.0-foss-2021a-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/m/MiGEC/MiGEC-1.2.9-Java-1.8.eb | 2 +- easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.13-Java-1.8.eb | 2 +- easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.3-Java-1.8.eb | 2 +- .../m/MinCED/MinCED-0.4.2-GCCcore-8.3.0-Java-11.eb | 2 +- .../m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb | 4 ++-- .../m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb | 2 +- .../m/MotionCor2/MotionCor2-1.2.6-GCCcore-8.2.0.eb | 2 +- .../m/MotionCor2/MotionCor2-1.3.1-GCCcore-8.3.0.eb | 2 +- .../m/MotionCor2/MotionCor2-1.3.2-GCCcore-8.3.0.eb | 2 +- .../m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb | 2 +- .../m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb | 2 +- .../m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb | 2 +- .../MuPeXI-1.2.0-foss-2018b-Perl-5.28.0-Python-2.7.15.eb | 2 +- .../m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb | 2 +- .../m/magma/magma-2.3.0-foss-2018a-CUDA-9.1.85.eb | 2 +- .../m/magma/magma-2.6.1-foss-2021a-CUDA-11.3.1.eb | 2 +- .../m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb | 2 +- .../m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb | 2 +- .../m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb | 2 +- .../m/metaWRAP/metaWRAP-1.2-foss-2018b-Python-2.7.15.eb | 2 +- .../m/metaWRAP/metaWRAP-1.2.2-foss-2019a-Python-2.7.15.eb | 4 ++-- .../m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb | 4 ++-- .../m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb | 2 +- .../easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb | 2 +- .../minieigen-0.5.4-intel-2018a-Python-2.7.14.eb | 2 +- easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/m/mold/mold-1.0.0-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/m/mold/mold-1.2.1-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/m/mold/mold-1.3.0-GCCcore-11.3.0.eb | 2 +- .../mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb | 4 ++-- .../mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb | 4 ++-- .../mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb | 4 ++-- .../mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb | 4 ++-- .../easyconfigs/n/NASM/NASM-2.11.08-GCCcore-5.4.0.eb | 2 +- .../n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb | 2 +- .../n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb | 2 +- .../n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb | 2 +- .../n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb | 4 ++-- .../n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb | 4 ++-- easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-1.3.0-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb | 2 +- .../n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-1.8.eb | 2 +- .../easyconfigs/n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-11.eb | 2 +- .../easyconfigs/n/NGS/NGS-2.10.4-GCCcore-8.3.0-Java-11.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-2.10.5-GCCcore-9.3.0.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-11.2.0.eb | 2 +- .../n/NGS/NGS-2.9.1-foss-2018a-Java-1.8.0_162.eb | 2 +- .../n/NGS/NGS-2.9.1-intel-2018a-Java-1.8.0_162.eb | 2 +- .../easyconfigs/n/NGS/NGS-2.9.3-foss-2018b-Java-1.8.eb | 2 +- .../n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb | 2 +- .../n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-19.07.0.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-19.12.0.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-20.01.0.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-20.04.1.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-20.10.0.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-21.03.0.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-21.08.0.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-21.10.6.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-22.04.0.eb | 2 +- .../nanopolish-0.10.2-foss-2018b-Python-2.7.15.eb | 2 +- .../nanopolish-0.10.2-intel-2018b-Python-2.7.15.eb | 2 +- .../nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb | 2 +- .../nanopolish-0.13.2-foss-2020a-Python-3.8.2.eb | 2 +- .../n/nanopolish/nanopolish-0.9.2-intel-2018a.eb | 2 +- .../easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb | 2 +- .../n/numba/numba-0.54.1-foss-2021b-CUDA-11.4.1.eb | 2 +- .../ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb | 4 ++-- .../OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb | 2 +- .../OSU-Micro-Benchmarks-5.9-gompi-2021a-CUDA-11.3.1.eb | 2 +- .../OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb | 2 +- .../OSU-Micro-Benchmarks-5.9-gompi-2022a-CUDA-11.7.0.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb | 2 +- .../easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-4.2.1-foss-2018a.eb | 2 +- .../easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb | 2 +- .../easyconfigs/o/Octave/Octave-4.2.1-intel-2017a-mt.eb | 2 +- .../easyconfigs/o/Octave/Octave-4.2.1-intel-2017a.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-4.2.2-foss-2018a.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-4.4.1-foss-2018b.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019a.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019b.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb | 2 +- .../OpenBabel-2.4.1-intel-2017b-Python-2.7.14.eb | 2 +- .../OpenBabel-2.4.1-intel-2018b-Python-2.7.15.eb | 2 +- .../OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-3.6.6.eb | 2 +- .../OpenBabel/OpenBabel-2.4.1-intel-2019a-Python-3.7.2.eb | 2 +- .../OpenBabel/OpenBabel-3.0.0-gompi-2019b-Python-3.7.4.eb | 2 +- .../OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb | 2 +- .../OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb | 2 +- .../easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb | 4 ++-- .../easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb | 4 ++-- .../easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb | 4 ++-- .../o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb | 4 ++-- .../o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb | 4 ++-- .../o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb | 4 ++-- .../o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb | 4 ++-- .../o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb | 4 ++-- .../o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb | 4 ++-- .../o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-2.7.14.eb | 4 ++-- .../OpenCV-3.4.1-foss-2018a-Python-3.6.4-contrib.eb | 4 ++-- .../o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-3.6.4.eb | 4 ++-- .../o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb | 4 ++-- .../o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-3.6.4.eb | 4 ++-- .../o/OpenCV/OpenCV-3.4.5-foss-2018b-Python-2.7.15.eb | 4 ++-- .../o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-2.7.15.eb | 4 ++-- .../o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-3.7.2.eb | 4 ++-- .../o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-2.7.15.eb | 4 ++-- .../o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-3.7.2.eb | 4 ++-- .../o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-2.7.15.eb | 4 ++-- .../o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb | 4 ++-- .../o/OpenCV/OpenCV-4.2.0-foss-2019b-Python-3.7.4.eb | 4 ++-- .../OpenCV-4.2.0-foss-2020a-Python-3.8.2-contrib.eb | 4 ++-- .../o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb | 4 ++-- .../o/OpenCV/OpenCV-4.2.0-fosscuda-2019b-Python-3.7.4.eb | 4 ++-- .../o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb | 4 ++-- .../o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb | 4 ++-- .../OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb | 8 ++++---- .../o/OpenCV/OpenCV-4.5.3-foss-2021a-contrib.eb | 4 ++-- .../o/OpenCV/OpenCV-4.5.5-foss-2021b-contrib.eb | 4 ++-- .../o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb | 4 ++-- .../o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/o/OpenMS/OpenMS-2.4.0-foss-2018b.eb | 2 +- .../o/OpenRefine/OpenRefine-2.7-Java-1.8.0_144.eb | 2 +- .../easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb | 2 +- .../o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb | 2 +- .../ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb | 2 +- .../ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../p/PCL/PCL-1.8.1-intel-2017b-Python-2.7.14.eb | 2 +- .../PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb | 2 +- .../PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb | 2 +- .../PCMSolver/PCMSolver-1.2.3-iimpi-2019b-Python-3.7.4.eb | 2 +- easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb | 2 +- .../p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb | 2 +- .../p/PIPITS/PIPITS-2.7-foss-2020a-Python-3.8.2.eb | 4 ++-- easybuild/easyconfigs/p/PIPITS/PIPITS-2.8-foss-2021a.eb | 4 ++-- ...Lplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb | 2 +- ...plot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb | 2 +- .../easyconfigs/p/PRSice/PRSice-2.2.12-GCCcore-8.3.0.eb | 2 +- .../easyconfigs/p/PRSice/PRSice-2.3.1-GCCcore-9.3.0.eb | 2 +- .../p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb | 2 +- .../easyconfigs/p/PTESFinder/PTESFinder-1-intel-2017b.eb | 2 +- easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb | 2 +- .../easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 2 +- .../easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 2 +- .../easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 2 +- .../PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb | 2 +- .../p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb | 2 +- .../p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb | 2 +- .../p/PostgreSQL/PostgreSQL-13.4-GCCcore-11.2.0.eb | 2 +- .../p/PostgreSQL/PostgreSQL-14.4-GCCcore-11.3.0.eb | 2 +- .../p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb | 2 +- ...CUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb | 2 +- .../p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb | 2 +- .../PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb | 2 +- .../p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb | 2 +- .../p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb | 2 +- .../p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb | 2 +- .../PyTorch-Lightning-1.5.9-foss-2021a-CUDA-11.3.1.eb | 2 +- .../PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb | 2 +- .../p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 4 ++-- .../p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 2 +- .../p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 4 ++-- .../easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb | 2 +- .../PyTorch/PyTorch-1.7.1-fosscuda-2020a-Python-3.8.2.eb | 2 +- .../easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 2 +- .../easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 2 +- .../p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 2 +- .../easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 2 +- .../p/Python/Python-2.7.18-GCCcore-10.3.0-bare.eb | 2 +- .../p/Python/Python-2.7.18-GCCcore-11.2.0-bare.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb | 2 +- .../p/Python/Python-2.7.18-GCCcore-11.3.0-bare.eb | 2 +- .../p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb | 2 +- .../easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb | 2 +- .../p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb | 2 +- .../easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb | 2 +- .../p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb | 2 +- .../easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb | 2 +- .../easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb | 2 +- .../pangolin-3.1.16-foss-2021b-pangoLEARN-2021-10-18.eb | 2 +- .../pangolin-3.1.16-foss-2021b-pangoLEARN-2021-11-25.eb | 2 +- ...arallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb | 2 +- ...arallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb | 2 +- easybuild/easyconfigs/p/picard/picard-2.18.14-Java-1.8.eb | 2 +- easybuild/easyconfigs/p/picard/picard-2.18.17-Java-1.8.eb | 2 +- .../easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb | 2 +- .../p/pkg-config/pkg-config-0.29.1-GCCcore-5.4.0.eb | 2 +- .../p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb | 2 +- .../p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb | 4 ++-- .../easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb | 4 ++-- .../easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb | 4 ++-- .../easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb | 4 ++-- easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb | 2 +- .../easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb | 2 +- easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb | 2 +- .../p/pybind11/pybind11-2.2.4-foss-2018a-Python-3.6.4.eb | 2 +- .../p/pybind11/pybind11-2.2.4-intel-2018b-Python-3.6.6.eb | 2 +- .../pybind11/pybind11-2.4.3-GCCcore-8.3.0-Python-3.7.4.eb | 2 +- ...python-weka-wrapper3-0.1.11-foss-2019b-Python-3.7.4.eb | 2 +- .../q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb | 2 +- .../q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb | 2 +- .../q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb | 2 +- .../q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb | 2 +- .../q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb | 2 +- .../q/QUAST/QUAST-5.0.2-foss-2020a-Python-3.8.2.eb | 2 +- .../q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb | 2 +- easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb | 2 +- easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021a.eb | 2 +- easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021b.eb | 2 +- .../easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb | 2 +- .../easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb | 2 +- .../q/Qualimap/Qualimap-2.2.1-foss-2019a-R-3.6.0.eb | 2 +- .../q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb | 2 +- .../q/Qualimap/Qualimap-2.2.1-foss-2021b-R-4.1.2.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb | 2 +- .../easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb | 2 +- .../easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb | 2 +- .../easyconfigs/r/R/R-3.3.3-intel-2016b-X11-20160819.eb | 2 +- .../easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 2 +- .../easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 2 +- .../easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb | 2 +- .../easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb | 2 +- .../r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb | 2 +- .../easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb | 2 +- .../easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb | 2 +- .../easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb | 2 +- .../easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb | 2 +- .../easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb | 2 +- .../easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb | 2 +- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb | 2 +- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 4 ++-- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 4 ++-- easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 4 ++-- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 4 ++-- .../r/RDKit/RDKit-2018.09.3-intel-2018b-Python-3.6.6.eb | 2 +- .../r/RDKit/RDKit-2019.09.3-foss-2019b-Python-3.7.4.eb | 2 +- .../r/RDKit/RDKit-2020.03.3-foss-2020a-Python-3.8.2.eb | 2 +- .../r/RDKit/RDKit-2020.03.3-intel-2020a-Python-3.8.2.eb | 2 +- .../r/RDKit/RDKit-2020.09.3-foss-2019b-Python-3.7.4.eb | 2 +- .../r/RELION/RELION-2.1-foss-2018a-CUDA-9.1.85.eb | 2 +- .../easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb | 2 +- .../easyconfigs/r/RNA-Bloom/RNA-Bloom-1.4.3-GCC-11.2.0.eb | 2 +- .../RNA-SeQC/RNA-SeQC-1.1.8-foss-2016b-Java-1.8.0_121.eb | 2 +- .../r/RNA-SeQC/RNA-SeQC-1.1.8-foss-2018b-Java-1.8.eb | 2 +- .../r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb | 2 +- .../r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb | 2 +- .../RStudio-Server-1.2.5033-fosscuda-2019b-Java-11.eb | 4 ++-- .../RStudio-Server-1.2.5042-foss-2019b-Java-11.eb | 4 ++-- .../RStudio-Server-1.3.1093-foss-2020a-Java-11-R-4.0.0.eb | 4 ++-- .../RStudio-Server-1.3.959-foss-2020a-Java-11-R-4.0.0.eb | 4 ++-- .../RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb | 4 ++-- ...RepeatMasker-4.0.8-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb | 2 +- ...ccifort-2017.4.196-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb | 2 +- .../RepeatMasker-4.0.8-intel-2018b-Perl-5.28.0-HMMER.eb | 2 +- .../RepeatMasker-4.0.9-p2-gompi-2019b-HMMER.eb | 2 +- .../easyconfigs/r/RheoTool/RheoTool-5.0-foss-2019b.eb | 2 +- .../easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb | 2 +- .../easyconfigs/r/Rust/Rust-1.56.0-GCCcore-11.2.0.eb | 2 +- .../easyconfigs/r/Rust/Rust-1.60.0-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb | 2 +- .../r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 4 ++-- .../s/SECAPR/SECAPR-1.1.15-foss-2019b-Python-2.7.16.eb | 6 +++--- .../s/SRPRISM/SRPRISM-3.1.1-GCCcore-8.2.0-Java-11.eb | 2 +- .../easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/s/SUMO/SUMO-1.12.0-foss-2021b.eb | 2 +- easybuild/easyconfigs/s/SUMO/SUMO-1.14.1-foss-2021b.eb | 2 +- .../s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb | 2 +- easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb | 2 +- .../SimpleElastix-1.1.0-foss-2019b-Python-3.7.4.eb | 2 +- .../s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb | 2 +- .../easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb | 2 +- ...-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb | 2 +- .../s/Spark/Spark-2.4.0-Hadoop-2.7-Java-1.8.eb | 2 +- .../s/Spark/Spark-2.4.0-foss-2018b-Python-2.7.15.eb | 2 +- ...-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb | 2 +- .../s/Spark/Spark-2.4.0-intel-2018b-Python-2.7.15.eb | 2 +- .../s/Spark/Spark-2.4.0-intel-2018b-Python-3.6.6.eb | 2 +- .../Spark-2.4.5-intel-2019b-Python-3.7.4-Java-1.8.eb | 2 +- .../s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb | 2 +- .../s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb | 2 +- .../s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb | 2 +- easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb | 2 +- .../easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/s/Spark/Spark-3.2.1-foss-2021b.eb | 2 +- .../SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb | 8 ++++---- .../SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb | 8 ++++---- .../s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb | 8 ++++---- .../s/StringTie/StringTie-1.3.5-GCCcore-8.2.0.eb | 2 +- .../s/Subversion/Subversion-1.10.0-foss-2017b.eb | 2 +- .../s/Subversion/Subversion-1.10.0-intel-2017b.eb | 2 +- ...iteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/s/Szip/Szip-2.1-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/s/sbt/sbt-1.0.2-Java-1.8.0_152.eb | 2 +- .../s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb | 2 +- .../s/shovill/shovill-0.9.0-foss-2018a-Python-2.7.14.eb | 4 ++-- .../s/shovill/shovill-1.0.4-foss-2018b-Python-2.7.15.eb | 4 ++-- .../easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb | 4 ++-- .../smooth-topk-1.0-20210817-foss-2021a-CUDA-11.3.1.eb | 2 +- .../snippy/snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb | 2 +- .../snpEff-5.0-GCCcore-9.3.0-Java-13-Python-3.8.2.eb | 2 +- .../s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb | 2 +- .../s/snpEff/snpEff-5.0e-GCCcore-11.2.0-Java-11.eb | 2 +- .../t/THetA/THetA-0.7-foss-2018b-Python-2.7.15.eb | 4 ++-- .../easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/t/TagDust/TagDust-2.33-GCCcore-8.3.0.eb | 2 +- .../TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb | 4 ++-- .../TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb | 2 +- .../t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 2 +- .../t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 2 +- .../TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb | 2 +- .../TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb | 2 +- .../t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb | 2 +- .../easyconfigs/t/Tracer/Tracer-1.7.1-GCCcore-8.2.0.eb | 2 +- .../t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb | 2 +- .../t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb | 2 +- .../t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb | 2 +- .../t/Trim_Galore/Trim_Galore-0.5.0-foss-2018b.eb | 2 +- .../Trim_Galore-0.5.0-intel-2018b-Python-3.6.6.eb | 2 +- .../Trim_Galore-0.6.0-foss-2018b-Python-2.7.15.eb | 2 +- .../Trim_Galore-0.6.0-foss-2018b-Python-3.6.6.eb | 2 +- .../Trim_Galore-0.6.1-foss-2018b-Python-2.7.15.eb | 2 +- .../Trim_Galore-0.6.1-foss-2018b-Python-3.6.6.eb | 2 +- .../Trim_Galore-0.6.2-GCCcore-8.2.0-Java-11.eb | 4 ++-- .../Trim_Galore-0.6.2-foss-2018b-Python-2.7.15.eb | 2 +- .../Trim_Galore-0.6.2-foss-2018b-Python-3.6.6.eb | 2 +- ...rim_Galore-0.6.5-GCCcore-8.3.0-Java-11-Python-3.7.4.eb | 4 ++-- .../Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb | 4 ++-- .../Trim_Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb | 4 ++-- .../t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb | 4 ++-- .../t/Trimmomatic/Trimmomatic-0.38-Java-1.8.eb | 2 +- .../t/Trinity/Trinity-2.10.0-foss-2019b-Python-3.7.4.eb | 4 ++-- .../easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb | 4 ++-- .../easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb | 4 ++-- .../easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017a.eb | 4 ++-- .../easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017b.eb | 4 ++-- .../easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb | 4 ++-- .../easyconfigs/t/Trinity/Trinity-2.8.4-foss-2018b.eb | 4 ++-- .../t/Trinity/Trinity-2.8.5-GCC-8.3.0-Java-11.eb | 2 +- .../Trinity-2.8.5-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 4 ++-- .../t/Trinity/Trinity-2.9.1-foss-2019b-Python-2.7.16.eb | 4 ++-- .../t/Trinity/Trinity-2.9.1-foss-2019b-Python-3.7.4.eb | 4 ++-- .../easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb | 2 +- .../t/topaz/topaz-0.2.5-foss-2021a-CUDA-11.3.1.eb | 2 +- .../torchvision-0.11.1-foss-2021a-CUDA-11.3.1.eb | 2 +- .../torchvision-0.11.3-foss-2021a-CUDA-11.3.1.eb | 2 +- .../easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-9.3.0.eb | 2 +- .../UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb | 2 +- .../UCX-CUDA-1.10.0-GCCcore-10.3.0-CUDA-11.3.1.eb | 2 +- .../UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb | 2 +- .../UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb | 2 +- .../UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb | 2 +- .../u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb | 2 +- .../u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb | 2 +- .../u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb | 2 +- .../Unicycler/Unicycler-0.4.7-foss-2019a-Python-3.7.2.eb | 4 ++-- .../Unicycler/Unicycler-0.4.8-gompi-2020a-Python-3.8.2.eb | 4 ++-- .../u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb | 4 ++-- .../u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb | 4 ++-- easybuild/easyconfigs/u/units/units-2.19-GCCcore-8.2.0.eb | 2 +- .../v/VMD/VMD-1.9.4a43-fosscuda-2019b-Python-3.7.4.eb | 2 +- .../easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb | 2 +- .../VirSorter-20160601-foss-2016a-Perl-5.22.1.eb | 4 ++-- .../Virtuoso-opensource-7.2.6.1-GCC-10.3.0.eb | 2 +- .../vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb | 4 ++-- easybuild/easyconfigs/w/WCT/WCT-4.6.0-Java-11.eb | 2 +- .../easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/x/X11/X11-20160819-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/x/X11/X11-20170129-gimkl-2017a.eb | 4 ++-- easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb | 2 +- .../XGBoost-20171120-intel-2017b-Java-1.8.0_152.eb | 2 +- .../x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb | 2 +- .../x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb | 4 ++-- easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb | 2 +- .../x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb | 2 +- .../x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb | 4 ++-- easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb | 4 ++-- easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.2.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.3.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-9.2.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb | 2 +- .../Xmipp-3.19.04-Apollo-foss-2019a-Python-2.7.15.eb | 2 +- .../Xmipp-3.19.04-Apollo-fosscuda-2019a-Python-2.7.15.eb | 2 +- .../x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb | 2 +- .../x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb | 2 +- .../xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb | 2 +- .../xcb-util-keysyms-0.4.0-intel-2016a.eb | 2 +- .../xcb-util-renderutil-0.3.9-foss-2016a.eb | 2 +- .../xcb-util-renderutil-0.3.9-intel-2016a.eb | 2 +- .../x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb | 2 +- .../x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb | 2 +- .../easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb | 2 +- .../easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb | 2 +- .../x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb | 2 +- .../y/Yade/Yade-2018.02b-intel-2018a-Python-2.7.14.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.1.0.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.1.0.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.5.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.2.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.3.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.4.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.1.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.4.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.2.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.3.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.4.0.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.3.0.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.1.0.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.2.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-9.5.0.eb | 2 +- .../z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb | 2 +- .../z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb | 2 +- .../z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb | 2 +- 1300 files changed, 1446 insertions(+), 1446 deletions(-) diff --git a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb index f40658d1411..539a0958608 100644 --- a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['ANTLR-%(version)s_cpp-headers.patch'] -dependencies = [('Java', '1.7.0_60', '', True)] +dependencies = [('Java', '1.7.0_60', '', SYSTEM)] configopts = "--disable-examples --disable-csharp" diff --git a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb index 8ba4070760d..72a027af04f 100644 --- a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['ANTLR-%(version)s_cpp-headers.patch'] -dependencies = [('Java', '1.7.0_60', '', True)] +dependencies = [('Java', '1.7.0_60', '', SYSTEM)] configopts = "--disable-examples --disable-csharp" diff --git a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb index 31ae0ccb152..0d8e1343e3d 100644 --- a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb @@ -20,7 +20,7 @@ pythonversion = '2.7.10' versionsuffix = "-Python-%s" % pythonversion dependencies = [ - ('Java', '1.8.0_60', '', True), + ('Java', '1.8.0_60', '', SYSTEM), ('Python', pythonversion), ] diff --git a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb index 00631356607..8b6c127a237 100644 --- a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb @@ -20,7 +20,7 @@ pythonversion = '2.7.10' versionsuffix = "-Python-%s" % pythonversion dependencies = [ - ('Java', '1.8.0_66', '', True), + ('Java', '1.8.0_66', '', SYSTEM), ('Python', pythonversion), ] diff --git a/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb index 41b26e296f8..c99f5de5a6b 100644 --- a/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb @@ -19,7 +19,7 @@ patches = [ dependencies = [ ('libpng', '1.6.6'), ('LibTIFF', '4.0.3'), - ('Java', '1.7.0_15', '', True), + ('Java', '1.7.0_15', '', SYSTEM), ('lynx', '2.8.7'), ('makedepend', '1.0.4'), ('imake', '1.0.5'), diff --git a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb index 938cb4bc7e4..174260cddaf 100644 --- a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb @@ -14,7 +14,7 @@ sources = ['%(name)s_%(version)s.tar.gz'] java = 'Java' javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) -dependencies = [(java, javaver, '', True)] +dependencies = [(java, javaver, '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb index 83c91ab617b..01cd8fffd9e 100644 --- a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb @@ -14,7 +14,7 @@ sources = ['%(name)s_%(version)s.tar.gz'] java = 'Java' javaver = '1.8.0_74' versionsuffix = '-%s-%s' % (java, javaver) -dependencies = [(java, javaver, '', True)] +dependencies = [(java, javaver, '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb index eb31afb5518..ec0b679c595 100644 --- a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb @@ -13,9 +13,9 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['beagle_release_%s.tar.gz' % version.replace('.', '_')] -dependencies = [('Java', '1.7.0_80', '', True)] +dependencies = [('Java', '1.7.0_80', '', SYSTEM)] -builddependencies = [('Autotools', '20150215', '', True)] +builddependencies = [('Autotools', '20150215', '', SYSTEM)] # parallel build does not work (to test) parallel = 1 diff --git a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb index eba16d5a4e3..ac6f731032d 100644 --- a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} # svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib sources = [SOURCE_TGZ] -dependencies = [('Java', '1.7.0_15', '', True)] +dependencies = [('Java', '1.7.0_15', '', SYSTEM)] builddependencies = [('Autotools', '20150215', '', ('GCC', '4.7.2'))] diff --git a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb index 6d20b44133f..371db8bef3c 100644 --- a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} # svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib sources = [SOURCE_TGZ] -dependencies = [('Java', '1.7.0_15', '', True)] +dependencies = [('Java', '1.7.0_15', '', SYSTEM)] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb index 0349d94e2ac..939c36e304f 100644 --- a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb +++ b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} # svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib sources = [SOURCE_TGZ] -dependencies = [('Java', '1.8.0_31', '', True)] +dependencies = [('Java', '1.8.0_31', '', SYSTEM)] builddependencies = [('Autotools', '20150215')] preconfigopts = './autogen.sh && ' diff --git a/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb b/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb index 847f0357417..0cfcc327bdb 100644 --- a/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb +++ b/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb @@ -30,7 +30,7 @@ dependencies = [ ('Boost', '1.51.0', '-Python-2.7.3'), ('SAMtools', '0.1.18'), ('Perl', '5.16.3', '-bare'), - ('Java', '1.7.0_10', '', True), + ('Java', '1.7.0_10', '', SYSTEM), ('libpng', '1.5.13'), ] diff --git a/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb b/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb index 3354b93931c..0b3d2f04c2b 100644 --- a/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb +++ b/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb @@ -30,7 +30,7 @@ dependencies = [ ('Boost', '1.51.0', '-Python-2.7.3'), ('SAMtools', '0.1.18'), ('Perl', '5.16.3', '-bare'), - ('Java', '1.7.0_10', '', True), + ('Java', '1.7.0_10', '', SYSTEM), ('libpng', '1.5.13'), ] diff --git a/easybuild/easyconfigs/__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb b/easybuild/easyconfigs/__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb index fc4d0275894..28db135235f 100644 --- a/easybuild/easyconfigs/__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb +++ b/easybuild/easyconfigs/__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = ['cplex_studio%s.linux-x86-64.bin' % ''.join(version.split('.'))] dependencies = [ - ('Java', '1.8.0_66', '', True), + ('Java', '1.8.0_66', '', SYSTEM), ] moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb index 77e43460d5c..5705d1a9f0d 100644 --- a/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb @@ -46,7 +46,7 @@ dependencies = [ ('CGAL', '4.0', versionsuffix), ('PETSc', '3.3-p2', versionsuffix), ('SLEPc', '3.3-p1', versionsuffix), - ('MTL4', '4.0.8878', '', True), + ('MTL4', '4.0.8878', '', SYSTEM), ('Trilinos', '10.12.2', versionsuffix), ('Sphinx', '1.1.3', versionsuffix), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb index f6b89c67c7a..851a565e755 100644 --- a/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb @@ -42,7 +42,7 @@ dependencies = [ ('CGAL', '4.7', versionsuffix), ('PETSc', '3.6.3', versionsuffix), ('SLEPc', '3.6.2', versionsuffix), - ('MTL4', '4.0.9555', '', True), + ('MTL4', '4.0.9555', '', SYSTEM), ('HDF5', '1.8.15-patch1'), ('Trilinos', '12.4.2', versionsuffix), ('Sphinx', '1.3.3', versionsuffix), diff --git a/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb index 573a00a1859..4c53065ba15 100644 --- a/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb @@ -23,7 +23,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.2.0'), - ('Java', '1.7.0_10', '', True), + ('Java', '1.7.0_10', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb index cfcf1c4b41a..c5f9edb822c 100644 --- a/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb @@ -23,7 +23,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.2.0'), - ('Java', '1.7.0_10', '', True), + ('Java', '1.7.0_10', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb b/easybuild/easyconfigs/__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb index 3968d910aa4..5bb43ab8b18 100644 --- a/easybuild/easyconfigs/__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} sources = ['otp_src_%(version)s.tar.gz'] source_urls = ['http://www.erlang.org/download'] -builddependencies = [('Java', '1.7.0_45', '', True)] +builddependencies = [('Java', '1.7.0_45', '', SYSTEM)] configopts = '--with-javac ' diff --git a/easybuild/easyconfigs/__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb index d05befd06c3..b12f25299be 100644 --- a/easybuild/easyconfigs/__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb @@ -18,7 +18,7 @@ dependencies = [ ('cURL', '7.27.0'), ('ncurses', '5.9'), ('libreadline', '6.2'), - ('Java', '1.7.0_10', '', True), + ('Java', '1.7.0_10', '', SYSTEM), ] parallel = 1 diff --git a/easybuild/easyconfigs/__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb index 2f7b37d7ff4..640ab72c71a 100644 --- a/easybuild/easyconfigs/__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb @@ -16,7 +16,7 @@ dependencies = [ ] builddependencies = [ - ('GHC', '6.12.3', '', True), + ('GHC', '6.12.3', '', SYSTEM), ('libxslt', '1.1.28'), ] diff --git a/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb b/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb index 7a5dd73b3c9..8db9f79f94f 100644 --- a/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ftp.gnu.org/gnu/gmp'] builddependencies = [ - ('Autotools', '20150215', '', True), + ('Autotools', '20150215', '', SYSTEM), ] # enable C++ interface diff --git a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb index 4634a7fb1a9..3caf8585701 100644 --- a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb @@ -26,7 +26,7 @@ dependencies = [ ('Ghostscript', '9.14'), ('GLib', '2.40.0'), ('GTS', '0.7.6'), - ('Java', '1.7.0_60', '', True), + ('Java', '1.7.0_60', '', SYSTEM), ('libpng', '1.6.12'), ('Pango', '1.36.7'), ('Perl', '5.20.0'), diff --git a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb index c9fd0d8f277..f0c9457cf81 100644 --- a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb @@ -28,7 +28,7 @@ dependencies = [ ('fontconfig', '2.11.94'), ('Ghostscript', '9.16'), ('GTS', '0.7.6', glibsuff), - ('Java', '1.7.0_80', '', True), + ('Java', '1.7.0_80', '', SYSTEM), ('libpng', '1.6.17'), ('Pango', '1.37.2'), ('Perl', '5.20.0'), diff --git a/easybuild/easyconfigs/__archive__/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb index 1b8304beca1..936ae21c317 100644 --- a/easybuild/easyconfigs/__archive__/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb @@ -25,8 +25,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} dependencies = [ ('GDB', '7.5.1'), - ('TotalView', '8.12.0-0', '-linux-x86-64', True), # provides MemoryScape - ('icc', '2013.5.192', '', True), # provides IDB in ictce/5.3.0 compatible mode + ('TotalView', '8.12.0-0', '-linux-x86-64', SYSTEM), # provides MemoryScape + ('icc', '2013.5.192', '', SYSTEM), # provides IDB in ictce/5.3.0 compatible mode ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb index a39dfd95472..6a56ae85cc2 100644 --- a/easybuild/easyconfigs/__archive__/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb @@ -21,9 +21,9 @@ description = """Common Set of Profilers""" toolchain = {'name': 'goolf', 'version': '1.4.10'} dependencies = [ - ('VTune', '2013_update10', '', True), - ('Inspector', '2013_update6', '', True), - ('itac', '8.0.0.011', '', True), + ('VTune', '2013_update10', '', SYSTEM), + ('Inspector', '2013_update6', '', SYSTEM), + ('itac', '8.0.0.011', '', SYSTEM), ('PAPI', '5.0.1'), ('Valgrind', '3.8.1'), ('binutils', '2.22'), # this one provides gprof diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb index 9272f98ff58..fac7767346e 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb @@ -23,8 +23,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), - ('vsc-mympirun', '3.4.2', '', True), - ('vsc-base', '2.1.2', '', True), + ('vsc-mympirun', '3.4.2', '', SYSTEM), + ('vsc-base', '2.1.2', '', SYSTEM), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb index a096633f0b1..f619e97afdd 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb @@ -23,8 +23,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), - ('vsc-mympirun', '3.4.2', '', True), - ('vsc-base', '2.1.2', '', True), + ('vsc-mympirun', '3.4.2', '', SYSTEM), + ('vsc-base', '2.1.2', '', SYSTEM), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb index c0a03ce83e5..eb3c96bcc41 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb @@ -23,8 +23,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), - ('vsc-mympirun', '3.4.2', '', True), - ('vsc-base', '2.1.2', '', True), + ('vsc-mympirun', '3.4.2', '', SYSTEM), + ('vsc-base', '2.1.2', '', SYSTEM), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb index b6761f74452..90c502a0495 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb @@ -23,8 +23,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), - ('vsc-mympirun', '3.4.2', '', True), - ('vsc-base', '2.1.2', '', True), + ('vsc-mympirun', '3.4.2', '', SYSTEM), + ('vsc-base', '2.1.2', '', SYSTEM), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb index f8c93660f1c..858b4f06340 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', True), + ('setuptools', '1.4.2', '', SYSTEM), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb index bcf97f426c7..e19609bcd3b 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', True), + ('setuptools', '1.4.2', '', SYSTEM), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb index 5a2ff293ea6..050fc9722ee 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', True), + ('setuptools', '1.4.2', '', SYSTEM), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb index b4fa5862100..8cec50e09ab 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', True), + ('setuptools', '1.4.2', '', SYSTEM), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb index 7cd4104ad9f..92eb557b169 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', True), + ('setuptools', '1.4.2', '', SYSTEM), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb b/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb index 3f166576635..f0bc1aefaff 100644 --- a/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb +++ b/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb @@ -13,7 +13,7 @@ source_urls = ['http://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s sources = ['%(namelower)s-%(version)s-64-bit.tar.gz'] dependencies = [ - ('Java', '1.7.0_80', '', True), + ('Java', '1.7.0_80', '', SYSTEM), ('Perl', '5.20.3'), ('libgd', '2.1.1'), ('Python', '2.7.10'), diff --git a/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb b/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb index 2388f280096..ec5a5e2789d 100644 --- a/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb +++ b/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb @@ -23,7 +23,7 @@ checksums = [ ] dependencies = [ - ('Java', '1.7.0_80', '', True), + ('Java', '1.7.0_80', '', SYSTEM), ('Perl', '5.20.3'), ('libgd', '2.1.1'), ('Python', '2.7.10'), diff --git a/easybuild/easyconfigs/__archive__/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/__archive__/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb index dafa45afa95..a7381adc66f 100644 --- a/easybuild/easyconfigs/__archive__/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/__archive__/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb @@ -20,7 +20,7 @@ java = 'Java' javaver = '1.7.0_75' versionsuffix = '-%s-%s' % (java, javaver) -builddependencies = [('ant', '1.9.6', '-Java-1.7.0_75', True)] +builddependencies = [('ant', '1.9.6', '-Java-1.7.0_75', SYSTEM)] dependencies = [('MPJ-Express', '0.44', '%(versionsuffix)s')] diff --git a/easybuild/easyconfigs/__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb b/easybuild/easyconfigs/__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb index fe336c46e0c..d334e3cb6ea 100644 --- a/easybuild/easyconfigs/__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb @@ -26,7 +26,7 @@ unpack_options = '--strip-components=1' builddependencies = [ ('CMake', '3.4.3'), - ('Autotools', '20150215', '', True), + ('Autotools', '20150215', '', SYSTEM), ] dependencies = [ @@ -34,7 +34,7 @@ dependencies = [ ('zlib', '1.2.8'), ('samblaster', '0.1.24'), ('SAMtools', '1.3.1'), - ('Sambamba', '0.6.6', '', True), + ('Sambamba', '0.6.6', '', SYSTEM), ('gawk', '4.0.2'), ] diff --git a/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb index 92964498140..904997dd1d9 100644 --- a/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] sources = ['stable_release-%s.zip' % version.replace('.', '-')] dependencies = [ - ('Java', '1.7.0_79', '', True), + ('Java', '1.7.0_79', '', SYSTEM), ('Python', '2.7.9'), ('HDF5', '1.8.9'), ('libxml2', '2.9.2'), diff --git a/easybuild/easyconfigs/__archive__/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/__archive__/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb index e553dd3905a..ac36c94964b 100644 --- a/easybuild/easyconfigs/__archive__/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/__archive__/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb @@ -24,7 +24,7 @@ versionsuffix = '-%s-%s' % (java, javaver) builddependencies = [('CMake', '2.8.12')] dependencies = [ - (java, javaver, '', True), + (java, javaver, '', SYSTEM), ] # compile JNI wrapper library as described in docs diff --git a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb index 4231bf81f8c..3a1bccbc96e 100644 --- a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb +++ b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb @@ -31,8 +31,8 @@ dependencies = [ ('libpng', '1.6.12'), ('LibTIFF', '4.0.3'), ('JasPer', '1.900.1'), - ('Java', '1.7.0_79', '', True), - ('ant', '1.9.3', '-Java-%(javaver)s', True), + ('Java', '1.7.0_79', '', SYSTEM), + ('ant', '1.9.3', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.40.0') ] diff --git a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb index bf5ac8dc56d..b495fa3ffb7 100644 --- a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb @@ -31,8 +31,8 @@ dependencies = [ ('libpng', '1.6.12'), ('LibTIFF', '4.0.3'), ('JasPer', '1.900.1'), - ('Java', '1.7.0_60', '', True), - ('ant', '1.9.3', '-Java-%(javaver)s', True), + ('Java', '1.7.0_60', '', SYSTEM), + ('ant', '1.9.3', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.40.0') ] diff --git a/easybuild/easyconfigs/__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb index 8ad72ec52f4..3599c26e381 100644 --- a/easybuild/easyconfigs/__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb @@ -16,7 +16,7 @@ dependencies = [ ] builddependencies = [ - ('FCM', '2.3.1', '', True), + ('FCM', '2.3.1', '', SYSTEM), ('Perl', '5.16.3'), ] diff --git a/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb index ba3147aeda1..41390bba2c2 100644 --- a/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} dependencies = [ ('make', '3.82'), - ('Java', '1.7.0_10', '', True), + ('Java', '1.7.0_10', '', SYSTEM), ('Bash', '4.2'), ('tcsh', '6.18.01'), ('Tcl', '8.5.12'), diff --git a/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb index e1d90973574..ea816765bb3 100644 --- a/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} dependencies = [ ('make', '3.82'), - ('Java', '1.7.0_10', '', True), + ('Java', '1.7.0_10', '', SYSTEM), ('Bash', '4.2'), ('tcsh', '6.18.01'), ('Tcl', '8.5.12'), diff --git a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb index 9948217fd4e..239d653b543 100644 --- a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb @@ -7,7 +7,7 @@ description = "PASHA is a parallel short read assembler for large genomes using toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -dependencies = [('tbb', '4.0.5.339', '', True)] +dependencies = [('tbb', '4.0.5.339', '', SYSTEM)] source_urls = ['http://downloads.sourceforge.net/pasha'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb index 4043dd5630c..c658a85d703 100644 --- a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb @@ -8,7 +8,7 @@ description = "PASHA is a parallel short read assembler for large genomes using toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -dependencies = [('tbb', '4.0.5.339', '', True)] +dependencies = [('tbb', '4.0.5.339', '', SYSTEM)] source_urls = ['http://downloads.sourceforge.net/pasha'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb index 161ca2d3837..7c33ed3c62f 100644 --- a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb @@ -8,7 +8,7 @@ description = "PASHA is a parallel short read assembler for large genomes using toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -dependencies = [('tbb', '4.0.5.339', '', True)] +dependencies = [('tbb', '4.0.5.339', '', SYSTEM)] source_urls = ['http://downloads.sourceforge.net/pasha'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index 8b0668a68f1..8391bc11951 100644 --- a/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -19,7 +19,7 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2014b'} dependencies = [ - ('Java', '1.7.0_60', '', True), + ('Java', '1.7.0_60', '', SYSTEM), ('libreadline', '6.3'), ('zlib', '1.2.8'), # OS dependency should be preferred if the os version is more recent then this version, diff --git a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb index e8adea5cdda..5afdb61e1c4 100644 --- a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb @@ -20,7 +20,7 @@ source_urls = [ mpich_opts = '--enable-static' dependencies = [ - ('pscom', '5.0.48-1', '', True), + ('pscom', '5.0.48-1', '', SYSTEM), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb index 9bf66b57282..0b59ed106c8 100644 --- a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb +++ b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb @@ -20,7 +20,7 @@ mpich_opts = '--enable-static' threaded = True dependencies = [ - ('pscom', '5.0.48-1', '', True), + ('pscom', '5.0.48-1', '', SYSTEM), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb index 8251dde430d..9c841513aa2 100644 --- a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb @@ -17,7 +17,7 @@ source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] mpich_opts = '--enable-static' dependencies = [ - ('pscom', '5.0.48-1', '', True), + ('pscom', '5.0.48-1', '', SYSTEM), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb index c6290e63183..09cc0738ddc 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.5.13'), # for plotting in R - ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_10', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb index b23784df275..cff665b0ada 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.5.13'), # for plotting in R - ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_10', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb index 4bb85edabe4..7d9a9a6b9be 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.5.13'), # for plotting in R - ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_10', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb index b5a30ff434c..70a3f64db0d 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.5.13'), # for plotting in R - ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_10', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb index 419fa691885..8fcddd02617 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.2'), # for plotting in R - ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_15', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb index 2437804b50b..cd8a6bcddf6 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.2'), # for plotting in R - ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_15', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb index c0064ba6a8c..a85fdf5d8fc 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.2'), # for plotting in R - ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_21', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb index 3b03bc30042..8939ec6a4eb 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.2'), # for plotting in R - ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_21', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb index 7db65a77f3e..edd7812782e 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.6'), # for plotting in R - ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_21', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb index 1c63079ab4a..5aa63fa961d 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.6'), # for plotting in R - ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_21', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb index ea1488b7501..b3be0a49a90 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.6'), # for plotting in R - ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_15', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb index 72798af0c69..bb2cdf29ef3 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.6'), # for plotting in R - ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_15', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb index 7b3d9ff4712..cac8a78c01f 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.9'), # for plotting in R - ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb index 4125b82ac4e..faed73f4aef 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.9'), # for plotting in R - ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb index 0b46e45f459..e9736a0d521 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb @@ -17,7 +17,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.12'), # for plotting in R ('libjpeg-turbo', '1.3.1'), # for plotting in R - ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb index 33df27d4460..8f2c4740b2d 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb @@ -17,7 +17,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.12'), # for plotting in R ('libjpeg-turbo', '1.3.1'), # for plotting in R - ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb index 3462ebf3f2c..f55402b39c8 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.12'), # for plotting in R ('libjpeg-turbo', '1.3.1'), # for plottting in R - ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb index 32f9e3876e9..cfb1fdded86 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb index 8dfe1121a12..6e9bb7dd130 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a-bare.eb index 95f4896bccf..c704735c37c 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb index 20b83d30bca..a2c3729ee62 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb index 2b252579399..c96c15e9389 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('NLopt', '2.4.2'), # for nloptr diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb index 1992cbe8043..db6599ad293 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('NLopt', '2.4.2'), # for nloptr diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-foss-2015a-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-foss-2015a-bare.eb index 83033319bd9..3de945fb60b 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-foss-2015a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb index 712ca683f37..35f77ae5f85 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb index fc8747efae8..034bec8b1d3 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.43.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb index dec3fef7965..9789a570017 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ] diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-intel-2015a-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-intel-2015a-bare.eb index 68941ac7809..282eb2bede6 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-intel-2015a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b-bare.eb index f4738f44f4b..f37ad6d3f33 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb index eb6d134dc02..77140a3bb18 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.43.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb index bf999bcdca7..4b3e1115ed6 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.43.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b-bare.eb index ad909a5e62b..25e622f04e6 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb index 28a924627e0..b00f07b4b09 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.43.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb index dba91bd2533..986af941152 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.45.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb index b503f4c6397..8bde637585c 100644 --- a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [ ('Boost', '1.55.0', versionsuffix), - ('tbb', '4.0.5.339', '', True), + ('tbb', '4.0.5.339', '', SYSTEM), ('Jellyfish', '2.1.3'), ('g2log', '1.0'), ] diff --git a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb index c80c41e1d54..93274668b83 100644 --- a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb @@ -27,7 +27,7 @@ builddependencies = [ dependencies = [ ('Boost', '1.59.0', versionsuffix), - ('tbb', '4.3.6.211', '', True), + ('tbb', '4.3.6.211', '', SYSTEM), ('Jellyfish', '2.2.3'), ('g2log', '1.0'), ] diff --git a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb index b4805f08e04..37c7bd731e4 100644 --- a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb @@ -29,7 +29,7 @@ builddependencies = [ dependencies = [ ('Boost', '1.59.0', versionsuffix), - ('tbb', '4.3.6.211', '', True), + ('tbb', '4.3.6.211', '', SYSTEM), ('Jellyfish', '2.2.4'), ('g2log', '1.0'), ] diff --git a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb index 878c68876e0..9317f21af8c 100644 --- a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb @@ -24,7 +24,7 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ ('Boost', '1.59.0', versionsuffix), - ('tbb', '4.3.6.211', '', True), + ('tbb', '4.3.6.211', '', SYSTEM), ('Jellyfish', '2.2.3'), ] builddependencies = [('CMake', '3.2.3')] diff --git a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb index 7699ae06d5a..0f6804b6b3c 100644 --- a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb @@ -24,7 +24,7 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ ('Boost', '1.59.0', versionsuffix), - ('tbb', '4.3.6.211', '', True), + ('tbb', '4.3.6.211', '', SYSTEM), ('Jellyfish', '2.2.4'), ] builddependencies = [('CMake', '3.2.3')] diff --git a/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb index f895fa63df1..dffa4ab145e 100644 --- a/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb @@ -16,7 +16,7 @@ source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s' install_cmd = "cp -a %(namelower)s_zip/* %(installdir)s && chmod +x %(installdir)s/%(namelower)s" dependencies = [ - ('FastQC', '0.10.1', '-Java-1.7.0_80', True), + ('FastQC', '0.10.1', '-Java-1.7.0_80', SYSTEM), ('cutadapt', '1.5', '-Python-2.7.10'), ] diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb index 821333d6ef7..abd5e0edeaa 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb @@ -19,8 +19,8 @@ sources = ['v%(version)s.tar.gz'] patches = ['Trinity-%(version)s_plugins-Makefile.patch'] dependencies = [ - ('Java', '1.7.0_80', '', True), - ('ant', '1.9.6', '-Java-%(javaver)s', True), + ('Java', '1.7.0_80', '', SYSTEM), + ('ant', '1.9.6', '-Java-%(javaver)s', SYSTEM), ('ncurses', '5.9'), ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb index 014e8ca4110..7fb8a37a67b 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb @@ -19,8 +19,8 @@ sources = ['v%(version)s.tar.gz'] patches = ['Trinity-2.0.4_plugins-Makefile.patch'] dependencies = [ - ('Java', '1.7.0_80', '', True), - ('ant', '1.9.6', '-Java-%(javaver)s', True), + ('Java', '1.7.0_80', '', SYSTEM), + ('ant', '1.9.6', '-Java-%(javaver)s', SYSTEM), ('ncurses', '5.9'), ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb index 71643e32bd6..063da9c3d98 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - (java, javaver, '', True), + (java, javaver, '', SYSTEM), ('ant', '1.9.6', '-%s-%s' % (java, javaver), True), ('Bowtie', '1.1.2'), ('Bowtie2', '2.2.6'), diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb index dcb9ea5cadb..2092bcc77db 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb @@ -24,7 +24,7 @@ java = 'Java' javaver = '1.7.0_10' dependencies = [ - (java, javaver, '', True), + (java, javaver, '', SYSTEM), ('ant', '1.8.4', '-%s-%s' % (java, javaver), True), ('ncurses', '5.9'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb index 7f5d5792225..afb90c64534 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb @@ -25,7 +25,7 @@ java = 'Java' javaver = '1.7.0_10' dependencies = [ - (java, javaver, '', True), + (java, javaver, '', SYSTEM), ('ant', '1.8.4', '-%s-%s' % (java, javaver), True), ('ncurses', '5.9'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb index f6e15e437ab..10bbd992eac 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb @@ -23,7 +23,7 @@ java = 'Java' javaver = '1.7.0_15' dependencies = [ - (java, javaver, '', True), + (java, javaver, '', SYSTEM), ('ant', '1.9.0', '-%s-%s' % (java, javaver), True), ('ncurses', '5.9'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb index dfd259613d8..50efb697da2 100644 --- a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb @@ -16,8 +16,8 @@ python = 'Python' pyver = '2.7.6' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - ('vsc-processcontrol', '1.0', '', True), - ('vsc-mympirun', version, '', True), + ('vsc-processcontrol', '1.0', '', SYSTEM), + ('vsc-mympirun', version, '', SYSTEM), (python, pyver), ('SCOOP', '0.6.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb index 1bbd44502a0..8afa94b6137 100644 --- a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb @@ -16,8 +16,8 @@ python = 'Python' pyver = '2.7.10' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', True), - ('vsc-mympirun', '3.4.2', '', True), + ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', SYSTEM), + ('vsc-mympirun', '3.4.2', '', SYSTEM), (python, pyver), ('SCOOP', '0.6.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb index 24d1ff604f7..f2a99790fa6 100644 --- a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb @@ -16,8 +16,8 @@ python = 'Python' pyver = '2.7.10' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', True), - ('vsc-mympirun', '3.4.2', '', True), + ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', SYSTEM), + ('vsc-mympirun', '3.4.2', '', SYSTEM), (python, pyver), ('SCOOP', '0.6.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb index f5d80fe9e55..99d0531e740 100644 --- a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb +++ b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.4', '', True), + ('gettext', '0.19.4', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb index 4c118e934ff..9c13936bba0 100644 --- a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215', '', ('GCC', '4.7.2')), - ('gettext', '0.18.2', '', True), + ('gettext', '0.18.2', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb index 43117900f60..df2d19b7d0b 100644 --- a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.18.2', '', True), + ('gettext', '0.18.2', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb index 63e623f082d..092e66d8068 100644 --- a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb @@ -20,7 +20,7 @@ pyver = '2.7.9' versionsuffix = '-Python-%s' % pyver dependencies = [ - ('Java', '1.8.0_40', '', True), + ('Java', '1.8.0_40', '', SYSTEM), ('Python', pyver), # should have a working sqlite, and provide numpy/mpi4py ('LibTIFF', '4.0.4beta'), ('HDF5', '1.8.14'), diff --git a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb index 18d8b11833b..3f34c8c15f5 100644 --- a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb +++ b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb @@ -12,6 +12,6 @@ sources = ['Xmipp-%(version)s-src.tar.gz'] toolchain = {'name': 'goolf', 'version': '1.4.10'} # note: all other dependencies are taken care of by Xmipp itself -dependencies = [('Java', '1.7.0_80', '', True)] +dependencies = [('Java', '1.7.0_80', '', SYSTEM)] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb index d6d8c64ef43..294af452fee 100644 --- a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb @@ -20,7 +20,7 @@ pyver = '2.7.9' versionsuffix = '-Python-%s' % pyver dependencies = [ - ('Java', '1.8.0_40', '', True), + ('Java', '1.8.0_40', '', SYSTEM), ('Python', pyver), # should have a working sqlite, and provide numpy/mpi4py ('LibTIFF', '4.0.4beta'), ('HDF5', '1.8.14'), diff --git a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.22-iccifort-2019.5.281.eb b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.22-iccifort-2019.5.281.eb index 855e80e9b9d..29a1e735bcb 100644 --- a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.22-iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.22-iccifort-2019.5.281.eb @@ -16,10 +16,10 @@ checksums = [ '05090efb306fc84d09f007a848ce0d0472f8633633b0a6eaf86ab075d092bc0d', # ABRA2-2.22_fix-Makefile.patch ] -builddependencies = [('Maven', '3.6.3', '', True)] +builddependencies = [('Maven', '3.6.3', '', SYSTEM)] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('BWA', '0.7.17'), ] diff --git a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb index f62a0b1e28b..b06c4f9ab4d 100644 --- a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb @@ -16,10 +16,10 @@ checksums = [ '05090efb306fc84d09f007a848ce0d0472f8633633b0a6eaf86ab075d092bc0d', # ABRA2-2.22_fix-Makefile.patch ] -builddependencies = [('Maven', '3.6.3', '', True)] +builddependencies = [('Maven', '3.6.3', '', SYSTEM)] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('BWA', '0.7.17'), ] diff --git a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb index f93ab230e6b..842e9e8cdfe 100644 --- a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb @@ -16,10 +16,10 @@ checksums = [ '05090efb306fc84d09f007a848ce0d0472f8633633b0a6eaf86ab075d092bc0d', # ABRA2-2.22_fix-Makefile.patch ] -builddependencies = [('Maven', '3.6.3', '', True)] +builddependencies = [('Maven', '3.6.3', '', SYSTEM)] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('BWA', '0.7.17'), ] diff --git a/easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb b/easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb index c9a3002ee86..176bd70202f 100644 --- a/easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb +++ b/easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb @@ -21,7 +21,7 @@ checksums = ['2d361fcc2b800c3daaf25692988af6105669cba2ff513aba82f36089beb2839f'] dependencies = [ ('Perl', '5.32.0'), - ('Java', '13', '', True), + ('Java', '13', '', SYSTEM), ('BioPerl', '1.7.8'), ('HMMER', '3.3.2'), ('EMBOSS', '6.6.0', local_javasuffix), diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb index 7f7064ef519..740009f42a3 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb @@ -21,7 +21,7 @@ checksums = [ ] builddependencies = [('binutils', '2.35')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.3.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.3.0-Java-11.eb index e1357bf2785..dca4fd3a96b 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.3.0-Java-11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.3.0-Java-11.eb @@ -21,7 +21,7 @@ checksums = [ ] builddependencies = [('binutils', '2.36.1')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.2.0-Java-11.eb index 05e3b23c3c8..10c24b2e952 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.2.0-Java-11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.2.0-Java-11.eb @@ -22,7 +22,7 @@ checksums = [ builddependencies = [('binutils', '2.37')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.3.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.3.0-Java-11.eb index 5c290512f99..034e0e39566 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.3.0-Java-11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.3.0-Java-11.eb @@ -22,7 +22,7 @@ checksums = [ builddependencies = [('binutils', '2.38')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-7.3.0.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-7.3.0.eb index 8b3f8a98607..89f841e46fa 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-7.3.0.eb @@ -20,7 +20,7 @@ checksums = [ ] builddependencies = [('binutils', '2.30')] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.2.0.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.2.0.eb index 25422d7f57a..d7596e6036d 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.2.0.eb @@ -20,7 +20,7 @@ checksums = [ ] builddependencies = [('binutils', '2.31.1')] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.3.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.3.0-Java-11.eb index 492d77e6e4f..a3ead0bb703 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.3.0-Java-11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.3.0-Java-11.eb @@ -21,7 +21,7 @@ checksums = [ ] builddependencies = [('binutils', '2.32')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-9.3.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-9.3.0-Java-11.eb index 39ff4c9c5da..25632498de1 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-9.3.0-Java-11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-9.3.0-Java-11.eb @@ -21,7 +21,7 @@ checksums = [ ] builddependencies = [('binutils', '2.34')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb index ddbfe7c0922..654825d9ff3 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_includes.patch'] dependencies = [ - ('Java', '1.8.0_74', '', True), + ('Java', '1.8.0_74', '', SYSTEM), ('Python', '2.7.11'), ] diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2017b.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2017b.eb index 10ff1403b09..12cc04a02e7 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2017b.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2017b.eb @@ -19,7 +19,7 @@ checksums = [ 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch ] -dependencies = [('Java', '1.8.0_152', '', True)] +dependencies = [('Java', '1.8.0_152', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018a-Python-2.7.14.eb index 3a34a478986..f1981196919 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018a-Python-2.7.14.eb @@ -21,7 +21,7 @@ checksums = [ ] dependencies = [ - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ('Python', '2.7.14'), ] diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b.eb index 867b9d56beb..7bc12739569 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b.eb @@ -19,7 +19,7 @@ checksums = [ 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2019a.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2019a.eb index ba4fd58a573..51bebed49f8 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2019a.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2019a.eb @@ -20,7 +20,7 @@ checksums = [ ] builddependencies = [('binutils', '2.31.1')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb index e00f225a130..123c3e1e968 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_includes.patch'] dependencies = [ - ('Java', '1.8.0_131', '', True), + ('Java', '1.8.0_131', '', SYSTEM), ('Python', '2.7.13'), ] diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b-Python-2.7.14.eb index 132b4a836cc..408bb64f951 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b-Python-2.7.14.eb @@ -21,7 +21,7 @@ checksums = [ ] dependencies = [ - ('Java', '1.8.0_152', '', True), + ('Java', '1.8.0_152', '', SYSTEM), ('Python', '2.7.14'), ] diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b.eb index ec6fe2656ce..d0f5a966868 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b.eb @@ -19,7 +19,7 @@ checksums = [ 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch ] -dependencies = [('Java', '1.8.0_152', '', True)] +dependencies = [('Java', '1.8.0_152', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2018a-Python-3.6.4.eb index e1528a3b461..39bdcb9da81 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2018a-Python-3.6.4.eb @@ -21,7 +21,7 @@ checksums = [ ] dependencies = [ - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ('Python', '3.6.4'), ] diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb index 8ccff72840b..4595800f99c 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb @@ -29,7 +29,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Boost', '1.76.0'), ('Python', '3.9.5'), ('OpenCV', '4.5.3', '-CUDA-%(cudaver)s-contrib'), diff --git a/easybuild/easyconfigs/a/ASTRID/ASTRID-2.2.1-gompi-2019a.eb b/easybuild/easyconfigs/a/ASTRID/ASTRID-2.2.1-gompi-2019a.eb index ea1dba9f73d..4a752357e25 100644 --- a/easybuild/easyconfigs/a/ASTRID/ASTRID-2.2.1-gompi-2019a.eb +++ b/easybuild/easyconfigs/a/ASTRID/ASTRID-2.2.1-gompi-2019a.eb @@ -18,7 +18,7 @@ checksums = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('phylokit', '1.0'), ('Boost', '1.70.0'), ] diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb index 05ffdaeea4e..7911a59e768 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb @@ -17,7 +17,7 @@ builddependencies = [ dependencies = [ ('Python', '3.9.5'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('SciPy-bundle', '2021.05'), ('PyYAML', '5.4.1'), ('TensorFlow', '2.6.0', versionsuffix), diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb index 3307a0c7c2b..2ab59fb243c 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb @@ -17,7 +17,7 @@ builddependencies = [ dependencies = [ ('Python', '3.9.5'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('SciPy-bundle', '2021.05'), ('PyYAML', '5.4.1'), ('TensorFlow', '2.6.0', versionsuffix), diff --git a/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb b/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb index d3c79474bb6..1f73638a1c1 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb @@ -27,7 +27,7 @@ patches = [ ] dependencies = [ - ('CUDA', '7.5.18', '', True), + ('CUDA', '7.5.18', '', SYSTEM), ('netCDF', '4.4.0'), ('netCDF-Fortran', '4.4.4'), ('Python', '2.7.11'), diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb index 4193c584dca..5b391327a36 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb @@ -23,7 +23,7 @@ patches = ['Amber-%(version)s_fix-hardcoding.patch', dependencies = [ - ('CUDA', '7.5.18', '', True), + ('CUDA', '7.5.18', '', SYSTEM), ('netCDF', '4.4.0'), ('netCDF-Fortran', '4.4.4'), ('Python', '2.7.11'), diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb index 5a8159af3bb..431f7a09b12 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb @@ -42,7 +42,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('libreadline', '8.0'), ('matplotlib', '3.2.1', '-Python-%(pyver)s'), - ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', SYSTEM), ('netCDF-Fortran', '4.5.2'), ('netCDF', '4.7.4'), ('Perl', '5.30.2'), diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb index fc45e8660c5..638decc861e 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb @@ -53,7 +53,7 @@ dependencies = [ ('PnetCDF', '1.12.2'), ('Tkinter', '3.8.6'), ('X11', '20201008'), - ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', SYSTEM), ] # Some CUDA tests differs from expected results diff --git a/easybuild/easyconfigs/a/AmrPlusPlus/AmrPlusPlus-2.0-20200114-GCC-8.3.0.eb b/easybuild/easyconfigs/a/AmrPlusPlus/AmrPlusPlus-2.0-20200114-GCC-8.3.0.eb index c2864dc231d..6cdb4f111e7 100644 --- a/easybuild/easyconfigs/a/AmrPlusPlus/AmrPlusPlus-2.0-20200114-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/a/AmrPlusPlus/AmrPlusPlus-2.0-20200114-GCC-8.3.0.eb @@ -32,11 +32,11 @@ sources = [{ checksums = ['04af67517b752e15b5add27f4584f8c11293a0ed1353d3c1dd60c3c6e2dcb329'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('BWA', '0.7.17'), - ('Trimmomatic', '0.39', '-Java-%(javashortver)s', True), + ('Trimmomatic', '0.39', '-Java-%(javashortver)s', SYSTEM), ('SAMtools', '1.10'), - ('Nextflow', '19.12.0', '', True), + ('Nextflow', '19.12.0', '', SYSTEM), ] local_exe_files = [ diff --git a/easybuild/easyconfigs/a/ArrayFire/ArrayFire-3.6.4-foss-2018b-CUDA-9.2.88.eb b/easybuild/easyconfigs/a/ArrayFire/ArrayFire-3.6.4-foss-2018b-CUDA-9.2.88.eb index 8549e014005..7efc990a687 100644 --- a/easybuild/easyconfigs/a/ArrayFire/ArrayFire-3.6.4-foss-2018b-CUDA-9.2.88.eb +++ b/easybuild/easyconfigs/a/ArrayFire/ArrayFire-3.6.4-foss-2018b-CUDA-9.2.88.eb @@ -29,7 +29,7 @@ builddependencies = [ dependencies = [ ('Boost', '1.67.0'), - ('CUDA', local_cudaver, '', True), + ('CUDA', local_cudaver, '', SYSTEM), ] separate_build_dir = True diff --git a/easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb index 90e04c1f06b..7998e273f4c 100644 --- a/easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb @@ -21,7 +21,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['6557df95eed99323befddcef6b8da8b67eba22476efccd1e69a87ffdf075e5f4'] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] parallel = 1 diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-4.9.2.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-4.9.2.eb index d2c6124a0ad..fed83b82ecb 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-4.9.2.eb @@ -19,7 +19,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.3.0.eb index 7d84000783a..029fc124736 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.3.0.eb @@ -19,7 +19,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb index b0b5d3dc351..76f7bbb3a51 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb @@ -19,7 +19,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.1.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.1.0.eb index 47f11e88e4c..acd3e293abe 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.1.0.eb @@ -19,7 +19,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.2.0.eb index 0d4d4fbba39..f8696b70aa8 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.2.0.eb @@ -19,7 +19,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.3.0.eb index 56c44c440ee..8c7c17b1767 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.3.0.eb @@ -19,7 +19,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.2.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.2.eb index d469fdb58f5..263e4f8bb5e 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.2.eb @@ -31,7 +31,7 @@ checksums = [ dependencies = [('Autoconf', '2.69')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/automake', 'bin/aclocal'], diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.3.0.eb index 9d0d0b21a79..a2333fa888f 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.3.0.eb @@ -31,7 +31,7 @@ checksums = [ dependencies = [('Autoconf', '2.69')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/automake', 'bin/aclocal'], diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb index 3ee3bf9adf7..b62e65b9410 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb @@ -31,7 +31,7 @@ checksums = [ dependencies = [('Autoconf', '2.69')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/automake', 'bin/aclocal'], diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.1.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.1.0.eb index 1b4be92da39..c36cbe68b6a 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.1.0.eb @@ -31,7 +31,7 @@ checksums = [ dependencies = [('Autoconf', '2.69')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/automake', 'bin/aclocal'], diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.2.0.eb index c8c1c5b5d60..d0a1c837755 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.2.0.eb @@ -31,7 +31,7 @@ checksums = [ dependencies = [('Autoconf', '2.69')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/automake', 'bin/aclocal'], diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb index e447b6af5a2..8ba57370da3 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb @@ -31,7 +31,7 @@ checksums = [ dependencies = [('Autoconf', '2.69')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/automake', 'bin/aclocal'], diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.eb b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.eb index 1ffd386831a..ed1e72fae99 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.eb @@ -17,7 +17,7 @@ sources = ['apache-%(name)s-%(version)s-src.tar.gz'] checksums = ['68f7ced0aa15d1f9f672f23d67c86deaf728e9576936313cfbff4f7a0e6ce382'] # specify dependency on Java/1.8 "wrapper", rather than a specific Java version -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] builddependencies = [('JUnit', '4.12', versionsuffix)] diff --git a/easybuild/easyconfigs/a/arcasHLA/arcasHLA-0.2.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/arcasHLA/arcasHLA-0.2.0-foss-2019b-Python-3.7.4.eb index bc81df83420..816d044d50f 100644 --- a/easybuild/easyconfigs/a/arcasHLA/arcasHLA-0.2.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/arcasHLA/arcasHLA-0.2.0-foss-2019b-Python-3.7.4.eb @@ -24,7 +24,7 @@ dependencies = [ ('SAMtools', '1.10'), ('pigz', '2.4'), ('git', '2.23.0', '-nodocs'), - ('git-lfs', '2.11.0', '', True), + ('git-lfs', '2.11.0', '', SYSTEM), ] # Download and install the reference database (1.8 GB) diff --git a/easybuild/easyconfigs/a/aria2/aria2-1.35.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/aria2/aria2-1.35.0-GCCcore-10.3.0.eb index 341a8dd97ca..c0280bde061 100644 --- a/easybuild/easyconfigs/a/aria2/aria2-1.35.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/a/aria2/aria2-1.35.0-GCCcore-10.3.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('libxml2', '2.9.10'), ('SQLite', '3.35.4'), ('c-ares', '1.17.2'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "--without-gnutls --with-openssl --enable-libaria2 --enable-static" diff --git a/easybuild/easyconfigs/a/aria2/aria2-1.36.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/aria2/aria2-1.36.0-GCCcore-11.3.0.eb index 591b1cbcd46..baafaf4f5e3 100644 --- a/easybuild/easyconfigs/a/aria2/aria2-1.36.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/a/aria2/aria2-1.36.0-GCCcore-11.3.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('libxml2', '2.9.13'), ('SQLite', '3.38.3'), ('c-ares', '1.18.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "--without-gnutls --with-openssl --enable-libaria2 --enable-static" diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019a.eb index b598e539cc1..25065d06f05 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019a.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019a.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ - ('Eigen', '3.3.7', '', True) + ('Eigen', '3.3.7', '', SYSTEM) ] preconfigopts = "sh bootstrap && " diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019b.eb index be0c9d7dedd..69babe0c5ea 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019b.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019b.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ - ('Eigen', '3.3.7', '', True) + ('Eigen', '3.3.7', '', SYSTEM) ] preconfigopts = "sh bootstrap && " diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-intel-2019b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-intel-2019b.eb index e60710e4b02..f262b1d4d67 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-intel-2019b.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-intel-2019b.eb @@ -24,7 +24,7 @@ builddependencies = [ ] dependencies = [ - ('Eigen', '3.3.7', '', True) + ('Eigen', '3.3.7', '', SYSTEM) ] separate_build_dir = True diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb index 574183e62e3..6a4cd8d698a 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb @@ -20,7 +20,7 @@ dependencies = [ ('Biopython', '1.72', versionsuffix), ('Pysam', '0.15.1', versionsuffix), ('BWA', '0.7.17'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('minimap2', '2.13'), ('SAMtools', '1.9'), ('MUSCLE', '3.8.31'), @@ -33,8 +33,8 @@ dependencies = [ ('python-parasail', '1.1.16', versionsuffix), ('PhyML', '3.3.20190321'), ('nodejs', '12.16.1'), - ('goalign', '0.3.2', '', True), - ('gotree', '0.4.0', '', True), + ('goalign', '0.3.2', '', SYSTEM), + ('gotree', '0.4.0', '', SYSTEM), ('rampart', '1.2.0rc3', versionsuffix), ('libdeflate', '1.5'), ('nanopolish', '0.13.1', versionsuffix), diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb index c4995246973..80e2cc8068d 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -33,8 +33,8 @@ dependencies = [ ('python-parasail', '1.2.4'), ('PhyML', '3.3.20200621'), ('nodejs', '12.19.0'), - ('goalign', '0.3.2', '', True), - ('gotree', '0.4.0', '', True), + ('goalign', '0.3.2', '', SYSTEM), + ('gotree', '0.4.0', '', SYSTEM), ('rampart', '1.2.0'), ('libdeflate', '1.7'), ('nanopolish', '0.13.3'), diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb index d90fb13229d..3d6512a5f33 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_112', '', True)] +dependencies = [('Java', '1.8.0_112', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-37.93-foss-2018a.eb b/easybuild/easyconfigs/b/BBMap/BBMap-37.93-foss-2018a.eb index eeb78bfbdb9..53aeebfca89 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-37.93-foss-2018a.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-37.93-foss-2018a.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['21be384f8535094b8b4695134b0b132863e6599811b8ea2d311960b7ba88df8f'] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-37.93-intel-2018a.eb b/easybuild/easyconfigs/b/BBMap/BBMap-37.93-intel-2018a.eb index 4c2ee3855a4..c5b17a83ed9 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-37.93-intel-2018a.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-37.93-intel-2018a.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['21be384f8535094b8b4695134b0b132863e6599811b8ea2d311960b7ba88df8f'] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.26-foss-2018b.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.26-foss-2018b.eb index 350359097a1..f8bdee8c943 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.26-foss-2018b.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.26-foss-2018b.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['e439709d6d294aae5938cb253c8640f8e0dfeb227d5b01ce17c37e9871a458b4'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.50b-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.50b-GCC-8.2.0-2.31.1.eb index 0c565ba0482..1e4f8b426cf 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.50b-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.50b-GCC-8.2.0-2.31.1.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['b3b8eefc2e32d035fb7c1732048dca81e367a7e5e43416c993c88683fc19ade7'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.76-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.76-GCC-8.2.0-2.31.1.eb index a3018663e1c..1356c84ed94 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.76-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.76-GCC-8.2.0-2.31.1.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['4f6e3c6a3b56c8514ddcd9e2bebe0f2c89698b16f3af9f52916f55d2a59f406b'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.79-GCC-8.3.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.79-GCC-8.3.0.eb index 90bb802ed78..d0cb1b445ca 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.79-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.79-GCC-8.3.0.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['72891105b6d3e190b5b1d60fb964077a997cf5d2647c472b213a6dd46e1ca07c'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.87-iccifort-2020.1.217.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.87-iccifort-2020.1.217.eb index 980626868d9..772b81bc312 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.87-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.87-iccifort-2020.1.217.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['22ab642b8af88faf208a56763158da895004c5231df572d3163ce52fbfb63240'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb index 94e6c8540fe..d0f16e3b3bd 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['a366531c566da5e7246ccf707b6770a92246c1cfe29fd30dc2d800c0d82269f1'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-9.3.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-9.3.0.eb index 6d1053ec36a..45b3f610c87 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-9.3.0.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['a366531c566da5e7246ccf707b6770a92246c1cfe29fd30dc2d800c0d82269f1'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.96-GCC-10.3.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.96-GCC-10.3.0.eb index d3215416acf..9088c7a0387 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.96-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.96-GCC-10.3.0.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['18d9c89b02c0ab044b2795a65f6236b2262a494ed83d27e31750437b350ef080'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.98-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.98-GCC-11.2.0.eb index e2bd5bd4075..d439a3560c1 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.98-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.98-GCC-11.2.0.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['cdc3b8e0530c4a83a728d28da31f0e7ead2bc233d4bf21cd1916572c9b2d0e0e'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BLT/BLT-20181223-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/BLT/BLT-20181223-GCCcore-11.2.0.eb index 3d71f64de88..19c368807ef 100644 --- a/easybuild/easyconfigs/b/BLT/BLT-20181223-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/BLT/BLT-20181223-GCCcore-11.2.0.eb @@ -28,7 +28,7 @@ dependencies = [ ('freetype', '2.11.0'), ('expat', '2.4.1'), ('SQLite', '3.36'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = '--with-tcl=$EBROOTTCL --with-tk=$EBROOTTK --enable-shared' diff --git a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.2-intel-2019a.eb b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.2-intel-2019a.eb index 6b33d7c53c6..9f70e27003e 100644 --- a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.2-intel-2019a.eb +++ b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.2-intel-2019a.eb @@ -19,7 +19,7 @@ dependencies = [ ('GeneMark-ET', '4.38'), ('BamTools', '2.5.1'), ('SAMtools', '1.9'), - ('GenomeThreader', '1.7.1', '-Linux_x86_64-64bit', True), + ('GenomeThreader', '1.7.1', '-Linux_x86_64-64bit', SYSTEM), ('spaln', '2.3.3c'), ('Exonerate', '2.4.0'), ('BLAST+', '2.9.0'), diff --git a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.5-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.5-intel-2019b-Python-3.7.4.eb index e356a0da97b..33487e8713e 100644 --- a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.5-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.5-intel-2019b-Python-3.7.4.eb @@ -20,7 +20,7 @@ dependencies = [ ('GeneMark-ET', '4.57'), ('BamTools', '2.5.1'), ('SAMtools', '1.10'), - ('GenomeThreader', '1.7.3', '-Linux_x86_64-64bit', True), + ('GenomeThreader', '1.7.3', '-Linux_x86_64-64bit', SYSTEM), ('spaln', '2.4.03'), ('Exonerate', '2.4.0'), ('BLAST+', '2.9.0'), diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.10.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.10.0-GCCcore-6.4.0.eb index 76b9371ed08..d2534be82ac 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.10.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.10.0-GCCcore-6.4.0.eb @@ -16,6 +16,6 @@ checksums = [ ] builddependencies = [('binutils', '2.28')] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.11.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.11.0-GCCcore-6.4.0.eb index 5829b4dc01c..ee1d8079476 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.11.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.11.0-GCCcore-6.4.0.eb @@ -12,6 +12,6 @@ sources = ['%(namelower)s-%(version)s-dist.zip'] checksums = ['abfeccc94728cb46be8dbb3507a23ccffbacef9fbda96a977ef4ea8d6ab0d384'] builddependencies = [('binutils', '2.28')] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.11.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.11.1-GCCcore-6.4.0.eb index 7d06a6a61a7..6f59179f3cd 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.11.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.11.1-GCCcore-6.4.0.eb @@ -12,6 +12,6 @@ sources = ['%(namelower)s-%(version)s-dist.zip'] checksums = ['e8d762bcc01566fa50952c8028e95cfbe7545a39b8ceb3a0d0d6df33b25b333f'] builddependencies = [('binutils', '2.28')] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.12.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.12.0-GCCcore-6.4.0.eb index ba628d6babe..2596352a994 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.12.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.12.0-GCCcore-6.4.0.eb @@ -12,6 +12,6 @@ sources = ['%(namelower)s-%(version)s-dist.zip'] checksums = ['3b3e7dc76d145046fdc78db7cac9a82bc8939d3b291e53a7ce85315feb827754'] builddependencies = [('binutils', '2.28')] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.16.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.16.0-GCCcore-6.4.0.eb index 9553e22d089..8215c28cdfc 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.16.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.16.0-GCCcore-6.4.0.eb @@ -16,6 +16,6 @@ checksums = [ ] builddependencies = [('binutils', '2.28')] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.16.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.16.0-GCCcore-7.3.0.eb index d6095508300..95378852161 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.16.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.16.0-GCCcore-7.3.0.eb @@ -16,6 +16,6 @@ checksums = [ ] builddependencies = [('binutils', '2.30')] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.18.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.18.0-GCCcore-7.3.0.eb index 088dbc8deb5..d7273df067b 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.18.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.18.0-GCCcore-7.3.0.eb @@ -21,7 +21,7 @@ builddependencies = [ ('Zip', '3.0'), ] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-7.3.0.eb index c98144ae9a1..5fd1011783f 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-7.3.0.eb @@ -21,7 +21,7 @@ builddependencies = [ ('Zip', '3.0'), ] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-8.2.0.eb index 72f11b4ee5b..59d5f18e87f 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-8.2.0.eb @@ -20,6 +20,6 @@ builddependencies = [ ('Python', '3.7.2'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.25.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.25.2-GCCcore-8.2.0.eb index 5de84907639..74f98e271dd 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.25.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.25.2-GCCcore-8.2.0.eb @@ -21,6 +21,6 @@ builddependencies = [ ('Python', '3.7.2'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.2.0.eb index 62c42905710..9a23b912978 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.2.0.eb @@ -21,6 +21,6 @@ builddependencies = [ ('Python', '3.7.2'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb index bf9db9bef97..b6becac4ae4 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb @@ -21,6 +21,6 @@ builddependencies = [ ('Python', '3.7.4'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.2.0.eb index 699ad4853c3..da42845ee5c 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.2.0.eb @@ -26,6 +26,6 @@ builddependencies = [ ('Python', '3.7.2'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb index 720da63a770..a859c64611e 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb @@ -26,6 +26,6 @@ builddependencies = [ ('Python', '3.7.4'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb index 9544908a761..4a205b4f676 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb @@ -27,6 +27,6 @@ builddependencies = [ ('Python', '3.8.2'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.7.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.7.0-GCCcore-6.4.0.eb index 386939c6183..279f3636e1b 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.7.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.7.0-GCCcore-6.4.0.eb @@ -12,6 +12,6 @@ sources = ['%(namelower)s-%(version)s-dist.zip'] checksums = ['a084a9c5d843e2343bf3f319154a48abe3d35d52feb0ad45dec427a1c4ffc416'] builddependencies = [('binutils', '2.28')] -dependencies = [('Java', '1.8.0_152', '', True)] +dependencies = [('Java', '1.8.0_152', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-1.1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-1.1.0-GCCcore-8.3.0.eb index 52fd06b9233..8ed77b68a9b 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-1.1.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-1.1.0-GCCcore-8.3.0.eb @@ -25,6 +25,6 @@ builddependencies = [ ('Python', '3.7.4'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb index 64cebdfa53f..3c49531cee4 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Python', '3.8.6'), ('Zip', '3.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] runtest = True testopts = ' '.join([ diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-8.3.0.eb index 106e2146849..1a5d8224c02 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-8.3.0.eb @@ -20,6 +20,6 @@ builddependencies = [ ('Python', '3.7.4'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.4.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.4.1-GCCcore-8.3.0.eb index fd6d2288410..54da4a210b6 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.4.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.4.1-GCCcore-8.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Python', '3.7.4'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] runtest = True testopts = ' '.join([ diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.6.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.6.0-GCCcore-9.3.0.eb index 386bdf9a4c8..6daf4172fef 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.6.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.6.0-GCCcore-9.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Python', '3.8.2'), ('Zip', '3.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] runtest = True testopts = ' '.join([ diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.1-GCCcore-8.3.0.eb index 1088865bda9..2877264df72 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.1-GCCcore-8.3.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('Python', '3.7.4'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] runtest = True testopts = ' '.join([ diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb index 6b259a49b41..f5408193257 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('Python', '3.8.6'), ('Zip', '3.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] runtest = True testopts = ' '.join([ diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.3.0.eb index 32ed844cbb5..aecd7128568 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.3.0.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Zip', '3.0'), ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] runtest = True diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb index 8c61b1cbe83..76adb8a37b4 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb @@ -29,7 +29,7 @@ builddependencies = [ ('Zip', '3.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] runtest = True testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-8.3.0.eb index c72ee0d0455..ddadf77aa93 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-8.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ('Zip', '3.0'), ('UnZip', '6.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] runtest = True testopts = ' '.join([ diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2-GCCcore-11.2.0.eb index 0a321f837b9..8680e49eb46 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2-GCCcore-11.2.0.eb @@ -35,7 +35,7 @@ builddependencies = [ ('Zip', '3.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] runtest = True testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-5.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-5.1.1-GCCcore-11.3.0.eb index 793f0a2c12f..2550749a059 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-5.1.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-5.1.1-GCCcore-11.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ('Zip', '3.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] runtest = True testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." diff --git a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb index 8b901156428..ca38ef74542 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb @@ -22,7 +22,7 @@ source_urls = ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(ver sources = ['BEASTv%(version)s.tgz'] dependencies = [ - ('Java', '1.8.0_74', '', True), + ('Java', '1.8.0_74', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb index 10b75ac34ee..8f2c406f424 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb @@ -18,7 +18,7 @@ sources = ['BEAST.v%(version)s.Linux.tgz'] checksums = ['05dcc619c2e10163f2c1089ec66149f6e53ec5a0583cd2cb8ffdccbbdb1d8183'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), # this is not mandatory but beagle-lib is recommended by developers ('beagle-lib', '3.1.2'), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb index 9fe7a6ae5b3..8176cae55eb 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb index ac0a67174d3..0768a39fbc4 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb index ef2c714b609..8a0e1981820 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb index 60fefc39bf5..a06558cc2cb 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.3.eb index d968d2c56be..79f08754508 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.3.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.4.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.4.eb index 01ec53eafb9..cd8a216a60e 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.4.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb index 0fc748e278b..2703ab53907 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.4.0.eb index 82200e98744..585c3a2730a 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.4.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.5.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.5.0.eb index 61b101b4d57..ab8762d3b91 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.5.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb index dab8d891914..0294b6dc75e 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.2.0.eb index da4efd77c4a..fc56131f50f 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.2.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.3.0.eb index 5a746f36187..5b4b26b3b8a 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.3.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb index cd56e251253..0c3cd239602 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb @@ -24,7 +24,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.28', '', True), + ('binutils', '2.28', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb index cfb4a2fcbf0..e43482d5649 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.28', '', True), + ('binutils', '2.28', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.2.0.eb index 0e32b008b26..ce7fec7fcfa 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.2.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.29', '', True), + ('binutils', '2.29', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.3.0.eb index ec463c45cfa..2de144d05ab 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.3.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.30', '', True), + ('binutils', '2.30', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-8.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-8.1.0.eb index d0e9458243e..6ed65c27da2 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-8.1.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.30', '', True), + ('binutils', '2.30', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-5.5.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-5.5.0.eb index a9e1ab6bf9f..5209b761d92 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-5.5.0.eb @@ -16,7 +16,7 @@ checksums = ['cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.3.0.eb index 0dfdab7a31f..4043ac56cd3 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.3.0.eb @@ -16,7 +16,7 @@ checksums = ['cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.4.0.eb index e7ec0780223..db24b4bf394 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.4.0.eb @@ -20,7 +20,7 @@ checksums = ['cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.28', '', True), + ('binutils', '2.28', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.2.0.eb index b38f9eaef5a..966f9bd8f1e 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.2.0.eb @@ -16,7 +16,7 @@ checksums = ['cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.29', '', True), + ('binutils', '2.29', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.3.0.eb index 957290a803b..eb4866bb158 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.3.0.eb @@ -16,7 +16,7 @@ checksums = ['cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.30', '', True), + ('binutils', '2.30', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.1.0.eb index ec067261a20..65af1da859e 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.1.0.eb @@ -16,7 +16,7 @@ checksums = ['cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.30', '', True), + ('binutils', '2.30', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.2.0.eb index 56d6cbacbbf..35c51fb65f2 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.2.0.eb @@ -16,7 +16,7 @@ checksums = ['cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.31.1', '', True), + ('binutils', '2.31.1', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.2.2-GCCcore-7.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.2.2-GCCcore-7.4.0.eb index 89abd0d346f..fcc092af430 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.2.2-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.2.2-GCCcore-7.4.0.eb @@ -16,7 +16,7 @@ checksums = ['3ffd2201041c6c56064b4bdad4dfb8959751efbefa823775242b4f32aa37786c'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.31.1', '', True), + ('binutils', '2.31.1', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.2.0.eb index e6731677f86..93c8a305b46 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.2.0.eb @@ -16,7 +16,7 @@ checksums = ['0fda1d034185397430eb7b0c9e140fb37e02fbfc53b90252fa5575e382b6dbd1'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.31.1', '', True), + ('binutils', '2.31.1', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.3.0.eb index d6c005dfb35..cea2cb041fc 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.3.0.eb @@ -16,7 +16,7 @@ checksums = ['0fda1d034185397430eb7b0c9e140fb37e02fbfc53b90252fa5575e382b6dbd1'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.4.0.eb index 2530ede83d4..a9eb850d760 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.4.0.eb @@ -16,7 +16,7 @@ checksums = ['0fda1d034185397430eb7b0c9e140fb37e02fbfc53b90252fa5575e382b6dbd1'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb index b46a869bd63..0fb633083da 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb @@ -16,7 +16,7 @@ checksums = ['0fda1d034185397430eb7b0c9e140fb37e02fbfc53b90252fa5575e382b6dbd1'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.2.0.eb index 5193a9f616f..358a90c1322 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.2.0.eb @@ -16,7 +16,7 @@ checksums = ['0fda1d034185397430eb7b0c9e140fb37e02fbfc53b90252fa5575e382b6dbd1'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb index c20e3f3948d..7924ce69695 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ checksums = ['34e201d963156618a0ea5bc87220f660a1e08403dd3c7c7903d4f38db3f40039'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.35', '', True), + ('binutils', '2.35', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-9.3.0.eb index 2da53fce904..f9deb82e85d 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-9.3.0.eb @@ -16,7 +16,7 @@ checksums = ['34e201d963156618a0ea5bc87220f660a1e08403dd3c7c7903d4f38db3f40039'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.34', '', True), + ('binutils', '2.34', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.6.1-GCCcore-10.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.6.1-GCCcore-10.1.0.eb index b30667a9417..adb0912d13d 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.6.1-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.6.1-GCCcore-10.1.0.eb @@ -16,7 +16,7 @@ checksums = ['1120f8bfe2cc13e5e1e3f671dc41b1a535ca5a75a70d5b349c19da9d4389f74d'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.34', '', True), + ('binutils', '2.34', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb index 55d04ef9b9d..8edc3c84d84 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ checksums = ['1dd952839cf0d5a8178c691eeae40dc48fa50d18dcce648b1ad9ae0195367d13'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.35', '', True), + ('binutils', '2.35', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-10.3.0.eb index 8c2f1680328..1b290ba82b4 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-10.3.0.eb @@ -16,7 +16,7 @@ checksums = ['69dc0bb46ea8fc307d4ca1e0b61c8c355eb207d0b0c69f4f8462328e74d7b9ea'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.1.0.eb index d5ee76339b3..6add8cb0941 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.1.0.eb @@ -16,7 +16,7 @@ checksums = ['69dc0bb46ea8fc307d4ca1e0b61c8c355eb207d0b0c69f4f8462328e74d7b9ea'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.2.0.eb index c272626ed8f..2f5f0c2547d 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.2.0.eb @@ -16,7 +16,7 @@ checksums = ['69dc0bb46ea8fc307d4ca1e0b61c8c355eb207d0b0c69f4f8462328e74d7b9ea'] builddependencies = [ ('M4', '1.4.19'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.37', '', True), + ('binutils', '2.37', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-9.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-9.4.0.eb index 7b61d615084..e5d42bae065 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-9.4.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-9.4.0.eb @@ -16,7 +16,7 @@ checksums = ['69dc0bb46ea8fc307d4ca1e0b61c8c355eb207d0b0c69f4f8462328e74d7b9ea'] builddependencies = [ ('M4', '1.4.19'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.3.0.eb index 4ec9c1c877b..51a53e9d6fa 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.3.0.eb @@ -16,7 +16,7 @@ checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] builddependencies = [ ('M4', '1.4.19'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.38', '', True), + ('binutils', '2.38', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.1.0.eb index 88bd7102234..d87bb83ccc5 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.1.0.eb @@ -16,7 +16,7 @@ checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] builddependencies = [ ('M4', '1.4.19'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.38', '', True), + ('binutils', '2.38', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.2.0.eb index 4c8dc227e18..adcb9e42b3c 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.2.0.eb @@ -16,7 +16,7 @@ checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] builddependencies = [ ('M4', '1.4.19'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.39', '', True), + ('binutils', '2.39', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-9.5.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-9.5.0.eb index 56c2cc38d82..82a5c2763df 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-9.5.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-9.5.0.eb @@ -16,7 +16,7 @@ checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] builddependencies = [ ('M4', '1.4.19'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.38', '', True), + ('binutils', '2.38', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb b/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb index 8b80ac71ba2..f85a0804f2a 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb @@ -24,7 +24,7 @@ dependencies = [ ('libGLU', '9.0.0'), ('OpenColorIO', '1.1.0'), # for advanced color management ('OpenImageIO', '1.8.16'), # required for cycles render engine - ('CUDA', local_cuda_ver, '', True), + ('CUDA', local_cuda_ver, '', SYSTEM), ] builddependencies = [('CMake', '3.12.1')] diff --git a/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb b/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb index b0ee97e8f9e..6210023c8d0 100644 --- a/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb +++ b/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['http://download.bpipe.org/versions/'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('Java', '1.8.0_131', '', True)] +dependencies = [('Java', '1.8.0_131', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/bpipe', 'lib/bpipe.jar'], diff --git a/easybuild/easyconfigs/b/bcgTree/bcgTree-1.0.10-intel-2018a-Perl-5.26.1.eb b/easybuild/easyconfigs/b/bcgTree/bcgTree-1.0.10-intel-2018a-Perl-5.26.1.eb index 616d4405ec0..19bf7119f78 100644 --- a/easybuild/easyconfigs/b/bcgTree/bcgTree-1.0.10-intel-2018a-Perl-5.26.1.eb +++ b/easybuild/easyconfigs/b/bcgTree/bcgTree-1.0.10-intel-2018a-Perl-5.26.1.eb @@ -17,7 +17,7 @@ dependencies = [ ('Perl', '5.26.1'), ('HMMER', '3.1b2'), ('MUSCLE', '3.8.31'), - ('Gblocks', '0.91b', '', True), + ('Gblocks', '0.91b', '', SYSTEM), ('RAxML', '8.2.11', '-hybrid-avx2'), ] diff --git a/easybuild/easyconfigs/b/bcgTree/bcgTree-1.1.0-intel-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/b/bcgTree/bcgTree-1.1.0-intel-2018b-Perl-5.28.0.eb index 4f4b3613521..374d15e26a6 100644 --- a/easybuild/easyconfigs/b/bcgTree/bcgTree-1.1.0-intel-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/b/bcgTree/bcgTree-1.1.0-intel-2018b-Perl-5.28.0.eb @@ -17,7 +17,7 @@ dependencies = [ ('Perl', '5.28.0'), ('HMMER', '3.2.1'), ('MUSCLE', '3.8.31'), - ('Gblocks', '0.91b', '', True), + ('Gblocks', '0.91b', '', SYSTEM), ('RAxML', '8.2.12', '-hybrid-avx2'), ] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb index 76868b55c45..fa78496309d 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['beagle_release_%s.tar.gz' % version.replace('.', '_')] -dependencies = [('Java', '1.8.0_74', '', True)] +dependencies = [('Java', '1.8.0_74', '', SYSTEM)] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2017a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2017a.eb index 88be4437d43..f69171cc680 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2017a.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2017a.eb @@ -13,7 +13,7 @@ source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['beagle_release_%s.tar.gz' % version.replace('.', '_')] checksums = ['82ff13f4e7d7bffab6352e4551dfa13afabf82bff54ea5761d1fc1e78341d7de'] -dependencies = [('Java', '1.8.0_144', '', True)] +dependencies = [('Java', '1.8.0_144', '', SYSTEM)] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.1-foss-2018a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.1-foss-2018a.eb index 8ea77e9a5bd..ca5de62a8c9 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.1-foss-2018a.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.1-foss-2018a.eb @@ -13,7 +13,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['d94b3b440ea64c564005f4eadceff8d502129dd22369f6045e40121ca383a6ca'] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] builddependencies = [('Autotools', '20170619')] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.1-intel-2018a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.1-intel-2018a.eb index 11f42e93a75..0b71e37b50f 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.1-intel-2018a.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.1-intel-2018a.eb @@ -13,7 +13,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['d94b3b440ea64c564005f4eadceff8d502129dd22369f6045e40121ca383a6ca'] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] builddependencies = [('Autotools', '20170619')] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b-CUDA-9.2.88.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b-CUDA-9.2.88.eb index 32be3e9381f..8df8f31d4d3 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b-CUDA-9.2.88.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b-CUDA-9.2.88.eb @@ -15,8 +15,8 @@ sources = ['v%(version)s.tar.gz'] checksums = ['59a7081b61ead0a5738e813c6fcfb614d2c5bb49c29b28609de8e2b51bea3ec0'] dependencies = [ - ('Java', '1.8', '', True), - ('CUDA', local_cuda_ver, '', True), + ('Java', '1.8', '', SYSTEM), + ('CUDA', local_cuda_ver, '', SYSTEM), ] builddependencies = [('Autotools', '20180311')] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b.eb index d3d114b1a46..571ffcfac1f 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b.eb @@ -12,7 +12,7 @@ source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['59a7081b61ead0a5738e813c6fcfb614d2c5bb49c29b28609de8e2b51bea3ec0'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] builddependencies = [('Autotools', '20180311')] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb index f40b3b1712f..e676c19b2af 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('pkg-config', '0.29.2'), ('pocl', '1.6'), ] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-8.2.0-2.31.1.eb index d300d9d5ff7..d464264930a 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-8.2.0-2.31.1.eb @@ -12,7 +12,7 @@ source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] builddependencies = [('Autotools', '20180311')] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-9.3.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-9.3.0.eb index f0dc7a138e7..f7afb71fa1b 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-9.3.0.eb @@ -12,7 +12,7 @@ source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] builddependencies = [('Autotools', '20180311')] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-gcccuda-2019b.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-gcccuda-2019b.eb index ecacb7868ce..97e7108bf28 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-gcccuda-2019b.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-gcccuda-2019b.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('pkg-config', '0.29.2'), ('pocl', '1.4'), ] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index ce1ff6795f0..67aec4c48d2 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -12,7 +12,7 @@ source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] builddependencies = [('Autotools', '20180311')] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index 08e10d150ca..dfa2e11582d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb index 9709696cf5d..7627c686af3 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index d6e68008e5b..9be29fca484 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb index 9ec7a3f3f32..0e86573cab6 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb @@ -16,7 +16,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb index f411442d121..f331b902250 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb @@ -16,7 +16,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb index 4eee9df8fa2..e631c72676f 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb @@ -16,7 +16,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb index d7c829040f2..ecd95aca019 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked instatically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb index 2ae6ba18a54..7122f8fed1d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb @@ -16,7 +16,7 @@ builddependencies = [ # zlib required, but being linked instatically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.5.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.5.0.eb index 2d41305b4cf..1ff0485bfc7 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.5.0.eb @@ -16,7 +16,7 @@ builddependencies = [ # zlib required, but being linked instatically, so not a runtime dep ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb index d95c058f0c8..c9f35fe7a36 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb @@ -17,7 +17,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb index 215aaf0cb28..847c265d57c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb index 88e16771dff..00cbe46a478 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb index 9346ceba7e7..e56efe34428 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb index 93b20c17e20..0759f7aae9e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.3'), ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb index 3cdec71af84..43d45b40723 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb @@ -15,7 +15,7 @@ builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain, # to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb index 7b12c3e7b9b..6cacb8636c8 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.3'), ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb index c35f4248bb2..ec297ac8a27 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb index 562cf4dc332..9ecaf6bc39b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb index 51db6bef353..f20a4a66372 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb index 3db9b24875c..3d6ec7437bb 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb @@ -19,7 +19,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.2.2'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb index ef31e6f73c4..8876efd1b6c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb @@ -19,7 +19,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.5'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb index 5e7624cfb62..a1384a814f7 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.3.2'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb index 2482db7b76a..7283ba452d4 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.3.2'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.2.0.eb index c7966387725..beeca4aff16 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.2.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.3.2'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-10.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-10.1.0.eb index fb99acd8de8..e7807685469 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-10.1.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.6.1'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-9.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-9.3.0.eb index f74f0325c09..34dc183b567 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-9.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.5.3'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb index c3fb942ee7d..43435891a60 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.7.1'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-10.3.0.eb index 8a7c407a6bb..6dd4731d702 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-10.3.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.7.6'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-11.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-11.1.0.eb index 9d954efae4e..4b6a60c48f3 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-11.1.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.7.6'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-8.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-8.4.0.eb index 5fe10da2880..efcc5a27842 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-8.4.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.3.2'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-9.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-9.4.0.eb index 9440aa2ae70..cdcea5ab36a 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-9.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-9.4.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.7.6'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.37-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.37-GCCcore-11.2.0.eb index 2f25a58407b..e655d705347 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.37-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.37-GCCcore-11.2.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.7.6'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-11.3.0.eb index da7b3d38de5..ddecfa4f7db 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-11.3.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.8.2'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-12.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-12.1.0.eb index fdfefe7c042..3710a56f322 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-12.1.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.8.2'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-9.5.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-9.5.0.eb index 9e8ca91c080..bea25508b1e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-9.5.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-9.5.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.8.2'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.39-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.39-GCCcore-12.2.0.eb index c8ec4f59243..f105d46cf0e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.39-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.39-GCCcore-12.2.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.8.2'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb index 138a0a59d7f..86e013bcdfd 100644 --- a/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'cstd': 'c++03'} builddependencies = [ - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021a-CUDA-11.3.1.eb index 1cba3eeb025..60d41ad83e5 100644 --- a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021a-CUDA-11.3.1.eb @@ -12,7 +12,7 @@ description = """This module sets a group of environment variables for compilers toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('UCX-CUDA', '1.10.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021b-CUDA-11.4.1.eb index 2aa49ff982a..b72970646fb 100644 --- a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021b-CUDA-11.4.1.eb @@ -12,7 +12,7 @@ description = """This module sets a group of environment variables for compilers toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('UCX-CUDA', '1.11.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022a-CUDA-11.7.0.eb index c1b49d2a91a..c3cb995d63e 100644 --- a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022a-CUDA-11.7.0.eb @@ -12,7 +12,7 @@ description = """This module sets a group of environment variables for compilers toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('UCX-CUDA', '1.12.1', versionsuffix), ] diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb index d9104ae02c8..aeea4de6789 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb @@ -18,6 +18,6 @@ checksums = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb index 333dfab361e..8ff51f5bd3e 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb @@ -18,6 +18,6 @@ checksums = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2021b.eb b/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2021b.eb index 7622ed76c90..6dcf10dda3d 100644 --- a/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2021b.eb +++ b/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2021b.eb @@ -24,7 +24,7 @@ dependencies = [ ('PnetCDF', '1.12.3'), ('Subversion', '1.14.1'), ('git', '2.33.1', '-nodocs'), - ('git-lfs', '3.2.0', '', True), + ('git-lfs', '3.2.0', '', SYSTEM), ] components = [ diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb index 843dd43347b..a891c0367b1 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.10.0'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb index c34f9e1cc3a..b4f032df4ee 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.10.0'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb index 4c9db1623b7..7cceb21f898 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.9.1'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb index 020c81029d7..55e0812e853 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.10.1'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb index 7e6d5bdcc6f..fa530f73cc2 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.10.0'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb index f9297a5a469..08ece993edb 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.10.2'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb index 1c2a60faa0a..4b1ed1907c7 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.10.2'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb index e8f39c66d57..8f439a24c42 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.11.4'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb index dc1d8abbeca..693040076f8 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.11.4'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb index 27070c69ab0..b0310dabbf2 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.10.2'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb index 4d717d55089..83445a5c0a6 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb @@ -15,7 +15,7 @@ checksums = ['59464b1eaee892f2223ba570a7642892c999e29524ab102a6efd7c29c94a29f7'] builddependencies = [ ('CMake', '3.13.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb index 7af7769dea5..e2824c61604 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb @@ -15,7 +15,7 @@ checksums = ['59464b1eaee892f2223ba570a7642892c999e29524ab102a6efd7c29c94a29f7'] builddependencies = [ ('CMake', '3.13.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb index 06c6212ddb5..8258003e2a5 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb @@ -15,7 +15,7 @@ checksums = ['d4ec2528b88a7c3a07b0b86db96c216822f85b951bf4bc7f9d1f26bf6c369afe'] builddependencies = [ ('CMake', '3.15.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb index 5872c04d23b..b0045e26225 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb @@ -15,7 +15,7 @@ checksums = ['d4ec2528b88a7c3a07b0b86db96c216822f85b951bf4bc7f9d1f26bf6c369afe'] builddependencies = [ ('CMake', '3.15.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb index 18103c12dc1..217755142f3 100644 --- a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb @@ -14,7 +14,7 @@ dependencies = [ ('TopHat', '2.1.1'), ('Cufflinks', '2.2.1'), ('BEDTools', '2.26.0'), - ('Kent_tools', '20171107', '-linux.x86_64', True), + ('Kent_tools', '20171107', '-linux.x86_64', SYSTEM), ('STAR', '2.5.3a'), ('BWA', '0.7.17'), ('segemehl', '0.2.0'), diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb index edff9ff989f..2362960ae99 100644 --- a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb @@ -18,7 +18,7 @@ dependencies = [ ('TopHat', '2.1.0', versionsuffix), ('Cufflinks', '2.2.1'), ('BEDTools', '2.27.1'), - ('Kent_tools', '20180716', '-linux.x86_64', True), + ('Kent_tools', '20180716', '-linux.x86_64', SYSTEM), ('STAR', '2.6.0c'), ('BWA', '0.7.17'), ('segemehl', '0.2.0'), diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.3.0.eb index 8407f07472a..8c8d1b0745c 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.3.0.eb @@ -24,7 +24,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('cURL', '7.76.0'), ('libarchive', '3.5.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.21.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.21.1-GCCcore-11.2.0.eb index 60e004e5627..e09ed862f94 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.21.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.21.1-GCCcore-11.2.0.eb @@ -24,7 +24,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('cURL', '7.78.0'), ('libarchive', '3.5.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb index 7d88407d378..87996bb065a 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb @@ -24,7 +24,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('cURL', '7.78.0'), ('libarchive', '3.5.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.23.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.23.1-GCCcore-11.3.0.eb index d6c0f58b8ae..069c6a25c27 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.23.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.23.1-GCCcore-11.3.0.eb @@ -24,7 +24,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('cURL', '7.83.0'), ('libarchive', '3.6.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb index 6b1b02e8197..113d81b7610 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb @@ -22,7 +22,7 @@ dependencies = [ ('scikit-learn', '0.19.1', versionsuffix), ('MEGAHIT', '1.1.3', versionsuffix), ('BEDTools', '2.27.1'), - ('picard', '2.18.27', '-Java-1.8', True), + ('picard', '2.18.27', '-Java-1.8', SYSTEM), ('SAMtools', '1.6'), ('Bowtie2', '2.3.4.1'), ('parallel', '20171122'), diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb index 30bfadb038e..22128baa385 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb @@ -22,7 +22,7 @@ dependencies = [ ('scikit-learn', '0.19.1', versionsuffix), ('MEGAHIT', '1.1.3', versionsuffix), ('BEDTools', '2.27.1'), - ('picard', '2.18.27', '-Java-1.8', True), + ('picard', '2.18.27', '-Java-1.8', SYSTEM), ('SAMtools', '1.6'), ('Bowtie2', '2.3.4.1'), ('parallel', '20171122'), diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb index b8d52d0019d..dc99d2aeb67 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb @@ -23,7 +23,7 @@ dependencies = [ ('scikit-learn', '0.20.2', versionsuffix), ('MEGAHIT', '1.1.4', versionsuffix), ('BEDTools', '2.27.1'), - ('picard', '2.18.27', '-Java-1.8', True), + ('picard', '2.18.27', '-Java-1.8', SYSTEM), ('SAMtools', '1.9'), ('Bowtie2', '2.3.4.2'), ('parallel', '20190222'), diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb index f1334d88a22..df708ac5e1f 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb @@ -27,7 +27,7 @@ dependencies = [ ('scikit-learn', '0.20.3'), ('MEGAHIT', '1.2.8'), ('BEDTools', '2.28.0'), - ('picard', '2.21.1', '-Java-11', True), + ('picard', '2.21.1', '-Java-11', SYSTEM), ('SAMtools', '1.9'), ('Bowtie2', '2.3.5.1'), ('parallel', '20190622'), diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb index 9c7b23d10c7..e8a5cb71f32 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb @@ -25,7 +25,7 @@ dependencies = [ ('GSL', '2.6'), ('MEGAHIT', '1.2.9', versionsuffix), ('parallel', '20210322'), - ('picard', '2.25.0', '-Java-11', True), + ('picard', '2.25.0', '-Java-11', SYSTEM), ('Pysam', '0.16.0.1', versionsuffix), ('SAMtools', '1.11'), ('scikit-learn', '0.20.4', versionsuffix), diff --git a/easybuild/easyconfigs/c/CPLEX/CPLEX-12.10-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/c/CPLEX/CPLEX-12.10-GCCcore-8.3.0-Python-3.7.4.eb index 854f8a57c6c..2bb7d98cdcf 100644 --- a/easybuild/easyconfigs/c/CPLEX/CPLEX-12.10-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CPLEX/CPLEX-12.10-GCCcore-8.3.0-Python-3.7.4.eb @@ -19,7 +19,7 @@ checksums = ['cd530eb9c6d446bd18b5dc5a3d61070bfad92c3efd6565d2d8e31a2acfb496f7'] builddependencies = [('binutils', '2.32')] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Python', '3.7.4'), ] diff --git a/easybuild/easyconfigs/c/CPLEX/CPLEX-12.9-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/CPLEX/CPLEX-12.9-GCCcore-8.2.0.eb index a35951482e9..4ccf2abec92 100644 --- a/easybuild/easyconfigs/c/CPLEX/CPLEX-12.9-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/c/CPLEX/CPLEX-12.9-GCCcore-8.2.0.eb @@ -20,7 +20,7 @@ multi_deps = {'Python': ['3.7.2', '2.7.15']} builddependencies = [('binutils', '2.31.1')] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb index 4024c882cdb..e815134c6ec 100644 --- a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb @@ -24,11 +24,11 @@ checksums = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '2.7.18'), ('SciPy-bundle', '2020.11', '-Python-%(pyver)s'), ('matplotlib', '2.2.5', '-Python-%(pyver)s'), - ('Trimmomatic', '0.39', '-Java-%(javashortver)s', True), + ('Trimmomatic', '0.39', '-Java-%(javashortver)s', SYSTEM), ('FLASH', '2.2.00'), ('SAMtools', '1.11'), ('Bowtie2', '2.4.2'), diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb index 10d20ead474..e1a264c229a 100644 --- a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb @@ -23,11 +23,11 @@ checksums = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('matplotlib', '3.3.3'), - ('Trimmomatic', '0.39', '-Java-%(javashortver)s', True), + ('Trimmomatic', '0.39', '-Java-%(javashortver)s', SYSTEM), ('FLASH', '2.2.00'), ('SAMtools', '1.11'), ('Bowtie2', '2.4.2'), diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-GCC-9.3.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-GCC-9.3.0.eb index c193a9b0bcd..23109630c34 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-GCC-9.3.0.eb @@ -10,7 +10,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = {'name': 'GCC', 'version': '9.3.0'} -dependencies = [('CUDAcore', '11.0.2', '', True)] +dependencies = [('CUDAcore', '11.0.2', '', SYSTEM)] altroot = 'CUDAcore' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-iccifort-2020.1.217.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-iccifort-2020.1.217.eb index 7f77cc256bf..a2eecc5b703 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-iccifort-2020.1.217.eb @@ -10,7 +10,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = {'name': 'iccifort', 'version': '2020.1.217'} -dependencies = [('CUDAcore', '11.0.2', '', True)] +dependencies = [('CUDAcore', '11.0.2', '', SYSTEM)] altroot = 'CUDAcore' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb index d6d90b81331..02cea32f4a5 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb @@ -10,7 +10,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = {'name': 'GCC', 'version': '10.2.0'} -dependencies = [('CUDAcore', version, '', True)] +dependencies = [('CUDAcore', version, '', SYSTEM)] altroot = 'CUDAcore' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb index c9848f32320..60c8e706731 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb @@ -10,7 +10,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -dependencies = [('CUDAcore', version, '', True)] +dependencies = [('CUDAcore', version, '', SYSTEM)] altroot = 'CUDAcore' diff --git a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb index bcf0c9ef120..cf48d75ac7f 100644 --- a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb @@ -29,8 +29,8 @@ dependencies = [ ('glog', '0.3.4'), ('gflags', '2.1.2'), ('OpenCV', '3.1.0'), - ('CUDA', local_cudaversion, '', True), - ('cuDNN', '4.0', '', True), + ('CUDA', local_cudaversion, '', SYSTEM), + ('cuDNN', '4.0', '', SYSTEM), ('LMDB', '0.9.18'), ('LevelDB', '1.18'), ('snappy', '1.1.3'), diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2017b-Python-2.7.14.eb index dea47b25389..4b4cf0047b5 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2017b-Python-2.7.14.eb @@ -31,7 +31,7 @@ dependencies = [ ] builddependencies = [ ('SCons', '3.0.1', versionsuffix), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('googletest', '1.8.0'), ('fmt', '3.0.2'), ] diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2017a-Python-2.7.13.eb index 2aca050dae2..a34dff6cd90 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2017a-Python-2.7.13.eb @@ -30,7 +30,7 @@ dependencies = [ builddependencies = [ ('SCons', '2.5.1', versionsuffix), ('3to2', '1.1.1', versionsuffix), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('fmt', '3.0.2'), ('googletest', '1.8.0'), ] diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2017b-Python-2.7.14.eb index adf2eb1798e..cd969a41467 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2017b-Python-2.7.14.eb @@ -31,7 +31,7 @@ dependencies = [ ] builddependencies = [ ('SCons', '3.0.1', versionsuffix), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('fmt', '3.0.2'), ('googletest', '1.8.0'), ] diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2018a-Python-2.7.14.eb index 49e2af27122..396bc3cc844 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2018a-Python-2.7.14.eb @@ -31,7 +31,7 @@ dependencies = [ ] builddependencies = [ ('SCons', '3.0.1', versionsuffix), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('fmt', '3.0.2'), ('googletest', '1.8.0'), ] diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.4.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.4.0-intel-2018a-Python-2.7.14.eb index dd2f84d5e11..64fbb834858 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.4.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.4.0-intel-2018a-Python-2.7.14.eb @@ -21,7 +21,7 @@ dependencies = [ ] builddependencies = [ ('SCons', '3.0.1', versionsuffix), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('fmt', '3.0.2'), ('googletest', '1.8.0'), ] diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-2.7.14.eb index c6904d99cd1..55855240f3f 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-2.7.14.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} dependencies = [ ('Python', '2.7.14'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.1b2'), ('matplotlib', '2.1.0', versionsuffix), diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-3.6.3.eb index e714707c6e2..5e8e0e8c81c 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-3.6.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} dependencies = [ ('Python', '3.6.3'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.1b2'), ('matplotlib', '2.1.0', versionsuffix), diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2018b-Python-2.7.15.eb index a86d3eb6269..f4962c34698 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2018b-Python-2.7.15.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} dependencies = [ ('Python', '2.7.15'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), ('matplotlib', '2.2.3', versionsuffix), diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-2.7.14.eb index 3896c5c1e88..be840290424 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-2.7.14.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} dependencies = [ ('Python', '2.7.14'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.1b2'), ('matplotlib', '2.1.0', versionsuffix), diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-3.6.3.eb index a37f08d8828..d4b79112d0a 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-3.6.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} dependencies = [ ('Python', '3.6.3'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.1b2'), ('matplotlib', '2.1.0', versionsuffix), diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2019a-Python-2.7.15.eb index 4514d763794..ff1a1fe08e9 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2019a-Python-2.7.15.eb @@ -22,7 +22,7 @@ checksums = ['0dcf31eab5e340a0fff37d7a5091d46d9269b0708db8f789adcd7cbd2a09a2b7'] # https://github.com/Ecogenomics/CheckM/blob/master/setup.py dependencies = [ ('Python', '2.7.15'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), ('SciPy-bundle', '2019.03'), # numpy diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb index b5127b17c53..3930c1d64ba 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb @@ -32,7 +32,7 @@ checksums = [ dependencies = [ ('Python', '2.7.18'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), ('SciPy-bundle', '2020.11', versionsuffix), diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.2-foss-2019b-Python-3.7.4.eb index 5c9942d78bd..76cd653d9bc 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.2-foss-2019b-Python-3.7.4.eb @@ -34,7 +34,7 @@ checksums = [ # https://github.com/Ecogenomics/CheckM/blob/master/setup.py dependencies = [ ('Python', '3.7.4'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), ('SciPy-bundle', '2019.10', versionsuffix), # numpy diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.2-intel-2019b-Python-3.7.4.eb index 59a8d8608ce..07591763a36 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.2-intel-2019b-Python-3.7.4.eb @@ -34,7 +34,7 @@ checksums = [ # https://github.com/Ecogenomics/CheckM/blob/master/setup.py dependencies = [ ('Python', '3.7.4'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), ('SciPy-bundle', '2019.10', versionsuffix), # numpy diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021a.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021a.eb index a7e58e823a7..7fb4d447164 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021a.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021a.eb @@ -33,7 +33,7 @@ checksums = [ # https://github.com/Ecogenomics/CheckM/blob/master/setup.py dependencies = [ ('Python', '3.9.5'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), ('SciPy-bundle', '2021.05'), # numpy diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb index c1bc07048f5..9cf5f49131d 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb @@ -34,7 +34,7 @@ checksums = [ # https://github.com/Ecogenomics/CheckM/blob/master/setup.py dependencies = [ ('Python', '3.9.6'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), ('SciPy-bundle', '2021.10'), # numpy diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-intel-2020a-Python-3.8.2.eb index 27fd970b63a..c7dd8d34897 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-intel-2020a-Python-3.8.2.eb @@ -34,7 +34,7 @@ checksums = [ # https://github.com/Ecogenomics/CheckM/blob/master/setup.py dependencies = [ ('Python', '3.8.2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.3.1'), ('SciPy-bundle', '2020.03', versionsuffix), # numpy diff --git a/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb index dead5e2ce6a..60ac440d2d1 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -57,7 +57,7 @@ dependencies = [ ('Z3', '4.8.11'), ('libffi', '3.3'), ('elfutils', '0.185'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] builddependencies = [ diff --git a/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb index 42c8ecf704e..f051e776913 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -57,7 +57,7 @@ dependencies = [ ('Z3', '4.8.12'), ('libffi', '3.4.2'), ('elfutils', '0.185'), - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ] builddependencies = [ diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb index b4f7a627ae0..ea670d2cb0c 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb @@ -54,7 +54,7 @@ dependencies = [ ('binutils', '2.31.1'), ('ncurses', '6.1'), ('GMP', '6.1.2'), - ('CUDA', local_cudaver, '', True), + ('CUDA', local_cudaver, '', SYSTEM), ] builddependencies = [ diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb index 7a92cacfd67..dddce517cbc 100644 --- a/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb @@ -13,9 +13,9 @@ builddependencies = [('Cython', '0.29.22')] dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), - ('cuTENSOR', '1.2.2.5', '-CUDA-%(cudaver)s', True), + ('cuTENSOR', '1.2.2.5', '-CUDA-%(cudaver)s', SYSTEM), ] use_pip = True diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2018b.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2018b.eb index 744472a8a39..c3ad4a5a02a 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2018b.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2018b.eb @@ -24,7 +24,7 @@ checksums = [ ] builddependencies = [ - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('SAMtools', '0.1.20'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-gompi-2019b.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-gompi-2019b.eb index 81654b4596c..5ec63582c06 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-gompi-2019b.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-gompi-2019b.eb @@ -24,7 +24,7 @@ checksums = [ ] builddependencies = [ - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('SAMtools', '0.1.20'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2017b.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2017b.eb index 89252c31854..c322edc64a1 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2017b.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2017b.eb @@ -15,7 +15,7 @@ checksums = [ '9199390a11376ffba0583741752faca277c82ce3ab665a66ba8dc5991c45088f', # Cufflinks-2.2.1_fix-boost-inc.patch ] -builddependencies = [('Eigen', '3.3.4', '', True)] +builddependencies = [('Eigen', '3.3.4', '', SYSTEM)] dependencies = [ ('Boost', '1.65.1'), ('SAMtools', '0.1.20'), diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2018a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2018a.eb index 11a20f70733..94cc688d081 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2018a.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2018a.eb @@ -16,7 +16,7 @@ checksums = [ ] builddependencies = [ - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('SAMtools', '0.1.20'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-gompi-2019a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-gompi-2019a.eb index fb65a457aae..881426fe576 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-gompi-2019a.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-gompi-2019a.eb @@ -16,7 +16,7 @@ sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_ checksums = ['444c632083a473fe4fd99ff189cef5bbd95daee0912e8eefe79534bf225fbcb6'] builddependencies = [ - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('Autotools', '20180311'), ('SAMtools', '1.9'), ] diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.49.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.49.1-GCCcore-5.4.0.eb index a4c5a87e6b9..34bc1da2fd4 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.49.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.49.1-GCCcore-5.4.0.eb @@ -17,7 +17,7 @@ source_urls = ['http://curl.haxx.se/download/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['ff3e80c1ca6a068428726cd7dd19037a47cc538ce58ef61c59587191039b2ca6'] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb index 09811fccdee..28584d265c3 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb index 8d7f087e2b7..9c8d5222d95 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.76.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.76.0-GCCcore-10.3.0.eb index 0c3b29d5863..27b19b6d9c6 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.76.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.76.0-GCCcore-10.3.0.eb @@ -30,7 +30,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = '--with-zlib' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.78.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.78.0-GCCcore-11.2.0.eb index e66d05453ca..ad57d96beb2 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.78.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.78.0-GCCcore-11.2.0.eb @@ -27,7 +27,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = '--with-zlib ' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.83.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.83.0-GCCcore-11.3.0.eb index 4a4ad41cdfe..2813650a0d3 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.83.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.83.0-GCCcore-11.3.0.eb @@ -27,7 +27,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.12'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = '--with-zlib ' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb index 69ff9b82788..7ff88d2ae52 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb @@ -27,7 +27,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.12'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = '--with-zlib ' diff --git a/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb b/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb index ff486b7b508..d3b3a9cf790 100755 --- a/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb +++ b/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb @@ -25,7 +25,7 @@ start_dir = 'src' files_to_copy = ['Linux-amd64/*'] dependencies = [ - ('Java', '1.8.0_112', '', True), + ('Java', '1.8.0_112', '', SYSTEM), ('Perl', '5.24.0'), ('gnuplot', '5.0.5'), ] diff --git a/easybuild/easyconfigs/c/canu/canu-1.8-GCCcore-8.2.0-Perl-5.28.1.eb b/easybuild/easyconfigs/c/canu/canu-1.8-GCCcore-8.2.0-Perl-5.28.1.eb index 5c98cf65e4e..5eb3e8890bb 100644 --- a/easybuild/easyconfigs/c/canu/canu-1.8-GCCcore-8.2.0-Perl-5.28.1.eb +++ b/easybuild/easyconfigs/c/canu/canu-1.8-GCCcore-8.2.0-Perl-5.28.1.eb @@ -16,7 +16,7 @@ checksums = ['30ecfe574166f54f79606038830f68927cf0efab33bdc3c6e43fd1448fa0b2e4'] builddependencies = [('binutils', '2.31.1')] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Perl', '5.28.1'), ('gnuplot', '5.2.6'), ] diff --git a/easybuild/easyconfigs/c/canu/canu-1.8-foss-2017b-Perl-5.26.0.eb b/easybuild/easyconfigs/c/canu/canu-1.8-foss-2017b-Perl-5.26.0.eb index 31877e3e7dd..54dd03ba54b 100644 --- a/easybuild/easyconfigs/c/canu/canu-1.8-foss-2017b-Perl-5.26.0.eb +++ b/easybuild/easyconfigs/c/canu/canu-1.8-foss-2017b-Perl-5.26.0.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['30ecfe574166f54f79606038830f68927cf0efab33bdc3c6e43fd1448fa0b2e4'] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Perl', '5.26.0'), ('gnuplot', '5.2.2'), ('Boost', '1.65.1'), diff --git a/easybuild/easyconfigs/c/canu/canu-1.8-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/c/canu/canu-1.8-foss-2018b-Perl-5.28.0.eb index 1066c169c5e..114020eb165 100644 --- a/easybuild/easyconfigs/c/canu/canu-1.8-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/c/canu/canu-1.8-foss-2018b-Perl-5.28.0.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['30ecfe574166f54f79606038830f68927cf0efab33bdc3c6e43fd1448fa0b2e4'] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Perl', '5.28.0'), ('gnuplot', '5.2.5'), ('Boost', '1.67.0'), diff --git a/easybuild/easyconfigs/c/canu/canu-1.8-intel-2017b-Perl-5.26.0.eb b/easybuild/easyconfigs/c/canu/canu-1.8-intel-2017b-Perl-5.26.0.eb index e74e3dbe8b9..75b1d610731 100644 --- a/easybuild/easyconfigs/c/canu/canu-1.8-intel-2017b-Perl-5.26.0.eb +++ b/easybuild/easyconfigs/c/canu/canu-1.8-intel-2017b-Perl-5.26.0.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['30ecfe574166f54f79606038830f68927cf0efab33bdc3c6e43fd1448fa0b2e4'] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Perl', '5.26.0'), ('gnuplot', '5.2.2'), ('Boost', '1.65.1'), diff --git a/easybuild/easyconfigs/c/canu/canu-1.9-GCCcore-8.3.0-Java-11.eb b/easybuild/easyconfigs/c/canu/canu-1.9-GCCcore-8.3.0-Java-11.eb index a1185d44d41..b9a96798841 100644 --- a/easybuild/easyconfigs/c/canu/canu-1.9-GCCcore-8.3.0-Java-11.eb +++ b/easybuild/easyconfigs/c/canu/canu-1.9-GCCcore-8.3.0-Java-11.eb @@ -16,7 +16,7 @@ checksums = ['6b086ab6086c050752166500378bc4b3b3543d4c617863e894d296171cee3385'] builddependencies = [('binutils', '2.32')] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Perl', '5.30.0'), ('gnuplot', '5.2.8'), ] diff --git a/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb index 7a7d3c59ec8..1a81cacc467 100644 --- a/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb @@ -19,7 +19,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Perl', '5.32.0'), ('gnuplot', '5.4.1'), ] diff --git a/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-9.3.0-Java-11.eb b/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-9.3.0-Java-11.eb index 990e0dcabec..8e5ee7b58b9 100644 --- a/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-9.3.0-Java-11.eb +++ b/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-9.3.0-Java-11.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Perl', '5.30.2'), ('gnuplot', '5.2.8'), ] diff --git a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0-Java-11.eb b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0-Java-11.eb index 42b5f5b32b9..441c3224e45 100644 --- a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0-Java-11.eb +++ b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0-Java-11.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Perl', '5.32.1'), ('gnuplot', '5.4.2'), ] diff --git a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0.eb index 688753bfca0..1eff45bbc43 100644 --- a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0.eb @@ -19,7 +19,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Perl', '5.32.1'), ('gnuplot', '5.4.2'), ] diff --git a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.2.0.eb index 946fb4dd038..4d58483415e 100644 --- a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.2.0.eb @@ -19,7 +19,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Perl', '5.34.0'), ('gnuplot', '5.4.2'), ] diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 7d60fb1c61d..8356b39778a 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -18,7 +18,7 @@ builddependencies = [ dependencies = [ ('Python', '3.8.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('SciPy-bundle', '2020.11'), ('leidenalg', '0.8.3'), ('hyperopt', '0.2.5'), diff --git a/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb index 5a14fa765f1..c4b1c45f09f 100644 --- a/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ ('Python', '3.9.5'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('SciPy-bundle', '2021.05'), ('PyTorch-Lightning', '1.5.9', versionsuffix), ('torchvision', '0.11.1', versionsuffix), diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb index 8a1c4c6c03a..87813b35bd9 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb @@ -35,7 +35,7 @@ dependencies = [ ('LibTIFF', '4.2.0'), ('GSL', '2.7'), ('wxWidgets', '3.1.5'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] configopts = '--enable-openmp ' diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-FCC-4.5.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-FCC-4.5.0.eb index eb7933a6c04..3552aab690a 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-FCC-4.5.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-FCC-4.5.0.eb @@ -23,7 +23,7 @@ checksums = [ builddependencies = [('binutils', '2.36.1')] -dependencies = [('OpenSSL', '1.1', '', True)] +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.3.0.eb index 4b461e5efbd..2d38e9742d4 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.3.0.eb @@ -23,7 +23,7 @@ checksums = [ builddependencies = [('binutils', '2.36.1')] -dependencies = [('OpenSSL', '1.1', '', True)] +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.2.0.eb index 94dd6b092b5..e05ffa92185 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.2.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [('binutils', '2.37')] -dependencies = [('OpenSSL', '1.1', '', True)] +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.3.0.eb index 21b56c74451..1217b252c49 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.3.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [('binutils', '2.38')] -dependencies = [('OpenSSL', '1.1', '', True)] +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.1.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.1.0.eb index d33d1cd6305..0d52a3be447 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.1.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [('binutils', '2.38')] -dependencies = [('OpenSSL', '1.1', '', True)] +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.2.0.eb index c78178d6997..515c85e1a9c 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.2.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [('binutils', '2.31.1')] -dependencies = [('OpenSSL', '1.1', '', True)] +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.3.0.eb index 0c21b4fc363..1a66d75ceb1 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.3.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [('binutils', '2.32')] -dependencies = [('OpenSSL', '1.1', '', True)] +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb index 5f7fbe14d4a..094f7bc25d2 100644 --- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb @@ -16,7 +16,7 @@ dependencies = [ ('Perl', '5.34.0'), ('MariaDB', '10.6.4'), ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] options = {'modulename': 'DBD::mysql'} diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb index eb71c16f467..6d67a433eb4 100644 --- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb @@ -16,7 +16,7 @@ dependencies = [ ('Perl', '5.34.1'), ('MariaDB', '10.9.3'), ('zlib', '1.2.12'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] options = {'modulename': 'DBD::mysql'} diff --git a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb index f7c16f218ab..2e64cfeb8f1 100644 --- a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ('zlib', '1.2.11'), ('libjpeg-turbo', '2.0.6'), ('LibTIFF', '4.3.0'), diff --git a/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2018.1.0.post1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2018.1.0.post1-foss-2018a-Python-3.6.4.eb index 61ccdb3b120..197ea4e94e2 100644 --- a/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2018.1.0.post1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2018.1.0.post1-foss-2018a-Python-3.6.4.eb @@ -34,7 +34,7 @@ dependencies = [ ('Trilinos', '12.12.1', versionsuffix), ('zlib', '1.2.11'), ('libxml2', '2.9.7'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('PLY', '3.11', versionsuffix), ('VTK', '8.1.0', versionsuffix), ('petsc4py', '3.9.1', versionsuffix), diff --git a/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2019.1.0.post0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2019.1.0.post0-foss-2019b-Python-3.7.4.eb index 51c770e09cc..067b5659b17 100644 --- a/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2019.1.0.post0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2019.1.0.post0-foss-2019b-Python-3.7.4.eb @@ -33,7 +33,7 @@ dependencies = [ ('Trilinos', '12.12.1', versionsuffix), ('zlib', '1.2.11'), ('libxml2', '2.9.9'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('PLY', '3.11', versionsuffix), ('VTK', '8.2.0', versionsuffix), ('petsc4py', '3.12.0', versionsuffix), diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb index 020b8f5f672..e06ee84b7f4 100644 --- a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb @@ -13,7 +13,7 @@ dependencies = [ ('R', '4.0.3'), ('R-bundle-Bioconductor', '3.12', '-R-%(rver)s'), ('tMAE', '1.0.0', '-R-%(rver)s'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('GATK', '4.2.0.0', '-Java-%(javaver)s'), ('Graphviz', '2.47.0', '-Java-%(javaver)s'), ('Python', '3.8.6'), @@ -23,7 +23,7 @@ dependencies = [ ('HTSlib', '1.11'), # for tabix ('SAMtools', '1.11'), ('BCFtools', '1.11'), - ('Pandoc', '2.13', '', True), + ('Pandoc', '2.13', '', SYSTEM), ] # postinstallcmds for pandoc are required to avoid that import fails because pandoc/definitions dir is not installed diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb index 014ae7c311e..8091ae5611b 100644 --- a/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb @@ -13,7 +13,7 @@ dependencies = [ ('R', '4.0.3'), ('R-bundle-Bioconductor', '3.12', '-R-%(rver)s'), ('tMAE', '1.0.0', '-R-%(rver)s'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('GATK', '4.2.0.0', '-Java-%(javaver)s'), ('Graphviz', '2.47.0', '-Java-%(javaver)s'), ('Python', '3.8.6'), @@ -23,7 +23,7 @@ dependencies = [ ('HTSlib', '1.11'), # for tabix ('SAMtools', '1.11'), ('BCFtools', '1.11'), - ('Pandoc', '2.13', '', True), + ('Pandoc', '2.13', '', SYSTEM), ] exts_list = [ diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb index db1db5f1d92..64d414e98e3 100644 --- a/easybuild/easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb @@ -13,7 +13,7 @@ dependencies = [ ('R', '4.1.2'), ('R-bundle-Bioconductor', '3.14', '-R-%(rver)s'), ('tMAE', '1.0.1', '-R-%(rver)s'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('GATK', '4.2.3.0', '-Java-%(javaver)s'), ('Graphviz', '2.50.0'), ('Python', '3.9.6'), @@ -23,7 +23,7 @@ dependencies = [ ('HTSlib', '1.14'), # for tabix ('SAMtools', '1.14'), ('BCFtools', '1.14'), - ('Pandoc', '2.13', '', True), + ('Pandoc', '2.13', '', SYSTEM), ] exts_list = [ diff --git a/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb index 3cfdd856379..1a94e28f534 100644 --- a/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('PyTorch', '1.10.0', versionsuffix), diff --git a/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb b/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb index 5077e846a5f..43608ef12b5 100644 --- a/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb @@ -18,7 +18,7 @@ source_urls = ['https://bitbucket.org/nrg/dicombrowser/downloads/'] sources = ['%(name)s-%(version)s-bin-with-dependencies.jar'] dependencies = [ - ('Java', '1.7.0_80', '', True), + ('Java', '1.7.0_80', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb index 90fd7aad74c..3b4f5c86dc5 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ checksums = ['af667887bd7a87dc0dbf9ac8d86c96b552dfb8ca9c790ed1cbffaa6131573f6b'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ('CMake', '3.7.2'), ('flex', '2.6.3'), ('Bison', '3.0.4'), diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb index 45622c59260..737412283c0 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb @@ -30,7 +30,7 @@ checksums = [ srcdir = 'src/source' builddependencies = [ - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('CMake', '3.21.1'), ] diff --git a/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb index c9fb8927779..319fbdda612 100644 --- a/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb @@ -10,7 +10,7 @@ description = "Efficient Multi-Scale 3D Convolutional Neural Network for Segment toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('TensorFlow', '2.6.0', versionsuffix), ('SciPy-bundle', '2021.05'), diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb index e62049c61b8..3448b11526f 100644 --- a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb @@ -25,7 +25,7 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('cuDNN', '8.2.1.32', versionsuffix, True), ] diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb index eaf6f22dc12..e32b7fad6ce 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb @@ -42,7 +42,7 @@ builddependencies = [('CMake', '3.18.4')] dependencies = [ ('X11', '20201008'), ('libharu', '2.3.0'), - ('Java', '13', '', True), + ('Java', '13', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.2.0-2.31.1.eb index a4cabd71a43..df004f43de0 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.2.0-2.31.1.eb @@ -37,7 +37,7 @@ builddependencies = [('CMake', '3.13.3')] dependencies = [ ('X11', '20190311'), ('libharu', '2.3.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.3.0-Java-11.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.3.0-Java-11.eb index e34109b6a96..aee6c64e90f 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.3.0-Java-11.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.3.0-Java-11.eb @@ -42,7 +42,7 @@ builddependencies = [('CMake', '3.15.3')] dependencies = [ ('X11', '20190717'), ('libharu', '2.3.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb index 0d6ccf3dc76..08887154a33 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb @@ -29,7 +29,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.3.0'), - ('Java', '1.7.0_80', '', True), + ('Java', '1.7.0_80', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb index 1e20c9bdaa4..ab468ed2c59 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb @@ -36,7 +36,7 @@ builddependencies = [('CMake', '3.11.4')] dependencies = [ ('X11', '20180604'), ('libharu', '2.3.0'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb index 2b478b1b9ea..11a7dcee8c2 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb @@ -39,7 +39,7 @@ builddependencies = [('CMake', '3.20.1')] dependencies = [ ('X11', '20210518'), ('libharu', '2.3.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021b.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021b.eb index 9471b613f8d..84ecb49dc1e 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021b.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021b.eb @@ -39,7 +39,7 @@ builddependencies = [('CMake', '3.22.1')] dependencies = [ ('X11', '20210802'), ('libharu', '2.3.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 3a560dce5d2..c5ee371b0db 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -37,7 +37,7 @@ builddependencies = [('CMake', '3.13.3')] dependencies = [ ('X11', '20190311'), ('libharu', '2.3.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb index fc0789ffe30..71a682b454e 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb @@ -35,7 +35,7 @@ dependencies = [ ('X11', local_x11ver), ('libgd', '2.2.4'), ('libharu', '2.3.0'), - ('Java', '1.8.0_144', '', True), + ('Java', '1.8.0_144', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb index d6fa49965ac..8796b8995a5 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb @@ -29,7 +29,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.3.0'), - ('Java', '1.7.0_80', '', True), + ('Java', '1.7.0_80', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2018b.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2018b.eb index 6c9d498a0a4..9da803147ab 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2018b.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2018b.eb @@ -33,7 +33,7 @@ dependencies = [ ('X11', '20180604'), ('libgd', '2.2.5'), ('libharu', '2.3.0'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index 328732419a3..8f17e9edb17 100644 --- a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -21,7 +21,7 @@ checksums = ['22229f19332d4fd08eb3bf60198211bda674f51632b977c9d7fd09531e09dd8d'] builddependencies = [('CMake', '3.11.4')] dependencies = [ - ('ispc', '1.10.0', '', True), + ('ispc', '1.10.0', '', SYSTEM), ('tbb', '2018_U5'), ] diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-5.4.0.eb index a00b575cac8..4cf6ddc59a4 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-5.4.0.eb @@ -10,7 +10,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori toolchain = {'name': 'GCCcore', 'version': '5.4.0'} toolchainopts = {'pic': True} -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] source_urls = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')] sources = [SOURCE_TAR_BZ2] diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-6.3.0.eb index e68f2d8d88a..b897f140c89 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-6.3.0.eb @@ -15,7 +15,7 @@ sources = [SOURCE_TAR_BZ2] checksums = ['d9e50ff2d19b3538bd2127902a89987474e1a4db8e43a66a4d1a712ab9a504ff'] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['include/expat.h', 'lib/libexpat.a', 'lib/libexpat.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb index 20703396833..fdb59680efe 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ - ('NASM', '2.12.02', '', True), + ('NASM', '2.12.02', '', SYSTEM), ('x264', '20170406'), ('X11', '20170129'), # pulls in bzip2 and zlib ] diff --git a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb index 4cb227e1d23..0e1c47bba9b 100644 --- a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb @@ -17,8 +17,8 @@ dependencies = [ ('FSL', '5.0.11', versionsuffix), ('ANTs', '2.3.1', versionsuffix), ('AFNI', '18.3.00', versionsuffix), - ('C3D', '1.0.0', '', True), - ('FreeSurfer', '6.0.1', '-centos6_x86_64', True), + ('C3D', '1.0.0', '', SYSTEM), + ('FreeSurfer', '6.0.1', '-centos6_x86_64', SYSTEM), ('ICA-AROMA', '0.4.4-beta', versionsuffix), ('Seaborn', '0.9.0', versionsuffix), ('PyYAML', '3.13', versionsuffix), diff --git a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb index b12cefc9057..81bb446518f 100644 --- a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb @@ -17,8 +17,8 @@ dependencies = [ ('FSL', '5.0.11', versionsuffix), ('ANTs', '2.3.1', versionsuffix), ('AFNI', '18.3.00', versionsuffix), - ('C3D', '1.0.0', '', True), - ('FreeSurfer', '6.0.1', '-centos6_x86_64', True), + ('C3D', '1.0.0', '', SYSTEM), + ('FreeSurfer', '6.0.1', '-centos6_x86_64', SYSTEM), ('ICA-AROMA', '0.4.4-beta', versionsuffix), ('Seaborn', '0.9.0', versionsuffix), ('PyYAML', '3.13', versionsuffix), diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb index f96cf15c130..e5ab2e466bf 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb @@ -60,7 +60,7 @@ dependencies = [ ('VTK', '8.1.1', local_python_suffix), ('GSL', '2.5'), ('Qwt', '6.1.4'), - ('CUDA', local_CUDA_ver, '', True), + ('CUDA', local_CUDA_ver, '', SYSTEM), ] # FSLDIR needs to be defined when running postinstall to get the correct shebang diff --git a/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb index 38ff91c345f..2e329e07f19 100644 --- a/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ ('Python', '3.9.5'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('SciPy-bundle', '2021.05'), ('PyYAML', '5.4.1'), ('Biopython', '1.79'), diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-1.8.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-1.8.eb index 9251dd40828..daee979d9db 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-1.8.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-1.8.eb @@ -21,7 +21,7 @@ checksums = [ '684701634440864750c9a0b99d81e122a1def78672d436daf5497bff61d9a356', # FastQC_shebang.patch ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] postinstallcmds = ["chmod +x %(installdir)s/fastqc"] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-11.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-11.eb index f075347905b..ef747fd9625 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-11.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-11.eb @@ -25,7 +25,7 @@ checksums = [ '684701634440864750c9a0b99d81e122a1def78672d436daf5497bff61d9a356', # FastQC_shebang.patch ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] postinstallcmds = ["chmod +x %(installdir)s/fastqc"] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.9-Java-11.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.9-Java-11.eb index bbe1b9f0240..5fa46779ccc 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.9-Java-11.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.9-Java-11.eb @@ -25,7 +25,7 @@ checksums = [ '684701634440864750c9a0b99d81e122a1def78672d436daf5497bff61d9a356', # FastQC_shebang.patch ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] postinstallcmds = ["chmod +x %(installdir)s/fastqc"] diff --git a/easybuild/easyconfigs/f/FastViromeExplorer/FastViromeExplorer-20180422-foss-2019b.eb b/easybuild/easyconfigs/f/FastViromeExplorer/FastViromeExplorer-20180422-foss-2019b.eb index 0fad82d9d44..e16acdff154 100644 --- a/easybuild/easyconfigs/f/FastViromeExplorer/FastViromeExplorer-20180422-foss-2019b.eb +++ b/easybuild/easyconfigs/f/FastViromeExplorer/FastViromeExplorer-20180422-foss-2019b.eb @@ -14,7 +14,7 @@ sources = [{'download_filename': 'FastViromeExplorer-%s.tar.gz' % local_commit, checksums = ['3a8e7842e83539cd36f619f1e01761e2c5b87a44a5f51328287b6dd20ef47384'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('kallisto', '0.46.1'), ('SAMtools', '1.10'), ] diff --git a/easybuild/easyconfigs/f/Ferret/Ferret-7.3-intel-2017b.eb b/easybuild/easyconfigs/f/Ferret/Ferret-7.3-intel-2017b.eb index 3c6dcc5750c..afc3e88aa32 100644 --- a/easybuild/easyconfigs/f/Ferret/Ferret-7.3-intel-2017b.eb +++ b/easybuild/easyconfigs/f/Ferret/Ferret-7.3-intel-2017b.eb @@ -22,7 +22,7 @@ dependencies = [ ('cURL', '7.56.0'), ('ncurses', '6.0'), ('libreadline', '7.0'), - ('Java', '1.8.0_152', '', True), + ('Java', '1.8.0_152', '', SYSTEM), ] parallel = 1 diff --git a/easybuild/easyconfigs/f/Ferret/Ferret-7.5.0-foss-2019b.eb b/easybuild/easyconfigs/f/Ferret/Ferret-7.5.0-foss-2019b.eb index 1b061234a1c..ad0059c286e 100644 --- a/easybuild/easyconfigs/f/Ferret/Ferret-7.5.0-foss-2019b.eb +++ b/easybuild/easyconfigs/f/Ferret/Ferret-7.5.0-foss-2019b.eb @@ -24,7 +24,7 @@ dependencies = [ ('cURL', '7.66.0'), ('ncurses', '6.1'), ('libreadline', '8.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] # /bin/csh is required for installation by bin/make_executable_tar, bin/make_environment_tar diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-20170530.eb b/easybuild/easyconfigs/f/Fiji/Fiji-20170530.eb index b1a1a6b217b..b7dd6766d3f 100644 --- a/easybuild/easyconfigs/f/Fiji/Fiji-20170530.eb +++ b/easybuild/easyconfigs/f/Fiji/Fiji-20170530.eb @@ -14,7 +14,7 @@ source_urls = ['https://downloads.imagej.net/fiji/Life-Line/'] sources = ['%(namelower)s-nojre-%(version)s.zip'] checksums = ['cf9fb45c48b22a7888b479968477f1f7a300a9c833e47244cbe0d1e93890bd20'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] postinstallcmds = [ # Remove binaries for other platforms diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-20191119-2057.eb b/easybuild/easyconfigs/f/Fiji/Fiji-20191119-2057.eb index 3309bd66a45..c4f26af3680 100644 --- a/easybuild/easyconfigs/f/Fiji/Fiji-20191119-2057.eb +++ b/easybuild/easyconfigs/f/Fiji/Fiji-20191119-2057.eb @@ -17,7 +17,7 @@ sources = [{ }] checksums = ['7fad8e8f8676edbcfe7eb979421ab163e8d48bb7950a815f7821cbe58b8bb051'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] postinstallcmds = [ # Remove binaries for other platforms diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-20201104-1356.eb b/easybuild/easyconfigs/f/Fiji/Fiji-20201104-1356.eb index efe07f936b3..aac8b8d8de9 100644 --- a/easybuild/easyconfigs/f/Fiji/Fiji-20201104-1356.eb +++ b/easybuild/easyconfigs/f/Fiji/Fiji-20201104-1356.eb @@ -17,7 +17,7 @@ sources = [{ }] checksums = ['ea60c212f0c123c2e947f0171b3a3ec83c38f0a6bd4c2bf2d5a5c53ba5e464cb'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] postinstallcmds = [ # Remove binaries for other platforms diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb index d84be83b2a1..f779e1cdeac 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb @@ -17,7 +17,7 @@ builddependencies = [ ('BLIS', '0.8.1'), # imkl is commented out, since installing it requires accepting the Intel oneAPI EULA; # note: also commented out the lines below to add imkl to 'backends'! - # ('imkl', {'arch=x86_64': '2021.4.0', 'arch=*': False}, '', True), + # ('imkl', {'arch=x86_64': '2021.4.0', 'arch=*': False}, '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb index e56c85b532c..8467c1d6f61 100644 --- a/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('libreadline', '8.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = '--with-openssl' diff --git a/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb index 5db5fc0424e..6d3a32e9eac 100644 --- a/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb @@ -13,7 +13,7 @@ github_account = 'ndaniel' toolchain = {'name': 'foss', 'version': '2019b'} dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '2.7.16'), ('SciPy-bundle', '2019.10', versionsuffix), ('Biopython', '1.75', versionsuffix), @@ -24,7 +24,7 @@ dependencies = [ ('Kent_tools', '401'), # required for liftOver ('SRA-Toolkit', '2.10.4'), ('STAR', '2.7.2b'), - ('picard', '2.21.6', '-Java-11', True), # optional + ('picard', '2.21.6', '-Java-11', SYSTEM), # optional ('Velvet', '1.2.10', '-mt-kmer_191'), # optional ('openpyxl', '2.6.4', versionsuffix), # optional ('parallel', '20190922'), # optional diff --git a/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.30-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.30-foss-2019b-Python-2.7.16.eb index 1f85b510834..19f5df4c694 100644 --- a/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.30-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.30-foss-2019b-Python-2.7.16.eb @@ -13,7 +13,7 @@ github_account = 'ndaniel' toolchain = {'name': 'foss', 'version': '2019b'} dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '2.7.16'), ('SciPy-bundle', '2019.10', versionsuffix), ('Biopython', '1.75', versionsuffix), @@ -24,7 +24,7 @@ dependencies = [ ('Kent_tools', '401'), # required for liftOver ('SRA-Toolkit', '2.10.4'), ('STAR', '2.7.2b'), - ('picard', '2.21.6', '-Java-11', True), # optional + ('picard', '2.21.6', '-Java-11', SYSTEM), # optional ('Velvet', '1.2.10', '-mt-kmer_191'), # optional ('openpyxl', '2.6.4', versionsuffix), # optional ('parallel', '20190922'), # optional diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb index ac2d9ea1647..f93575efa78 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb index 72d2805b5fe..5845a2c4a99 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb index facf8e7f13d..6dfeb43eb04 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb index a28470817bb..77843fba611 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb index 68344b21cb3..db2144c50dd 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb index f579ff8a965..152ebf1d622 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb index bf74b3065c0..fd99cc06be2 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb @@ -14,6 +14,6 @@ checksums = ['71dd1b58158c935027104c830c019e48c73250708af5def45ea256c789318948'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.28', '', True)] +builddependencies = [('binutils', '2.28', '', SYSTEM)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb index b7b82f91973..92ac3157fe7 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb index 73279c6d88c..18c962e0803 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb index 954dea0d03b..adf1e7911c6 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb index ee9b4ed94d3..171d19af2db 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb index 51d6c9f7b63..1f313caa5a3 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb index 43cfdfac42c..cafaa07872a 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb index fea26879081..50026211e06 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ('Bison', '3.0.4'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb index e7dd6de964c..b8bb432df65 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ('Bison', '3.0.4'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb index 28c855c205d..8f9ab00f288 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ('Bison', '3.0.4'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.28', '', True), + ('binutils', '2.28', '', SYSTEM), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.1.0.eb index e615af45793..b0c78713c4d 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.1.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.6.1'), ('help2man', '1.47.15'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.34', '', True), + ('binutils', '2.34', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb index d6bae199dd3..f9dd97bb264 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.7.1'), ('help2man', '1.47.16'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.35', '', True), + ('binutils', '2.35', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.3.0.eb index cf948060781..9c8be6a9616 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.7.6'), ('help2man', '1.48.3'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.1.0.eb index 4ca376c2d43..0b7ca6dcc6a 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.1.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.7.6'), ('help2man', '1.48.3'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb index bd40de3b73d..78207419ed1 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.7.6'), ('help2man', '1.48.3'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.37', '', True), + ('binutils', '2.37', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.3.0.eb index c0e17568f86..dcf62626f8b 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.8.2'), ('help2man', '1.49.2'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.38', '', True), + ('binutils', '2.38', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.1.0.eb index b515d9c39a5..98d514c2d78 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.1.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.8.2'), ('help2man', '1.49.2'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.38', '', True), + ('binutils', '2.38', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.2.0.eb index b953ed29dab..63776909de0 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.8.2'), ('help2man', '1.49.2'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.39', '', True), + ('binutils', '2.39', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-5.5.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-5.5.0.eb index ffa930b4898..6e2346cb45a 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-5.5.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.0.5'), ('help2man', '1.47.5'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.3.0.eb index 20fcbab0a05..9f150f124f7 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.3.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ('Bison', '3.0.5'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] # glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.4.0.eb index 17af2c37c99..9879fbf3e84 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.4.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.0.5'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.28', '', True), + ('binutils', '2.28', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.2.0.eb index 85ed2ec7911..e22e1391359 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.0.5'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.29', '', True), + ('binutils', '2.29', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.3.0.eb index 94729110abe..aed4ab61424 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.0.5'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.30', '', True), + ('binutils', '2.30', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.4.0.eb index ae0550f73c3..179da80d419 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.4.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.2.2'), ('help2man', '1.47.8'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.31.1', '', True), + ('binutils', '2.31.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.1.0.eb index ac19425d0d4..92b958e6a97 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.1.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.0.5'), ('help2man', '1.47.6'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.30', '', True), + ('binutils', '2.30', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.2.0.eb index 01fb067c997..059e88ff05c 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.0.5'), ('help2man', '1.47.7'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.31.1', '', True), + ('binutils', '2.31.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.3.0.eb index f5fc0ba9248..11a535f092d 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.3.2'), ('help2man', '1.47.8'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.4.0.eb index 36aad7de33d..39338043fd8 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.4.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.3.2'), ('help2man', '1.47.8'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.1.0.eb index 256f72bf9e9..b1e5c067383 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.1.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.3.2'), ('help2man', '1.47.10'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.2.0.eb index 6a58f80946f..de9e537294f 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.3.2'), ('help2man', '1.47.10'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.3.0.eb index 5f380c6db6e..f61ebc628c7 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.5.3'), ('help2man', '1.47.12'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.34', '', True), + ('binutils', '2.34', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.4.0.eb index 7d4dffd6bd2..6cae0620be3 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.4.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.7.6'), ('help2man', '1.48.3'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.5.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.5.0.eb index 56f3743d5ab..24974f71c4d 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.5.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.5.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.8.2'), ('help2man', '1.49.2'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.38', '', True), + ('binutils', '2.38', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb index fc9583cf3bc..8f37cf904d2 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb @@ -20,7 +20,7 @@ dependencies = [ # use same binutils version that was used when building GCCcore toolchain builddependencies = [ - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ('pkg-config', '0.29.1'), ] diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb index 0b86b4b9dbd..d9df0e9ca8d 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb @@ -20,7 +20,7 @@ dependencies = [ # use same binutils version that was used when building GCCcore toolchain builddependencies = [ - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ('pkg-config', '0.29.2'), ] diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb index 2ff9e6f9623..4c6ef6f4dd4 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb @@ -20,7 +20,7 @@ dependencies = [ # use same binutils version that was used when building GCCcore toolchain builddependencies = [ - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ('pkg-config', '0.29.2'), ] diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-5.4.0.eb index 266f40adb09..191eede5cf5 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-5.4.0.eb @@ -18,7 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] configopts = '--with-harfbuzz=no' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb index f01c0208b56..c1cfebce521 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb @@ -18,7 +18,7 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] configopts = '--with-harfbuzz=no' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb index 2b17c553f92..eb85cf2630c 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb @@ -20,7 +20,7 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] configopts = '--with-harfbuzz=no' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb index a9afba8996d..f8625f2b6eb 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb @@ -19,7 +19,7 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] configopts = '--with-harfbuzz=no' diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.10.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.10.0-foss-2018b-Python-3.6.6.eb index f77438c3055..08f154e2df5 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.10.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.10.0-foss-2018b-Python-3.6.6.eb @@ -39,7 +39,7 @@ checksums = ['6a149750dfcdb250e07198cf1726d2f0958d2b8f257618b3b585194c4c392283'] dependencies = [ ('Python', '3.6.6'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.12.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.12.0-foss-2018b-Python-3.6.6.eb index 389c8248e1e..2b2f1c7f916 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.12.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.12.0-foss-2018b-Python-3.6.6.eb @@ -35,7 +35,7 @@ checksums = ['733134303f4961dec589247ff006612b7a94171fab8913c5d44c836aa086865f'] dependencies = [ ('Python', '3.6.6'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-2.7.14.eb index 4a926a82dd9..5b5158ceae2 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-2.7.14.eb @@ -34,7 +34,7 @@ checksums = ['801bbb181c275cfabc96dc0cb21f3f901634cec11efde9ba9c8b91e2834feef4'] dependencies = [ ('Python', '2.7.14'), - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-3.6.4.eb index 597a6f976c6..f1cff8ec83e 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-3.6.4.eb @@ -34,7 +34,7 @@ checksums = ['801bbb181c275cfabc96dc0cb21f3f901634cec11efde9ba9c8b91e2834feef4'] dependencies = [ ('Python', '3.6.4'), - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.5.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.5.1-foss-2018a-Python-3.6.4.eb index c6bfdc3bc56..0eb7cbd64a4 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.5.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.5.1-foss-2018a-Python-3.6.4.eb @@ -35,7 +35,7 @@ checksums = ['3847f540beeb02651f0cf8f14bb0c6ed4e837f1ea73bc6d04cbe38d217c1b25f'] dependencies = [ ('Python', '3.6.4'), - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.7.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.7.0-intel-2018a-Python-2.7.14.eb index e82571bce37..ba6dfc0ee3a 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.7.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.7.0-intel-2018a-Python-2.7.14.eb @@ -35,7 +35,7 @@ checksums = ['9dda57e82471e67151a442c4751308b6db4e88db315b2f5ed10a41f0b2acbf7c'] dependencies = [ ('Python', '2.7.14'), - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.7.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.7.0-intel-2018a-Python-3.6.4.eb index 4570b7031c6..0a969762ea5 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.7.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.7.0-intel-2018a-Python-3.6.4.eb @@ -35,7 +35,7 @@ checksums = ['9dda57e82471e67151a442c4751308b6db4e88db315b2f5ed10a41f0b2acbf7c'] dependencies = [ ('Python', '3.6.4'), - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.8.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.8.1-foss-2018b-Python-2.7.15.eb index 77b1b7f821b..ced47b570c5 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.8.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.8.1-foss-2018b-Python-2.7.15.eb @@ -35,7 +35,7 @@ checksums = ['e4bb082d8c8826d4f8bc8c2f83811d0e81e5088b99099d3396d284f82fbf28c9'] dependencies = [ ('Python', '2.7.15'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.8.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.8.1-foss-2018b-Python-3.6.6.eb index 7e9fea1dd4b..2007bd75f4d 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.8.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.8.1-foss-2018b-Python-3.6.6.eb @@ -35,7 +35,7 @@ checksums = ['e4bb082d8c8826d4f8bc8c2f83811d0e81e5088b99099d3396d284f82fbf28c9'] dependencies = [ ('Python', '3.6.6'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb index d559c597928..a883aa385e9 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb @@ -35,7 +35,7 @@ checksums = ['148aa061328d922a570d0120d88f27e61e5da877f542206f4d77f2d788b7d21d'] dependencies = [ ('Python', '3.6.6'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.2.0-GCCcore-8.2.0-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.2.0-GCCcore-8.2.0-Java-1.8.eb index 259b1fc261c..48b0ca81c08 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.1.2.0-GCCcore-8.2.0-Java-1.8.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.2.0-GCCcore-8.2.0-Java-1.8.eb @@ -36,7 +36,7 @@ checksums = ['ffc5f9b3d4b35772ee5dac3060b59dc657f30e830745160671d84d732c30dc65'] multi_deps = {'Python': ['3.7.2', '2.7.15']} dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.3.0-GCCcore-8.3.0-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.3.0-GCCcore-8.3.0-Java-1.8.eb index dd822ef8725..988b75dedf0 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.1.3.0-GCCcore-8.3.0-Java-1.8.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.3.0-GCCcore-8.3.0-Java-1.8.eb @@ -36,7 +36,7 @@ checksums = ['56fd4f03b15a8a01eaa4629f62e3ab15e4d4b957c787efd2d5629b2658c3df0a'] multi_deps = {'Python': ['3.7.4', '2.7.16']} dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.4.1-GCCcore-8.3.0-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.4.1-GCCcore-8.3.0-Java-1.8.eb index 6e29aeb7a94..59f9839ebb3 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.1.4.1-GCCcore-8.3.0-Java-1.8.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.4.1-GCCcore-8.3.0-Java-1.8.eb @@ -36,7 +36,7 @@ checksums = ['21ae694cfc8b7447381ad5ce62ed4af22e53a228b12495bdcca7df0c73b09cea'] multi_deps = {'Python': ['3.7.4', '2.7.16']} dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.4.1-GCCcore-8.3.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.4.1-GCCcore-8.3.0-Java-11.eb index 6f9d693a6ff..105c7c506f8 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.1.4.1-GCCcore-8.3.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.4.1-GCCcore-8.3.0-Java-11.eb @@ -36,7 +36,7 @@ checksums = ['21ae694cfc8b7447381ad5ce62ed4af22e53a228b12495bdcca7df0c73b09cea'] multi_deps = {'Python': ['3.7.4', '2.7.16']} dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-1.8.eb index d0ea17e1743..4296a3c1049 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-1.8.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-1.8.eb @@ -36,7 +36,7 @@ checksums = ['6fc152c2cae0cc54c7c4cfdfd865a64f7054a820f7d02ca2549511af1dd9882b'] multi_deps = {'Python': ['3.8.2', '2.7.18']} dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-11.eb index 03050c2a5c7..007404e1392 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-11.eb @@ -36,7 +36,7 @@ checksums = ['6fc152c2cae0cc54c7c4cfdfd865a64f7054a820f7d02ca2549511af1dd9882b'] multi_deps = {'Python': ['3.8.2', '2.7.18']} dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.8.1-GCCcore-9.3.0-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.8.1-GCCcore-9.3.0-Java-1.8.eb index 18bc8061965..f93742a9063 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.1.8.1-GCCcore-9.3.0-Java-1.8.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.8.1-GCCcore-9.3.0-Java-1.8.eb @@ -36,7 +36,7 @@ checksums = ['42e6de5059232df1ad5785c68c39a53dc1b54afe7bb086d0129f4dc95fb182bc'] multi_deps = {'Python': ['3.8.2', '2.7.18']} dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb index 610d9d24aa1..097bd00e48f 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb @@ -34,7 +34,7 @@ sources = ['gatk-%(version)s.zip'] checksums = ['dd11cc8e3bc7a23c2c226366428f0908c902765eabbc1c641c736c06b80aaf78'] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Python', '3.8.6'), ] diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb index f11ab541250..515f6cea9b1 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb @@ -34,7 +34,7 @@ sources = ['gatk-%(version)s.zip'] checksums = ['dd11cc8e3bc7a23c2c226366428f0908c902765eabbc1c641c736c06b80aaf78'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.8.6'), ] diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.3.0-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.3.0-GCCcore-11.2.0-Java-11.eb index cd0447168d9..e965471f65a 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.2.3.0-GCCcore-11.2.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.3.0-GCCcore-11.2.0-Java-11.eb @@ -35,7 +35,7 @@ sources = ['gatk-%(version)s.zip'] checksums = ['12fbd03142311419a050dba8009d615ee8faceb32b46aad8f4448dafd61e11eb'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.9.6'), ] diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.5.0-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.5.0-GCCcore-11.2.0-Java-11.eb index 49709d4a376..d9e3451ed2f 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.2.5.0-GCCcore-11.2.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.5.0-GCCcore-11.2.0-Java-11.eb @@ -35,7 +35,7 @@ sources = ['gatk-%(version)s.zip'] checksums = ['203f17868f0a73a8322d2f8bd568b9f7b4bb81e36d37db5b6a142d8050ef049f'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.9.6'), ] diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.6.1-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.6.1-GCCcore-11.2.0-Java-11.eb index 3b8c9ff85d5..1d4af9b3398 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.2.6.1-GCCcore-11.2.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.6.1-GCCcore-11.2.0-Java-11.eb @@ -35,7 +35,7 @@ sources = ['gatk-%(version)s.zip'] checksums = ['1125cfc862301d437310506c8774d36c3a90d00d52c7b5d6b59dac7241203628'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.9.6'), ] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb index ecc2aa7e0a6..c99c15a13e4 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('CUDAcore', local_cudaversion, '', True), # needed by GDRCopy binaries, which are tools for testing + ('CUDAcore', local_cudaversion, '', SYSTEM), # needed by GDRCopy binaries, which are tools for testing ('Check', '0.15.2'), ] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb index 4e78c65fb6b..accc04a5bde 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('CUDAcore', local_cudaversion, '', True), # needed by GDRCopy binaries, which are tools for testing + ('CUDAcore', local_cudaversion, '', SYSTEM), # needed by GDRCopy binaries, which are tools for testing ('Check', '0.15.2'), ] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb index 63ed61f6150..864159cc441 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('CUDAcore', local_cudaversion, '', True), + ('CUDAcore', local_cudaversion, '', SYSTEM), ('Check', '0.15.2'), ] diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2016b.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2016b.eb index 8606dd48d2a..66240220c01 100644 --- a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2016b.eb @@ -18,7 +18,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['9b22a61f01af27e60d483cb7bca73e397d8ca4719c741349a8551984c6c33976'] builddependencies = [ - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb index 4824b4d661d..149f74bea8f 100644 --- a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb @@ -18,7 +18,7 @@ sources = ['%(version)s.tar.gz'] checksums = ['6beeed4a9e727a96fdea9e86e39bbe9cbc9f0540ad3a1053814e95b0863a7e6b'] builddependencies = [ - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-foss-2018b-Python-3.6.6.eb index d489fda525c..06af8a8bbb1 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-foss-2018b-Python-3.6.6.eb @@ -29,7 +29,7 @@ dependencies = [ ('ASE', '3.16.2', versionsuffix), ('libxc', '3.0.1'), ('libvdwxc', '0.3.2'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-intel-2018b-Python-3.6.6.eb index 8e5a3d625fa..fa75dd66180 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-intel-2018b-Python-3.6.6.eb @@ -28,7 +28,7 @@ dependencies = [ ('Python', '3.6.6'), ('ASE', '3.16.2', versionsuffix), ('libxc', '3.0.1'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6.eb b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6.eb index 6a5eb1c4ce2..660743db68a 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6.eb @@ -28,7 +28,7 @@ dependencies = [ ('ASE', local_aseversion, local_pythonsuffix), ('libxc', '3.0.1'), # Old version to maintain consistency with AtomPAW and ABINIT. ('libvdwxc', '0.3.2'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2019a-Python-3.7.2.eb index ed31bbedf0e..6c10491a0d2 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2019a-Python-3.7.2.eb @@ -27,7 +27,7 @@ dependencies = [ ('ASE', '3.18.0', versionsuffix), ('libxc', '4.3.4'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6.eb b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6.eb index c06fe0fe7ca..3158794bf1a 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6.eb @@ -28,7 +28,7 @@ dependencies = [ ('Python', '3.6.6'), ('ASE', local_aseversion, local_pythonsuffix), ('libxc', '3.0.1'), # Old version to maintain consistency with AtomPAW and ABINIT. - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2019a-Python-3.7.2.eb index 337d63d58b0..b6da87b17cc 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2019a-Python-3.7.2.eb @@ -26,7 +26,7 @@ dependencies = [ ('SciPy-bundle', '2019.03'), ('ASE', '3.18.0', versionsuffix), ('libxc', '4.3.4'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb index 06c705f51cb..67b6ba7a5f0 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb @@ -32,7 +32,7 @@ dependencies = [ ('ASE', '3.19.0', versionsuffix), ('libxc', '4.3.4'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb index fc6b25cdb3d..e2df43f33a3 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb @@ -32,7 +32,7 @@ dependencies = [ ('SciPy-bundle', '2019.10', versionsuffix), ('ASE', '3.19.0', versionsuffix), ('libxc', '4.3.4'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4.eb index 31e4e602dc0..3226c8a9aca 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4.eb @@ -34,7 +34,7 @@ dependencies = [ ('ASE', _aseversion, _pythonsuffix), ('libxc', '4.3.4'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb index 1b322074614..6758eb60891 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb @@ -29,7 +29,7 @@ dependencies = [ ('ASE', '3.20.1'), ('libxc', '4.3.4'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4.eb index 7535f24c1a0..d19ddaf4ded 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4.eb @@ -33,7 +33,7 @@ dependencies = [ ('SciPy-bundle', '2019.10', _pythonsuffix), ('ASE', _aseversion, _pythonsuffix), ('libxc', '4.3.4'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb index 861a80e2fd1..0714f4060f1 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb @@ -29,7 +29,7 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('ASE', '3.20.1'), ('libxc', '4.3.4'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb index 7a2e4989e8a..7c888723000 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb @@ -29,7 +29,7 @@ dependencies = [ ('ASE', _aseversion), ('libxc', '4.3.4'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb index 1f22f89cc83..978ddc9ef57 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb @@ -28,7 +28,7 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('ASE', _aseversion), ('libxc', '4.3.4'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb index 582e90ea73b..465fd9c9b07 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb @@ -30,7 +30,7 @@ dependencies = [ ('ASE', _aseversion), ('libxc', '4.3.4'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2021a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2021a.eb index 4abf305f2a6..2abce4c3ad2 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2021a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2021a.eb @@ -28,7 +28,7 @@ dependencies = [ ('ASE', '3.22.0'), ('libxc', '5.1.5'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb index bba61ad1209..56885619470 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb @@ -30,7 +30,7 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('ASE', _aseversion), ('libxc', '4.3.4'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2021b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2021b.eb index e3d8e921b48..cc8928a6e81 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2021b.eb @@ -31,7 +31,7 @@ dependencies = [ ('libxc', '5.1.6'), ('PyYAML', '5.4.1'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb index b400a2bd2c3..a5bf81c6abc 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb @@ -31,7 +31,7 @@ dependencies = [ ('libxc', '5.2.3'), ('libvdwxc', '0.4.0'), ('PyYAML', '6.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2021b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2021b.eb index 1ca56803196..343180bbb51 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2021b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2021b.eb @@ -30,7 +30,7 @@ dependencies = [ ('ASE', '3.22.1'), ('libxc', '5.1.6'), ('PyYAML', '5.4.1'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb index 58087303e00..126147e70d5 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb @@ -30,7 +30,7 @@ dependencies = [ ('ASE', '3.22.1'), ('libxc', '5.2.3'), ('PyYAML', '6.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' diff --git a/easybuild/easyconfigs/g/GRNBoost/GRNBoost-20171009-intel-2017b-Java-1.8.0_152.eb b/easybuild/easyconfigs/g/GRNBoost/GRNBoost-20171009-intel-2017b-Java-1.8.0_152.eb index 633322c56c4..a8e13772a67 100644 --- a/easybuild/easyconfigs/g/GRNBoost/GRNBoost-20171009-intel-2017b-Java-1.8.0_152.eb +++ b/easybuild/easyconfigs/g/GRNBoost/GRNBoost-20171009-intel-2017b-Java-1.8.0_152.eb @@ -16,7 +16,7 @@ sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_ builddependencies = [('sbt', '1.0.2', versionsuffix, True)] dependencies = [ - ('Java', '1.8.0_152', '', True), + ('Java', '1.8.0_152', '', SYSTEM), ('XGBoost', '20171120', versionsuffix), ('Spark', '2.2.0', '-Hadoop-2.6' + versionsuffix, True), ] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb index aa8b7a249fd..60b10be1daf 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb @@ -69,7 +69,7 @@ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('networkx', '2.5.1'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('PLUMED', _plumedver), ('UCX-CUDA', '1.10.0', _cuda_suffix), ] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb index a3519c9ca33..88ab48e3311 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb @@ -65,7 +65,7 @@ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('networkx', '2.5.1'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('UCX-CUDA', '1.10.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb index bbe65cdd01e..f54123b4866 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb @@ -74,7 +74,7 @@ dependencies = [ ('SciPy-bundle', '2021.10'), ('networkx', '2.6.3'), ('PLUMED', _plumedver), - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('UCX-CUDA', '1.11.2', _cuda_suffix), ] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb index 3226925397d..2ae42d897ca 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb @@ -66,7 +66,7 @@ dependencies = [ ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), ('networkx', '2.6.3'), - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('UCX-CUDA', '1.11.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb index 083ad67f279..b3f086375fe 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb @@ -19,7 +19,7 @@ dependencies = [('GStreamer', '0.10.36')] # does not work with Bison 3.x builddependencies = [ - ('Bison', '2.7', '', True), + ('Bison', '2.7', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb index 74bd62f7515..b77d7997cff 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb @@ -21,7 +21,7 @@ dependencies = [ # does not work with Bison 3.x builddependencies = [ - ('Bison', '2.7', '', True), + ('Bison', '2.7', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb index 23b2a931e08..7c60f600376 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb @@ -19,7 +19,7 @@ dependencies = [('GStreamer', '0.10.36')] # does not work with Bison 3.x builddependencies = [ - ('Bison', '2.7', '', True), + ('Bison', '2.7', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb index 60907564e6e..37624651adc 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb @@ -19,7 +19,7 @@ dependencies = [('GStreamer', '0.10.36')] # does not work with Bison 3.x builddependencies = [ - ('Bison', '2.7', '', True), + ('Bison', '2.7', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb index 858a8095477..d7288a32aba 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb @@ -19,7 +19,7 @@ dependencies = [('GStreamer', '0.10.36')] # does not work with Bison 3.x builddependencies = [ - ('Bison', '2.7', '', True), + ('Bison', '2.7', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb index 663148178bc..69edf4e5879 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb @@ -18,7 +18,7 @@ checksums = ['7a193e2a66b0d7411160ef2a373184c8aa3cdeaa576fa270be346716220d9606'] dependencies = [('GStreamer', '1.6.4')] builddependencies = [ - ('Bison', '3.0.4', '', True), + ('Bison', '3.0.4', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb index 0c4cb354f0c..178b50575df 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb @@ -23,7 +23,7 @@ dependencies = [ builddependencies = [ ('Autotools', '20150215'), ('pkg-config', '0.29.1'), - ('Bison', '3.0.4', '', True), + ('Bison', '3.0.4', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb index 31e79963a2f..c3a7851b678 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb @@ -23,7 +23,7 @@ dependencies = [ # does not work with Bison 3.x builddependencies = [ - ('Bison', '2.7', '', True), + ('Bison', '2.7', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb index 941ced47c5b..dd3738d82c9 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb @@ -23,8 +23,8 @@ dependencies = [ # does not work with Bison 3.x builddependencies = [ - ('flex', '2.6.4', '', True), - ('Bison', '2.7', '', True), + ('flex', '2.6.4', '', SYSTEM), + ('Bison', '2.7', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb index 49d0445dfd4..fd95931f5df 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb @@ -23,7 +23,7 @@ dependencies = [ # does not work with Bison 3.x builddependencies = [ - ('Bison', '2.7', '', True), + ('Bison', '2.7', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb index df0cc749083..d24fcda642a 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb @@ -23,7 +23,7 @@ dependencies = [ # does not work with Bison 3.x builddependencies = [ - ('Bison', '2.7', '', True), + ('Bison', '2.7', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb index 0fd9f637575..c7044fe5592 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb @@ -22,7 +22,7 @@ dependencies = [ ] builddependencies = [ - ('Bison', '3.0.4', '', True), + ('Bison', '3.0.4', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb index c6e3c5bf573..f73039f0fbb 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb @@ -15,7 +15,7 @@ dependencies = [ ('matplotlib', '2.2.3', versionsuffix), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.1'), ('FastTree', '2.1.10'), ] diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb index 96d22c898b8..baa0455e8d4 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb @@ -19,7 +19,7 @@ dependencies = [ ('matplotlib', '2.2.4', versionsuffix), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.2'), ('FastTree', '2.1.11'), ] diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb index 89a5cfe9651..234c38d3b4a 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb @@ -19,7 +19,7 @@ dependencies = [ ('matplotlib', '2.2.4', versionsuffix), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.2'), ('FastTree', '2.1.11'), ] diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.0.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.0.2-intel-2019b-Python-3.7.4.eb index a3ec2738504..c35fe8da4a6 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.0.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.0.2-intel-2019b-Python-3.7.4.eb @@ -23,7 +23,7 @@ dependencies = [ ('matplotlib', '3.1.1', versionsuffix), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.3'), ('FastTree', '2.1.11'), ] diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.3.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.3.0-intel-2020a-Python-3.8.2.eb index 54dc20a75fc..13e7349e42f 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.3.0-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.3.0-intel-2020a-Python-3.8.2.eb @@ -23,7 +23,7 @@ dependencies = [ ('matplotlib', '3.2.1', versionsuffix), ('prodigal', '2.6.3'), ('HMMER', '3.3.1'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.31'), ('FastTree', '2.1.11'), ('tqdm', '4.47.0'), diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb index 0ff0be7b625..5f2ae473469 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('matplotlib', '3.3.3'), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.33'), ('FastTree', '2.1.11'), ('tqdm', '4.56.2'), diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb index d0bc5d3e526..d40e1ff699c 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('matplotlib', '3.3.3'), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.33'), ('FastTree', '2.1.11'), ('tqdm', '4.56.2'), diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2021a.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2021a.eb index 05e89644664..8022a696c23 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2021a.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2021a.eb @@ -22,7 +22,7 @@ dependencies = [ ('matplotlib', '3.4.2'), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.33'), ('FastTree', '2.1.11'), ('tqdm', '4.61.2'), diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb index 2e0232fed40..4d81bd500b9 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('matplotlib', '3.3.3'), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.33'), ('FastTree', '2.1.11'), ('tqdm', '4.56.2'), diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-foss-2021a.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-foss-2021a.eb index 3d85efa5db7..741d72ebed0 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-foss-2021a.eb @@ -22,7 +22,7 @@ dependencies = [ ('matplotlib', '3.4.2'), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.33'), ('FastTree', '2.1.11'), ('Mash', '2.3'), diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-intel-2021b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-intel-2021b.eb index f1bc9b730fe..d7ed1a25516 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-intel-2021b.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-intel-2021b.eb @@ -22,7 +22,7 @@ dependencies = [ ('matplotlib', '3.4.3'), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.33'), ('FastTree', '2.1.11'), ('tqdm', '4.62.3'), diff --git a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.2-foss-2020a-Python-3.8.2.eb index 1e00e8c37de..112304a7a38 100644 --- a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.2-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.2-foss-2020a-Python-3.8.2.eb @@ -15,7 +15,7 @@ checksums = ['54923ca971d68620aaf036a324b554084b00f7c209b0b3a234f815c82ee6d079'] dependencies = [ ('Python', '3.8.2'), - ('Bandage', '0.8.1', '_Centos', True), + ('Bandage', '0.8.1', '_Centos', SYSTEM), ('SciPy-bundle', '2020.03', versionsuffix), ('sympy', '1.6.2', versionsuffix), ('SPAdes', '3.14.1', versionsuffix), diff --git a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb index 095a77b88cf..2eabe89e524 100644 --- a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb @@ -15,7 +15,7 @@ checksums = ['ee3dc807e0fb59c1788717a155238115d7a860191f686ef2c5a5b685aa2a2948'] dependencies = [ ('Python', '3.8.6'), - ('Bandage', '0.8.1', '_Centos', True), + ('Bandage', '0.8.1', '_Centos', SYSTEM), ('SciPy-bundle', '2020.11'), ('sympy', '1.7.1'), ('SPAdes', '3.15.2'), diff --git a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb index b8e860947db..65e2cb11638 100644 --- a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ builddependencies = [ dependencies = [ ('Python', '3.8.6'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] use_pip = True diff --git a/easybuild/easyconfigs/g/Go/Go-1.12.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/g/Go/Go-1.12.1-GCCcore-7.3.0.eb index efe696b4984..da1e8ab0a6a 100644 --- a/easybuild/easyconfigs/g/Go/Go-1.12.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/g/Go/Go-1.12.1-GCCcore-7.3.0.eb @@ -17,7 +17,7 @@ checksums = ['0be127684df4b842a64e58093154f9d15422f1405f1fcff4b2c36ffc6a15818a'] builddependencies = [ ('binutils', '2.30'), # go requires Go to install from source, see https://golang.org/doc/install/source - ('Go', '1.12', '', True), + ('Go', '1.12', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb index ef9c393d1a7..5584942b29c 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb @@ -21,7 +21,7 @@ dependencies = [ ('freetype', '2.6.5'), ('Ghostscript', '9.20'), ('GTS', '0.7.6'), - ('Java', '1.8.0_92', '', True), + ('Java', '1.8.0_92', '', SYSTEM), ('libpng', '1.6.24'), ('Pango', '1.40.3'), ('Perl', '5.24.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb index 50d0e0b4494..2a678bb2b9e 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb @@ -21,7 +21,7 @@ dependencies = [ ('freetype', '2.6.5'), ('Ghostscript', '9.20'), ('GTS', '0.7.6'), - ('Java', '1.8.0_92', '', True), + ('Java', '1.8.0_92', '', SYSTEM), ('libpng', '1.6.24'), ('Pango', '1.40.3'), ('Perl', '5.24.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b-Python-2.7.15.eb index 3393732425c..062902b979a 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b-Python-2.7.15.eb @@ -54,7 +54,7 @@ dependencies = [ ('Gdk-Pixbuf', '2.36.12'), ('Ghostscript', '9.23'), ('GTS', '0.7.6'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('libgd', '2.2.5'), ('Pango', '1.42.4'), ('Perl', '5.28.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b.eb index dad37c034a9..15a13ec7078 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b.eb @@ -51,7 +51,7 @@ dependencies = [ ('Gdk-Pixbuf', '2.36.12'), ('Ghostscript', '9.23'), ('GTS', '0.7.6'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('libgd', '2.2.5'), ('Pango', '1.42.4'), ('Perl', '5.28.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-intel-2018a.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-intel-2018a.eb index ae0ee795432..604d4417f17 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-intel-2018a.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-intel-2018a.eb @@ -41,7 +41,7 @@ dependencies = [ ('freetype', '2.9'), ('Ghostscript', '9.22', '-cairo-1.14.12'), ('GTS', '0.7.6'), - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ('libpng', '1.6.34'), ('Pango', '1.41.1'), ('Perl', '5.26.1'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-GCCcore-8.3.0-Java-11.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-GCCcore-8.3.0-Java-11.eb index bc1b89f5f65..7ac2a75670e 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-GCCcore-8.3.0-Java-11.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-GCCcore-8.3.0-Java-11.eb @@ -40,7 +40,7 @@ dependencies = [ ('Gdk-Pixbuf', '2.38.2'), ('Ghostscript', '9.50'), ('GTS', '0.7.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('libgd', '2.2.5'), ('Pango', '1.44.7'), ('Perl', '5.30.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b-Python-3.7.4.eb index 1ca2e2d4744..26ac994d037 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b-Python-3.7.4.eb @@ -44,7 +44,7 @@ dependencies = [ ('Gdk-Pixbuf', '2.38.2'), ('Ghostscript', '9.50'), ('GTS', '0.7.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('libgd', '2.2.5'), ('Pango', '1.44.7'), ('Perl', '5.30.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b.eb index def5b531355..bd1974fc84c 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b.eb @@ -38,7 +38,7 @@ dependencies = [ ('Gdk-Pixbuf', '2.38.2'), ('Ghostscript', '9.50'), ('GTS', '0.7.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('libgd', '2.2.5'), ('Pango', '1.44.7'), ('Perl', '5.30.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11-Python-3.8.2.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11-Python-3.8.2.eb index ac21ce695d2..f19b861f72c 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11-Python-3.8.2.eb @@ -33,7 +33,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.8.2'), ('FriBidi', '1.0.9'), ('Gdk-Pixbuf', '2.40.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11.eb index 5d7b20ee277..e532aad271a 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11.eb @@ -32,7 +32,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('FriBidi', '1.0.9'), ('Gdk-Pixbuf', '2.40.0'), ('Ghostscript', '9.52'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb index fe7ec68c3fe..740e71bf496 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb @@ -33,7 +33,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.8.6'), ('FriBidi', '1.0.10'), ('Gdk-Pixbuf', '2.40.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.2-GCCcore-10.3.0.eb index 82bbddffe8d..efaf644fa43 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.2-GCCcore-10.3.0.eb @@ -32,7 +32,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.9.5'), ('FriBidi', '1.0.10'), ('Gdk-Pixbuf', '2.42.6'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.50.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.50.0-GCCcore-11.2.0.eb index f2fff0736b3..e96a04c6708 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.50.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.50.0-GCCcore-11.2.0.eb @@ -32,7 +32,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.9.6'), ('FriBidi', '1.0.10'), ('Gdk-Pixbuf', '2.42.6'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb index 574ffbd5cd3..a2f44ff0ff8 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb @@ -32,7 +32,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.10.4'), ('FriBidi', '1.0.12'), ('Gdk-Pixbuf', '2.42.8'), diff --git a/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb index 4f4fa3e2f0c..35dbf494bc9 100644 --- a/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] configopts = " --enable-error-on-warning=no" diff --git a/easybuild/easyconfigs/g/gRPC/gRPC-1.44.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/gRPC/gRPC-1.44.0-GCCcore-11.2.0.eb index 7c7a4e106cf..a7c26ea7739 100644 --- a/easybuild/easyconfigs/g/gRPC/gRPC-1.44.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/gRPC/gRPC-1.44.0-GCCcore-11.2.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ('Abseil', '20210324.2'), ('c-ares', '1.18.1'), ('protobuf', '3.17.3'), diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-5.4.0.eb index 4a9705e7ef7..7bbdba6432e 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-5.4.0.eb @@ -24,7 +24,7 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb index 691a5661ac0..7acb30d5912 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb @@ -24,7 +24,7 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' diff --git a/easybuild/easyconfigs/g/gifsicle/gifsicle-1.92-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/gifsicle/gifsicle-1.92-GCCcore-8.2.0.eb index ec28d95cf35..a56f14839cf 100644 --- a/easybuild/easyconfigs/g/gifsicle/gifsicle-1.92-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/gifsicle/gifsicle-1.92-GCCcore-8.2.0.eb @@ -18,7 +18,7 @@ checksums = ['f8a944f47faa9323bcc72c6e2239e0608bf30693894aee61512aba107a4c6b55'] toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -builddependencies = [('binutils', '2.31.1', '', True)] +builddependencies = [('binutils', '2.31.1', '', SYSTEM)] configure_cmd = "./bootstrap.sh && ./configure" diff --git a/easybuild/easyconfigs/g/git/git-2.32.0-GCCcore-10.3.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.32.0-GCCcore-10.3.0-nodocs.eb index 5559af9962b..6a9f8e88f5b 100644 --- a/easybuild/easyconfigs/g/git/git-2.32.0-GCCcore-10.3.0-nodocs.eb +++ b/easybuild/easyconfigs/g/git/git-2.32.0-GCCcore-10.3.0-nodocs.eb @@ -27,7 +27,7 @@ dependencies = [ ('expat', '2.2.9'), ('gettext', '0.21'), ('Perl', '5.32.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] preconfigopts = 'make configure && ' diff --git a/easybuild/easyconfigs/g/git/git-2.33.1-GCCcore-11.2.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.33.1-GCCcore-11.2.0-nodocs.eb index ed7c62fbd3b..08aff1076cb 100644 --- a/easybuild/easyconfigs/g/git/git-2.33.1-GCCcore-11.2.0-nodocs.eb +++ b/easybuild/easyconfigs/g/git/git-2.33.1-GCCcore-11.2.0-nodocs.eb @@ -30,7 +30,7 @@ dependencies = [ ('expat', '2.4.1'), ('gettext', '0.21'), ('Perl', '5.34.0'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] preconfigopts = 'make configure && ' diff --git a/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb index b4bb0d64474..214a4cc7228 100644 --- a/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb +++ b/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb @@ -30,7 +30,7 @@ dependencies = [ ('expat', '2.4.8'), ('gettext', '0.21'), ('Perl', '5.34.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] preconfigopts = 'make configure && ' diff --git a/easybuild/easyconfigs/g/gubbins/gubbins-2.4.0.eb b/easybuild/easyconfigs/g/gubbins/gubbins-2.4.0.eb index 3bd71c3f03d..c209965f2eb 100644 --- a/easybuild/easyconfigs/g/gubbins/gubbins-2.4.0.eb +++ b/easybuild/easyconfigs/g/gubbins/gubbins-2.4.0.eb @@ -30,7 +30,7 @@ channels = ['r', 'conda-forge', 'bioconda'] requirements = '%(namelower)s=%(version)s python=3.6' dependencies = [ - ('Miniconda3', '4.7.10', '', True) + ('Miniconda3', '4.7.10', '', SYSTEM) ] sanity_check_commands = [('gubbins', '-h')] diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb index cb15f9404ed..795f421b233 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb @@ -29,7 +29,7 @@ checksums = [ builddependencies = [ ('binutils', '2.35'), - ('Maven', '3.6.3', '', True), + ('Maven', '3.6.3', '', SYSTEM), ('protobuf', '2.5.0'), # *must* be this version - https://issues.apache.org/jira/browse/HADOOP-13363 ('CMake', '3.18.4'), ('snappy', '1.1.8'), @@ -39,7 +39,7 @@ builddependencies = [ # https://cwiki.apache.org/confluence/display/HADOOP/Hadoop+Java+Versions dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('libtirpc', '1.3.1'), ] diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-8.3.0-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-8.3.0-native.eb index c1fa9fa3cdc..039bc9f1132 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-8.3.0-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-8.3.0-native.eb @@ -29,7 +29,7 @@ checksums = [ builddependencies = [ ('binutils', '2.32'), - ('Maven', '3.6.3', '', True), + ('Maven', '3.6.3', '', SYSTEM), ('protobuf', '2.5.0'), # *must* be this version - https://issues.apache.org/jira/browse/HADOOP-13363 ('CMake', '3.15.3'), ('snappy', '1.1.7'), @@ -39,7 +39,7 @@ builddependencies = [ # https://cwiki.apache.org/confluence/display/HADOOP/Hadoop+Java+Versions dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('libtirpc', '1.2.6'), ] diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.9.2-GCCcore-7.3.0-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.9.2-GCCcore-7.3.0-native.eb index 1e22b4574c8..22aad2469d9 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.9.2-GCCcore-7.3.0-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.9.2-GCCcore-7.3.0-native.eb @@ -24,7 +24,7 @@ checksums = [ builddependencies = [ ('binutils', '2.30'), - ('Maven', '3.6.0', '', True), + ('Maven', '3.6.0', '', SYSTEM), ('protobuf', '2.5.0'), # *must* be this version ('CMake', '3.12.1'), ('snappy', '1.1.7'), @@ -32,7 +32,7 @@ builddependencies = [ ('bzip2', '1.0.6'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] build_native_libs = True diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb index 4ad47ea0521..6933ece700e 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb @@ -16,7 +16,7 @@ builddependencies = [ ('flatbuffers', '2.0.0'), ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('UCX-CUDA', '1.10.0', local_cuda_suffix), ('NCCL', '2.10.3', local_cuda_suffix), ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb index 1a551228e8f..ff4cb82b3f6 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb @@ -18,7 +18,7 @@ builddependencies = [ dependencies = [ ('Python', '3.9.5'), ('PyYAML', '5.4.1'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('NCCL', '2.10.3', local_cuda_suffix), ('PyTorch', local_pt_version, local_cuda_suffix), ] diff --git a/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb index 08c0a3b716c..0bb49bddc8e 100644 --- a/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} builddependencies = [ ('binutils', '2.36.1'), - ('Java', '11', '', True), # needed by ANTLR runtime + ('Java', '11', '', SYSTEM), # needed by ANTLR runtime ] dependencies = [ diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.1.0.eb index 2c4fe36c213..594056facd2 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.1.0.eb @@ -14,7 +14,7 @@ checksums = ['f371cbfd63f879065422b58fa6b81e21870cd791ef6e11d4528608204aa4dcfb'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.2.0.eb index b2566498fcf..4aa3a420ef1 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.2.0.eb @@ -14,7 +14,7 @@ checksums = ['f371cbfd63f879065422b58fa6b81e21870cd791ef6e11d4528608204aa4dcfb'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.12-GCCcore-9.3.0.eb index 10eb7812dcd..77bffeabf8a 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.12-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.12-GCCcore-9.3.0.eb @@ -14,7 +14,7 @@ checksums = ['7d0ba64cf9d16ec97cc11aafb659b55aa7bdec99072ff2aec5fcecf0fbeab160'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.34', '', True), + ('binutils', '2.34', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.15-GCCcore-10.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.15-GCCcore-10.1.0.eb index 2d8893f9c12..113edba6b65 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.15-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.15-GCCcore-10.1.0.eb @@ -14,7 +14,7 @@ checksums = ['c25a35b30eceb315361484b0ff1f81c924e8ee5c8881576f1ee762f001dbcd1c'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.34', '', True), + ('binutils', '2.34', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb index 16eb74c38c5..48daa7126a1 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb @@ -14,7 +14,7 @@ checksums = ['3ef8580c5b86e32ca092ce8de43df204f5e6f714b0cd32bc6237e6cd0f34a8f4'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.35', '', True), + ('binutils', '2.35', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb index 0d730043fba..1257db05441 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_XZ] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb index 4931b9f6ce3..3ff4d3ef78f 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_XZ] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb index c354ad33693..c1f8fcc9061 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb @@ -18,7 +18,7 @@ checksums = ['d4ecf697d13f14dd1a78c5995f06459bff706fd1ce593d1c02d81667c0207753'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.28', '', True), + ('binutils', '2.28', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb index f487ba55300..402e97d506e 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_XZ] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.28', '', True), + ('binutils', '2.28', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.2.0.eb index 63e4b751a13..ab49db02c27 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.2.0.eb @@ -14,7 +14,7 @@ checksums = ['d4ecf697d13f14dd1a78c5995f06459bff706fd1ce593d1c02d81667c0207753'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.29', '', True), + ('binutils', '2.29', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.3.0.eb index 50e6f6e2199..d125e15db98 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.3.0.eb @@ -14,7 +14,7 @@ checksums = ['d4ecf697d13f14dd1a78c5995f06459bff706fd1ce593d1c02d81667c0207753'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.30', '', True), + ('binutils', '2.30', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.5-GCCcore-5.5.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.5-GCCcore-5.5.0.eb index 54568207731..c429f8c03fd 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.5-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.5-GCCcore-5.5.0.eb @@ -14,7 +14,7 @@ checksums = ['7ca60b2519fdbe97f463fe2df66a6188d18b514bfd44127d985f0234ee2461b1'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.6-GCCcore-8.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.6-GCCcore-8.1.0.eb index a6acf99d4a7..8a4a5572203 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.6-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.6-GCCcore-8.1.0.eb @@ -14,7 +14,7 @@ checksums = ['d91b0295b72a638e4a564f643e4e6d1928779131f628c00f356c13bf336de46f'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.30', '', True), + ('binutils', '2.30', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.7-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.7-GCCcore-8.2.0.eb index 3de5a41822f..81085956428 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.7-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.7-GCCcore-8.2.0.eb @@ -14,7 +14,7 @@ checksums = ['585b8e88ed04bdb426403cf7d9b0c0bb9c7630755b0096c2b018a024b29bec0d'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.31.1', '', True), + ('binutils', '2.31.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-7.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-7.4.0.eb index d2c9f0677aa..d71469d2a1a 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-7.4.0.eb @@ -14,7 +14,7 @@ checksums = ['528f6a81ad34cbc76aa7dce5a82f8b3d2078ef065271ab81fda033842018a8dc'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.31.1', '', True), + ('binutils', '2.31.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.3.0.eb index 21de8022b13..2c4f4f0dbdb 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.3.0.eb @@ -14,7 +14,7 @@ checksums = ['528f6a81ad34cbc76aa7dce5a82f8b3d2078ef065271ab81fda033842018a8dc'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.4.0.eb index 08d063f0300..6d131fe3331 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.4.0.eb @@ -14,7 +14,7 @@ checksums = ['528f6a81ad34cbc76aa7dce5a82f8b3d2078ef065271ab81fda033842018a8dc'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-10.3.0.eb index 8697c849e41..2253777a680 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-10.3.0.eb @@ -14,7 +14,7 @@ checksums = ['8361ff3c643fbd391064e97e5f54592ca28b880eaffbf566a68e0ad800d1a8ac'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.1.0.eb index c5323938915..7b7405ce180 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.1.0.eb @@ -14,7 +14,7 @@ checksums = ['8361ff3c643fbd391064e97e5f54592ca28b880eaffbf566a68e0ad800d1a8ac'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.2.0.eb index dd03b0d33f5..ea6ea4b507b 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.2.0.eb @@ -14,7 +14,7 @@ checksums = ['8361ff3c643fbd391064e97e5f54592ca28b880eaffbf566a68e0ad800d1a8ac'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.37', '', True), + ('binutils', '2.37', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-9.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-9.4.0.eb index a3563b02d50..2e1ff3703b1 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-9.4.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-9.4.0.eb @@ -14,7 +14,7 @@ checksums = ['8361ff3c643fbd391064e97e5f54592ca28b880eaffbf566a68e0ad800d1a8ac'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-11.3.0.eb index 26957da215e..d434ddefe0d 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-11.3.0.eb @@ -14,7 +14,7 @@ checksums = ['9e2e0e213a7e0a36244eed6204d902b6504602a578b6ecd15268b1454deadd36'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.38', '', True), + ('binutils', '2.38', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.1.0.eb index b76db7f347c..6c618e880ac 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.1.0.eb @@ -14,7 +14,7 @@ checksums = ['9e2e0e213a7e0a36244eed6204d902b6504602a578b6ecd15268b1454deadd36'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.38', '', True), + ('binutils', '2.38', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.2.0.eb index 712e28926d5..3fa0f481563 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.2.0.eb @@ -14,7 +14,7 @@ checksums = ['9e2e0e213a7e0a36244eed6204d902b6504602a578b6ecd15268b1454deadd36'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.39', '', True), + ('binutils', '2.39', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-9.5.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-9.5.0.eb index 19d7895e8f1..dbe1f931596 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-9.5.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-9.5.0.eb @@ -14,7 +14,7 @@ checksums = ['9e2e0e213a7e0a36244eed6204d902b6504602a578b6ecd15268b1454deadd36'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.38', '', True), + ('binutils', '2.38', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb b/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb index d06d9b20df6..ee5c6c8ec69 100644 --- a/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('Clang', '11.0.1'), - # ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', True), + # ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', SYSTEM), # ('Python', '3.8.6'), ] diff --git a/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.2.0.eb index be49af696cf..28463835271 100644 --- a/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.2.0.eb @@ -28,7 +28,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb b/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb index 94664ec45e6..4e2be23df1d 100644 --- a/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb +++ b/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb @@ -23,7 +23,7 @@ dependencies = [ ('SciPy-bundle', '2019.10', local_python_versionsuffix), # for numpy, scipy ('networkx', '2.4', local_python_versionsuffix), ('scikit-learn', '0.21.3', local_python_versionsuffix), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Spark', '2.4.5', versionsuffix), ] diff --git a/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.5-fosscuda-2020b.eb b/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.5-fosscuda-2020b.eb index 4f7660f2938..8a744cd8d26 100644 --- a/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.5-fosscuda-2020b.eb @@ -20,7 +20,7 @@ dependencies = [ ('networkx', '2.5'), ('scikit-learn', '0.23.2'), ('tqdm', '4.56.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Spark', '3.1.1'), ] diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.12.3-Java-11.eb b/easybuild/easyconfigs/i/IGV/IGV-2.12.3-Java-11.eb index 0005d342b59..7e992b8bba5 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.12.3-Java-11.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.12.3-Java-11.eb @@ -22,7 +22,7 @@ source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_ sources = ['%(name)s_%(version)s.zip'] checksums = ['c87a109deb35994e1b28dee80b5acfd623ec3257f031fcd9cfce008cd32a4cf2'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] sanity_check_paths = { 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb b/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb index 175e1547ee9..1716dc4a133 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb @@ -22,7 +22,7 @@ source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_ sources = ['%(name)s_%(version)s.zip'] checksums = ['44efdd0500dd6ace8e1c70dad0d758d9ab90492b391d2af4a416f03808fee471'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] sanity_check_paths = { 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.8.0-Java-11.eb b/easybuild/easyconfigs/i/IGV/IGV-2.8.0-Java-11.eb index 870e1a93e0d..9369fb4f3ad 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.8.0-Java-11.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.8.0-Java-11.eb @@ -22,7 +22,7 @@ source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_ sources = ['%(name)s_%(version)s.zip'] checksums = ['33f3ac57017907b931f90c35b63b2de2e4f8d2452f0fbb5be39d30288fc9b2c6'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] sanity_check_paths = { 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.9.4-Java-11.eb b/easybuild/easyconfigs/i/IGV/IGV-2.9.4-Java-11.eb index 3e9176b8a21..f257993866e 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.9.4-Java-11.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.9.4-Java-11.eb @@ -22,7 +22,7 @@ source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_ sources = ['%(name)s_%(version)s.zip'] checksums = ['05717ec6d0386a5eafe93c8b1af371c0013355eae74312b78eae5fdd99fc5fc1'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] sanity_check_paths = { 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb index fa2d35b964b..d3a1580f52b 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb @@ -34,7 +34,7 @@ checksums = [ dependencies = [ ('LibTIFF', '4.1.0'), ('Qt5', '5.14.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('HDF5', '1.10.7'), ('Python', '3.8.6'), ] diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb index d2bc021cbb9..1f1c6e82c8a 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb @@ -37,7 +37,7 @@ checksums = [ dependencies = [ ('LibTIFF', '4.1.0'), ('Qt5', '5.14.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('HDF5', '1.10.7'), ('Python', '3.8.6'), ] diff --git a/easybuild/easyconfigs/i/INTEGRATE-Neo/INTEGRATE-Neo-1.2.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/INTEGRATE-Neo/INTEGRATE-Neo-1.2.1-foss-2018b-Python-3.6.6.eb index abf9e6ec074..78711215507 100644 --- a/easybuild/easyconfigs/i/INTEGRATE-Neo/INTEGRATE-Neo-1.2.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/INTEGRATE-Neo/INTEGRATE-Neo-1.2.1-foss-2018b-Python-3.6.6.eb @@ -22,7 +22,7 @@ dependencies = [ ('Python', '3.6.6'), ('BWA', '0.7.17'), ('HLAminer', '1.4', '-Perl-5.28.0'), - ('netMHC', '4.0a', '', True), + ('netMHC', '4.0a', '', SYSTEM), ] start_dir = '%(name)s-V-%(version)s' diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb index aec8a7ac610..ad5e295f908 100644 --- a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb @@ -17,7 +17,7 @@ checksums = ['9614092de7a157de82c9cc402b19cc8bfa0cb0ffc93b91817875c2b4bb46a284'] builddependencies = [ ('CMake', '3.12.1'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [('zlib', '1.2.11')] diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-intel-2019b.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-intel-2019b.eb index a27292fd82e..cb0a9baa6c5 100644 --- a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-intel-2019b.eb +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-intel-2019b.eb @@ -16,7 +16,7 @@ checksums = ['9614092de7a157de82c9cc402b19cc8bfa0cb0ffc93b91817875c2b4bb46a284'] builddependencies = [ ('CMake', '3.15.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [('zlib', '1.2.11')] diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.6-intel-2018a.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.6-intel-2018a.eb index 66ddae35864..a3b9c543ee0 100644 --- a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.6-intel-2018a.eb +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.6-intel-2018a.eb @@ -16,7 +16,7 @@ checksums = ['31bc44e3a79edb889f3e2ed396d1492b8e38d93437b2ae64deb452867929dc56'] builddependencies = [ ('CMake', '3.10.2'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] dependencies = [('zlib', '1.2.11')] diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb index 8108fd7121c..4d7e044fc45 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb @@ -24,7 +24,7 @@ checksums = ['b352060d8b7289916a3cb033dfdbcf423423ba474643b79706966e679268e3d7'] builddependencies = [ ('CMake', '3.15.3'), ('Bison', '3.3.2'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb index 62e178a70de..a435dbd1e32 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb @@ -30,7 +30,7 @@ checksums = ['c6b3c33ecc73104c906e0e1a1bfaa41a09af24bf53a4ec5e5c265d7e82bdf69f'] builddependencies = [ ('CMake', '3.13.3'), ('Bison', '3.0.5'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb index 091109392a2..63a9196709b 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb @@ -30,7 +30,7 @@ checksums = ['c6b3c33ecc73104c906e0e1a1bfaa41a09af24bf53a4ec5e5c265d7e82bdf69f'] builddependencies = [ ('CMake', '3.15.3'), ('Bison', '3.3.2'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb index 7d9f547d493..ac587d50840 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb @@ -16,7 +16,7 @@ sources = ['ij%(version_major)s%(version_minor)s-src.zip'] checksums = ['1fe77bedd792f095bc51d7b12083319b04124bb82f2dc5eb0552089880cf1a4f'] # specify dependency on Java/1.8 "wrapper", rather than a specific Java version -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] builddependencies = [('ant', '1.10.1', '-Java-%(javaver)s')] diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.26-65.0-intel-2017b.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.26-65.0-intel-2017b.eb index 76b2b69e139..03a9b9f0119 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.26-65.0-intel-2017b.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.26-65.0-intel-2017b.eb @@ -26,7 +26,7 @@ checksums = [ ] dependencies = [ - ('Java', '1.8.0_152', '', True), + ('Java', '1.8.0_152', '', SYSTEM), ('Perl', '5.26.0'), ('libgd', '2.2.5'), ('Python', '2.7.14'), diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.27-66.0-intel-2017b.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.27-66.0-intel-2017b.eb index 1542ef84a85..bb69e1b65bb 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.27-66.0-intel-2017b.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.27-66.0-intel-2017b.eb @@ -26,7 +26,7 @@ checksums = [ ] dependencies = [ - ('Java', '1.8.0_152', '', True), + ('Java', '1.8.0_152', '', SYSTEM), ('Perl', '5.26.0'), ('libgd', '2.2.5'), ('Python', '2.7.14'), diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.28-67.0-intel-2018a.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.28-67.0-intel-2018a.eb index c82158bd56c..129c5160aa2 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.28-67.0-intel-2018a.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.28-67.0-intel-2018a.eb @@ -26,7 +26,7 @@ checksums = [ ] dependencies = [ - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ('Perl', '5.26.1'), ('libgd', '2.2.5'), ('Python', '2.7.14'), diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb index b3d5765b73d..fdfeaac821f 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb @@ -18,7 +18,7 @@ sources = ['%(namelower)s-%(version)s-64-bit.tar.gz'] checksums = ['50a03c47fb16c669c265e99ba05c4a8558b82047f713c9945f362d3d4be6069a'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Perl', '5.32.1'), ('libgd', '2.3.1'), ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb index 3107c097d4a..d4535511479 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb @@ -23,7 +23,7 @@ checksums = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Perl', '5.32.1'), ('libgd', '2.3.1'), ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb b/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb index 95b0d643515..90f8eac533d 100644 --- a/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb +++ b/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb @@ -15,7 +15,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['a71718d418fb8b1afacbe2b3a6b91fd50cadc9e12c0b532739b955e455913b0b'] dependencies = [ - ('Java', '15', '', True), + ('Java', '15', '', SYSTEM), ('minimap2', '2.22'), ('HTSlib', '1.14'), ('SAMtools', '1.14'), diff --git a/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb index 56433fb0b9c..1cdc59d3ecd 100644 --- a/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb @@ -34,7 +34,7 @@ dependencies = [ ('ImageMagick', '6.9.4-8'), ('STAMP', '1.3'), ('Cluster-Buster', '20160106'), - ('Kent_tools', '20130806', '-linux.x86_64', True), + ('Kent_tools', '20130806', '-linux.x86_64', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021b.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021b.eb index 8a42ae8abf5..03a7f2798db 100644 --- a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021b.eb @@ -6,6 +6,6 @@ description = "FFTW interfaces using Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2021b'} -dependencies = [('imkl', version, '', True)] +dependencies = [('imkl', version, '', SYSTEM)] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021b.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021b.eb index e1f4249fb2b..e411b2b3923 100644 --- a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021b.eb +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021b.eb @@ -6,6 +6,6 @@ description = "FFTW interfaces using Intel oneAPI Math Kernel Library" toolchain = {'name': 'iimpi', 'version': '2021b'} -dependencies = [('imkl', version, '', True)] +dependencies = [('imkl', version, '', SYSTEM)] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.0.1-iimpi-2022.00.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.0.1-iimpi-2022.00.eb index 2eaf7432065..07d65f3a80f 100644 --- a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.0.1-iimpi-2022.00.eb +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.0.1-iimpi-2022.00.eb @@ -6,6 +6,6 @@ description = "FFTW interfaces using Intel oneAPI Math Kernel Library" toolchain = {'name': 'iimpi', 'version': '2022.00'} -dependencies = [('imkl', version, '', True)] +dependencies = [('imkl', version, '', SYSTEM)] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022.05.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022.05.eb index 1d2d73b038e..203a8e9f0ef 100644 --- a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022.05.eb +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022.05.eb @@ -6,6 +6,6 @@ description = "FFTW interfaces using Intel oneAPI Math Kernel Library" toolchain = {'name': 'iimpi', 'version': '2022.05'} -dependencies = [('imkl', version, '', True)] +dependencies = [('imkl', version, '', SYSTEM)] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022a.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022a.eb index d81a631f10f..a18ad2d9d36 100644 --- a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022a.eb +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022a.eb @@ -6,6 +6,6 @@ description = "FFTW interfaces using Intel oneAPI Math Kernel Library" toolchain = {'name': 'iimpi', 'version': '2022a'} -dependencies = [('imkl', version, '', True)] +dependencies = [('imkl', version, '', SYSTEM)] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/intel/intel-2021b.eb b/easybuild/easyconfigs/i/intel/intel-2021b.eb index 68916794a30..8d5b83ca141 100644 --- a/easybuild/easyconfigs/i/intel/intel-2021b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2021b.eb @@ -15,7 +15,7 @@ dependencies = [ ('binutils', '2.37', '', ('GCCcore', local_gccver)), ('intel-compilers', local_comp_ver), ('impi', local_comp_ver, '', ('intel-compilers', local_comp_ver)), - ('imkl', local_comp_ver, '', True), + ('imkl', local_comp_ver, '', SYSTEM), ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), ] diff --git a/easybuild/easyconfigs/i/intel/intel-2022.00.eb b/easybuild/easyconfigs/i/intel/intel-2022.00.eb index 756e76c67c6..d4c1c743073 100644 --- a/easybuild/easyconfigs/i/intel/intel-2022.00.eb +++ b/easybuild/easyconfigs/i/intel/intel-2022.00.eb @@ -15,7 +15,7 @@ dependencies = [ ('binutils', '2.37', '', ('GCCcore', local_gccver)), ('intel-compilers', local_comp_ver), ('impi', '2021.5.0', '', ('intel-compilers', local_comp_ver)), - ('imkl', local_comp_ver, '', True), + ('imkl', local_comp_ver, '', SYSTEM), ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), ] diff --git a/easybuild/easyconfigs/i/intel/intel-2022.05.eb b/easybuild/easyconfigs/i/intel/intel-2022.05.eb index b78b8a46bb5..1dd52139097 100644 --- a/easybuild/easyconfigs/i/intel/intel-2022.05.eb +++ b/easybuild/easyconfigs/i/intel/intel-2022.05.eb @@ -15,7 +15,7 @@ dependencies = [ ('binutils', '2.38', '', ('GCCcore', local_gccver)), ('intel-compilers', local_comp_ver), ('impi', '2021.6.0', '', ('intel-compilers', local_comp_ver)), - ('imkl', local_comp_ver, '', True), + ('imkl', local_comp_ver, '', SYSTEM), ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), ] diff --git a/easybuild/easyconfigs/i/intel/intel-2022a.eb b/easybuild/easyconfigs/i/intel/intel-2022a.eb index b9eb05d6541..59f22dc713b 100644 --- a/easybuild/easyconfigs/i/intel/intel-2022a.eb +++ b/easybuild/easyconfigs/i/intel/intel-2022a.eb @@ -15,7 +15,7 @@ dependencies = [ ('binutils', '2.38', '', ('GCCcore', local_gccver)), ('intel-compilers', local_comp_ver), ('impi', '2021.6.0', '', ('intel-compilers', local_comp_ver)), - ('imkl', local_comp_ver, '', True), + ('imkl', local_comp_ver, '', SYSTEM), ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), ] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.eb index d773a1008c5..9c828ff708b 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.eb @@ -17,7 +17,7 @@ sources = ['%(namelower)s-%(version)s.jar'] checksums = ['59721f0805e223d84b90677887d9ff567dc534d7c502ca903c0c2b17f05c116a'] # specify dependency on Java/1.8 "wrapper", rather than a specific Java version -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] sanity_check_paths = { 'files': sources, diff --git a/easybuild/easyconfigs/j/Jasmine/Jasmine-1.1.4-GCC-11.2.0-Java-15.eb b/easybuild/easyconfigs/j/Jasmine/Jasmine-1.1.4-GCC-11.2.0-Java-15.eb index 811d9481443..781822576b5 100644 --- a/easybuild/easyconfigs/j/Jasmine/Jasmine-1.1.4-GCC-11.2.0-Java-15.eb +++ b/easybuild/easyconfigs/j/Jasmine/Jasmine-1.1.4-GCC-11.2.0-Java-15.eb @@ -15,7 +15,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['b52e13964b41f7659368965cd9e0537b151a6b52cf41dc8634ba67b1384113ec'] dependencies = [ - ('Java', '15', '', True), + ('Java', '15', '', SYSTEM), ('Iris', '1.0.5', versionsuffix), ] diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb index 3457f1b8086..97b36ac60d2 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb @@ -18,7 +18,7 @@ dependencies = [ ('IPython', '7.25.0'), ('Mako', '1.1.4'), ('configurable-http-proxy', '4.4.0'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] use_pip = True diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb index f138187813d..039ed9bd0d2 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('flatbuffers-python', '1.12'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb index 770de325d37..d9c4a4c51a4 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('cuDNN', '8.2.1.32', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb index a4992725207..387bbe5cc6c 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('cuDNN', '8.4.1.50', versionsuffix, True), ('NCCL', '2.12.12', versionsuffix), ('Python', '3.10.4'), diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb index 20d0ce315f7..92459f0310c 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('cuDNN', '8.2.1.32', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb index 6fbb4b351ab..46515f5f9c2 100644 --- a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [ ('Python', '3.9.5'), ('JupyterHub', '1.4.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ('aiohttp', '3.8.1'), ] diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb index e5ec4e0190e..23a32baffb9 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb @@ -21,7 +21,7 @@ dependencies = [ ('libpng', '1.6.37'), ('zlib', '1.2.11'), ('util-linux', '2.36'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb index 6e386edc292..866d7dadb81 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('libpng', '1.6.37'), ('zlib', '1.2.11'), ('util-linux', '2.37'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ('freetype', '2.11.0'), ] diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb index 5649a33478f..bb60e5f730f 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb @@ -56,7 +56,7 @@ dependencies = [ ('FFmpeg', '4.2.1'), ('Voro++', '0.4.6'), ('kim-api', '2.1.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('yaff', '1.6.0', local_python_versionsuffix), ('PLUMED', '2.5.3', local_python_versionsuffix), ] diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb index 722f37b89e8..a96f4e1bf04 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb @@ -60,7 +60,7 @@ dependencies = [ ('FFmpeg', '4.2.1'), ('Voro++', '0.4.6'), ('kim-api', '2.1.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('yaff', '1.6.0', local_python_versionsuffix), ('PLUMED', '2.5.3', local_python_versionsuffix), ] diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb index b380301035a..3b651f5bb18 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb @@ -56,7 +56,7 @@ dependencies = [ ('FFmpeg', '4.2.1'), ('Voro++', '0.4.6'), ('kim-api', '2.1.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('yaff', '1.6.0', local_python_versionsuffix), ('PLUMED', '2.5.3', local_python_versionsuffix), ] diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb index f8494e9734b..f6d6351c64b 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb @@ -63,7 +63,7 @@ dependencies = [ ('FFmpeg', '4.2.1'), ('Voro++', '0.4.6'), ('kim-api', '2.1.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('yaff', '1.6.0', local_python_versionsuffix), ('PLUMED', '2.5.3', local_python_versionsuffix), ] diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb index 35c2a48a208..23b825e617b 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb @@ -56,7 +56,7 @@ dependencies = [ ('FFmpeg', '4.2.1'), ('Voro++', '0.4.6'), ('kim-api', '2.1.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('yaff', '1.6.0', local_python_versionsuffix), ('PLUMED', '2.5.3', local_python_versionsuffix), ] diff --git a/easybuild/easyconfigs/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb index f509313572d..a022ed94c45 100644 --- a/easybuild/easyconfigs/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb @@ -17,7 +17,7 @@ builddependencies = [ ('CMake', '3.18.4'), ('Ninja', '1.10.1'), # building LDC from source required LDC 0.17.x - ('LDC', '0.17.6', '-%(arch)s', True), + ('LDC', '0.17.6', '-%(arch)s', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/LDC/LDC-1.26.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LDC/LDC-1.26.0-GCCcore-10.3.0.eb index 01d38679892..55231353b25 100644 --- a/easybuild/easyconfigs/l/LDC/LDC-1.26.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/LDC/LDC-1.26.0-GCCcore-10.3.0.eb @@ -17,7 +17,7 @@ builddependencies = [ ('CMake', '3.20.1'), ('Ninja', '1.10.2'), # building LDC from source required LDC 0.17.x - ('LDC', '0.17.6', '-%(arch)s', True), + ('LDC', '0.17.6', '-%(arch)s', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/LOHHLA/LOHHLA-2018.11.05-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/l/LOHHLA/LOHHLA-2018.11.05-foss-2018b-R-3.5.1.eb index e8d3bf16a0c..ea74d83de75 100644 --- a/easybuild/easyconfigs/l/LOHHLA/LOHHLA-2018.11.05-foss-2018b-R-3.5.1.eb +++ b/easybuild/easyconfigs/l/LOHHLA/LOHHLA-2018.11.05-foss-2018b-R-3.5.1.eb @@ -29,7 +29,7 @@ dependencies = [ ('BEDTools', '2.27.1'), ('SAMtools', '1.9'), ('novoalign', '3.09.01', versionsuffix), - ('picard', '2.18.27', '-Java-1.8', True), + ('picard', '2.18.27', '-Java-1.8', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/LiBis/LiBis-20200428-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/l/LiBis/LiBis-20200428-foss-2019b-Python-3.7.4.eb index 1788ec1f1d8..4eadb4441ed 100644 --- a/easybuild/easyconfigs/l/LiBis/LiBis-20200428-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/l/LiBis/LiBis-20200428-foss-2019b-Python-3.7.4.eb @@ -24,7 +24,7 @@ checksums = [ dependencies = [ ('Python', '3.7.4'), - ('FastQC', '0.11.9', '-Java-11', True), + ('FastQC', '0.11.9', '-Java-11', SYSTEM), ('SciPy-bundle', '2019.10', versionsuffix), # pandas ('matplotlib', '3.1.1', versionsuffix), ('cutadapt', '2.7', versionsuffix), diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.4.2-intel-2018a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.4.2-intel-2018a.eb index f36862909d7..a9f94d66090 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.4.2-intel-2018a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.4.2-intel-2018a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('Autotools', '20170619'), ('GMP', '6.1.2'), ('Boost', '1.66.0', '-Python-2.7.14'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('Python', '2.7.14'), ] diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.5.0-gompi-2019a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.5.0-gompi-2019a.eb index 7bdd390fc27..ea2d5040ce7 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.5.0-gompi-2019a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.5.0-gompi-2019a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('Autotools', '20180311'), ('GMP', '6.1.2'), ('Boost', '1.70.0'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('Python', '2.7.15'), ] diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.5.0-iimpi-2019a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.5.0-iimpi-2019a.eb index 3983e2d6057..87d30d047ad 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.5.0-iimpi-2019a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.5.0-iimpi-2019a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('Autotools', '20180311'), ('GMP', '6.1.2'), ('Boost', '1.70.0'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('Python', '2.7.15'), ] diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb index 29c369131f2..f0c3fff870f 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb @@ -13,7 +13,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb index 52b296562ea..7fb4df0019e 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb @@ -13,7 +13,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb index 5d0e481e2b0..f0d08dd8dd7 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb @@ -13,7 +13,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb index ecc53857740..d3c68c53159 100644 --- a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb index 8068f14ea72..9b673d9b132 100644 --- a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb index b9a8c3b204c..2e7d6b7a9f3 100644 --- a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb @@ -15,7 +15,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('fixesproto', '5.0'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb index bbe2ea95f7e..1eb5c2b11e2 100644 --- a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb @@ -15,7 +15,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('fixesproto', '5.0'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb index dcc203e11e3..4d51c3577b5 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb @@ -15,7 +15,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('xextproto', '7.3.0'), ('libpthread-stubs', '0.3'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('kbproto', '1.0.7'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb index ba7aa8aa456..40f48498460 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb @@ -15,7 +15,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('xextproto', '7.3.0'), ('libpthread-stubs', '0.3'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('kbproto', '1.0.7'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb index 76dc5940533..9478bc5d4a6 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('libpthread-stubs', '0.3'), ('inputproto', '2.3.1'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb index d0b72a86ea2..bcc8bb91b85 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('libpthread-stubs', '0.3'), ('inputproto', '2.3.1'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb index 5af14da529b..f215f8541e5 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('libpthread-stubs', '0.3'), ('inputproto', '2.3.1'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb index 8117c7c96b3..50f49048f36 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb @@ -17,7 +17,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb index b95d581275b..7512c727f34 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb index 1cc411ee297..c06e453df9d 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb @@ -17,7 +17,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb index 6589aeeb492..f5d786fdb45 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb index 2f7d28f58a9..e95534157b7 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('fixesproto', '5.0'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('libpthread-stubs', '0.3'), ('xtrans', '1.3.5'), ] diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb index 028286d1610..c23a7491a1f 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('fixesproto', '5.0'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('libpthread-stubs', '0.3'), ('xtrans', '1.3.5'), ] diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb index 7f990b2124d..787ed0a6b96 100644 --- a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('xorg-macros', '1.19.0'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('libpthread-stubs', '0.3'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb index 7e2411fa015..20acc539c5d 100644 --- a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('xorg-macros', '1.19.0'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('libpthread-stubs', '0.3'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb index 62c62161692..1f7e10f14bb 100644 --- a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('libpthread-stubs', '0.3'), ('randrproto', '1.5.0'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb index d6e4b7406dd..66d8e8e7988 100644 --- a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('libpthread-stubs', '0.3'), ('randrproto', '1.5.0'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb index b4c2ef6a53d..f3c947b005a 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb index 2c473580acb..c981feacb52 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb index c7e832fe55b..61d8f22229f 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('kbproto', '1.0.7'), ('xorg-macros', '1.19.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('libpthread-stubs', '0.3'), ('xextproto', '7.3.0'), ('inputproto', '2.3.1'), diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb index e12535727a9..4401fe752de 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('kbproto', '1.0.7'), ('xorg-macros', '1.19.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('libpthread-stubs', '0.3'), ('xextproto', '7.3.0'), ('inputproto', '2.3.1'), diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-10.3.0.eb index 9f8743b3091..df8e63cdd74 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-10.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), ('XZ', '5.2.5'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-11.2.0.eb index a5bba4c08fc..c0609d8718e 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-11.2.0.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), ('XZ', '5.2.5'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-11.3.0.eb index bb86f508a75..2f0d0841e1b 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-11.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.12'), ('XZ', '5.2.5'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb index fe73b8ae707..8c219ad876e 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb @@ -18,7 +18,7 @@ sources = ['%(name)s-%(version)s-stable.tar.gz'] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-10.3.0.eb index b5cc4b2c7c0..a5d36861e3f 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-10.3.0.eb @@ -29,7 +29,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.2.0.eb index ce86a4e932c..03d032cf290 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.2.0.eb @@ -26,7 +26,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb index 09681e8d363..d88edcd0b49 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb @@ -26,7 +26,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.12'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-5.4.0.eb index 380578da359..1013ed198c1 100644 --- a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-5.4.0.eb @@ -20,7 +20,7 @@ checksums = [ '078bec207fc3d5a0581f2a952d1c014b76a6e84a93a6a089ff9b9fe5b3908cb9', # libffi-3.2.1_fix-include-location.patch ] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.3.0.eb index 363d1410af2..072c87fca91 100644 --- a/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ dependencies = [ ('PCRE', '8.44'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.1.1-GCCcore-11.2.0.eb index 085a5fb9f66..67f2252522d 100644 --- a/easybuild/easyconfigs/l/libgit2/libgit2-1.1.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.1.1-GCCcore-11.2.0.eb @@ -23,7 +23,7 @@ builddependencies = [ dependencies = [ ('PCRE', '8.45'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.4.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.4.3-GCCcore-11.3.0.eb index c1884e0bb10..24bafd95d41 100644 --- a/easybuild/easyconfigs/l/libgit2/libgit2-1.4.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.4.3-GCCcore-11.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ dependencies = [ ('PCRE', '8.45'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb index c2a203f1b2d..0e6381d00bb 100644 --- a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb @@ -12,7 +12,7 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb index 8fe50e9968e..33ce05138dc 100644 --- a/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-5.4.0.eb index 160e79719f9..4343922d7ce 100644 --- a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-5.4.0.eb @@ -13,7 +13,7 @@ source_urls = ['https://ftpmirror.gnu.org/gnu/libidn'] sources = [SOURCELOWER_TAR_GZ] checksums = ['e1cb1db3d2e249a6a3eb6f0946777c2e892d5c5dc7bd91c74394fc3a01cab8b5'] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/idn2', 'lib/libidn2.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.0-GCCcore-5.4.0.eb index 886c796fe1a..0a3c4a9ccac 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.0-GCCcore-5.4.0.eb @@ -19,7 +19,7 @@ dependencies = [ ('NASM', '2.11.08'), ] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] configopts = "--with-jpeg8" runtest = "test" diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-5.4.0.eb index c90941e7e9e..5c9da9b3258 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-5.4.0.eb @@ -15,7 +15,7 @@ checksums = ['be46e0d14ccac3800f816ae860d191a1187a40164b7552c44afeee97a9caa0a3'] dependencies = [('zlib', '1.2.8')] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb index f33c3fbc3e1..5679b67d18b 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('zlib', '1.2.11')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-6.3.0.eb index 49f53a9c0c2..9cb10e36685 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-6.3.0.eb @@ -16,7 +16,7 @@ checksums = ['b6cec903e74e9fdd7b5bbcde0ab2415dd12f2f9e84d9e4d9ddd2ba26a41623b2'] dependencies = [('zlib', '1.2.11')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb index 8c7fd2019e9..156f6db5ca5 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('zlib', '1.2.11')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb index 4e54ffba1c2..21a8965354a 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb @@ -20,7 +20,7 @@ checksums = [ '46317932e1af8c5e0916930e545a354f5ce821f34fa1c5b40619b77e50400ffd', # libreadline-6.3-bugfix.patch ] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] dependencies = [('ncurses', '6.0')] diff --git a/easybuild/easyconfigs/l/libsamplerate/libsamplerate-0.1.9-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libsamplerate/libsamplerate-0.1.9-GCCcore-8.2.0.eb index 3e47dc3c618..d0959ea0cea 100644 --- a/easybuild/easyconfigs/l/libsamplerate/libsamplerate-0.1.9-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libsamplerate/libsamplerate-0.1.9-GCCcore-8.2.0.eb @@ -15,7 +15,7 @@ checksums = ['0a7eb168e2f21353fb6d84da152e4512126f7dc48ccb0be80578c565413444c1'] builddependencies = [ ('binutils', '2.31.1'), # need to include gompi too to ensure FFTW can be loaded in case hierarchical module naming scheme is used - ('gompi', '2019a', '', True), + ('gompi', '2019a', '', SYSTEM), # FFTW is only required for tests ('FFTW', '3.3.8', '', ('gompi', '2019a')), ] diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb index e8763aba9c4..82f2dfb2315 100644 --- a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.2.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.2.eb index fdb971d5a6b..5cb32f20da8 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.2.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.3.0.eb index 42794e4902b..11b1fbaf2be 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.3.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb index e7ade18cd5e..2e615320fc8 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb index 09f8321dfd0..91409103d4c 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb index f8debfbbbad..763a4f1aefd 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb index f22547e6446..fe4f7047b25 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb index a3916dbea56..5e2eece33bb 100644 --- a/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb @@ -21,9 +21,9 @@ checksums = ['099e85d8ba3c3d849ce05b8ba2791dd25cd042a813be947fb321b0676ef71883'] builddependencies = [ ('binutils', '2.36.1'), ('CMake', '3.20.1'), - ('cxxopts', '3.0.0', '', True), - ('ELFIO', '3.9', '', True), - ('termcolor', '2.0.0', '', True), + ('cxxopts', '3.0.0', '', SYSTEM), + ('ELFIO', '3.9', '', SYSTEM), + ('termcolor', '2.0.0', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb index c1f1541e7ad..e97d8ea1348 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} sources = [SOURCELOWER_TAR_XZ] source_urls = [GNU_SOURCE] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] parallel = 1 diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb index 7a2944d9e46..965a763a8c8 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('pkg-config', '0.29'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb index ab5bcf6b380..3ec05ecfbde 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ] diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb index c69ddcedb6e..4f81dd3b454 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('pkg-config', '0.29'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb index 2ec01ebf7f2..835f4ff45f3 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb @@ -16,7 +16,7 @@ checksums = ['0bb3cfd46dbd90066bf4d7de3cad73ec1024c7325a4a0cbf5f4a0d4fa91155fb'] builddependencies = [ ('binutils', '2.28'), ('pkg-config', '0.29.2'), - ('xcb-proto', '1.13', '', True), + ('xcb-proto', '1.13', '', SYSTEM), ('xproto', '7.0.31'), ('libpthread-stubs', '0.4'), ('xorg-macros', '1.19.1'), diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb index 54ae8147222..690edb297f9 100644 --- a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb @@ -22,7 +22,7 @@ dependencies = [ builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb index b3bcbc8fa66..7c8c84e827d 100644 --- a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb @@ -22,7 +22,7 @@ dependencies = [ builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-5.4.0.eb index 346410c130c..7cfd54f4e1b 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-5.4.0.eb @@ -22,6 +22,6 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb index b71554c4dfa..f5aef73bc13 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb @@ -21,6 +21,6 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.5-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.5-GCCcore-6.3.0.eb index 8452f3187e2..42dac0e7a79 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.5-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.5-GCCcore-6.3.0.eb @@ -22,6 +22,6 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb index d33516e092f..6d0bea61d24 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['ba65236116de8326d83378b2bd929879fa185195bc530b9d1aba72107910b6b3'] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb index fe7ed2be661..d198d46a308 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb index 0f3443b3e7f..da1de09fb7b 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb index 23ce8933d1c..085515a2705 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb index 7886d1c9ada..4fc80e53b4a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb index 7b223299334..0a707b51b00 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb index 45af326f45d..5f4d20ef856 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb index e2473bcff4d..c3716a65a86 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb index d7aa39079a3..fe316e7657a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb index 8f7d944e2e1..a8faaec3954 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCCcore -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb index 70f9de4b636..388f76f2753 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb index 9bd978b3ec9..bd7b15d0f99 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.34', '', True)] +builddependencies = [('binutils', '2.34', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb index 50594f87ece..40d8acc91af 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.35', '', True)] +builddependencies = [('binutils', '2.35', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb index e7dee0ddd89..aaa4eda2c91 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.36.1', '', True)] +builddependencies = [('binutils', '2.36.1', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb index e63d5912066..c1852324b5b 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.36.1', '', True)] +builddependencies = [('binutils', '2.36.1', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb index 13063f1b7f6..90f3441ae31 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb index 362ecb6b5e5..44174916f39 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb @@ -19,7 +19,7 @@ checksums = [ 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb index 7d867eee4d9..bb84008fe0d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb index 19fb0b8badd..42ac0537642 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb index 33da257c441..abedf0b58b2 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb @@ -24,7 +24,7 @@ checksums = [ # use same binutils version that was used when building GCC toolchain builddependencies = [ - ('binutils', '2.28', '', True), + ('binutils', '2.28', '', SYSTEM), ] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb index 4f300fc47cf..70675bd26d4 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.28', '', True)] +builddependencies = [('binutils', '2.28', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb index f4ec9a042e1..95c1d432cdf 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.29', '', True)] +builddependencies = [('binutils', '2.29', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb index 709134121bf..d435d9cf19f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.30', '', True)] +builddependencies = [('binutils', '2.30', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb index 89a858a24f8..18817b26e32 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.31.1', '', True)] +builddependencies = [('binutils', '2.31.1', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb index a92a076f9bc..f268c01aaed 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.30', '', True)] +builddependencies = [('binutils', '2.30', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb index 3f8004316c4..cdf833ca394 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.31.1', '', True)] +builddependencies = [('binutils', '2.31.1', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb index 0d5a496fbf0..b21fcafc4f7 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.32', '', True)] +builddependencies = [('binutils', '2.32', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb index c52483a837d..30d2b32da00 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.32', '', True)] +builddependencies = [('binutils', '2.32', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb index 7cb0d843963..aac98bc3c12 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.32', '', True)] +builddependencies = [('binutils', '2.32', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb index 2d1822b6404..c70532aeb1f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.32', '', True)] +builddependencies = [('binutils', '2.32', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb index 5e4d0740ee7..61100b9eb44 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.34', '', True)] +builddependencies = [('binutils', '2.34', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.0.eb index 0f426d46de5..7818364f1ae 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.37', '', True)] +builddependencies = [('binutils', '2.37', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.3.0.eb index dfdd4df8d10..41a76cb08ba 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.3.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.38', '', True)] +builddependencies = [('binutils', '2.38', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.1.0.eb index b0d85861200..7e38a77b438 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.1.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.38', '', True)] +builddependencies = [('binutils', '2.38', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.2.0.eb index 568d60035ca..4061197926d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.2.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.39', '', True)] +builddependencies = [('binutils', '2.39', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.4.0.eb index 6e539babe63..e59b0628b8e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.4.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.36.1', '', True)] +builddependencies = [('binutils', '2.36.1', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.5.0.eb index 95d679a09cf..e586ce4a60a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.5.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.38', '', True)] +builddependencies = [('binutils', '2.38', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb index 7009268301e..17a1f835e91 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} dependencies = [ ('Python', '2.7.14'), - ('MATLAB', version, '', True) + ('MATLAB', version, '', SYSTEM) ] # Since this setup.py does not provide a separate --build-base for the install diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb index d7fcbc99902..55b0c6ce81f 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} dependencies = [ ('Python', '3.6.3'), - ('MATLAB', version, '', True) + ('MATLAB', version, '', SYSTEM) ] # Since this setup.py does not provide a separate --build-base for the install diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb index fc816ba2323..14e3d088e33 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} dependencies = [ ('Python', '2.7.14'), - ('MATLAB', version, '', True) + ('MATLAB', version, '', SYSTEM) ] # Since this setup.py does not provide a separate --build-base for the install diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb index 0c39c8a729c..76000b4dc4a 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} dependencies = [ ('Python', '3.6.3'), - ('MATLAB', version, '', True) + ('MATLAB', version, '', SYSTEM) ] # Since this setup.py does not provide a separate --build-base for the install diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb index 7ce8669e278..8ac5cb405dc 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} multi_deps = {'Python': ['3.7.4', '2.7.16']} dependencies = [ - ('MATLAB', version, '', True) + ('MATLAB', version, '', SYSTEM) ] use_pip = False diff --git a/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb b/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb index f41f912592a..13a5f06fec5 100644 --- a/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb @@ -13,7 +13,7 @@ source_urls = ['https://github.com/matsim-org/matsim/releases/download/%(namelow sources = ['%(namelower)s-%(version)s.zip'] dependencies = [ - ('Java', '1.8.0_112', '', True), + ('Java', '1.8.0_112', '', SYSTEM), ('X11', '20160819'), ] diff --git a/easybuild/easyconfigs/m/MATSim/MATSim-14.0-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/m/MATSim/MATSim-14.0-GCCcore-11.2.0-Java-11.eb index dd2b476ec76..0c14fa80736 100644 --- a/easybuild/easyconfigs/m/MATSim/MATSim-14.0-GCCcore-11.2.0-Java-11.eb +++ b/easybuild/easyconfigs/m/MATSim/MATSim-14.0-GCCcore-11.2.0-Java-11.eb @@ -14,7 +14,7 @@ sources = ['%(namelower)s-%(version)s-release.zip'] checksums = ['17c7b785678cacd937f5df5b8c80398b73e2e9ceb07cc1ebd175fc94a65ce3c4'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Mesa', '21.1.7'), ('X11', '20210802'), ] diff --git a/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb b/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb index 3b6f548fcac..e26b1a04135 100644 --- a/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb +++ b/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb @@ -24,7 +24,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '13', '', True), + ('Java', '13', '', SYSTEM), ('MDSplus', version), ] diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index 9b8ad14bb5f..05e8b2e18a0 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] sources = ['stable_release-%s.zip' % version.replace('.', '-')] dependencies = [ - ('Java', '1.7.0_79', '', True), + ('Java', '1.7.0_79', '', SYSTEM), ('Python', '2.7.11'), ('HDF5', '1.8.16'), ('libxml2', '2.9.3'), diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb index d8d121944ac..97b0d2699a0 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb @@ -21,7 +21,7 @@ sources = ['mpj-v%s.tar.gz' % (version.replace('.', '_'))] builddependencies = [('CMake', '3.5.2')] dependencies = [ - ('Java', '1.8.0_92', '', True), + ('Java', '1.8.0_92', '', SYSTEM), ] # compile JNI wrapper library as described in docs diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-2.7.16.eb index 7f066294b57..61d2d07255f 100644 --- a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-2.7.16.eb @@ -15,7 +15,7 @@ sources = ['%s.tar.gz' % local_commit] checksums = ['7140934dc653ee5edf807120a8e9cf23a0bf72f01bbe4dfbe2a15206ce6812db'] builddependencies = [ - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-3.7.4.eb index 7163dd84d46..186b2b4b72a 100644 --- a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-3.7.4.eb @@ -15,7 +15,7 @@ sources = ['%s.tar.gz' % local_commit] checksums = ['7140934dc653ee5edf807120a8e9cf23a0bf72f01bbe4dfbe2a15206ce6812db'] builddependencies = [ - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC2-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC2-foss-2017a-Python-2.7.13.eb index aa0e747a561..b8433c3a9de 100644 --- a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC2-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC2-foss-2017a-Python-2.7.13.eb @@ -14,7 +14,7 @@ sources = ['%(version)s.tar.gz'] checksums = ['88187f3498f4ee215b2a51d16acb7f2e6c33217e72403a7d48c2ec5da6e2218b'] builddependencies = [ - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC3-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC3-intel-2018a-Python-2.7.14.eb index fc29aa69abd..aaddadd44e2 100644 --- a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC3-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC3-intel-2018a-Python-2.7.14.eb @@ -14,7 +14,7 @@ sources = ['%(version)s.tar.gz'] checksums = ['1eebd96d476772b4f1aaad2d362af575e70fd2de0bede61a658758ffd9793b4d'] builddependencies = [ - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb index 55513948cde..c6e9f493935 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb @@ -34,7 +34,7 @@ dependencies = [ ('Boost', '1.77.0'), # needed by OQGraph ('Judy', '1.0.5'), # needed by OQGraph ('PCRE2', '10.37'), - ('OpenSSL', '1.1', '', True), # runtime dep for mysql and PCRE2 for mysqltest + ('OpenSSL', '1.1', '', SYSTEM), # runtime dep for mysql and PCRE2 for mysqltest ] separate_build_dir = True diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb index 0742cb59603..12a89338f1e 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb @@ -34,7 +34,7 @@ dependencies = [ ('Boost', '1.79.0'), # needed by OQGraph ('Judy', '1.0.5'), # needed by OQGraph ('PCRE2', '10.40'), - ('OpenSSL', '1.1', '', True), # runtime dep for mysql and PCRE2 for mysqltest + ('OpenSSL', '1.1', '', SYSTEM), # runtime dep for mysql and PCRE2 for mysqltest ] separate_build_dir = True diff --git a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0-foss-2021a-CUDA-11.3.1.eb index 121bec87c85..6e267773c52 100644 --- a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0-foss-2021a-CUDA-11.3.1.eb @@ -12,7 +12,7 @@ genome/transriptome.""" toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('h5py', '3.2.1'), diff --git a/easybuild/easyconfigs/m/MiGEC/MiGEC-1.2.9-Java-1.8.eb b/easybuild/easyconfigs/m/MiGEC/MiGEC-1.2.9-Java-1.8.eb index c1dfbf5a270..ca85b3b0c8f 100644 --- a/easybuild/easyconfigs/m/MiGEC/MiGEC-1.2.9-Java-1.8.eb +++ b/easybuild/easyconfigs/m/MiGEC/MiGEC-1.2.9-Java-1.8.eb @@ -19,7 +19,7 @@ source_urls = ['https://github.com/mikessh/migec/releases/download/%(version)s/' sources = ['%(namelower)s-%(version)s.zip'] checksums = ['4a9ace1ab932d06154cdd3eaf6724f55c8dc5c3ce68108b8a4d30ecb0d58ea7e'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] sanity_check_paths = { 'files': ['migec', 'migec-%(version)s.jar'], diff --git a/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.13-Java-1.8.eb b/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.13-Java-1.8.eb index 4287f32cf3f..93646ef7373 100644 --- a/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.13-Java-1.8.eb +++ b/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.13-Java-1.8.eb @@ -19,7 +19,7 @@ source_urls = ['https://github.com/milaboratory/mixcr/releases/download/v%(versi sources = ['%(namelower)s-%(version)s.zip'] checksums = ['f0b32efadf6dae95819cd90cf49978e48797fc9f2685af1fd282a47d3f9fda08'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] sanity_check_paths = { 'files': ['mixcr', 'mixcr.jar'], diff --git a/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.3-Java-1.8.eb b/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.3-Java-1.8.eb index 864fd64611c..b1db223674b 100644 --- a/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.3-Java-1.8.eb +++ b/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.3-Java-1.8.eb @@ -19,7 +19,7 @@ source_urls = ['https://github.com/milaboratory/mixcr/releases/download/v%(versi sources = ['%(namelower)s-%(version)s.zip'] checksums = ['a969d815f8e7a8c3ffe082fdfe8f63cadbef7820b9299d648a454fe9480c72af'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] sanity_check_paths = { 'files': ['mixcr', 'mixcr.jar'], diff --git a/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0-Java-11.eb b/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0-Java-11.eb index 4cb42765502..5301799bdd2 100644 --- a/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0-Java-11.eb +++ b/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0-Java-11.eb @@ -19,7 +19,7 @@ sources = ['%(version)s.tar.gz'] checksums = ['35b6ee22fe6bdc26a31d0203a7dcc6bd1a19fd6733c60d80ceb44431884af165'] builddependencies = [('binutils', '2.32')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] # minced executable has to be in the same directory as jar files_to_copy = [(['minced', 'minced.jar'], 'bin')] diff --git a/easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb index d5bfff12153..e33cd3c0183 100644 --- a/easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb @@ -18,7 +18,7 @@ checksums = ['13fc5d3c6f41a6eb17498dfb1e69735a2b3f4e62ac7393d3ed71ea9502038841'] dependencies = [ ('Python', '3.6.6'), ('Perl', '5.28.0'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('libgd', '2.2.5'), ('Biopython', '1.72', versionsuffix), ('BioPerl', '1.7.2', '-Perl-%(perlver)s'), @@ -28,7 +28,7 @@ dependencies = [ ('SAMtools', '1.9'), ('Infernal', '1.1.2'), ('ETE', '3.1.1', versionsuffix), - ('tbl2asn', '20200302', '-linux64', True), + ('tbl2asn', '20200302', '-linux64', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb b/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb index cf0f71ea2bc..7402e2f2b74 100644 --- a/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb @@ -26,7 +26,7 @@ builddependencies = [('CMake', '3.22.1')] dependencies = { ('flex', '2.6.4'), - ('Bison', '3.8.2', '', True) + ('Bison', '3.8.2', '', SYSTEM) } files_to_copy = ['bin'] diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.2.6-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.2.6-GCCcore-8.2.0.eb index eb939d50379..25197a7fbf6 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.2.6-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.2.6-GCCcore-8.2.0.eb @@ -36,7 +36,7 @@ checksums = [ # of MotionCor2 builddependencies = [ ('binutils', '2.31.1'), - ('CUDA', '10.1.105', '', True), + ('CUDA', '10.1.105', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.1-GCCcore-8.3.0.eb index dfaa5e0b7fd..3989ce20c54 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.1-GCCcore-8.3.0.eb @@ -36,7 +36,7 @@ checksums = [ # of MotionCor2 builddependencies = [ ('binutils', '2.32'), - ('CUDA', '10.1.243', '', True), + ('CUDA', '10.1.243', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.2-GCCcore-8.3.0.eb index c0a0396d15d..29958aa847c 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.2-GCCcore-8.3.0.eb @@ -36,7 +36,7 @@ checksums = [ # of MotionCor2 builddependencies = [ ('binutils', '2.32'), - ('CUDA', '10.1.243', '', True), + ('CUDA', '10.1.243', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb index 4f2bf4aeabb..0bbb8322a60 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb @@ -34,7 +34,7 @@ checksums = ['5a1b952f46816e396b918b92fcb118376c02be3636371bd6fcef00f315685b8d'] # of MotionCor2 builddependencies = [ ('binutils', '2.35'), - ('CUDAcore', '11.1.1', '', True), + ('CUDAcore', '11.1.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb index ed127443bf8..836b2d4668c 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb @@ -32,7 +32,7 @@ checksums = ['128f5cdf83b5023204c10b4801baa13f0a56a950e0bc6e0ed26c7f3aa1df59d7'] # of MotionCor2 builddependencies = [ ('binutils', '2.35'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb index 642b53c9aeb..632abd81b22 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb @@ -32,7 +32,7 @@ checksums = ['128f5cdf83b5023204c10b4801baa13f0a56a950e0bc6e0ed26c7f3aa1df59d7'] # of MotionCor2 builddependencies = [ ('binutils', '2.36.1'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MuPeXI/MuPeXI-1.2.0-foss-2018b-Perl-5.28.0-Python-2.7.15.eb b/easybuild/easyconfigs/m/MuPeXI/MuPeXI-1.2.0-foss-2018b-Perl-5.28.0-Python-2.7.15.eb index 839d7674129..4fcc2d91235 100644 --- a/easybuild/easyconfigs/m/MuPeXI/MuPeXI-1.2.0-foss-2018b-Perl-5.28.0-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/MuPeXI/MuPeXI-1.2.0-foss-2018b-Perl-5.28.0-Python-2.7.15.eb @@ -23,7 +23,7 @@ checksums = [ dependencies = [ ('Python', '2.7.15'), ('Perl', '5.28.0'), - ('netMHCpan', '4.0a', '', True), + ('netMHCpan', '4.0a', '', SYSTEM), ('VEP', '94.0', '-Perl-%(perlver)s'), ('Biopython', '1.72', '-Python-%(pyver)s'), ('psutil', '5.4.7', '-Python-%(pyver)s'), diff --git a/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb index 6a07a625057..af248bb974a 100644 --- a/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb @@ -27,7 +27,7 @@ dependencies = [ ('matplotlib', '2.2.4', versionsuffix), ('prodigal', '2.6.3'), ('fetchMG', '1.0'), - ('UCLUST', '1.2.22q', '-i86linux64', True), + ('UCLUST', '1.2.22q', '-i86linux64', SYSTEM), ('CD-HIT', '4.8.1'), ('tsne', '0.1.8', versionsuffix), ] diff --git a/easybuild/easyconfigs/m/magma/magma-2.3.0-foss-2018a-CUDA-9.1.85.eb b/easybuild/easyconfigs/m/magma/magma-2.3.0-foss-2018a-CUDA-9.1.85.eb index 0791cbd4c8e..36e4ae6c390 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.3.0-foss-2018a-CUDA-9.1.85.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.3.0-foss-2018a-CUDA-9.1.85.eb @@ -20,7 +20,7 @@ checksums = [ '47e734cf30577b563377c946fb7897da2fd53d050f7e4fe83d8bb11b8d157913', # magma-2.3.0-fix-makefile.patch ] -dependencies = [('CUDA', local_cuda_ver, '', True)] +dependencies = [('CUDA', local_cuda_ver, '', SYSTEM)] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/magma/magma-2.6.1-foss-2021a-CUDA-11.3.1.eb index 8b6cf89878b..18427a5c0bf 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.1-foss-2021a-CUDA-11.3.1.eb @@ -24,7 +24,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb index da5c2d7e1a5..e1b180e8d15 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb @@ -24,7 +24,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb index de1fa80521a..5c0b53f2a56 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('CMake', '3.23.1'), ] dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('UCX-CUDA', '1.12.1', versionsuffix), ] diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb index b7d5d70c2df..fb935602693 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ source_urls = [XORG_UTIL_SOURCE] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ('xproto', '7.0.31'), ('xorg-macros', '1.19.1'), ] diff --git a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2-foss-2018b-Python-2.7.15.eb index 0340543f67d..4e25ce407a7 100644 --- a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2-foss-2018b-Python-2.7.15.eb @@ -36,7 +36,7 @@ dependencies = [ ('Seaborn', '0.9.0', versionsuffix), ('BLAST+', '2.7.1'), ('Bowtie2', '2.3.4.2'), - ('FastQC', '0.11.8', '-Java-1.8', True), + ('FastQC', '0.11.8', '-Java-1.8', SYSTEM), ('Trim_Galore', '0.6.0', versionsuffix), ('bmtagger', '3.101'), ('taxator-tk', '1.3.3'), diff --git a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2.2-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2.2-foss-2019a-Python-2.7.15.eb index c8c34cc86a5..9e626cd3f73 100644 --- a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2.2-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2.2-foss-2019a-Python-2.7.15.eb @@ -21,7 +21,7 @@ sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_ checksums = ['67e1d86cafc20a8b2713000d18a169a25b4a7dd7c2d4433b51b2e8ad1d4627ff'] builddependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] # see https://github.com/bxlab/metaWRAP/blob/master/installation/dependancies.md @@ -44,7 +44,7 @@ dependencies = [ ('Seaborn', '0.9.0', versionsuffix), ('BLAST+', '2.9.0'), ('Bowtie2', '2.3.5.1'), - ('FastQC', '0.11.8', '-Java-11', True), + ('FastQC', '0.11.8', '-Java-11', SYSTEM), ('Trim_Galore', '0.6.2', '-Java-11'), ('bmtagger', '3.101'), ('taxator-tk', '1.3.3'), diff --git a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb index bb979fb26e2..382b15693e9 100644 --- a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb @@ -17,7 +17,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['ffdbccf340dc0b1ebd0ad6f222e3bdef1e22bbd6e4e5156bf93500a3a834dd52'] builddependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] # see https://github.com/bxlab/metaWRAP/blob/master/installation/dependancies.md @@ -30,7 +30,7 @@ dependencies = [ ('Bowtie2', '2.4.2'), ('BWA', '0.7.17'), ('CheckM', '1.0.18', versionsuffix), - ('FastQC', '0.11.9', '-Java-11', True), + ('FastQC', '0.11.9', '-Java-11', SYSTEM), ('Kraken', '1.1.1'), ('KronaTools', '2.8'), ('MEGAHIT', '1.2.9', versionsuffix), diff --git a/easybuild/easyconfigs/m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb index 388d152019f..e87d9e19fd7 100644 --- a/easybuild/easyconfigs/m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb @@ -19,7 +19,7 @@ dependencies = [ ('Bowtie2', '2.3.2'), ('Bowtie', '1.1.2'), ('SAMtools', '1.6'), - ('picard', '2.6.0', '-Java-1.8.0_131', True), + ('picard', '2.6.0', '-Java-1.8.0_131', SYSTEM), ('GSL', '2.3'), ] diff --git a/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb index c66bd30a717..ffeef5eccb8 100644 --- a/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb +++ b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb @@ -19,7 +19,7 @@ dependencies = [ ('Bowtie2', '2.4.4'), ('Bowtie', '1.3.1'), ('SAMtools', '1.14'), - ('picard', '2.25.1', '-Java-11', True), + ('picard', '2.25.1', '-Java-11', SYSTEM), ('GSL', '2.7'), ('Kent_tools', '422'), ] diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.4-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.4-intel-2018a-Python-2.7.14.eb index 4a532cf4fe8..fd51cdde93e 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.4-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.4-intel-2018a-Python-2.7.14.eb @@ -19,7 +19,7 @@ checksums = [ builddependencies = [('Boost.Python', '1.66.0', versionsuffix)] dependencies = [ - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('Python', '2.7.14'), ] diff --git a/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb index d5203935c90..c7fdb119d30 100644 --- a/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb @@ -19,7 +19,7 @@ builddependencies = [ dependencies = [ ('xxHash', '0.8.0'), ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/m/mold/mold-1.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/mold/mold-1.0.0-GCCcore-11.2.0.eb index 98e1d3c8a65..abcdedea8e6 100644 --- a/easybuild/easyconfigs/m/mold/mold-1.0.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/mold/mold-1.0.0-GCCcore-11.2.0.eb @@ -19,7 +19,7 @@ builddependencies = [ dependencies = [ ('xxHash', '0.8.0'), ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/m/mold/mold-1.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mold/mold-1.2.1-GCCcore-11.3.0.eb index fe82f3d27ad..7dbc871c42a 100644 --- a/easybuild/easyconfigs/m/mold/mold-1.2.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/mold/mold-1.2.1-GCCcore-11.3.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ] dependencies = [ ('zlib', '1.2.12'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/m/mold/mold-1.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mold/mold-1.3.0-GCCcore-11.3.0.eb index e78902943a2..874c4beff87 100644 --- a/easybuild/easyconfigs/m/mold/mold-1.3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/mold/mold-1.3.0-GCCcore-11.3.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ] dependencies = [ ('zlib', '1.2.12'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb index 321116d715d..c76c50c23f9 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb @@ -14,8 +14,8 @@ checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] dependencies = [ ('Python', '2.7.15'), - ('vsc-base', '2.8.3', '', True), - ('vsc-mympirun', '4.1.8', '', True), + ('vsc-base', '2.8.3', '', SYSTEM), + ('vsc-mympirun', '4.1.8', '', SYSTEM), ('matplotlib', '2.2.4', versionsuffix), ('h5py', '2.9.0'), ('mpi4py', '3.0.2', '-timed-pingpong'), diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb index e26533855e6..194aa344082 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb @@ -14,8 +14,8 @@ checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] dependencies = [ ('Python', '2.7.13'), - ('vsc-base', '2.5.8', '', True), - ('vsc-mympirun', '4.0.2', '', True), + ('vsc-base', '2.5.8', '', SYSTEM), + ('vsc-mympirun', '4.0.2', '', SYSTEM), ('matplotlib', '2.0.2', versionsuffix), ('h5py', '2.7.1', versionsuffix), ('mpi4py', '2.0.0', versionsuffix + '-timed-pingpong'), diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb index 7c14b8aa091..9c4144e7c47 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb @@ -14,8 +14,8 @@ checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] dependencies = [ ('Python', '2.7.14'), - ('vsc-base', '2.8.1', '', True), - ('vsc-mympirun', '4.1.5', '', True), + ('vsc-base', '2.8.1', '', SYSTEM), + ('vsc-mympirun', '4.1.5', '', SYSTEM), ('matplotlib', '2.1.2', versionsuffix), ('h5py', '2.7.1', versionsuffix), ('mpi4py', '3.0.0', versionsuffix + '-timed-pingpong'), diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb index 5c72b2d9539..6202bc1f6ce 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb @@ -14,8 +14,8 @@ checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] dependencies = [ ('Python', '2.7.15'), - ('vsc-base', '2.8.3', '', True), - ('vsc-mympirun', '4.1.8', '', True), + ('vsc-base', '2.8.3', '', SYSTEM), + ('vsc-mympirun', '4.1.8', '', SYSTEM), ('matplotlib', '2.2.4', versionsuffix), ('h5py', '2.9.0'), ('mpi4py', '3.0.2', '-timed-pingpong'), diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-GCCcore-5.4.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-GCCcore-5.4.0.eb index 59d28ad1fac..4cb8911d18f 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-GCCcore-5.4.0.eb @@ -12,7 +12,7 @@ source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['9da3a0291a0bdc06305b7ba194f1e2c2b55ae6f11210b4af43729868149d5445'] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/nasm'], diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb index ce83714e0e1..16e18e8e36e 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -16,7 +16,7 @@ checksums = ['55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'] builddependencies = [('binutils', '2.36.1')] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('UCX-CUDA', '1.10.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb index 6375266362f..63927a18ac1 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -16,7 +16,7 @@ checksums = ['55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'] builddependencies = [('binutils', '2.37')] dependencies = [ - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('UCX-CUDA', '1.11.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb index 026964019f7..2282286a915 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb @@ -16,7 +16,7 @@ checksums = ['49b4fbfeebf1f62f6ceb69e72504045d8d1b4e7609e3c2477906f3004c7e2d82'] builddependencies = [('binutils', '2.38')] dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('UCX-CUDA', '1.12.1', versionsuffix), ] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb index cbf8532c70e..81fa9b3dfaa 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -10,8 +10,8 @@ communication primitives that are performance optimized for NVIDIA GPUs.""" toolchain = {'name': 'GCCcore', 'version': local_gcc_ver} -builddependencies = [('GCC', local_gcc_ver, '', True)] -dependencies = [('CUDAcore', local_cuda_version, '', True)] +builddependencies = [('GCC', local_gcc_ver, '', SYSTEM)] +dependencies = [('CUDAcore', local_cuda_version, '', SYSTEM)] github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb index 50bb04e3b90..140a12a4575 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -10,8 +10,8 @@ communication primitives that are performance optimized for NVIDIA GPUs.""" toolchain = {'name': 'GCCcore', 'version': local_gcc_ver} -builddependencies = [('GCC', local_gcc_ver, '', True)] -dependencies = [('CUDAcore', local_cuda_version, '', True)] +builddependencies = [('GCC', local_gcc_ver, '', SYSTEM)] +dependencies = [('CUDAcore', local_cuda_version, '', SYSTEM)] github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb index 5ebb8f01ff7..abba6ab7b5b 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_92', '', True)] +dependencies = [('Java', '1.8.0_92', '', SYSTEM)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb index ed0e37836cc..5375c605408 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_77', '', True)] +dependencies = [('Java', '1.8.0_77', '', SYSTEM)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb index 8b032e04685..e2ec60825f6 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_92', '', True)] +dependencies = [('Java', '1.8.0_92', '', SYSTEM)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.3.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-GCCcore-6.4.0.eb index 85280ff5970..c6bfafd32a6 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-1.3.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-GCCcore-6.4.0.eb @@ -13,7 +13,7 @@ source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['803c650a6de5bb38231d9ced7587f3ab788b415cac04b0ef4152546b18713ef2'] -dependencies = [('Java', '1.8.0_192', '', True)] +dependencies = [('Java', '1.8.0_192', '', SYSTEM)] builddependencies = [ ('binutils', '2.28'), diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb index 8d0219a7422..fc51bb5ca7f 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_121', '', True)] +dependencies = [('Java', '1.8.0_121', '', SYSTEM)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-1.8.eb b/easybuild/easyconfigs/n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-1.8.eb index bc20255c082..de7c2047d29 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-1.8.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-1.8.eb @@ -20,7 +20,7 @@ checksums = ['4139adff83af213d7880bc80d1c0f5ee9b00c6c4e615d00aa47aaa267e40ed25'] builddependencies = [('binutils', '2.31.1')] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-11.eb b/easybuild/easyconfigs/n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-11.eb index f32799f658e..c95aef751b3 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-11.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-11.eb @@ -20,7 +20,7 @@ checksums = ['4139adff83af213d7880bc80d1c0f5ee9b00c6c4e615d00aa47aaa267e40ed25'] builddependencies = [('binutils', '2.31.1')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.10.4-GCCcore-8.3.0-Java-11.eb b/easybuild/easyconfigs/n/NGS/NGS-2.10.4-GCCcore-8.3.0-Java-11.eb index bf41fbf66b7..04f599cb3a4 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.10.4-GCCcore-8.3.0-Java-11.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.10.4-GCCcore-8.3.0-Java-11.eb @@ -15,7 +15,7 @@ builddependencies = [ ('Perl', '5.30.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] default_easyblock = 'ConfigureMake' default_component_specs = { diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.10.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/NGS/NGS-2.10.5-GCCcore-9.3.0.eb index 8a3ae837e9e..c6f2f988ec1 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.10.5-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.10.5-GCCcore-9.3.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('Perl', '5.30.2'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] default_easyblock = 'ConfigureMake' default_component_specs = { diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb index 3ca4af87ce9..3ef383ecc8b 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('Perl', '5.32.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] default_easyblock = 'ConfigureMake' default_component_specs = { diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.3.0.eb index f07787644a5..9c8a9ae5026 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.3.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('Perl', '5.32.1'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] default_easyblock = 'ConfigureMake' default_component_specs = { diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-11.2.0.eb index d410657900f..785c1683f20 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-11.2.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('Perl', '5.34.0', '-minimal'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] default_easyblock = 'ConfigureMake' default_component_specs = { diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.9.1-foss-2018a-Java-1.8.0_162.eb b/easybuild/easyconfigs/n/NGS/NGS-2.9.1-foss-2018a-Java-1.8.0_162.eb index 8c00266c360..1255f097104 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.9.1-foss-2018a-Java-1.8.0_162.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.9.1-foss-2018a-Java-1.8.0_162.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['c24c93bd70ed198a44c6b9dba0d6704edc90f228f832f2fef21fa5342303fc50'] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.9.1-intel-2018a-Java-1.8.0_162.eb b/easybuild/easyconfigs/n/NGS/NGS-2.9.1-intel-2018a-Java-1.8.0_162.eb index ec99368e887..6f21a2ce8b4 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.9.1-intel-2018a-Java-1.8.0_162.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.9.1-intel-2018a-Java-1.8.0_162.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['c24c93bd70ed198a44c6b9dba0d6704edc90f228f832f2fef21fa5342303fc50'] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.9.3-foss-2018b-Java-1.8.eb b/easybuild/easyconfigs/n/NGS/NGS-2.9.3-foss-2018b-Java-1.8.eb index b65402280d4..37d4558ef19 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.9.3-foss-2018b-Java-1.8.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.9.3-foss-2018b-Java-1.8.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['d16cdf340f4c66e449cc490a222e54e9074cd15fe0938cb75b951a72985f757d'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb index 492ce96c1a9..bd388fb7582 100644 --- a/easybuild/easyconfigs/n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb +++ b/easybuild/easyconfigs/n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb @@ -17,7 +17,7 @@ source_urls = [ sources = ['%(namelower)s_%(version)s.tar.gz'] checksums = ['661a5bb626164c145ae9c5ba5c3d9c30b0ecc1b83d86eae25d83745324906f7e'] -builddependencies = [('Eigen', '3.3.7', '', True)] +builddependencies = [('Eigen', '3.3.7', '', SYSTEM)] dependencies = [('R', '3.5.1')] diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb index 5c22660ad0b..db905d3342f 100644 --- a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb @@ -27,7 +27,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('UCX-CUDA', '1.12.1', versionsuffix), ('NCCL', '2.12.12', versionsuffix), ] diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb index 4c737da9890..b145b8018a3 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb @@ -17,7 +17,7 @@ sources = ['%(namelower)s-%(version)s-all'] checksums = ['10d96864489a5d6b4de3a730307871ca865e2f1c49a14cd5c4051cae5dca8d8e'] # specify dependency on Java/1.8 "wrapper", rather than a specific Java version -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] install_cmd = "[ -d %(builddir)s/bin ] || mkdir -p %(installdir)s/bin &&" install_cmd += "cp %(builddir)s/nextflow-%(version)s-all %(installdir)s/bin &&" diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.07.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.07.0.eb index 1e97a00e55f..87b4b238692 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.07.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.07.0.eb @@ -17,7 +17,7 @@ sources = ['%(namelower)s-%(version)s-all'] checksums = ['6f7069b43f395c5d902321745d37988fed7ef84d2006ea00be0df19de97c1986'] # specify dependency on Java/1.8 "wrapper", rather than a specific Java version -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] install_cmd = "[ -d %(builddir)s/bin ] || mkdir -p %(installdir)s/bin &&" install_cmd += "cp %(builddir)s/%(namelower)s-%(version)s-all %(installdir)s/bin &&" diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.12.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.12.0.eb index 4cb30cd7747..f7ce8ad37cd 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.12.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.12.0.eb @@ -24,7 +24,7 @@ sources = ['v%(version)s-edge.tar.gz'] checksums = ['16d38a14aeab636531da6d5d1894898d13a359c5f699eefcfb433fc3340e1b8a'] # specify dependency on Java/11 "wrapper", rather than a specific Java version -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] skipsteps = ['configure', 'build'] diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-20.01.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-20.01.0.eb index 012c69b71df..90347313e4c 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-20.01.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-20.01.0.eb @@ -25,7 +25,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['011b0b74df612a001bee05c75ee3eb93caff76eb2facd39527a092b86c3373ab'] # specify dependency on Java/11 "wrapper", rather than a specific Java version -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] skipsteps = ['configure', 'build'] diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-20.04.1.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-20.04.1.eb index cf8212fe26f..f55c9aac668 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-20.04.1.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-20.04.1.eb @@ -25,7 +25,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['ec939568585454cad3ab1a4f6510f0dee707e02ce44324bd43a05e5601d28136'] # specify dependency on Java/11 "wrapper", rather than a specific Java version -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] skipsteps = ['configure', 'build'] diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-20.10.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-20.10.0.eb index 01b4e6dcf2f..029737900a7 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-20.10.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-20.10.0.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['5ebf674c75ff73cd7a090921942fb1234653f50beaac09962022f20fa2ef4fc9'] # specify dependency on Java/11 "wrapper", rather than a specific Java version -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] skipsteps = ['configure', 'build'] diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-21.03.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-21.03.0.eb index d7d137ebdf3..4ee8f8aca28 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-21.03.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-21.03.0.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s-edge.tar.gz'] checksums = ['7b10fe1d8cf5dc6aba810e36b28aa360cd186cd583208542422daf1f08089692'] # specify dependency on Java/11 "wrapper", rather than a specific Java version -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] skipsteps = ['configure', 'build'] diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-21.08.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-21.08.0.eb index 7e99ffb9bd6..42acc235e75 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-21.08.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-21.08.0.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s-edge.tar.gz'] checksums = ['ab47af92e6f5c5c08a43b70e60cc3d8720e267a507f21af62ac24805b02a2e8b'] # specify dependency on Java/13 "wrapper", rather than a specific Java version -dependencies = [('Java', '13', '', True)] +dependencies = [('Java', '13', '', SYSTEM)] skipsteps = ['configure', 'build'] diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-21.10.6.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-21.10.6.eb index ed4ceee4b28..d610c0c4a0d 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-21.10.6.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-21.10.6.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['91b108cba321cb5500e2e811c446b04aee152dc2f97cb2cf4ae00eeecd4f332f'] # specify dependency on Java/13 "wrapper", rather than a specific Java version -dependencies = [('Java', '13', '', True)] +dependencies = [('Java', '13', '', SYSTEM)] skipsteps = ['configure', 'build'] diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-22.04.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.04.0.eb index 14616b6305d..1dd727aee12 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-22.04.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.04.0.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['4547a82228d1ad8615dd9916cd47a64a397405058579c0557cd11540633713ad'] # specify dependency on Java/11 "wrapper", rather than a specific Java version -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] skipsteps = ['configure', 'build'] diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.10.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.10.2-foss-2018b-Python-2.7.15.eb index 801d95801e6..91d4c8cbd71 100644 --- a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.10.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.10.2-foss-2018b-Python-2.7.15.eb @@ -22,7 +22,7 @@ checksums = [ 'f8b1ce2c07adb56b4f13337ef008e124255f86cdb7e74e4233afa8dca878ee1a', # fast5-v0.6.5.tar.gz ] -builddependencies = [('Eigen', '3.3.5', '', True)] +builddependencies = [('Eigen', '3.3.5', '', SYSTEM)] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.10.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.10.2-intel-2018b-Python-2.7.15.eb index 6799dfdb146..98affa6d3c8 100644 --- a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.10.2-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.10.2-intel-2018b-Python-2.7.15.eb @@ -22,7 +22,7 @@ checksums = [ 'f8b1ce2c07adb56b4f13337ef008e124255f86cdb7e74e4233afa8dca878ee1a', # fast5-v0.6.5.tar.gz ] -builddependencies = [('Eigen', '3.3.4', '', True)] +builddependencies = [('Eigen', '3.3.4', '', SYSTEM)] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb index 8bfbce42b87..ec682cb63db 100644 --- a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb @@ -22,7 +22,7 @@ checksums = [ 'f8b1ce2c07adb56b4f13337ef008e124255f86cdb7e74e4233afa8dca878ee1a', # fast5-v0.6.5.tar.gz ] -builddependencies = [('Eigen', '3.3.7', '', True)] +builddependencies = [('Eigen', '3.3.7', '', SYSTEM)] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.2-foss-2020a-Python-3.8.2.eb index 5a800af7bf5..edaace23ac2 100644 --- a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.2-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.2-foss-2020a-Python-3.8.2.eb @@ -23,7 +23,7 @@ checksums = [ 'f8b1ce2c07adb56b4f13337ef008e124255f86cdb7e74e4233afa8dca878ee1a', # fast5-v0.6.5.tar.gz ] -builddependencies = [('Eigen', '3.3.7', '', True)] +builddependencies = [('Eigen', '3.3.7', '', SYSTEM)] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.9.2-intel-2018a.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.9.2-intel-2018a.eb index f7f74b3e462..b6658ad065b 100644 --- a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.9.2-intel-2018a.eb +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.9.2-intel-2018a.eb @@ -21,7 +21,7 @@ checksums = [ 'f8b1ce2c07adb56b4f13337ef008e124255f86cdb7e74e4233afa8dca878ee1a', # fast5-v0.6.5.tar.gz ] -builddependencies = [('Eigen', '3.3.4', '', True)] +builddependencies = [('Eigen', '3.3.4', '', SYSTEM)] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb index a8a803600e1..52735d76539 100644 --- a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb @@ -35,7 +35,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ('nghttp3', '0.6.0'), ('Python', '3.9.6'), ('libxml2', '2.9.10'), diff --git a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb index 72ff0976e45..2c658278a18 100644 --- a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb @@ -29,7 +29,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ('GnuTLS', '3.7.3'), ('nghttp3', '0.6.0'), ('libev', '4.33'), diff --git a/easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b-CUDA-11.4.1.eb index f3783e2fc9e..60d55c02ccc 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b-CUDA-11.4.1.eb @@ -18,7 +18,7 @@ dependencies = [ ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), ('LLVM', '12.0.1'), - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ] use_pip = True diff --git a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb index 02d864af126..a2434cbbc44 100644 --- a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -27,7 +27,7 @@ checksums = [ ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('ONNX', '1.11.0'), ('flatbuffers-python', '2.0'), diff --git a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb index 9c57ffb879e..6e9d0724196 100644 --- a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb @@ -30,9 +30,9 @@ local_gurobiver = '8.1.1' dependencies = [ ('Python', '3.7.2'), ('zlib', '1.2.11'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), # Gurobi is optional - ('Gurobi', local_gurobiver, '', True), + ('Gurobi', local_gurobiver, '', SYSTEM), ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb index 81a663791de..cd846a70218 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TGZ] checksums = ['cb5ce4e2e68ed012d9952e96ef880a802058c87a1d840a2093b19bddc7faa165'] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('UCX-CUDA', '1.10.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021a-CUDA-11.3.1.eb index 45ef99c6337..bc0b6fe9631 100755 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021a-CUDA-11.3.1.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['d619740a1c2cc7c02a9763931546b320d0fa4093c415ff3873c2958e121c0609'] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('UCX-CUDA', '1.10.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb index 65c303f62cb..6122b5221dd 100755 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['d619740a1c2cc7c02a9763931546b320d0fa4093c415ff3873c2958e121c0609'] dependencies = [ - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('UCX-CUDA', '1.11.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022a-CUDA-11.7.0.eb index f081748a1b9..f1ffbd93b35 100755 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022a-CUDA-11.7.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['d619740a1c2cc7c02a9763931546b320d0fa4093c415ff3873c2958e121c0609'] dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('NCCL', '2.12.12', versionsuffix), ('UCX-CUDA', '1.12.1', versionsuffix), ('UCC-CUDA', '1.0.0', versionsuffix), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb index ff686a0a357..5c5cf246ba1 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.58'), ('GL2PS', '1.3.9'), ('gnuplot', '5.0.3'), - ('Java', '1.8.0_72', '', True), + ('Java', '1.8.0_72', '', SYSTEM), ('zlib', '1.2.8'), ('Mesa', '11.1.2'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb index ce3a19f67d0..c2c9f653f54 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.60'), ('GL2PS', '1.3.9'), ('gnuplot', '5.0.5'), - ('Java', '1.8.0_112', '', True), + ('Java', '1.8.0_112', '', SYSTEM), ('zlib', '1.2.8'), ('Mesa', '12.0.2'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-foss-2018a.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-foss-2018a.eb index 433b701f926..bd551db8f61 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-foss-2018a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-foss-2018a.eb @@ -40,7 +40,7 @@ dependencies = [ ('GLPK', '4.65'), ('GL2PS', '1.4.0'), ('gnuplot', '5.2.2'), - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '17.3.6'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb index ea85cfeafc9..20d927dc1fb 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb @@ -33,7 +33,7 @@ dependencies = [ ('GLPK', '4.60'), ('GL2PS', '1.3.9'), ('gnuplot', '5.0.5'), - ('Java', '1.8.0_121', '', True), + ('Java', '1.8.0_121', '', SYSTEM), ('zlib', '1.2.8'), ('Mesa', '12.0.2'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a-mt.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a-mt.eb index f623cd98f9f..2f8f0f23352 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a-mt.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a-mt.eb @@ -37,7 +37,7 @@ dependencies = [ ('GLPK', '4.61'), ('GL2PS', '1.4.0'), ('gnuplot', '5.0.6'), - ('Java', '1.8.0_131', '', True), + ('Java', '1.8.0_131', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '17.0.2'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a.eb index 913fdc43d8f..e5240000ae6 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a.eb @@ -36,7 +36,7 @@ dependencies = [ ('GLPK', '4.61'), ('GL2PS', '1.4.0'), ('gnuplot', '5.0.6'), - ('Java', '1.8.0_131', '', True), + ('Java', '1.8.0_131', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '17.0.2'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.2-foss-2018a.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.2-foss-2018a.eb index 9f2386fc73e..3765993042c 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.2-foss-2018a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.2-foss-2018a.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.65'), ('GL2PS', '1.4.0'), ('gnuplot', '5.2.2'), - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '17.3.6'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.4.1-foss-2018b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.4.1-foss-2018b.eb index 843200f9542..5662e74132d 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.4.1-foss-2018b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.4.1-foss-2018b.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.65'), ('GL2PS', '1.4.0'), ('gnuplot', '5.2.5'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '18.1.1'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019a.eb b/easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019a.eb index 287bbf1c983..38880eb0332 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019a.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.65'), ('GL2PS', '1.4.0'), ('gnuplot', '5.2.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '19.0.1'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019b.eb b/easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019b.eb index b37ef2c4129..3a702aad19f 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019b.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.65'), ('GL2PS', '1.4.0'), ('gnuplot', '5.2.8'), - ('Java', '11.0.2', '', True), + ('Java', '11.0.2', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '19.1.7'), ('libGLU', '9.0.1'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb b/easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb index 3da5bd86b42..03e6837966e 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.65'), ('GL2PS', '1.4.2'), ('gnuplot', '5.4.1'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '20.2.1'), ('libGLU', '9.0.1'), diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2017b-Python-2.7.14.eb index 143c4e517cd..c100a2239ce 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2017b-Python-2.7.14.eb @@ -29,7 +29,7 @@ dependencies = [ ('Python', '2.7.14'), ('zlib', '1.2.11'), ('libxml2', '2.9.7'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] runtest = 'test' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-2.7.15.eb index 303e55408ce..1aac64ecdbe 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-2.7.15.eb @@ -29,7 +29,7 @@ dependencies = [ ('Python', '2.7.15'), ('zlib', '1.2.11'), ('libxml2', '2.9.8'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] runtest = 'test' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-3.6.6.eb index fe1c852d320..f10768b4b02 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-3.6.6.eb @@ -31,7 +31,7 @@ dependencies = [ ('Python', '3.6.6'), ('zlib', '1.2.11'), ('libxml2', '2.9.8'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] runtest = 'test' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2019a-Python-3.7.2.eb index ad1ddc252ce..263cec8636f 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2019a-Python-3.7.2.eb @@ -30,7 +30,7 @@ dependencies = [ ('Python', '3.7.2'), ('zlib', '1.2.11'), ('libxml2', '2.9.8'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] runtest = 'test' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.0.0-gompi-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.0.0-gompi-2019b-Python-3.7.4.eb index d49bf26cef7..2b022edef2d 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.0.0-gompi-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.0.0-gompi-2019b-Python-3.7.4.eb @@ -26,7 +26,7 @@ dependencies = [ ('Python', '3.7.4'), ('zlib', '1.2.11'), ('libxml2', '2.9.9'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('RapidJSON', '1.1.0'), ('cairo', '1.16.0'), # optional: for .png output ('Boost', '1.71.0'), # optional: for Maestro formats diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb index 6d911749614..cf4291bf2cc 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb @@ -37,7 +37,7 @@ dependencies = [ ('Python', '3.7.4'), ('zlib', '1.2.11'), ('libxml2', '2.9.9'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('RapidJSON', '1.1.0'), ('cairo', '1.16.0'), # optional: for .png output ('Boost', '1.71.0'), diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb index 7dbebd3a06a..77d78162002 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb @@ -36,7 +36,7 @@ dependencies = [ ('Python', '3.8.2'), ('zlib', '1.2.11'), ('libxml2', '2.9.10'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('RapidJSON', '1.1.0'), ('cairo', '1.16.0'), # optional: for .png output ('Boost', '1.72.0'), diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb index 70e5bf517cc..258ec7b63f6 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb @@ -31,8 +31,8 @@ dependencies = [ ('libpng', '1.6.21'), ('LibTIFF', '4.0.6'), ('JasPer', '1.900.1'), - ('Java', '1.7.0_80', '', True), - ('ant', '1.9.6', '-Java-%(javaver)s', True), + ('Java', '1.7.0_80', '', SYSTEM), + ('ant', '1.9.6', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.48.0'), ('GTK+', '2.24.30'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb index 71a179c34f1..f3e4bca8821 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb @@ -37,8 +37,8 @@ dependencies = [ ('libpng', '1.6.21'), ('LibTIFF', '4.0.6'), ('JasPer', '1.900.1'), - ('Java', '1.8.0_92', '', True), - ('ant', '1.9.7', '-Java-%(javaver)s', True), + ('Java', '1.8.0_92', '', SYSTEM), + ('ant', '1.9.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.48.0'), ('GTK+', '2.24.30'), ('GStreamer', '1.6.4'), diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb index c983e1fdf0b..c05ad6cd156 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb @@ -37,8 +37,8 @@ dependencies = [ ('libpng', '1.6.24'), ('LibTIFF', '4.0.6'), ('JasPer', '1.900.1'), - ('Java', '1.8.0_92', '', True), - ('ant', '1.9.7', '-Java-%(javaver)s', True), + ('Java', '1.8.0_92', '', SYSTEM), + ('ant', '1.9.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.49.5'), ('GTK+', '2.24.31'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb index 1ea167eadfc..56882999097 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb @@ -39,8 +39,8 @@ dependencies = [ ('libpng', '1.6.21'), ('LibTIFF', '4.0.6'), ('JasPer', '1.900.1'), - ('Java', '1.8.0_92', '', True), - ('ant', '1.9.7', '-Java-%(javaver)s', True), + ('Java', '1.8.0_92', '', SYSTEM), + ('ant', '1.9.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.48.0'), ('GTK+', '2.24.30'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb index 554cb1cb273..b5a7c1b3002 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb @@ -39,8 +39,8 @@ dependencies = [ ('libpng', '1.6.24'), ('LibTIFF', '4.0.6'), ('JasPer', '1.900.1'), - ('Java', '1.8.0_92', '', True), - ('ant', '1.9.7', '-Java-%(javaver)s', True), + ('Java', '1.8.0_92', '', SYSTEM), + ('ant', '1.9.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.49.5'), ('GTK+', '2.24.31'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb index 204d5064bea..c6c1d65f281 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb @@ -36,8 +36,8 @@ dependencies = [ ('libpng', '1.6.32'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.53.5'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb index 6727d4e58da..79e2cee0431 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb @@ -36,8 +36,8 @@ dependencies = [ ('libpng', '1.6.32'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.53.5'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb index 750d74b0485..74c953d5cba 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb @@ -38,8 +38,8 @@ dependencies = [ ('libpng', '1.6.29'), ('LibTIFF', '4.0.8'), ('JasPer', '2.0.12'), - ('Java', '1.8.0_144', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_144', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.53.5'), ('GTK+', '2.24.31'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb index 6d11e2ff77d..789d6aaf637 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb @@ -38,8 +38,8 @@ dependencies = [ ('libpng', '1.6.29'), ('LibTIFF', '4.0.8'), ('JasPer', '2.0.12'), - ('Java', '1.8.0_144', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_144', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.53.5'), ('GTK+', '2.24.31'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb index 293945598e4..8b301fd1a19 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb @@ -36,8 +36,8 @@ dependencies = [ ('libpng', '1.6.32'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.53.5'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb index 7c0fdad4b14..40f101d42e3 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb @@ -36,8 +36,8 @@ dependencies = [ ('libpng', '1.6.32'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.53.5'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-2.7.14.eb index 842fafdf34b..b5a104f5992 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-2.7.14.eb @@ -37,8 +37,8 @@ dependencies = [ ('libpng', '1.6.34'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8.0_162', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_162', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.54.3'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-3.6.4-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-3.6.4-contrib.eb index 74d3fa4a8c9..7df03a1aa93 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-3.6.4-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-3.6.4-contrib.eb @@ -42,8 +42,8 @@ dependencies = [ ('libpng', '1.6.34'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8.0_162', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_162', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.54.3'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-3.6.4.eb index a0370ed6840..ecd2995c966 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-3.6.4.eb @@ -37,8 +37,8 @@ dependencies = [ ('libpng', '1.6.34'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8.0_162', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_162', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.54.3'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb index e017af4d366..87b5199daa2 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb @@ -37,8 +37,8 @@ dependencies = [ ('libpng', '1.6.34'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8.0_162', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_162', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.54.3'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-3.6.4.eb index e9800cb3a37..91670fc7d49 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-3.6.4.eb @@ -37,8 +37,8 @@ dependencies = [ ('libpng', '1.6.34'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8.0_162', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_162', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.54.3'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.5-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.5-foss-2018b-Python-2.7.15.eb index 614a84cbc6b..9766e39c514 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.5-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.5-foss-2018b-Python-2.7.15.eb @@ -36,8 +36,8 @@ dependencies = [ ('libpng', '1.6.34'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8', '', True), - ('ant', '1.10.5', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('ant', '1.10.5', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.54.3'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-2.7.15.eb index 708d99f1e04..f9e7d4e506a 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-2.7.15.eb @@ -39,8 +39,8 @@ dependencies = [ ('libpng', '1.6.36'), ('LibTIFF', '4.0.10'), ('JasPer', '2.0.14'), - ('Java', '11', '', True), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.60.1'), ('GTK+', '3.24.8'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-3.7.2.eb index c01e9fa3946..5d57f174681 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-3.7.2.eb @@ -39,8 +39,8 @@ dependencies = [ ('libpng', '1.6.36'), ('LibTIFF', '4.0.10'), ('JasPer', '2.0.14'), - ('Java', '11', '', True), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.60.1'), ('GTK+', '3.24.8'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-2.7.15.eb index d32d54e08be..8acf1dbbfc3 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-2.7.15.eb @@ -39,8 +39,8 @@ dependencies = [ ('libpng', '1.6.36'), ('LibTIFF', '4.0.10'), ('JasPer', '2.0.14'), - ('Java', '11', '', True), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.60.1'), ('GTK+', '3.24.8'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-3.7.2.eb index 1e78bb05a9d..727c24fe4ec 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-3.7.2.eb @@ -39,8 +39,8 @@ dependencies = [ ('libpng', '1.6.36'), ('LibTIFF', '4.0.10'), ('JasPer', '2.0.14'), - ('Java', '11', '', True), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.60.1'), ('GTK+', '3.24.8'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-2.7.15.eb index fbd9e8d0fcf..ae5711df4af 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-2.7.15.eb @@ -36,8 +36,8 @@ dependencies = [ ('libpng', '1.6.34'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8', '', True), - ('ant', '1.10.5', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('ant', '1.10.5', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.54.3'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb index 0aa61fe1e65..23ce3d0dc51 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb @@ -36,8 +36,8 @@ dependencies = [ ('libpng', '1.6.34'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8', '', True), - ('ant', '1.10.5', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('ant', '1.10.5', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.54.3'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2019b-Python-3.7.4.eb index 9bc89cf3d0f..d38ec1d62da 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2019b-Python-3.7.4.eb @@ -37,8 +37,8 @@ dependencies = [ ('libpng', '1.6.37'), ('LibTIFF', '4.0.10'), ('JasPer', '2.0.14'), - ('Java', '11', '', True), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.62.0'), ('GTK+', '3.24.13'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2-contrib.eb index 8d9b3948a85..8870feae56a 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2-contrib.eb @@ -43,8 +43,8 @@ dependencies = [ ('libwebp', '1.1.0'), ('OpenEXR', '2.4.1'), ('JasPer', '2.0.14'), - ('Java', '11', '', True), - ('ant', '1.10.8', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.8', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.64.1'), ('GTK+', '3.24.17'), ('HDF5', '1.10.6'), # needed by hdf from contrib diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb index 49b5c8ba29b..bb85b7a793f 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb @@ -39,8 +39,8 @@ dependencies = [ ('libwebp', '1.1.0'), ('OpenEXR', '2.4.1'), ('JasPer', '2.0.14'), - ('Java', '11', '', True), - ('ant', '1.10.8', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.8', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.64.1'), ('GTK+', '3.24.17'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-fosscuda-2019b-Python-3.7.4.eb index 184171377df..7c1b760a1bc 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-fosscuda-2019b-Python-3.7.4.eb @@ -43,8 +43,8 @@ dependencies = [ ('libpng', '1.6.37'), ('LibTIFF', '4.0.10'), ('JasPer', '2.0.14'), - ('Java', '11', '', True), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.62.0'), ('GTK+', '3.24.13'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb index cf24b5ca039..f866015943d 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb @@ -45,8 +45,8 @@ dependencies = [ ('libwebp', '1.1.0'), ('OpenEXR', '2.5.5'), ('JasPer', '2.0.24'), - ('Java', '11', '', True), - ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.9', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.66.1'), ('GTK+', '3.24.23'), ('HDF5', '1.10.7'), # needed by hdf from contrib diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb index 5fe200231f7..6bd1dad125b 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb @@ -45,8 +45,8 @@ dependencies = [ ('libwebp', '1.1.0'), ('OpenEXR', '2.5.5'), ('JasPer', '2.0.24'), - ('Java', '11', '', True), - ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.9', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.66.1'), ('GTK+', '3.24.23'), ('HDF5', '1.10.7'), # needed by hdf from contrib diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb index f9b43027447..9c0af78eb10 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb @@ -45,13 +45,13 @@ dependencies = [ ('libwebp', '1.2.0'), ('OpenEXR', '3.0.1'), ('JasPer', '2.0.28'), - ('Java', '11', '', True), - ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.9', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.68.2'), ('GTK3', '3.24.29'), ('HDF5', '1.10.7'), # needed by hdf from contrib - ('CUDA', '11.3.1', '', True), - ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('CUDA', '11.3.1', '', SYSTEM), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), ] # XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-contrib.eb index 9dd6c211740..39fac2609e2 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-contrib.eb @@ -45,8 +45,8 @@ dependencies = [ ('libwebp', '1.2.0'), ('OpenEXR', '3.0.1'), ('JasPer', '2.0.28'), - ('Java', '11', '', True), - ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.9', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.68.2'), ('GTK3', '3.24.29'), ('HDF5', '1.10.7'), # needed by hdf from contrib diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-contrib.eb index 5b3d0e27351..86531a76eb5 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-contrib.eb @@ -45,8 +45,8 @@ dependencies = [ ('libwebp', '1.2.0'), ('OpenEXR', '3.1.1'), ('JasPer', '2.0.33'), - ('Java', '11', '', True), - ('ant', '1.10.11', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.11', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.69.1'), ('GTK3', '3.24.31'), ('HDF5', '1.12.1'), # needed by hdf from contrib diff --git a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb index b7b2f6058eb..10c57638036 100644 --- a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb @@ -26,8 +26,8 @@ builddependencies = [ ('patchelf', '0.12') ] dependencies = [ - ('CUDA', '11.3.1', '', True), - ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('CUDA', '11.3.1', '', SYSTEM), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), ('OpenCV', '4.5.3', '-CUDA-%(cudaver)s-contrib'), ('dlib', '19.22', '-CUDA-%(cudaver)s'), ('SDL2', '2.0.14'), diff --git a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb index f4797eae8eb..1d5296cc0d5 100644 --- a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb @@ -16,7 +16,7 @@ builddependencies = [ dependencies = [ ('Python', '3.9.5'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('SciPy-bundle', '2021.05'), ('PyYAML', '5.4.1'), ('Biopython', '1.79'), diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb index d52bab5ca43..61a9e74745f 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb @@ -35,7 +35,7 @@ separate_build_dir = True dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('SWIG', '4.0.2'), ] diff --git a/easybuild/easyconfigs/o/OpenMS/OpenMS-2.4.0-foss-2018b.eb b/easybuild/easyconfigs/o/OpenMS/OpenMS-2.4.0-foss-2018b.eb index c2c006a21f5..0be7211a54e 100644 --- a/easybuild/easyconfigs/o/OpenMS/OpenMS-2.4.0-foss-2018b.eb +++ b/easybuild/easyconfigs/o/OpenMS/OpenMS-2.4.0-foss-2018b.eb @@ -33,7 +33,7 @@ dependencies = [ ('Xerces-C++', '3.2.0'), ('LIBSVM', '3.23'), ('GLPK', '4.65'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('SQLite', '3.24.0'), ('bzip2', '1.0.6'), ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_144.eb b/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_144.eb index ff54cc30a4b..a5bd30ffa85 100644 --- a/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_144.eb +++ b/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_144.eb @@ -15,7 +15,7 @@ sources = ['%(version)s.tar.gz'] checksums = ['16f8c86db061d1c24f1fc64897eb23742e73415a019dd8ea3f39782de833146b'] builddependencies = [ - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ] dependencies = [ ('Java', '1.8.0_144'), diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb index 29256de39d1..86f569eb1f8 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.openssl.org/source/'] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb index 904ddedf279..f80a7efa49f 100644 --- a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb @@ -19,7 +19,7 @@ dependencies = [ ('Perl', '5.24.0'), ('MCL', '%s.%s' % (local_mcl_majver, local_mcl_minver)), ('BioPerl', '1.7.1', versionsuffix), - ('BLAST', '2.2.26', '-Linux_x86_64', True), + ('BLAST', '2.2.26', '-Linux_x86_64', SYSTEM), ] start_dir = 'ORTHOMCLV%(version)s' diff --git a/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb index c7f14efe011..09952eda5e0 100644 --- a/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb @@ -13,7 +13,7 @@ and run simple inference.""" toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('ONNX-Runtime', '1.10.0', versionsuffix), diff --git a/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb index 3336e2eb4a7..3298c090913 100644 --- a/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb @@ -13,7 +13,7 @@ and run simple inference.""" toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('ONNX-Runtime', '1.10.0', versionsuffix), diff --git a/easybuild/easyconfigs/p/PCL/PCL-1.8.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/PCL/PCL-1.8.1-intel-2017b-Python-2.7.14.eb index 47629d26e8e..710857fb134 100644 --- a/easybuild/easyconfigs/p/PCL/PCL-1.8.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PCL/PCL-1.8.1-intel-2017b-Python-2.7.14.eb @@ -22,7 +22,7 @@ checksums = [ builddependencies = [('CMake', '3.9.5')] dependencies = [ ('Boost', '1.65.1'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('FLANN', '1.8.4', versionsuffix), ('VTK', '8.0.1', versionsuffix), ('Qhull', '2015.2'), diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb index 017eaf7df0b..558337872ed 100644 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb @@ -24,7 +24,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.12.1'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] configopts = '-DEIGEN3_ROOT=$EBROOTEIGEN' diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb index 1483418bd8d..fc5b5e2cff7 100644 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb @@ -24,7 +24,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.13.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] configopts = '-DEIGEN3_ROOT=$EBROOTEIGEN' diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2019b-Python-3.7.4.eb index 4862bbfa6aa..ee6f7d3f34e 100644 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2019b-Python-3.7.4.eb @@ -18,7 +18,7 @@ checksums = ['d1ef6bdc268a2e719b36c85125c3543df7a26e1a738daf4483f4ded0c76f5b60'] builddependencies = [ ('CMake', '3.15.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb index 9dc98305542..484eb213be4 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb @@ -18,7 +18,7 @@ checksums = [ builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" diff --git a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb index 53475269537..ece457c65a0 100644 --- a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb @@ -18,7 +18,7 @@ source_urls = ['http://cmpg.unibe.ch/software/PGDSpider/'] sources = ['%(name)s_%(version)s.zip'] dependencies = [ - ('Java', '1.7.0_80', '', True), + ('Java', '1.7.0_80', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/PIPITS/PIPITS-2.7-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PIPITS/PIPITS-2.7-foss-2020a-Python-3.8.2.eb index 2167bd9bd68..a62393975f0 100644 --- a/easybuild/easyconfigs/p/PIPITS/PIPITS-2.7-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PIPITS/PIPITS-2.7-foss-2020a-Python-3.8.2.eb @@ -18,8 +18,8 @@ dependencies = [ ('FASTX-Toolkit', '0.0.14'), ('ITSx', '1.1.2'), ('HMMER', '3.3.1'), - ('RDP-Classifier', '2.13', '-Java-11', True), - ('SeqKit', '0.13.2', '', True), + ('RDP-Classifier', '2.13', '-Java-11', SYSTEM), + ('SeqKit', '0.13.2', '', SYSTEM), ] use_pip = True diff --git a/easybuild/easyconfigs/p/PIPITS/PIPITS-2.8-foss-2021a.eb b/easybuild/easyconfigs/p/PIPITS/PIPITS-2.8-foss-2021a.eb index 0d9fdbabdc7..e4b4218920f 100644 --- a/easybuild/easyconfigs/p/PIPITS/PIPITS-2.8-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PIPITS/PIPITS-2.8-foss-2021a.eb @@ -17,8 +17,8 @@ dependencies = [ ('FASTX-Toolkit', '0.0.14'), ('ITSx', '1.1.3'), ('HMMER', '3.3.2'), - ('RDP-Classifier', '2.13', '-Java-11', True), - ('SeqKit', '2.1.0', '', True), + ('RDP-Classifier', '2.13', '-Java-11', SYSTEM), + ('SeqKit', '2.1.0', '', SYSTEM), ] use_pip = True diff --git a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb index a77bf58f492..83910094da9 100644 --- a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.7.0_80', '', True), + ('Java', '1.7.0_80', '', SYSTEM), ('Python', '2.7.11'), ('Perl', '5.22.1'), ('Tcl', '8.6.4'), diff --git a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb index fb25f08bf9e..79bce614bbe 100644 --- a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.8'), - ('Java', '1.7.0_80', '', True), + ('Java', '1.7.0_80', '', SYSTEM), ('Python', '2.7.12'), ('Perl', '5.24.0'), ('cairo', '1.14.6'), diff --git a/easybuild/easyconfigs/p/PRSice/PRSice-2.2.12-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/PRSice/PRSice-2.2.12-GCCcore-8.3.0.eb index 4408537b08e..2e22ee69d17 100644 --- a/easybuild/easyconfigs/p/PRSice/PRSice-2.2.12-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/PRSice/PRSice-2.2.12-GCCcore-8.3.0.eb @@ -21,7 +21,7 @@ checksums = ['1e3d43f269ad6c4c703431e3a96084e7c85391e00061684d60a8599d4e158c84'] builddependencies = [ ('CMake', '3.15.3'), ('binutils', '2.32'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] files_to_copy = [(['bin/PRSice'], 'bin'), "README.md", "LICENSE"] diff --git a/easybuild/easyconfigs/p/PRSice/PRSice-2.3.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.1-GCCcore-9.3.0.eb index 0d030134301..1a07392a87c 100644 --- a/easybuild/easyconfigs/p/PRSice/PRSice-2.3.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.1-GCCcore-9.3.0.eb @@ -21,7 +21,7 @@ checksums = ['b4adec078d7101d00390e529c9cb6d935c50d60ae17db6fa044295767d3131a4'] builddependencies = [ ('CMake', '3.16.4'), ('binutils', '2.34'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] files_to_copy = [(['bin/PRSice'], 'bin'), "README.md", "LICENSE"] diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb index 99940a8a08d..e0de2012bfd 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -20,7 +20,7 @@ dependencies = [ ('Perl', '5.22.1'), ('libpsortb', '1.0'), ('BioPerl', '1.6.924', '-Perl-5.22.1'), - ('BLAST', '2.2.26', '-Linux_x86_64', True), + ('BLAST', '2.2.26', '-Linux_x86_64', SYSTEM), ('pftoolsV3', '20160324'), ] diff --git a/easybuild/easyconfigs/p/PTESFinder/PTESFinder-1-intel-2017b.eb b/easybuild/easyconfigs/p/PTESFinder/PTESFinder-1-intel-2017b.eb index c495729322c..1885396ad81 100644 --- a/easybuild/easyconfigs/p/PTESFinder/PTESFinder-1-intel-2017b.eb +++ b/easybuild/easyconfigs/p/PTESFinder/PTESFinder-1-intel-2017b.eb @@ -16,7 +16,7 @@ dependencies = [ ('Bowtie', '1.2.1.1'), ('Bowtie2', '2.3.3.1'), ('BEDTools', '2.26.0'), - ('Java', '1.8.0_152', '', True), + ('Java', '1.8.0_152', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb index 903ad1a1e1c..6b718496c02 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('ncurses', '6.2'), # for Term::ReadLine::Gnu ('libreadline', '8.1'), # for Term::ReadLine::Gnu ('DB', '18.1.40'), # for DB_File - ('OpenSSL', '1.1', '', True), # required for Net::SSLeay + ('OpenSSL', '1.1', '', SYSTEM), # required for Net::SSLeay ] exts_default_options = {'buildopts': 'CC="$CC"'} diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb index 947436d0265..c06f75ac1bd 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('ncurses', '6.2'), # for Term::ReadLine::Gnu ('libreadline', '8.1'), # for Term::ReadLine::Gnu ('DB', '18.1.40'), # for DB_File - ('OpenSSL', '1.1', '', True), # required for Net::SSLeay + ('OpenSSL', '1.1', '', SYSTEM), # required for Net::SSLeay ] # !! order of extensions is important !! diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index 63d38816c14..596de0bad6b 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -22,7 +22,7 @@ dependencies = [ ('ncurses', '6.2'), # for Term::ReadLine::Gnu ('libreadline', '8.1'), # for Term::ReadLine::Gnu ('DB', '18.1.40'), # for DB_File - ('OpenSSL', '1.1', '', True), # required for Net::SSLeay + ('OpenSSL', '1.1', '', SYSTEM), # required for Net::SSLeay ] # !! order of extensions is important !! diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb index 7354490d5e4..b998f1d93d0 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb @@ -22,7 +22,7 @@ dependencies = [ ('ncurses', '6.3'), # for Term::ReadLine::Gnu ('libreadline', '8.1.2'), # for Term::ReadLine::Gnu ('DB', '18.1.40'), # for DB_File - ('OpenSSL', '1.1', '', True), # required for Net::SSLeay + ('OpenSSL', '1.1', '', SYSTEM), # required for Net::SSLeay ] # !! order of extensions is important !! diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb index 2a1efcc2d51..1424b9a1a56 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb @@ -22,7 +22,7 @@ dependencies = [ ('ncurses', '6.3'), # for Term::ReadLine::Gnu ('libreadline', '8.1.2'), # for Term::ReadLine::Gnu ('DB', '18.1.40'), # for DB_File - ('OpenSSL', '1.1', '', True), # required for Net::SSLeay + ('OpenSSL', '1.1', '', SYSTEM), # required for Net::SSLeay ] # !! order of extensions is important !! diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb index 98b660aba06..4b0003f906b 100644 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb @@ -36,7 +36,7 @@ dependencies = [ ('SEPP', '4.3.10', versionsuffix), ('trimAl', '1.4.1'), ('BLAST+', '2.10.1'), - ('USEARCH', '11.0.667-i86linux32', '', True), + ('USEARCH', '11.0.667-i86linux32', '', SYSTEM), ('DIAMOND', '2.0.4'), ] diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb index 0e70c4e11de..7d564d27db0 100644 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb @@ -36,7 +36,7 @@ dependencies = [ ('SEPP', '4.5.0'), ('trimAl', '1.4.1'), ('BLAST+', '2.11.0'), - ('USEARCH', '11.0.667-i86linux32', '', True), + ('USEARCH', '11.0.667-i86linux32', '', SYSTEM), ('DIAMOND', '2.0.11'), ] diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb index bbe63ecc522..eb61569278c 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb @@ -30,7 +30,7 @@ builddependencies = [ dependencies = [ ('libreadline', '8.1'), ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = '--with-python --with-openssl' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.4-GCCcore-11.2.0.eb index 8c788d103e7..5cf9564e87f 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.4-GCCcore-11.2.0.eb @@ -30,7 +30,7 @@ builddependencies = [ dependencies = [ ('libreadline', '8.1'), ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = '--with-python --with-openssl' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-14.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-14.4-GCCcore-11.3.0.eb index f3972f8c07f..ae344d6e856 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-14.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-14.4-GCCcore-11.3.0.eb @@ -30,7 +30,7 @@ builddependencies = [ dependencies = [ ('libreadline', '8.1.2'), ('zlib', '1.2.12'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = '--with-python --with-openssl' diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb index 2899a206f1b..ce30da2a7da 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb @@ -15,7 +15,7 @@ checksums = ['a7dbdac7e2f0c0d2ad98f5f281d5a9d29d6673b3c20210e261b96e9a2d0b6e37'] dependencies = [ ('Python', '2.7.12'), - ('CUDA', '8.0.61', '', True), + ('CUDA', '8.0.61', '', SYSTEM), ('Boost', '1.61.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb index 4d6b28f646a..fcdf4189ca2 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} dependencies = [ ('Python', '2.7.14'), - ('CUDA', '9.0.176', '', True), + ('CUDA', '9.0.176', '', SYSTEM), ('Boost.Python', '1.65.1', '-Python-%(pyver)s'), ('Mako', '1.0.7', '-Python-%(pyver)s'), ('pytest', '3.8.2', '-Python-%(pyver)s'), diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb index e98942047c3..13947e02b8c 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb @@ -15,7 +15,7 @@ checksums = ['6b5a9384e38c603ee429f8a6bee424532db7b3505027ce22f7e18ad19564b563'] dependencies = [ ('Python', '2.7.14'), - ('CUDA', '9.1.85', '', True), + ('CUDA', '9.1.85', '', SYSTEM), ('Boost.Python', '1.66.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb index a3f849bd92e..1d9ef9ef9e6 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb @@ -15,7 +15,7 @@ checksums = ['7079f7738e83ee79ae26f0827ada29fe55921fec9760201199cc2bfb69446c92'] dependencies = [ ('Python', '3.6.4'), - ('CUDA', '9.1.85', '', True), + ('CUDA', '9.1.85', '', SYSTEM), ('Boost.Python', '1.66.0', '-Python-%(pyver)s'), ] diff --git a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb index 134d0b6c5f4..b2c7e5f1d25 100644 --- a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb @@ -23,7 +23,7 @@ checksums = ['0799e6c3021d6e163ef7250853922fc365c3fb94246c2cb0984381741b83ea98'] dependencies = [ ('Python', '2.7.12'), ('PyCogent', '1.9', versionsuffix), - ('UCLUST', '1.2.22q', '-i86linux64', True), + ('UCLUST', '1.2.22q', '-i86linux64', SYSTEM), ] options = {'modulename': '%(namelower)s'} diff --git a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb index 3d6d9af5489..d4fd449da32 100644 --- a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb @@ -24,7 +24,7 @@ checksums = ['0799e6c3021d6e163ef7250853922fc365c3fb94246c2cb0984381741b83ea98'] dependencies = [ ('Python', '2.7.15'), ('PyCogent', '1.9', versionsuffix), - ('UCLUST', '1.2.22q', '-i86linux64', True), + ('UCLUST', '1.2.22q', '-i86linux64', SYSTEM), ] options = {'modulename': '%(namelower)s'} diff --git a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb index 651a588075e..dcf058b6b89 100644 --- a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb @@ -19,7 +19,7 @@ sources = ['%(version)s.tar.gz'] dependencies = [ ('Python', '2.7.12'), ('PyCogent', '1.5.3', versionsuffix), - ('UCLUST', '1.2.22q', '-i86linux64', True), + ('UCLUST', '1.2.22q', '-i86linux64', SYSTEM), ] options = {'modulename': 'pynast'} diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a-CUDA-11.3.1.eb index e8d997ccd68..cf88ff010b2 100644 --- a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a-CUDA-11.3.1.eb @@ -10,7 +10,7 @@ description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML resea toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('PyTorch', '1.10.0', versionsuffix), ('tqdm', '4.61.2'), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb index 2a45738b149..b6ac75df40b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb @@ -72,7 +72,7 @@ builddependencies = [('CMake', '3.10.2')] dependencies = [ ('Python', '3.6.4'), ('PyYAML', '3.12', '-Python-%(pyver)s'), - ('CUDA', local_cuda_ver, '', True), + ('CUDA', local_cuda_ver, '', SYSTEM), ('magma', '2.3.0', '-CUDA-%s' % local_cuda_ver), ('cuDNN', '7.0.5', '-CUDA-%s' % local_cuda_ver, True), ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index cecec914c70..3dedead0354 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -73,7 +73,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions ('Python', '3.9.5'), ('protobuf', '3.17.3'), @@ -87,7 +87,7 @@ dependencies = [ ('numactl', '2.0.14'), ('FFmpeg', '4.3.2'), ('Pillow', '8.2.0'), - ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.6.1', '-CUDA-%(cudaver)s'), ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), ('expecttest', '0.1.3'), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb index a7ff2a282f4..938b94c4f93 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -86,7 +86,7 @@ dependencies = [ ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), ('expecttest', '0.1.3'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 5aba12b3957..37b6a8f47f0 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -63,7 +63,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions ('Python', '3.9.5'), ('protobuf', '3.17.3'), @@ -77,7 +77,7 @@ dependencies = [ ('numactl', '2.0.14'), ('FFmpeg', '4.3.2'), ('Pillow', '8.2.0'), - ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.6.1', '-CUDA-%(cudaver)s'), ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), ('expecttest', '0.1.3'), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb index 20dd004271e..1e64c9e1b94 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb @@ -277,7 +277,7 @@ dependencies = [ ('numactl', '2.0.13'), ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020a-Python-3.8.2.eb index 5483fb70434..64428626873 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020a-Python-3.8.2.eb @@ -320,7 +320,7 @@ dependencies = [ ('numactl', '2.0.13'), ('FFmpeg', '4.2.2'), ('Pillow', '7.0.0', versionsuffix), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index 5b00155d13b..63ff087989b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -28,7 +28,7 @@ dependencies = [ ('numactl', '2.0.13'), ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb index a32c54ea29e..90e96f96e04 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -97,7 +97,7 @@ dependencies = [ ('numactl', '2.0.13'), ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index b4662e2722d..bcfc0d48d26 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -99,7 +99,7 @@ dependencies = [ ('numactl', '2.0.13'), ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ('imkl', '2020.4.304'), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index e7070b8d189..55ca64a6024 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -98,7 +98,7 @@ dependencies = [ ('numactl', '2.0.13'), ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.3.0-bare.eb index 6f6385c7887..5ce78d117e8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.3.0-bare.eb @@ -24,7 +24,7 @@ dependencies = [ ('libreadline', '8.1'), ('ncurses', '6.2'), ('SQLite', '3.35.4'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0-bare.eb index 1975150da07..32a0a66ea27 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0-bare.eb @@ -24,7 +24,7 @@ dependencies = [ ('libreadline', '8.1'), ('ncurses', '6.2'), ('SQLite', '3.36'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb index c9a13925842..40d1364f4e5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('SQLite', '3.36'), ('GMP', '6.2.1'), # required for pycrypto ('libffi', '3.4.2'), # required for cryptography - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.3.0-bare.eb index 30621d2d5a4..f2ad29b3f79 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.3.0-bare.eb @@ -24,7 +24,7 @@ dependencies = [ ('libreadline', '8.1.2'), ('ncurses', '6.3'), ('SQLite', '3.38.3'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb index c1e834e461b..2209fb0498b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb @@ -27,7 +27,7 @@ dependencies = [ ('SQLite', '3.38.3'), ('XZ', '5.2.5'), ('libffi', '3.4.2'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb index 0d94ec7e686..1cfac838d2c 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb @@ -29,7 +29,7 @@ dependencies = [ ('XZ', '5.2.5'), ('GMP', '6.2.1'), # required for pycrypto ('libffi', '3.4.2'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb index d4ac365a6cb..451ff497b6e 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb @@ -27,7 +27,7 @@ dependencies = [ ('SQLite', '3.35.4'), ('XZ', '5.2.5'), ('libffi', '3.3'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb index 577405f03b6..f225ea27ce8 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb @@ -29,7 +29,7 @@ dependencies = [ ('XZ', '5.2.5'), ('GMP', '6.2.1'), # required for pycrypto ('libffi', '3.3'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb index 6ce8d0e64b2..44e990e3147 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb @@ -27,7 +27,7 @@ dependencies = [ ('SQLite', '3.36'), ('XZ', '5.2.5'), ('libffi', '3.4.2'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb index d729015147b..707d986560a 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb @@ -29,7 +29,7 @@ dependencies = [ ('XZ', '5.2.5'), ('GMP', '6.2.1'), # required for pycrypto ('libffi', '3.4.2'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb index 0e997ce499e..fa0cc0df4bd 100644 --- a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb @@ -20,7 +20,7 @@ dependencies = [ ('libffi', '3.2.1'), ] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/p11-kit', 'bin/trust'] + diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb index a782c5e9a6a..b84ba84bea4 100644 --- a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} dependencies = [ ('Biopython', '1.78'), - ('gofasta', '0.0.5', '', True), + ('gofasta', '0.0.5', '', SYSTEM), ('minimap2', '2.18'), ('Pysam', '0.16.0.1'), ('Python', '3.8.6'), diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-10-18.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-10-18.eb index 6d54365d3d7..9ed7733f533 100644 --- a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-10-18.eb +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-10-18.eb @@ -19,7 +19,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ ('Biopython', '1.79'), - ('gofasta', '0.0.5', '', True), + ('gofasta', '0.0.5', '', SYSTEM), ('minimap2', '2.22'), ('Pysam', '0.17.0'), ('Python', '3.9.6'), diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-11-25.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-11-25.eb index ebc0440bf2b..7057ca7d244 100644 --- a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-11-25.eb +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-11-25.eb @@ -19,7 +19,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ ('Biopython', '1.79'), - ('gofasta', '0.0.5', '', True), + ('gofasta', '0.0.5', '', SYSTEM), ('minimap2', '2.22'), ('Pysam', '0.17.0'), ('Python', '3.9.6'), diff --git a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb index c92a89c0b3d..99145dac6d6 100644 --- a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb @@ -26,7 +26,7 @@ builddependencies = [('binutils', '2.31.1')] dependencies = [ ('Python', '3.7.2'), - ('SRA-Toolkit', '2.9.6-1', '-centos_linux64', True) + ('SRA-Toolkit', '2.9.6-1', '-centos_linux64', SYSTEM) ] download_dep_fail = True diff --git a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb index 234ce1ed45d..b401fc90655 100644 --- a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb @@ -23,7 +23,7 @@ builddependencies = [('binutils', '2.34')] dependencies = [ ('Python', '3.8.2'), - ('SRA-Toolkit', '2.9.6-1', '-centos_linux64', True) + ('SRA-Toolkit', '2.9.6-1', '-centos_linux64', SYSTEM) ] download_dep_fail = True diff --git a/easybuild/easyconfigs/p/picard/picard-2.18.14-Java-1.8.eb b/easybuild/easyconfigs/p/picard/picard-2.18.14-Java-1.8.eb index ad1bce59ad9..58561192969 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.18.14-Java-1.8.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.18.14-Java-1.8.eb @@ -36,7 +36,7 @@ checksums = ['4941719941a46c72e72a3b160ff8b8fc7e2af90198004bd727526ce522ae8575'] postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] sanity_check_paths = { 'files': ['picard.jar'], diff --git a/easybuild/easyconfigs/p/picard/picard-2.18.17-Java-1.8.eb b/easybuild/easyconfigs/p/picard/picard-2.18.17-Java-1.8.eb index 570181a5407..88b4346cba4 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.18.17-Java-1.8.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.18.17-Java-1.8.eb @@ -36,7 +36,7 @@ checksums = ['f51f64824072f26dc5d0932376929b20e6f66ff478810bcf8145792773f5474f'] postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] sanity_check_paths = { 'files': ['picard.jar'], diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb index 185ce92b1dc..6b79129e1de 100644 --- a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ source_urls = ['http://cairographics.org/releases/'] sources = [SOURCE_TAR_GZ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-5.4.0.eb index 0320934f75e..a5ae68a1194 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-5.4.0.eb @@ -17,7 +17,7 @@ checksums = ['beb43c9e064555469bd4390dcfd8030b1536e0aa103f08d7abf7ae8cac0cb001'] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] # don't use PAX, it might break. diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb index dadba07804c..876023e3f43 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb @@ -19,7 +19,7 @@ patches = [ builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] # don't use PAX, it might break. diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb index b75a0d85ea9..60acff26e4a 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb @@ -16,7 +16,7 @@ source_urls = ['https://pkg-config.freedesktop.org/releases/'] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] # don't use PAX, it might break. diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb index 97e2f412b2c..275ef39e9b8 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb @@ -22,9 +22,9 @@ checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] dependencies = [ ('BioPerl', '1.7.2', '-Perl-5.28.1'), ('BLAST+', '2.9.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('parallel', '20190622'), - ('tbl2asn', '20220427', '-linux64', True), + ('tbl2asn', '20220427', '-linux64', SYSTEM), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb index b0cb7c51077..fba179ce972 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb @@ -22,9 +22,9 @@ checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] dependencies = [ ('BioPerl', '1.7.2'), ('BLAST+', '2.9.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('parallel', '20190922'), - ('tbl2asn', '20220427', '-linux64', True), + ('tbl2asn', '20220427', '-linux64', SYSTEM), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb index 8f30af1ba54..d5adf00b384 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb @@ -22,10 +22,10 @@ checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] dependencies = [ ('BioPerl', '1.7.8'), ('BLAST+', '2.11.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Bio-SearchIO-hmmer', '1.7.3'), ('parallel', '20210322'), - ('tbl2asn', '20220427', '-linux64', True), + ('tbl2asn', '20220427', '-linux64', SYSTEM), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb index ebd872de355..39eb4f8fef4 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb @@ -22,10 +22,10 @@ checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] dependencies = [ ('BioPerl', '1.7.8'), ('BLAST+', '2.11.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Bio-SearchIO-hmmer', '1.7.3'), ('parallel', '20210622'), - ('tbl2asn', '20220427', '-linux64', True), + ('tbl2asn', '20220427', '-linux64', SYSTEM), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb index dfba4ffaa84..4af4cb4cfef 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb @@ -20,7 +20,7 @@ source_urls = [ mpich_opts = '--enable-static' dependencies = [ - ('pscom', '5.0.48-1', '', True), + ('pscom', '5.0.48-1', '', SYSTEM), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb index 1bfdad4fb7a..7c6c53dd6bf 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb @@ -20,7 +20,7 @@ mpich_opts = '--enable-static' threaded = True dependencies = [ - ('pscom', '5.0.48-1', '', True), + ('pscom', '5.0.48-1', '', SYSTEM), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb index 93f76f8af09..4937bd9d705 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb @@ -17,7 +17,7 @@ source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] mpich_opts = '--enable-static' dependencies = [ - ('pscom', '5.0.48-1', '', True), + ('pscom', '5.0.48-1', '', SYSTEM), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-foss-2018a-Python-3.6.4.eb index 6bd38d27263..24a72d64d3a 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-foss-2018a-Python-3.6.4.eb @@ -16,7 +16,7 @@ checksums = ['b69e83658513215b8d1443544d0549b7d231b9f201f6fc787a2b2218b408181e'] builddependencies = [ ('CMake', '3.12.1'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('pytest', '3.8.0', versionsuffix), ] dependencies = [('Python', '3.6.4')] diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-intel-2018b-Python-3.6.6.eb index 65b955a13b7..968a6a89f01 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-intel-2018b-Python-3.6.6.eb @@ -16,7 +16,7 @@ checksums = ['b69e83658513215b8d1443544d0549b7d231b9f201f6fc787a2b2218b408181e'] builddependencies = [ ('CMake', '3.12.1'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('pytest', '3.8.2', versionsuffix), ] dependencies = [('Python', '3.6.6')] diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.4.3-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.4.3-GCCcore-8.3.0-Python-3.7.4.eb index 37a8909ca53..fbdf9a41967 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.4.3-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.4.3-GCCcore-8.3.0-Python-3.7.4.eb @@ -19,7 +19,7 @@ checksums = [ builddependencies = [ ('binutils', '2.32'), ('CMake', '3.15.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [('Python', '3.7.4')] diff --git a/easybuild/easyconfigs/p/python-weka-wrapper3/python-weka-wrapper3-0.1.11-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/python-weka-wrapper3/python-weka-wrapper3-0.1.11-foss-2019b-Python-3.7.4.eb index b3f71b6a46b..eafbd05b096 100644 --- a/easybuild/easyconfigs/p/python-weka-wrapper3/python-weka-wrapper3-0.1.11-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/python-weka-wrapper3/python-weka-wrapper3-0.1.11-foss-2019b-Python-3.7.4.eb @@ -13,7 +13,7 @@ dependencies = [ ('Python', '3.7.4'), ('matplotlib', '3.1.1', versionsuffix), ('Pillow', '6.2.1'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] use_pip = True diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb index 341f884f89e..43f185c60fd 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb @@ -25,7 +25,7 @@ dependencies = [ ('Python', '3.5.2'), ('Perl', '5.24.0'), ('matplotlib', '1.5.3', versionsuffix), - ('Java', '1.8.0_131', '', True), + ('Java', '1.8.0_131', '', SYSTEM), ('Boost', '1.63.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb index f0f4d2c5b81..79f2d229658 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb @@ -23,7 +23,7 @@ dependencies = [ ('Python', '3.6.4'), ('Perl', '5.26.1'), ('matplotlib', '2.1.2', versionsuffix), - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ('Boost', '1.66.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb index f3b210b0ca5..da0694b350b 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '2.7.15'), ('Perl', '5.28.0'), ('matplotlib', '2.2.3', versionsuffix), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Boost', '1.67.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb index cef7ad2f682..aee9ee6a397 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb @@ -20,7 +20,7 @@ dependencies = [ ('Python', '2.7.15'), ('Perl', '5.28.1'), ('matplotlib', '2.2.4', versionsuffix), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Boost', '1.70.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb index 01960475b5e..9e7475ccdd8 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb @@ -20,7 +20,7 @@ dependencies = [ ('Python', '3.7.2'), ('Perl', '5.28.1'), ('matplotlib', '3.0.3', versionsuffix), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Boost', '1.70.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020a-Python-3.8.2.eb index 87ae71af604..e0f1cd1e1ce 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020a-Python-3.8.2.eb @@ -20,7 +20,7 @@ dependencies = [ ('Python', '3.8.2'), ('Perl', '5.30.2'), ('matplotlib', '3.2.1', versionsuffix), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Boost', '1.72.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb index 58f9709a656..81762184ba7 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb @@ -20,7 +20,7 @@ dependencies = [ ('Python', '2.7.18'), ('Perl', '5.32.0'), ('matplotlib', '2.2.5', versionsuffix), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Boost', '1.74.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb index 53e95a0065d..d0057cb1ac6 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.8.6'), ('Perl', '5.32.0'), ('matplotlib', '3.3.3'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Boost', '1.74.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021a.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021a.eb index 2fa06228d15..435b062ca1e 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021a.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021a.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.9.5'), ('Perl', '5.32.1'), ('matplotlib', '3.4.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Boost', '1.76.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021b.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021b.eb index eedf3ea7c27..6a2efd7b120 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021b.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021b.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.9.6'), ('Perl', '5.34.0'), ('matplotlib', '3.4.3'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Boost', '1.77.0'), ] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb index 26cc0e00521..d81dfc2eebd 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('pkg-config', '0.29.1'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb index 5bc3462602c..dc3c3684a36 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('pkg-config', '0.29.1'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-10.3.0.eb index 0d7bdcbe989..ec6b5ac968f 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-10.3.0.eb @@ -56,7 +56,7 @@ dependencies = [ ('snappy', '1.1.8'), ('JasPer', '2.0.28'), ('bzip2', '1.0.8'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb index 16cca743fc8..ab34684b136 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb @@ -61,7 +61,7 @@ dependencies = [ ('snappy', '1.1.9'), ('JasPer', '2.0.33'), ('bzip2', '1.0.8'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ('ICU', '69.1'), ] diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb index c12b05d90b1..a9d014e9d75 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb @@ -61,7 +61,7 @@ dependencies = [ ('snappy', '1.1.9'), ('JasPer', '2.0.33'), ('bzip2', '1.0.8'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ('ICU', '71.1'), ('nodejs', '16.15.1'), ] diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb index ea7a0361a22..5138261fdec 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb @@ -23,7 +23,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('pkg-config', '0.29.1'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb index cb2811a839e..cf7f35e5fee 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb @@ -23,7 +23,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('pkg-config', '0.29.1'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb index 316cae4a7e0..4309fafb895 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb @@ -23,7 +23,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('pkg-config', '0.29.1'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb index 6ddda44037e..db20d4633cd 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb @@ -23,7 +23,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('pkg-config', '0.29.1'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2019a-R-3.6.0.eb b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2019a-R-3.6.0.eb index 90bf997ca5c..35374dd4af2 100644 --- a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2019a-R-3.6.0.eb +++ b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2019a-R-3.6.0.eb @@ -16,7 +16,7 @@ sources = ['qualimap_v%(version)s.zip'] checksums = ['08f1d66e49c83c76c56c4225c53aee44f41e0592c8bdc84b8c4ecd975700e045'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('R', '3.6.0'), ('R-bundle-Bioconductor', '3.9', versionsuffix), ] diff --git a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb index 4b25f9686c6..70260a39f73 100644 --- a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb @@ -16,7 +16,7 @@ sources = ['qualimap_v%(version)s.zip'] checksums = ['08f1d66e49c83c76c56c4225c53aee44f41e0592c8bdc84b8c4ecd975700e045'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('R', '4.0.3'), ('R-bundle-Bioconductor', '3.12', versionsuffix), ] diff --git a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2021b-R-4.1.2.eb index fdbfeb2bd21..ee634ca5d69 100644 --- a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2021b-R-4.1.2.eb @@ -16,7 +16,7 @@ sources = ['qualimap_v%(version)s.zip'] checksums = ['08f1d66e49c83c76c56c4225c53aee44f41e0592c8bdc84b8c4ecd975700e045'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('R', '4.1.2'), ('R-bundle-Bioconductor', '3.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb index 503529a7dda..856611cdef4 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb index 4606a8754dd..8598fef3f0a 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.47.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb index 10bcf7e69ec..acb8163c2da 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.23'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb index aa995966ac0..cf10b5462d5 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb index f3ec1cac38c..c5c88c181d4 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb @@ -23,7 +23,7 @@ dependencies = [ ('libjpeg-turbo', '1.4.2'), # for plottting in R ('LibTIFF', '4.0.6'), # for plotting in R ('cairo', '1.14.6'), # for plotting in R - ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', versionsuffix), # for tcltk ('cURL', '7.47.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index 841c073f2b3..4f6c9a71091 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.47.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb index 067c596089e..84e20abc2e2 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb @@ -20,7 +20,7 @@ dependencies = [ ('libpng', '1.6.23'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb index cd605ba827a..32c2e7ab309 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb @@ -20,7 +20,7 @@ dependencies = [ ('libpng', '1.6.23'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb b/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb index ebe33155b56..724a3ceed71 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb @@ -20,7 +20,7 @@ dependencies = [ ('libpng', '1.6.23'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb index 13ed7e3b872..2f0044cf886 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb @@ -26,7 +26,7 @@ dependencies = [ ('libpng', '1.6.24'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2016b-X11-20160819.eb index c9d9b92cc47..c29dcf3fa05 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2016b-X11-20160819.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2016b-X11-20160819.eb @@ -27,7 +27,7 @@ dependencies = [ ('libpng', '1.6.24'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 11f7ae9944f..8436e30f382 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -26,7 +26,7 @@ dependencies = [ ('libpng', '1.6.29'), # for plotting in R ('libjpeg-turbo', '1.5.1'), # for plottting in R ('LibTIFF', '4.0.7'), - ('Java', '1.8.0_121', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_121', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.6'), # for tcltk ('Tk', '8.6.6'), # for tcltk ('cURL', '7.53.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index 01b9b412a37..c8fa9e81b36 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -26,7 +26,7 @@ dependencies = [ ('libpng', '1.6.29'), # for plotting in R ('libjpeg-turbo', '1.5.1'), # for plottting in R ('LibTIFF', '4.0.7'), - ('Java', '1.8.0_121', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_121', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.6'), # for tcltk ('Tk', '8.6.6'), # for tcltk ('cURL', '7.53.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb index 515080f4f37..e6902b752ee 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb @@ -32,7 +32,7 @@ dependencies = [ ('libpng', '1.6.24'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_141', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_141', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb b/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb index 93b5974cfca..25a9ce4249a 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.32'), # for plotting in R ('libjpeg-turbo', '1.5.2'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_152', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_152', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.7'), # for tcltk ('Tk', '8.6.7'), # for tcltk ('cURL', '7.55.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb index 72a1d8f4d5b..f09e4a993e8 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb @@ -31,7 +31,7 @@ dependencies = [ ('libpng', '1.6.32'), # for plotting in R ('libjpeg-turbo', '1.5.2'), # for plottting in R ('LibTIFF', '4.0.8'), - ('Java', '1.8.0_152', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_152', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.7'), # for tcltk ('Tk', '8.6.7'), # for tcltk ('cURL', '7.56.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb index 10a97cc8586..ea2dd212efd 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.32'), # for plotting in R ('libjpeg-turbo', '1.5.2'), # for plottting in R ('LibTIFF', '4.0.8'), - ('Java', '1.8.0_152', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_152', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.7'), # for tcltk ('Tk', '8.6.7'), # for tcltk ('cURL', '7.56.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb index 25d65103609..70cf55f16c3 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '1.5.3'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_162', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_162', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.8'), # for tcltk ('Tk', '8.6.8'), # for tcltk ('cURL', '7.58.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb index dc9f868dc2b..5422e8e8b16 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '1.5.3'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_162', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_162', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.8'), # for tcltk ('Tk', '8.6.8'), # for tcltk ('cURL', '7.58.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb index 83ac3843168..df2f0ef39b8 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '1.5.3'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_162', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_162', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.8'), # for tcltk ('Tk', '8.6.8'), # for tcltk ('cURL', '7.58.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb index 7c15c4437a8..0852baef0e8 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '1.5.3'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_162', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_162', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.8'), # for tcltk ('Tk', '8.6.8'), # for tcltk ('cURL', '7.58.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb index b13278061d0..3cf0f77bff8 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '2.0.0'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Tk', '8.6.8'), # for tcltk ('cURL', '7.60.0'), # for RCurl ('libxml2', '2.9.8'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb index b6425f1a0f4..75f04ccc800 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb @@ -36,7 +36,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '2.0.0'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Tk', '8.6.8'), # for tcltk ('cURL', '7.60.0'), # for RCurl ('libxml2', '2.9.8'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb index 72905166d7d..e0d6e243698 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb @@ -28,7 +28,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '2.0.0'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Tk', '8.6.8'), # for tcltk ('cURL', '7.60.0'), # for RCurl ('libxml2', '2.9.8'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb index 4fad425acdd..85c028d5c76 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb @@ -28,7 +28,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '2.0.0'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Tk', '8.6.8'), # for tcltk ('cURL', '7.60.0'), # for RCurl ('libxml2', '2.9.8'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb b/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb index b3dfeeb1012..4e4d1c99a5f 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb @@ -29,7 +29,7 @@ dependencies = [ ('libpng', '1.6.36'), # for plotting in R ('libjpeg-turbo', '2.0.2'), # for plottting in R ('LibTIFF', '4.0.10'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.9'), # for tcltk ('cURL', '7.63.0'), # for RCurl ('libxml2', '2.9.8'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb b/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb index df2b372cf23..f20ae1ce680 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb @@ -29,7 +29,7 @@ dependencies = [ ('libpng', '1.6.36'), # for plotting in R ('libjpeg-turbo', '2.0.2'), # for plottting in R ('LibTIFF', '4.0.10'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.9'), # for tcltk ('cURL', '7.63.0'), # for RCurl ('libxml2', '2.9.8'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb b/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb index 190263d2d3c..385c219696e 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb @@ -29,7 +29,7 @@ dependencies = [ ('libpng', '1.6.36'), # for plotting in R ('libjpeg-turbo', '2.0.2'), # for plottting in R ('LibTIFF', '4.0.10'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.9'), # for tcltk ('cURL', '7.63.0'), # for RCurl ('libxml2', '2.9.8'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index 0bc641a52fc..70af7d3e9fd 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -35,7 +35,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.3'), # for plottting in R ('LibTIFF', '4.0.10'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.9'), # for tcltk ('cURL', '7.66.0'), # for RCurl ('libxml2', '2.9.9'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index c455fc487cf..99a3664d030 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -35,7 +35,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.3'), # for plottting in R ('LibTIFF', '4.0.10'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.9'), # for tcltk ('cURL', '7.66.0'), # for RCurl ('libxml2', '2.9.9'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb index cabb0423e80..a3abe2e37ee 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb @@ -33,7 +33,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.3'), # for plottting in R ('LibTIFF', '4.0.10'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.9'), # for tcltk ('cURL', '7.66.0'), # for RCurl ('libxml2', '2.9.9'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb index dc8f3642b9a..ad7708d2b1f 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb @@ -29,7 +29,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.4'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.69.1'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index 9afb0e13b61..faa29bd2b3e 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -34,7 +34,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.4'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.69.1'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb index 4bd3700f409..e1e620b5669 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb @@ -34,7 +34,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.4'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.69.1'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 3226ee0f4bc..782f039b492 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index d35824d64ba..db5d9c9e47c 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 26d6cbdb27b..c7d07e5f2ac 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -36,7 +36,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 9c612d32b95..afc6216b0bf 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index febdb0ca5e7..bf2b31d78ee 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -33,7 +33,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index d1e5430a104..be10c211dc4 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -33,7 +33,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index 3bdb84f74b2..d7eb4353a4d 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -34,7 +34,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.6'), # for plottting in R ('LibTIFF', '4.2.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.11'), # for tcltk ('cURL', '7.76.0'), # for RCurl ('libxml2', '2.9.10'), # for XML @@ -51,7 +51,7 @@ dependencies = [ ('nodejs', '14.17.0'), # for V8 (required by rstan) ('GDAL', '3.3.0'), # for sf ('libgit2', '1.1.0'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 9c0872e0343..97750491d42 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -34,7 +34,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.6'), # for plottting in R ('LibTIFF', '4.3.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.11'), # for tcltk ('cURL', '7.78.0'), # for RCurl ('libxml2', '2.9.10'), # for XML @@ -52,7 +52,7 @@ dependencies = [ ('GDAL', '3.3.2'), # for sf ('MPFR', '4.1.0'), # for Rmpfr ('libgit2', '1.1.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb index 46ee68285da..6175f90d834 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -35,7 +35,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.6'), # for plottting in R ('LibTIFF', '4.3.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.11'), # for tcltk ('cURL', '7.78.0'), # for RCurl ('libxml2', '2.9.10'), # for XML @@ -53,7 +53,7 @@ dependencies = [ ('GDAL', '3.3.2'), # for sf ('MPFR', '4.1.0'), # for Rmpfr ('libgit2', '1.1.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 1dfdcecb129..b97f484e225 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -31,7 +31,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.1.3'), # for plottting in R ('LibTIFF', '4.3.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.12'), # for tcltk ('cURL', '7.83.0'), # for RCurl ('libxml2', '2.9.13'), # for XML @@ -49,7 +49,7 @@ dependencies = [ ('GDAL', '3.5.0'), # for sf ('MPFR', '4.1.0'), # for Rmpfr ('libgit2', '1.4.3'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2018.09.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2018.09.3-intel-2018b-Python-3.6.6.eb index 84be9e4f58f..5cec5783bdc 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2018.09.3-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2018.09.3-intel-2018b-Python-3.6.6.eb @@ -15,7 +15,7 @@ checksums = ['3be20bade43657c0d74617ab99ca30f872eaaedc314a87f690ac38e5ef590224'] builddependencies = [ ('CMake', '3.12.1'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2019.09.3-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2019.09.3-foss-2019b-Python-3.7.4.eb index d7db7604054..eb85dc0a82a 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2019.09.3-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2019.09.3-foss-2019b-Python-3.7.4.eb @@ -22,7 +22,7 @@ checksums = [ builddependencies = [ ('CMake', '3.15.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-foss-2020a-Python-3.8.2.eb index 0f3478b407f..3ddb556d58b 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-foss-2020a-Python-3.8.2.eb @@ -26,7 +26,7 @@ checksums = [ # https://rdkit.readthedocs.io/en/latest/Install.html#installing-prerequisites-from-source builddependencies = [ ('CMake', '3.16.4'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-intel-2020a-Python-3.8.2.eb index 9114ab335e8..33bde2b7c1f 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-intel-2020a-Python-3.8.2.eb @@ -26,7 +26,7 @@ checksums = [ # https://rdkit.readthedocs.io/en/latest/Install.html#installing-prerequisites-from-source builddependencies = [ ('CMake', '3.16.4'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2020.09.3-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2020.09.3-foss-2019b-Python-3.7.4.eb index 30280d9b65f..501cd89e3bc 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2020.09.3-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2020.09.3-foss-2019b-Python-3.7.4.eb @@ -24,7 +24,7 @@ checksums = [ # https://rdkit.readthedocs.io/en/latest/Install.html#installing-prerequisites-from-source builddependencies = [ ('CMake', '3.15.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2018a-CUDA-9.1.85.eb b/easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2018a-CUDA-9.1.85.eb index 747d228757a..c9c0251c232 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2018a-CUDA-9.1.85.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2018a-CUDA-9.1.85.eb @@ -23,7 +23,7 @@ checksums = [ builddependencies = [('CMake', '3.10.1')] dependencies = [ - ('CUDA', local_cuda_ver, '', True), + ('CUDA', local_cuda_ver, '', SYSTEM), ('X11', '20180131'), ('FLTK', '1.3.4'), ] diff --git a/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb b/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb index dbd242572b8..babe47dcf73 100644 --- a/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb @@ -13,7 +13,7 @@ sources = ['rnabloom_v%(version)s.tar.gz'] checksums = ['7418761ff99f24f0edc23772cfa517c3d7401eac98642dcb017d48fb35c6ee4a'] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('minimap2', '2.17'), ('Racon', '1.4.13'), ('ntCard', '1.2.1'), diff --git a/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.4.3-GCC-11.2.0.eb b/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.4.3-GCC-11.2.0.eb index 02ac929561f..86df5571106 100644 --- a/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.4.3-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.4.3-GCC-11.2.0.eb @@ -13,7 +13,7 @@ sources = ['rnabloom_v%(version)s.tar.gz'] checksums = ['819274d674fe350ae3a1e1136618d52a8abb941280f604c6777ea4540b299a38'] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('minimap2', '2.24'), ('Racon', '1.5.0'), ('ntCard', '1.2.1'), diff --git a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-foss-2016b-Java-1.8.0_121.eb b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-foss-2016b-Java-1.8.0_121.eb index 9ff75608237..f6ee37eac64 100644 --- a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-foss-2016b-Java-1.8.0_121.eb +++ b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-foss-2016b-Java-1.8.0_121.eb @@ -22,7 +22,7 @@ checksums = ['0a6a8cc885e77c7e7b75dafcfd2152e0d1031fa7aba2565250a46fbd98979793'] dependencies = [ ('BWA', '0.7.16a'), - ('Java', '1.8.0_121', '', True), + ('Java', '1.8.0_121', '', SYSTEM), ] modloadmsg = """To execute RNA-SeQC run: java -jar $EBROOTRNAMINSEQC/%(name)s_v%(version)s.jar\n""" diff --git a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-foss-2018b-Java-1.8.eb b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-foss-2018b-Java-1.8.eb index 75bf91935f7..22e20680911 100644 --- a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-foss-2018b-Java-1.8.eb +++ b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-foss-2018b-Java-1.8.eb @@ -22,7 +22,7 @@ checksums = ['0a6a8cc885e77c7e7b75dafcfd2152e0d1031fa7aba2565250a46fbd98979793'] dependencies = [ ('BWA', '0.7.17'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modloadmsg = "To execute RNA-SeQC run: java -jar $EBROOTRNAMINSEQC/%(name)s_v%(version)s.jar" diff --git a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb index 7cc11725a88..147016a5526 100644 --- a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb @@ -18,7 +18,7 @@ dependencies = [ ('Python', '3.6.6'), ('Pysam', '0.15.1', versionsuffix), ('scikit-learn', '0.20.0', versionsuffix), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] download_dep_fail = True diff --git a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb index dc9c93177cf..1a666f6fc94 100644 --- a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb @@ -18,7 +18,7 @@ dependencies = [ ('Python', '3.6.6'), ('Pysam', '0.15.1', versionsuffix), ('scikit-learn', '0.20.0', versionsuffix), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] download_dep_fail = True diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.2.5033-fosscuda-2019b-Java-11.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.2.5033-fosscuda-2019b-Java-11.eb index e68f58adf65..0e6ae1282eb 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.2.5033-fosscuda-2019b-Java-11.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.2.5033-fosscuda-2019b-Java-11.eb @@ -29,13 +29,13 @@ checksums = [ builddependencies = [ ('pkg-config', '0.29.2'), ('CMake', '3.15.3'), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ] dependencies = [ ('Boost', '1.71.0'), ('R', '3.6.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] osdependencies = [ diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.2.5042-foss-2019b-Java-11.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.2.5042-foss-2019b-Java-11.eb index 756445042c1..b91df14e310 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.2.5042-foss-2019b-Java-11.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.2.5042-foss-2019b-Java-11.eb @@ -29,13 +29,13 @@ checksums = [ builddependencies = [ ('pkg-config', '0.29.2'), ('CMake', '3.15.3'), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ] dependencies = [ ('Boost', '1.71.0'), ('R', '3.6.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] osdependencies = [ diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.3.1093-foss-2020a-Java-11-R-4.0.0.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.3.1093-foss-2020a-Java-11-R-4.0.0.eb index 4c871371f5e..80dfe9052a9 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.3.1093-foss-2020a-Java-11-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.3.1093-foss-2020a-Java-11-R-4.0.0.eb @@ -29,13 +29,13 @@ checksums = [ builddependencies = [ ('pkg-config', '0.29.2'), ('CMake', '3.16.4'), - ('ant', '1.10.8', '-Java-%(javaver)s', True), + ('ant', '1.10.8', '-Java-%(javaver)s', SYSTEM), ] dependencies = [ ('Boost', '1.72.0'), ('R', '4.0.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] osdependencies = [ diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.3.959-foss-2020a-Java-11-R-4.0.0.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.3.959-foss-2020a-Java-11-R-4.0.0.eb index 26f4b962160..2ef5e389064 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.3.959-foss-2020a-Java-11-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.3.959-foss-2020a-Java-11-R-4.0.0.eb @@ -25,13 +25,13 @@ checksums = [ builddependencies = [ ('pkg-config', '0.29.2'), ('CMake', '3.16.4'), - ('ant', '1.10.8', '-Java-%(javaver)s', True), + ('ant', '1.10.8', '-Java-%(javaver)s', SYSTEM), ] dependencies = [ ('Boost', '1.72.0'), ('R', '4.0.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] osdependencies = [ diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb index d163c925d0c..db9cd5d65bf 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb @@ -21,13 +21,13 @@ checksums = ['3af234180fd7cef451aef40faac2c7b52860f14a322244c1c7aede029814d261'] builddependencies = [ ('pkg-config', '0.29.2'), ('CMake', '3.20.1'), - ('ant', '1.10.11', '-Java-%(javaver)s', True), + ('ant', '1.10.11', '-Java-%(javaver)s', SYSTEM), ] dependencies = [ ('Boost', '1.76.0'), ('R', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('SOCI', '4.0.2'), ] diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb index e8ef0ee102f..786360704ba 100644 --- a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb @@ -14,7 +14,7 @@ checksums = ['e294396f49ec236626c47020ce3c893ba08a50bce204e1d51a074978d215b558'] dependencies = [ ('Perl', '5.26.0'), - ('TRF', '4.09', '-linux64', True), + ('TRF', '4.09', '-linux64', SYSTEM), ('HMMER', '3.1b2'), ] diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-iccifort-2017.4.196-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-iccifort-2017.4.196-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb index 52f3b80f931..7eafecb7975 100644 --- a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-iccifort-2017.4.196-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-iccifort-2017.4.196-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb @@ -14,7 +14,7 @@ checksums = ['e294396f49ec236626c47020ce3c893ba08a50bce204e1d51a074978d215b558'] dependencies = [ ('Perl', '5.26.0'), - ('TRF', '4.09', '-linux64', True), + ('TRF', '4.09', '-linux64', SYSTEM), ('HMMER', '3.1b2'), ] diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-intel-2018b-Perl-5.28.0-HMMER.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-intel-2018b-Perl-5.28.0-HMMER.eb index 49bf1b790e1..ffb217fc6f4 100644 --- a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-intel-2018b-Perl-5.28.0-HMMER.eb +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-intel-2018b-Perl-5.28.0-HMMER.eb @@ -14,7 +14,7 @@ checksums = ['e294396f49ec236626c47020ce3c893ba08a50bce204e1d51a074978d215b558'] dependencies = [ ('Perl', '5.28.0'), - ('TRF', '4.09', '-linux64', True), + ('TRF', '4.09', '-linux64', SYSTEM), ('HMMER', '3.2.1'), ] diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.9-p2-gompi-2019b-HMMER.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.9-p2-gompi-2019b-HMMER.eb index bb5f15e74c3..9f6c7bc0b01 100644 --- a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.9-p2-gompi-2019b-HMMER.eb +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.9-p2-gompi-2019b-HMMER.eb @@ -25,7 +25,7 @@ checksums = [ dependencies = [ ('Perl', '5.30.0'), - ('TRF', '4.09', '-linux64', True), + ('TRF', '4.09', '-linux64', SYSTEM), ('HMMER', '3.2.1'), ] diff --git a/easybuild/easyconfigs/r/RheoTool/RheoTool-5.0-foss-2019b.eb b/easybuild/easyconfigs/r/RheoTool/RheoTool-5.0-foss-2019b.eb index 86bb0bbf1ae..b9117db641e 100644 --- a/easybuild/easyconfigs/r/RheoTool/RheoTool-5.0-foss-2019b.eb +++ b/easybuild/easyconfigs/r/RheoTool/RheoTool-5.0-foss-2019b.eb @@ -15,7 +15,7 @@ checksums = ['2e0899684d6d7f9ddee0d93b39a6ed56262b171bc4e5536914645209b66003ed'] dependencies = [ ('OpenFOAM', '7', '-20200508'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('PETSc', '3.12.4', '-Python-3.7.4'), ] diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb index eaec7699da4..7eab5f3ec8d 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb index 2a008d86759..8d66638b61d 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb index 9f045c62c02..3916f14fbd9 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.56.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.56.0-GCCcore-11.2.0.eb index 58777add4e0..c70ed36ffd9 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.56.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.56.0-GCCcore-11.2.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-10.3.0.eb index 5eab0202819..0b1bb2ee921 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-10.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb index ecaf7753a89..0a1bf6c1485 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " diff --git a/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb index 6680caa1442..2a055d37ff0 100644 --- a/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} github_account = 'PhoenixDL' dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), # provides numpy ('PyTorch', '1.10.0', versionsuffix), diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index dbefc98c9f4..173bc41c41a 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -27,8 +27,8 @@ dependencies = [ ('R', '4.1.2'), ('BLAST+', '2.12.0'), ('AUGUSTUS', '3.4.0'), - ('Java', '11', '', True), - ('Maven', '3.6.3', '', True), + ('Java', '11', '', SYSTEM), + ('Maven', '3.6.3', '', SYSTEM), ('plotly.py', '5.4.0'), ('ETE', '3.1.2'), ('PyYAML', '5.4.1'), diff --git a/easybuild/easyconfigs/s/SECAPR/SECAPR-1.1.15-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/s/SECAPR/SECAPR-1.1.15-foss-2019b-Python-2.7.16.eb index f137d101fa2..e19b28dbb97 100644 --- a/easybuild/easyconfigs/s/SECAPR/SECAPR-1.1.15-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/s/SECAPR/SECAPR-1.1.15-foss-2019b-Python-2.7.16.eb @@ -17,16 +17,16 @@ dependencies = [ ('ABySS', '2.1.5'), ('Biopython', '1.75', versionsuffix), ('BWA', '0.7.17'), - ('picard', '2.21.6', '-Java-11', True), + ('picard', '2.21.6', '-Java-11', SYSTEM), ('BCFtools', '1.10.2'), ('EMBOSS', '6.6.0', '-Java-11'), - ('FastQC', '0.11.9', '-Java-11', True), + ('FastQC', '0.11.9', '-Java-11', SYSTEM), ('LASTZ', '1.04.03'), ('MAFFT', '7.453', '-with-extensions'), ('MUSCLE', '3.8.1551'), ('SAMtools', '1.10'), ('seqtk', '1.3'), - ('Trimmomatic', '0.39', '-Java-11', True), + ('Trimmomatic', '0.39', '-Java-11', SYSTEM), ('Trinity', '2.9.1', versionsuffix), ] diff --git a/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.1-GCCcore-8.2.0-Java-11.eb b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.1-GCCcore-8.2.0-Java-11.eb index dcc982d7e1f..ae01366c9ef 100644 --- a/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.1-GCCcore-8.2.0-Java-11.eb +++ b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.1-GCCcore-8.2.0-Java-11.eb @@ -20,7 +20,7 @@ checksums = ['11cd754087fc3a8a12362af6140949726d4c32f1097a7c387d116cc1cf7e234e'] builddependencies = [('binutils', '2.31.1')] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('NGS', '2.10.0', '-Java-11'), ('bzip2', '1.0.6'), ] diff --git a/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb index 41984431bdc..3aac6838fbf 100644 --- a/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb @@ -15,7 +15,7 @@ checksums = ['93e6864b7ab18be96584950227426102b545db7d6d02762490a43e1610b7eb9b'] builddependencies = [('binutils', '2.35')] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('NGS', '2.10.9'), ('bzip2', '1.0.8'), ] diff --git a/easybuild/easyconfigs/s/SUMO/SUMO-1.12.0-foss-2021b.eb b/easybuild/easyconfigs/s/SUMO/SUMO-1.12.0-foss-2021b.eb index fecda0386ee..5d5ce7762a7 100644 --- a/easybuild/easyconfigs/s/SUMO/SUMO-1.12.0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SUMO/SUMO-1.12.0-foss-2021b.eb @@ -23,7 +23,7 @@ checksums = [ builddependencies = [ ('CMake', '3.22.1'), ('SWIG', '4.0.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/s/SUMO/SUMO-1.14.1-foss-2021b.eb b/easybuild/easyconfigs/s/SUMO/SUMO-1.14.1-foss-2021b.eb index 17783cb2a67..fb78dda30bc 100644 --- a/easybuild/easyconfigs/s/SUMO/SUMO-1.14.1-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SUMO/SUMO-1.14.1-foss-2021b.eb @@ -23,7 +23,7 @@ checksums = [ builddependencies = [ ('CMake', '3.22.1'), ('SWIG', '4.0.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb index 30e5d21317c..eb4f55f2430 100644 --- a/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb @@ -23,7 +23,7 @@ checksums = [ builddependencies = [ ('CMake', '3.16.4'), ('SWIG', '4.0.1'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.3.0.eb index d65645b9dd5..d319f5ccfa1 100644 --- a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ dependencies = [ ('APR', '1.7.0'), ('APR-util', '1.6.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] buildopts = "APR=$EBROOTAPR/bin/apr-1-config APU=$EBROOTAPRMINUTIL/bin/apu-1-config" diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.2.0.eb index c6fb0da1ec0..72cdc72b88f 100644 --- a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.2.0.eb @@ -25,7 +25,7 @@ builddependencies = [ dependencies = [ ('APR', '1.7.0'), ('APR-util', '1.6.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] buildopts = "APR=$EBROOTAPR/bin/apr-1-config APU=$EBROOTAPRMINUTIL/bin/apu-1-config" diff --git a/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb b/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb index 3781b94855a..b6965d55e69 100644 --- a/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb @@ -29,7 +29,7 @@ checksums = [ builddependencies = [ ('CMake', '3.18.4'), - ('Cereal', '1.3.0', '', True), + ('Cereal', '1.3.0', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-1.1.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-1.1.0-foss-2019b-Python-3.7.4.eb index 03165ec8f41..29d9b21e0d8 100644 --- a/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-1.1.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-1.1.0-foss-2019b-Python-3.7.4.eb @@ -16,7 +16,7 @@ toolchainopts = {'pic': True} builddependencies = [ ('CMake', '3.15.3'), ('Bison', '3.3.2'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('googletest', '1.10.0'), ] diff --git a/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb index 35d4801c28d..01f18a9bb75 100644 --- a/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb @@ -23,7 +23,7 @@ dependencies = [ ('OrfM', '0.7.1'), ('HMMER', '3.2.1'), ('fxtract', '2.3'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('KronaTools', '2.7.1'), ('DIAMOND', '0.9.24'), ] diff --git a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb index 63485234dcb..996aeca133c 100644 --- a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb @@ -19,7 +19,7 @@ dependencies = [ ('Pysam', '0.17.0'), ('Biopython', '1.79'), ('SAMtools', '1.14'), - ('VarScan', '2.4.4', '-Java-11', True), + ('VarScan', '2.4.4', '-Java-11', SYSTEM), ('R', '4.1.2'), ('NextGenMap', '0.5.5'), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb b/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb index 0e81ab6be6c..31aafdd2c90 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb @@ -18,7 +18,7 @@ source_urls = [ checksums = ['86f33f6f4fe545cb848600004144f09b6e8413af47ce02c1203c3ecda075288d'] dependencies = [ - ('Java', '1.8.0_152', '', True), + ('Java', '1.8.0_152', '', SYSTEM), ('Python', '3.6.3'), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-Hadoop-2.7-Java-1.8.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-Hadoop-2.7-Java-1.8.eb index 073734a3f85..f14e575058a 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-Hadoop-2.7-Java-1.8.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-Hadoop-2.7-Java-1.8.eb @@ -17,7 +17,7 @@ source_urls = [ ] checksums = ['c93c096c8d64062345b26b34c85127a6848cff95a4bb829333a06b83222a5cfa'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/spark-shell'], diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-foss-2018b-Python-2.7.15.eb index 23510072e38..d780b9c3b02 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-foss-2018b-Python-2.7.15.eb @@ -19,7 +19,7 @@ checksums = ['c93c096c8d64062345b26b34c85127a6848cff95a4bb829333a06b83222a5cfa'] dependencies = [ ('Python', '2.7.15'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Hadoop', '2.9.2', '-native'), ('Arrow', '0.12.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb index 6fa3caf6ede..e643595c370 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb @@ -19,7 +19,7 @@ sources = ['%%(namelower)s-%%(version)s-bin-hadoop%s.tgz' % local_hadoopver] checksums = ['c93c096c8d64062345b26b34c85127a6848cff95a4bb829333a06b83222a5cfa'] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Python', '3.6.6'), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-2.7.15.eb index 387340456d0..f7991b20743 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-2.7.15.eb @@ -19,7 +19,7 @@ checksums = ['c93c096c8d64062345b26b34c85127a6848cff95a4bb829333a06b83222a5cfa'] dependencies = [ ('Python', '2.7.15'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Hadoop', '2.9.2', '-native'), ('Arrow', '0.12.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-3.6.6.eb index cd360504934..7dd10c2a0c7 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-3.6.6.eb @@ -19,7 +19,7 @@ checksums = ['c93c096c8d64062345b26b34c85127a6848cff95a4bb829333a06b83222a5cfa'] dependencies = [ ('Python', '3.6.6'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Hadoop', '2.9.2', '-native'), ('Arrow', '0.12.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.5-intel-2019b-Python-3.7.4-Java-1.8.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.5-intel-2019b-Python-3.7.4-Java-1.8.eb index f8644c9fdea..46a739bcb58 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.5-intel-2019b-Python-3.7.4-Java-1.8.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.5-intel-2019b-Python-3.7.4-Java-1.8.eb @@ -22,7 +22,7 @@ checksums = ['020be52524e4df366eb974d41a6e18fcb6efcaba9a51632169e917c74267dd81'] dependencies = [ ('Python', '3.7.4'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Hadoop', '2.10.0', '-native'), ('Arrow', '0.16.0', local_python_versionsuffix), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb index adae6b1c2c7..c7ad27d0aa2 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb @@ -18,7 +18,7 @@ checksums = ['98f6b92e5c476d7abb93cc179c2616aa5dc897da25753bd197e20ef54a28d945'] dependencies = [ ('Python', '2.7.15'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Hadoop', '2.9.2', '-native'), ('Arrow', '0.12.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb index df8e7e468b1..64cc3061e75 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb @@ -18,7 +18,7 @@ checksums = ['98f6b92e5c476d7abb93cc179c2616aa5dc897da25753bd197e20ef54a28d945'] dependencies = [ ('Python', '2.7.15'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Hadoop', '2.9.2', '-native'), ('Arrow', '0.12.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb index cecf3035382..fd433043377 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb @@ -20,7 +20,7 @@ checksums = ['4e0846207bf10311de43451bc99309086fce7990aaf54bf3038608b1981afbe7'] dependencies = [ ('Python', '3.8.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), # ('Hadoop', '2.10.0', '-native'), ('Arrow', '0.17.1', versionsuffix), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb index 5cb1ec3c5ee..c5815aa76aa 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb @@ -19,7 +19,7 @@ checksums = ['4e0846207bf10311de43451bc99309086fce7990aaf54bf3038608b1981afbe7'] dependencies = [ ('Python', '3.8.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), # ('Hadoop', '2.10.0', '-native'), ('Arrow', '0.17.1'), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb index b4585778e53..e08aae3577c 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb @@ -19,7 +19,7 @@ checksums = ['4e0846207bf10311de43451bc99309086fce7990aaf54bf3038608b1981afbe7'] dependencies = [ ('Python', '3.8.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), # ('Hadoop', '2.10.0', '-native'), ('Arrow', '0.17.1'), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.2.1-foss-2021b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.2.1-foss-2021b.eb index 7ae8baa1987..f9867229cb9 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.2.1-foss-2021b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.2.1-foss-2021b.eb @@ -19,7 +19,7 @@ checksums = ['224e058cb0c6fb68b39896427a3ccd11ae2246e9bf465b5e29e4fb192d39a59c'] dependencies = [ ('Python', '3.9.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), # ('Hadoop', '2.10.0', '-native'), ('Arrow', '6.0.0'), ] diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb index 99b2e9b26ea..a6aacdefcaf 100644 --- a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb @@ -34,12 +34,12 @@ dependencies = [ ('DIAMOND', '0.9.22'), ('MEGAHIT', '1.1.4', versionsuffix), ('minimap2', '2.13'), - ('Java', '1.8', '', True), - ('RDP-Classifier', '2.12', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('RDP-Classifier', '2.12', '-Java-%(javaver)s', SYSTEM), ('MetaBAT', '2.12.1', versionsuffix), ('MinPath', '1.4', versionsuffix), # depends on GPLK (which provides glpsol) ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), - ('Trimmomatic', '0.38', '-Java-%(javaver)s', True), + ('Trimmomatic', '0.38', '-Java-%(javaver)s', SYSTEM), ('AMOS', '3.1.0'), ('MaxBin', '2.2.6', '-Perl-%(perlver)s'), ('SPAdes', '3.13.0'), @@ -47,7 +47,7 @@ dependencies = [ ('canu', '1.8', '-Perl-%(perlver)s'), ('HMMER', '3.2.1'), ('MUMmer', '4.0.0beta2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ] keepsymlinks = True diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb index bc932b4a6c7..49bda51b080 100644 --- a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb @@ -33,12 +33,12 @@ dependencies = [ ('DIAMOND', '0.9.22'), ('MEGAHIT', '1.1.4', versionsuffix), ('minimap2', '2.13'), - ('Java', '1.8', '', True), - ('RDP-Classifier', '2.12', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('RDP-Classifier', '2.12', '-Java-%(javaver)s', SYSTEM), ('MetaBAT', '2.12.1', versionsuffix), ('MinPath', '1.4', versionsuffix), # depends on GPLK (which provides glpsol) ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), - ('Trimmomatic', '0.38', '-Java-%(javaver)s', True), + ('Trimmomatic', '0.38', '-Java-%(javaver)s', SYSTEM), ('AMOS', '3.1.0'), ('MaxBin', '2.2.6', '-Perl-%(perlver)s'), ('SPAdes', '3.13.0'), @@ -46,7 +46,7 @@ dependencies = [ ('canu', '1.8', '-Perl-%(perlver)s'), ('HMMER', '3.2.1'), ('MUMmer', '4.0.0beta2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('Short-Pair', '20170125', versionsuffix), ('SAMtools', '1.9'), ('CompareM', '0.0.23', versionsuffix), diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb index 492c34fe96c..f1a8cec6d8d 100644 --- a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb @@ -30,12 +30,12 @@ dependencies = [ ('DIAMOND', '2.0.13'), ('MEGAHIT', '1.2.9'), ('minimap2', '2.22'), - ('Java', '11', '', True), - ('RDP-Classifier', '2.13', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('RDP-Classifier', '2.13', '-Java-%(javaver)s', SYSTEM), ('MetaBAT', '2.15'), ('MinPath', '1.6'), # depends on GPLK (which provides glpsol) ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), - ('Trimmomatic', '0.39', '-Java-%(javaver)s', True), + ('Trimmomatic', '0.39', '-Java-%(javaver)s', SYSTEM), ('AMOS', '3.1.0'), ('MaxBin', '2.2.7'), ('SPAdes', '3.15.3'), @@ -43,7 +43,7 @@ dependencies = [ ('canu', '2.2'), ('HMMER', '3.3.2'), ('MUMmer', '4.0.0beta2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('Short-Pair', '20170125'), ('SAMtools', '1.14'), ('CompareM', '0.1.2'), diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.5-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.5-GCCcore-8.2.0.eb index 9721dbb7e51..b360d49ed19 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.5-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.5-GCCcore-8.2.0.eb @@ -14,7 +14,7 @@ source_urls = ['http://ccb.jhu.edu/software/%(namelower)s/dl/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['f16ec07d4869b7656bc1a9b6eb662fd9404c122d18431c845e93d810840c5db9'] -builddependencies = [('binutils', '2.31.1', '', True)] +builddependencies = [('binutils', '2.31.1', '', SYSTEM)] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.10.0-foss-2017b.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.10.0-foss-2017b.eb index 309d66a48c7..cd483fdf31e 100644 --- a/easybuild/easyconfigs/s/Subversion/Subversion-1.10.0-foss-2017b.eb +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.10.0-foss-2017b.eb @@ -30,7 +30,7 @@ dependencies = [ ('Python', '2.7.14'), ('Perl', '5.26.1'), ('Ruby', '2.4.2'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('SWIG', '3.0.12', '-Python-%(pyver)s'), ] diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.10.0-intel-2017b.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.10.0-intel-2017b.eb index 8d399be6349..ca96dc353d4 100644 --- a/easybuild/easyconfigs/s/Subversion/Subversion-1.10.0-intel-2017b.eb +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.10.0-intel-2017b.eb @@ -30,7 +30,7 @@ dependencies = [ ('Python', '2.7.14'), ('Perl', '5.26.1'), ('Ruby', '2.5.0'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('SWIG', '3.0.12', '-Python-%(pyver)s'), ] diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb index 2ef23ba8a82..0b9443692f3 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [ ('METIS', local_metis_ver), ('MPFR', '4.1.0'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-GCCcore-5.4.0.eb index d42e2e93387..b69c7feaf2e 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-GCCcore-5.4.0.eb @@ -15,7 +15,7 @@ checksums = ['a816d95d5662e8279625abdbea7d0e62157d7d1f028020b1075500bf483ed5ef'] configopts = "--with-pic" -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + diff --git a/easybuild/easyconfigs/s/sbt/sbt-1.0.2-Java-1.8.0_152.eb b/easybuild/easyconfigs/s/sbt/sbt-1.0.2-Java-1.8.0_152.eb index 09e6c9dafd7..8fa744e8aee 100644 --- a/easybuild/easyconfigs/s/sbt/sbt-1.0.2-Java-1.8.0_152.eb +++ b/easybuild/easyconfigs/s/sbt/sbt-1.0.2-Java-1.8.0_152.eb @@ -13,7 +13,7 @@ source_urls = ['https://github.com/sbt/sbt/releases/download/v%(version)s'] sources = [SOURCE_TGZ] checksums = ['c3f063d8122d87f0d80b25221d76b0a164e9247d35190f31ec360edcb4352ef0'] -dependencies = [('Java', '1.8.0_152', '', True)] +dependencies = [('Java', '1.8.0_152', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/sbt'], diff --git a/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb index 06f3fc97f7e..e45a4e372cc 100644 --- a/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/shar', 'bin/uudecode', 'bin/uuencode', 'bin/unshar'], diff --git a/easybuild/easyconfigs/s/shovill/shovill-0.9.0-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/s/shovill/shovill-0.9.0-foss-2018a-Python-2.7.14.eb index 86ecd27ae6a..45fe9061553 100644 --- a/easybuild/easyconfigs/s/shovill/shovill-0.9.0-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/shovill/shovill-0.9.0-foss-2018a-Python-2.7.14.eb @@ -23,11 +23,11 @@ dependencies = [ ('SKESA', '2.2'), ('MEGAHIT', '1.1.3', versionsuffix), ('KMC', '3.1.0'), - ('Pilon', '1.22', '-Java-1.8.0_162', True), + ('Pilon', '1.22', '-Java-1.8.0_162', SYSTEM), ('SPAdes', '3.12.0'), ('Lighter', '1.1.1'), ('FLASH', '1.2.11'), - ('Trimmomatic', '0.38', '-Java-1.8.0_162', True), + ('Trimmomatic', '0.38', '-Java-1.8.0_162', SYSTEM), ('Velvet', '1.2.10', '-mt-kmer_191'), ('pigz', '2.4'), ] diff --git a/easybuild/easyconfigs/s/shovill/shovill-1.0.4-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/shovill/shovill-1.0.4-foss-2018b-Python-2.7.15.eb index fed24b4cdcb..b5a0a68a8c9 100644 --- a/easybuild/easyconfigs/s/shovill/shovill-1.0.4-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/shovill/shovill-1.0.4-foss-2018b-Python-2.7.15.eb @@ -23,11 +23,11 @@ dependencies = [ ('SKESA', '2.3.0'), ('MEGAHIT', '1.1.4', versionsuffix), ('KMC', '3.1.0'), - ('Pilon', '1.23', '-Java-1.8', True), + ('Pilon', '1.23', '-Java-1.8', SYSTEM), ('SPAdes', '3.13.0'), ('Lighter', '1.1.2'), ('FLASH', '1.2.11'), - ('Trimmomatic', '0.38', '-Java-1.8', True), + ('Trimmomatic', '0.38', '-Java-1.8', SYSTEM), ('Velvet', '1.2.10', '-mt-kmer_191'), ('pigz', '2.4'), ('samclip', '0.2', '-Perl-5.28.0'), diff --git a/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb b/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb index d71b5e0fb90..dfc9a1c3943 100644 --- a/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb @@ -22,11 +22,11 @@ dependencies = [ ('SKESA', '2.4.0', '_saute.1.3.0_1'), ('MEGAHIT', '1.2.9'), ('KMC', '3.2.1'), - ('Pilon', '1.23', '-Java-11', True), + ('Pilon', '1.23', '-Java-11', SYSTEM), ('SPAdes', '3.15.3'), ('Lighter', '1.1.2'), ('FLASH', '2.2.00'), - ('Trimmomatic', '0.39', '-Java-11', True), + ('Trimmomatic', '0.39', '-Java-11', SYSTEM), ('Velvet', '1.2.10', '-mt-kmer_191'), ('pigz', '2.6'), ('samclip', '0.4.0'), diff --git a/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a-CUDA-11.3.1.eb index ecbc8b58ffd..9cdb80b108b 100644 --- a/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a-CUDA-11.3.1.eb @@ -11,7 +11,7 @@ description = "Smooth Loss Functions for Deep Top-k Classification" toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('tqdm', '4.61.2'), ('PyTorch', '1.10.0', versionsuffix), diff --git a/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb index 3d829256a63..aba93468232 100644 --- a/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb @@ -21,7 +21,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['7264e3819e249387effd3eba170ff49404b1cf7347dfa25944866f5aeb6b11c3'] dependencies = [ - ('Java', '13', '', True), + ('Java', '13', '', SYSTEM), ('Python', '3.8.2'), ('Perl', '5.30.2'), ('BioPerl', '1.7.7'), diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.0-GCCcore-9.3.0-Java-13-Python-3.8.2.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.0-GCCcore-9.3.0-Java-13-Python-3.8.2.eb index f3814608665..e05db5008e7 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-5.0-GCCcore-9.3.0-Java-13-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.0-GCCcore-9.3.0-Java-13-Python-3.8.2.eb @@ -15,7 +15,7 @@ sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] checksums = ['2b177440eb4a2c3bbfc8f50d4adf9e405f3dcfc05a31a55c96f773f07832af34'] dependencies = [ - ('Java', '13', '', True), + ('Java', '13', '', SYSTEM), ('Python', '3.8.2'), ('Perl', '5.30.2'), ] diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb index cfde903143c..2e5679be3cd 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb @@ -15,7 +15,7 @@ sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] checksums = ['85d907b5dd9e9008a0cf245956e3c9077a31e45f21a1b580d9b98a53fd8dcb9d'] dependencies = [ - ('Java', '13', '', True), + ('Java', '13', '', SYSTEM), ('Python', '3.8.6'), ('Perl', '5.32.0'), ] diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-11.2.0-Java-11.eb index a7a8a7334f4..3281c84b650 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-11.2.0-Java-11.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-11.2.0-Java-11.eb @@ -17,7 +17,7 @@ checksums = ['85d907b5dd9e9008a0cf245956e3c9077a31e45f21a1b580d9b98a53fd8dcb9d'] dependencies = [ # ignore website claim that Java 12+ is required, nothing is compiled for # anything newer than Java 11 - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.9.6'), ('Perl', '5.34.0'), ] diff --git a/easybuild/easyconfigs/t/THetA/THetA-0.7-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/THetA/THetA-0.7-foss-2018b-Python-2.7.15.eb index 003a47f61ba..bd37bacce14 100644 --- a/easybuild/easyconfigs/t/THetA/THetA-0.7-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/THetA/THetA-0.7-foss-2018b-Python-2.7.15.eb @@ -18,8 +18,8 @@ checksums = ['474452fa87a1ca0228137693bfede3200b91e4e166b2216c4bd24f8b270c1dea'] dependencies = [ ('Python', '2.7.15'), ('bnpy', '0.1.6', versionsuffix), - ('ant', '1.10.5', '-Java-1.8', True), # (Optional) needed for preprocessing script - # ('MATLAB', '2018b', '', True), # (Optional) provides interface to Matlab + ('ant', '1.10.5', '-Java-1.8', SYSTEM), # (Optional) needed for preprocessing script + # ('MATLAB', '2018b', '', SYSTEM), # (Optional) provides interface to Matlab ] cmds_map = [('', "ant")] diff --git a/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb index 003fb9008b0..fd542467800 100644 --- a/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb @@ -27,7 +27,7 @@ parallel = 1 builddependencies = [ ('binutils', '2.35'), - ('Pandoc', '2.10', '', True), + ('Pandoc', '2.10', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-8.3.0.eb index 5675584ba3d..cbf5ee21bc6 100644 --- a/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-8.3.0.eb @@ -23,7 +23,7 @@ parallel = 1 builddependencies = [ ('binutils', '2.32'), - ('Pandoc', '2.10', '', True), + ('Pandoc', '2.10', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb index 3bf1060dd25..ad59ec63441 100755 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb @@ -17,8 +17,8 @@ local_pymajmin = local_pymaj + local_pymin dependencies = [ ('Python', '%s.%s.2' % (local_pymaj, local_pymin)), ('protobuf-python', '3.3.0', local_pythonsuffix), - ('CUDA', '8.0.44', '', True), - ('cuDNN', '5.1', '-CUDA-8.0.44', True), + ('CUDA', '8.0.44', '', SYSTEM), + ('cuDNN', '5.1', '-CUDA-8.0.44', SYSTEM), ] exts_list = [ diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb index 5cae5dc8c13..54fdbc44964 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb @@ -18,7 +18,7 @@ builddependencies = [ ('pybind11', '2.4.3', versionsuffix), ] dependencies = [ - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ('Python', '3.8.2'), ('h5py', '2.10.0', versionsuffix), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index 0feb8006d4d..110b07df5a5 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -19,7 +19,7 @@ builddependencies = [ ('UnZip', '6.0'), ] dependencies = [ - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ('Python', '3.8.6'), # Next 2 are for h5py diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index c1662ad3a3b..b4daf67aaa3 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -19,7 +19,7 @@ builddependencies = [ ('UnZip', '6.0'), ] dependencies = [ - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ('Python', '3.8.6'), ('h5py', '3.1.0'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb index 59a083f5333..0ac39221678 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb @@ -19,7 +19,7 @@ builddependencies = [ ('UnZip', '6.0'), ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('cuDNN', '8.2.1.32', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb index bb846c638fc..8c4c862c922 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb @@ -19,7 +19,7 @@ builddependencies = [ ('UnZip', '6.0'), ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('cuDNN', '8.2.1.32', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb index 1cd3c17f6d0..24cafa17438 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb @@ -20,7 +20,7 @@ builddependencies = [ ('LLVM', '12.0.1'), # for debugging with llvm-symbolizer, to be removed ] dependencies = [ - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('cuDNN', '8.2.2.26', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.6'), diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb index c7c4aba1c1b..7acce00ef7d 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb @@ -19,7 +19,7 @@ checksums = ['5da6c2242ea72a991c8446d7fe7d35189ea346ef7d024c890397011114bf10fc'] dependencies = [ ('Python', '3.8.6'), ('libgpuarray', '0.7.6'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('SciPy-bundle', '2020.11'), ] diff --git a/easybuild/easyconfigs/t/Tracer/Tracer-1.7.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/t/Tracer/Tracer-1.7.1-GCCcore-8.2.0.eb index ee85d771a64..0cf3c7d492b 100644 --- a/easybuild/easyconfigs/t/Tracer/Tracer-1.7.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/t/Tracer/Tracer-1.7.1-GCCcore-8.2.0.eb @@ -18,7 +18,7 @@ sources = [{'download_filename': '%(name)s_v%(version)s.tgz', 'filename': SOURCE checksums = ['200d7ffa1e48994b71245994e299847ac2be72d3d5c37d9048418557e1d8c12e'] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Mesa', '19.0.1'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb index b6070a5118c..5a6e085b08a 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb @@ -21,7 +21,7 @@ source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s' install_cmd = "cp -a %(namelower)s_zip/* %(installdir)s && chmod +x %(installdir)s/%(namelower)s" dependencies = [ - ('FastQC', '0.11.5', '-Java-1.7.0_80', True), + ('FastQC', '0.11.5', '-Java-1.7.0_80', SYSTEM), ('cutadapt', '1.9.1', '-Python-2.7.12'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb index ed3b6794101..132db8b33b2 100755 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb @@ -21,7 +21,7 @@ source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s' install_cmd = "cp -a * %(installdir)s && chmod +x %(installdir)s/%(namelower)s" dependencies = [ - ('FastQC', '0.11.5', '-Java-1.7.0_80', True), + ('FastQC', '0.11.5', '-Java-1.7.0_80', SYSTEM), ('cutadapt', '1.9.1', '-Python-2.7.12'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb index 934d2bd4129..5dd29ffb263 100755 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb @@ -22,7 +22,7 @@ install_cmd = "cp -a * %(installdir)s && chmod +x %(installdir)s/%(namelower)s & install_cmd += "sed -i '1 i#!/usr/bin/env perl' %(installdir)s/%(namelower)s" dependencies = [ - ('FastQC', '0.11.5', '-Java-1.8.0_144', True), + ('FastQC', '0.11.5', '-Java-1.8.0_144', SYSTEM), ('cutadapt', '1.14', '-Python-2.7.13'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-foss-2018b.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-foss-2018b.eb index 751ec831e27..939e4aa653a 100755 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-foss-2018b.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-foss-2018b.eb @@ -15,7 +15,7 @@ sources = ['%(version)s.tar.gz'] checksums = ['9a7966bcfdea5d8c4f14c669904fb44693ac5d9392caa4d49dd11254a0a6753d'] dependencies = [ - ('FastQC', '0.11.8', '-Java-1.8', True), + ('FastQC', '0.11.8', '-Java-1.8', SYSTEM), ('cutadapt', '1.18', '-Python-3.6.6'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-intel-2018b-Python-3.6.6.eb index 54a9e8723f4..9fffbfd9a38 100755 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-intel-2018b-Python-3.6.6.eb @@ -16,7 +16,7 @@ sources = ['%(version)s.tar.gz'] checksums = ['9a7966bcfdea5d8c4f14c669904fb44693ac5d9392caa4d49dd11254a0a6753d'] dependencies = [ - ('FastQC', '0.11.8', '-Java-1.8', True), + ('FastQC', '0.11.8', '-Java-1.8', SYSTEM), ('cutadapt', '1.18', versionsuffix), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-2.7.15.eb index e30697fa9a2..50baaf11de7 100755 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-2.7.15.eb @@ -17,7 +17,7 @@ checksums = ['f374dfa4c94e2ad50c63276dda0f341fd95b29cb1d5a0e2ad56e8b0168b758ec'] dependencies = [ ('Python', '2.7.15'), - ('FastQC', '0.11.8', '-Java-1.8', True), + ('FastQC', '0.11.8', '-Java-1.8', SYSTEM), ('cutadapt', '1.18', versionsuffix), ('Perl', '5.28.0'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-3.6.6.eb index f03c582405b..d4df9526da5 100755 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-3.6.6.eb @@ -18,7 +18,7 @@ checksums = ['f374dfa4c94e2ad50c63276dda0f341fd95b29cb1d5a0e2ad56e8b0168b758ec'] dependencies = [ ('Python', '3.6.6'), # multi-core support requires Python 3.x + pigz ('pigz', '2.4'), - ('FastQC', '0.11.8', '-Java-1.8', True), + ('FastQC', '0.11.8', '-Java-1.8', SYSTEM), ('cutadapt', '1.18', versionsuffix), ('Perl', '5.28.0'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-2.7.15.eb index 96d93d982ce..aabeeaa87aa 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-2.7.15.eb @@ -22,7 +22,7 @@ checksums = ['658578c29d007fe66f9ab49608442be703a6fcf535db06eb82659c7edccb62b0'] dependencies = [ ('Python', '2.7.15'), ('Perl', '5.28.0'), - ('FastQC', '0.11.8', '-Java-1.8', True), + ('FastQC', '0.11.8', '-Java-1.8', SYSTEM), ('cutadapt', '1.18', versionsuffix) ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-3.6.6.eb index 07037434493..7a5caa1e5a3 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-3.6.6.eb @@ -23,7 +23,7 @@ dependencies = [ ('Python', '3.6.6'), # multi-core support requires Python 3.x + pigz ('pigz', '2.4'), ('Perl', '5.28.0'), - ('FastQC', '0.11.8', '-Java-1.8', True), + ('FastQC', '0.11.8', '-Java-1.8', SYSTEM), ('cutadapt', '1.18', versionsuffix) ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-GCCcore-8.2.0-Java-11.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-GCCcore-8.2.0-Java-11.eb index 2cd8ff63867..43cccd80beb 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-GCCcore-8.2.0-Java-11.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-GCCcore-8.2.0-Java-11.eb @@ -28,10 +28,10 @@ multi_deps = {'Python': ['3.7.2', '2.7.15']} builddependencies = [('binutils', '2.31.1')] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('pigz', '2.4'), ('Perl', '5.28.1'), - ('FastQC', '0.11.8', '-Java-11', True), + ('FastQC', '0.11.8', '-Java-11', SYSTEM), ('cutadapt', '1.18'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-2.7.15.eb index cf2e0c9f7dc..a8df5a83fbe 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-2.7.15.eb @@ -22,7 +22,7 @@ checksums = ['c50b841bdc294a6cdc6a27fb7bfbed1973541d20a68a4708584b817c58b3f376'] dependencies = [ ('Python', '2.7.15'), ('Perl', '5.28.0'), - ('FastQC', '0.11.8', '-Java-1.8', True), + ('FastQC', '0.11.8', '-Java-1.8', SYSTEM), ('cutadapt', '1.18', versionsuffix) ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-3.6.6.eb index b4fc90cc570..d6fb92d2cb4 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-3.6.6.eb @@ -23,7 +23,7 @@ dependencies = [ ('Python', '3.6.6'), # multi-core support requires Python 3.x + pigz ('pigz', '2.4'), ('Perl', '5.28.0'), - ('FastQC', '0.11.8', '-Java-1.8', True), + ('FastQC', '0.11.8', '-Java-1.8', SYSTEM), ('cutadapt', '1.18', versionsuffix) ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.5-GCCcore-8.3.0-Java-11-Python-3.7.4.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.5-GCCcore-8.3.0-Java-11-Python-3.7.4.eb index b7d71152b88..e3c7224c9f5 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.5-GCCcore-8.3.0-Java-11-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.5-GCCcore-8.3.0-Java-11-Python-3.7.4.eb @@ -27,10 +27,10 @@ builddependencies = [('binutils', '2.32')] dependencies = [ ('Python', '3.7.4'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('pigz', '2.4'), ('Perl', '5.30.0'), - ('FastQC', '0.11.9', '-Java-%(javaver)s', True), + ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), ('cutadapt', '2.7', '-Python-%(pyver)s'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb index add75646761..36e73454652 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb @@ -25,10 +25,10 @@ builddependencies = [('binutils', '2.35')] dependencies = [ ('Python', '2.7.18'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('pigz', '2.6'), ('Perl', '5.32.0'), - ('FastQC', '0.11.9', '-Java-%(javaver)s', True), + ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), ('cutadapt', '1.18', versionsuffix), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb index e55fe4ccfae..48d1f2c85a2 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb @@ -27,10 +27,10 @@ builddependencies = [('binutils', '2.34')] dependencies = [ ('Python', '3.8.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('pigz', '2.4'), ('Perl', '5.30.2'), - ('FastQC', '0.11.9', '-Java-%(javaver)s', True), + ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), ('cutadapt', '2.10', '-Python-%(pyver)s'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb index cf5350b94a4..495deb9a976 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb @@ -25,11 +25,11 @@ checksums = [ dependencies = [ ('Python', '3.9.5'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('pigz', '2.6'), ('Perl', '5.32.1'), ('cutadapt', '3.4'), - ('FastQC', '0.11.9', '-Java-%(javaver)s', True), + ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), ] postinstallcmds = [ diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.38-Java-1.8.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.38-Java-1.8.eb index da61b4d7b33..80d1c83a61f 100644 --- a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.38-Java-1.8.eb +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.38-Java-1.8.eb @@ -20,7 +20,7 @@ source_urls = ['http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/' sources = [SOURCE_ZIP] checksums = ['d428af42b6c400a2e7ee5e6b4cab490eddc621f949b086bd7dddb698dcf1647c'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] modloadmsg = """To execute Trimmomatic run: java -jar $EBROOTTRIMMOMATIC/trimmomatic-%(version)s.jar\n""" diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.10.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.10.0-foss-2019b-Python-3.7.4.eb index 009b1080766..5f6beb23aa6 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.10.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.10.0-foss-2019b-Python-3.7.4.eb @@ -30,8 +30,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ('Perl', '5.30.0'), ('Python', '3.7.4'), ('SciPy-bundle', '2019.10', versionsuffix), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb index b4e2affc990..65072fe8b8e 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb @@ -26,8 +26,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.8.0_92', '', True), - ('ant', '1.9.7', '-Java-%(javaver)s', True), + ('Java', '1.8.0_92', '', SYSTEM), + ('ant', '1.9.7', '-Java-%(javaver)s', SYSTEM), ('Bowtie', '1.1.2'), ('Bowtie2', '2.2.8'), ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb index 98a63c78c78..044419c7ace 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb @@ -25,8 +25,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.8.0_121', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_121', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('Bowtie', '1.1.2'), ('Bowtie2', '2.3.2'), ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017a.eb index b081019d430..834721f2ac7 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017a.eb @@ -28,8 +28,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.8.0_152', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_152', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('Bowtie', '1.1.2'), ('Bowtie2', '2.3.2'), ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017b.eb index 75a7be3a9af..29331247179 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017b.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017b.eb @@ -28,8 +28,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.8.0_152', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_152', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('Bowtie', '1.2.2'), ('Bowtie2', '2.3.4'), ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb index 35b020b401a..5e8309a25ee 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb @@ -27,8 +27,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.8.0_162', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_162', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('Bowtie', '1.2.2'), ('Bowtie2', '2.3.4.1'), ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.8.4-foss-2018b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.8.4-foss-2018b.eb index 655df5ae21a..2f8bbf8e3f6 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.8.4-foss-2018b.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.8.4-foss-2018b.eb @@ -19,8 +19,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.8', '', True), - ('ant', '1.10.5', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('ant', '1.10.5', '-Java-%(javaver)s', SYSTEM), ('Bowtie', '1.2.2'), ('Bowtie2', '2.3.4.2'), ('ncurses', '6.1'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.8.5-GCC-8.3.0-Java-11.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.8.5-GCC-8.3.0-Java-11.eb index aaf6957b7ae..8d8703a5561 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.8.5-GCC-8.3.0-Java-11.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.8.5-GCC-8.3.0-Java-11.eb @@ -26,7 +26,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('ant', '1.10.7', versionsuffix, True), ('Bowtie', '1.2.3'), ('Bowtie2', '2.3.5.1'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.8.5-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.8.5-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index eeef16155fb..654e032e6c6 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.8.5-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.8.5-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -25,8 +25,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.8', '', True), - ('ant', '1.10.5', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('ant', '1.10.5', '-Java-%(javaver)s', SYSTEM), ('Bowtie', '1.2.3'), ('Bowtie2', '2.3.5.1'), ('ncurses', '6.1'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2019b-Python-2.7.16.eb index 706bcf94ecb..3ca740f8aab 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2019b-Python-2.7.16.eb @@ -30,8 +30,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ('Perl', '5.30.0'), ('Python', '2.7.16'), ('SciPy-bundle', '2019.10', versionsuffix), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2019b-Python-3.7.4.eb index 92750de5d52..923a3cd1f94 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2019b-Python-3.7.4.eb @@ -30,8 +30,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ('Perl', '5.30.0'), ('Python', '3.7.4'), ('SciPy-bundle', '2019.10', versionsuffix), diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb index 7522e28d255..843aa1c597d 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb @@ -29,7 +29,7 @@ source_urls = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] dependencies = [('ncurses', '6.0')] diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-6.4.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-6.4.0.eb index fcc5a44425a..5586784fcf2 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-6.4.0.eb @@ -30,7 +30,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['b89de7064ab54dac454a266cfe5d8bf66940cb5ed048d0c30674ea62e7ecef9d'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.28', '', True)] +builddependencies = [('binutils', '2.28', '', SYSTEM)] dependencies = [('ncurses', '6.0')] diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb index bb013b1619c..0e32b78cf2d 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb @@ -15,7 +15,7 @@ source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a-CUDA-11.3.1.eb index 14ac4f4f602..6e1e1c39fdf 100644 --- a/easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a-CUDA-11.3.1.eb @@ -18,7 +18,7 @@ dependencies = [ ('PyTorch', '1.10.0', versionsuffix), ('torchvision', '0.11.1', versionsuffix), ('scikit-learn', '0.24.2'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] use_pip = True diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.11.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.11.1-foss-2021a-CUDA-11.3.1.eb index 7e64e72a452..d3755b1e9fc 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.11.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.11.1-foss-2021a-CUDA-11.3.1.eb @@ -17,7 +17,7 @@ dependencies = [ ('Python', '3.9.5'), ('Pillow-SIMD', '8.2.0'), ('PyTorch', '1.10.0', '-CUDA-%(cudaver)s'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] # Defaults. Can be changed with --cuda-compute-capabilities diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.11.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.11.3-foss-2021a-CUDA-11.3.1.eb index 3eb21ffbed3..7c591865f3a 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.11.3-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.11.3-foss-2021a-CUDA-11.3.1.eb @@ -14,7 +14,7 @@ checksums = ['b4c51d27589783e6e6941ecaa67b55f6f41633874ec37f80b64a0c92c3196e0c'] builddependencies = [('CMake', '3.20.1')] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('Pillow-SIMD', '8.2.0'), ('PyTorch', '1.10.0', versionsuffix), diff --git a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb index ebf9a1d24b8..41eb21d1767 100644 --- a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb @@ -19,7 +19,7 @@ source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e'] -builddependencies = [('binutils', '2.36.1', '', True)] +builddependencies = [('binutils', '2.36.1', '', SYSTEM)] start_dir = 'source' files_to_copy = [(['trimal', 'readal', 'statal'], 'bin')] diff --git a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-9.3.0.eb index a509e00b02e..52c4b51c8b1 100644 --- a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-9.3.0.eb @@ -16,7 +16,7 @@ github_account = 'scapella' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e'] -builddependencies = [('binutils', '2.34', '', True)] +builddependencies = [('binutils', '2.34', '', SYSTEM)] start_dir = 'source' files_to_copy = [(['trimal', 'readal', 'statal'], 'bin')] diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb index bf163fd4655..e213c78d3b7 100644 --- a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb @@ -33,7 +33,7 @@ builddependencies = [ dependencies = [ ('UCC', '1.0.0'), - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('UCX-CUDA', '1.12.1', '-CUDA-%(cudaver)s'), ('NCCL', '2.12.12', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.10.0-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.10.0-GCCcore-10.3.0-CUDA-11.3.1.eb index 67d9cdb0044..70a85299c29 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.10.0-GCCcore-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.10.0-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -35,7 +35,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), ('UCX', version), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('GDRCopy', '2.2'), ] diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb index 1dad569119f..ce3211904db 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -35,7 +35,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), ('UCX', version), - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('GDRCopy', '2.3'), ] diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb index bc3201ec688..d5f4602d19f 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -35,7 +35,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), ('UCX', version), - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('GDRCopy', '2.3'), ] diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb index 7bf9d3c8710..0fb175ca066 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb @@ -35,7 +35,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.12'), ('UCX', version), - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('GDRCopy', '2.3'), ] diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb index cc2d5938c65..bfafd2ff9cd 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -38,7 +38,7 @@ osdependencies = [OS_PKG_IBVERBS_DEV] dependencies = [ ('numactl', '2.0.13'), - ('CUDAcore', local_cudaversion, '', True), + ('CUDAcore', local_cudaversion, '', SYSTEM), ('GDRCopy', '2.1', versionsuffix), ] diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb index 48c65be2945..4f58f9acc83 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -30,7 +30,7 @@ osdependencies = [OS_PKG_IBVERBS_DEV] dependencies = [ ('numactl', '2.0.13'), - ('CUDAcore', local_cudaversion, '', True), + ('CUDAcore', local_cudaversion, '', SYSTEM), ('GDRCopy', '2.1', versionsuffix), ] diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb index fd3d6e7b5dc..11fabfc2ea7 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb @@ -30,7 +30,7 @@ osdependencies = [OS_PKG_IBVERBS_DEV] dependencies = [ ('numactl', '2.0.13'), - ('CUDAcore', local_cudaversion, '', True), + ('CUDAcore', local_cudaversion, '', SYSTEM), ('GDRCopy', '2.1', versionsuffix), ] diff --git a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.7-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.7-foss-2019a-Python-3.7.2.eb index 890acbbf6f4..a83700d58cd 100644 --- a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.7-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.7-foss-2019a-Python-3.7.2.eb @@ -17,12 +17,12 @@ checksums = ['a8cf65e46dc2694b0fbd4e9190c73a1f300921457aadfab27a1792b785620d63'] dependencies = [ ('Python', '3.7.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Bowtie2', '2.3.5.1'), ('SAMtools', '1.9'), ('SPAdes', '3.13.1'), ('Racon', '1.3.2'), - ('Pilon', '1.23', '-Java-%(javaver)s', True), + ('Pilon', '1.23', '-Java-%(javaver)s', SYSTEM), ('BLAST+', '2.9.0'), ] diff --git a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.8-gompi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.8-gompi-2020a-Python-3.8.2.eb index 70ef7ebfed1..ae461e506cd 100644 --- a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.8-gompi-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.8-gompi-2020a-Python-3.8.2.eb @@ -17,12 +17,12 @@ checksums = ['e948871e4de9db5964c9ca6f8f877c3cbe6a46f62052dfab52ffe0f45bbbd203'] dependencies = [ ('Python', '3.8.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Bowtie2', '2.4.1'), ('SAMtools', '1.10'), ('SPAdes', '3.14.1', versionsuffix), ('Racon', '1.4.13'), - ('Pilon', '1.23', '-Java-%(javaver)s', True), + ('Pilon', '1.23', '-Java-%(javaver)s', SYSTEM), ('BLAST+', '2.10.1'), ] diff --git a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb index 2e9b8f68fe0..1ca53bc8f78 100644 --- a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb +++ b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb @@ -16,12 +16,12 @@ checksums = ['84bea8f3e8f99a1e63e5230ffe474a696db8caa67569c3a96ae12906d32a35eb'] dependencies = [ ('Python', '3.9.5'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Bowtie2', '2.4.4'), ('SAMtools', '1.13'), ('SPAdes', '3.13.0'), ('Racon', '1.4.21'), - ('Pilon', '1.23', '-Java-%(javaver)s', True), + ('Pilon', '1.23', '-Java-%(javaver)s', SYSTEM), ('BLAST+', '2.11.0'), ] diff --git a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb index 712952beb6f..3fc79ebf2db 100644 --- a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb @@ -17,12 +17,12 @@ checksums = ['84a8709c9f2e624225410af702d779ffb0cb06f7c22c20e1f01b989945e08a47'] dependencies = [ ('Python', '3.9.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Bowtie2', '2.4.4'), ('SAMtools', '1.14'), ('SPAdes', '3.15.3'), ('Racon', '1.5.0'), - ('Pilon', '1.23', '-Java-%(javaver)s', True), + ('Pilon', '1.23', '-Java-%(javaver)s', SYSTEM), ('BLAST+', '2.12.0'), ] diff --git a/easybuild/easyconfigs/u/units/units-2.19-GCCcore-8.2.0.eb b/easybuild/easyconfigs/u/units/units-2.19-GCCcore-8.2.0.eb index 72f4c73aa6c..d86c35faedf 100644 --- a/easybuild/easyconfigs/u/units/units-2.19-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/u/units/units-2.19-GCCcore-8.2.0.eb @@ -17,7 +17,7 @@ checksums = ['4262136bdfc152b63ff5a9b93a7d80ce18b5e8bebdcffddc932dda769e306556'] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.31.1', '', True), + ('binutils', '2.31.1', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a43-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a43-fosscuda-2019b-Python-3.7.4.eb index 5c2bcb96f52..331d66698e0 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a43-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a43-fosscuda-2019b-Python-3.7.4.eb @@ -54,7 +54,7 @@ dependencies = [ ('FFmpeg', '4.2.1'), ('ImageMagick', '7.0.9-5'), ('ACTC', '1.1'), - ('OptiX', '6.5.0', '', True), + ('OptiX', '6.5.0', '', SYSTEM), ('zlib', '1.2.11'), ('libpng', '1.6.37'), ] diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb index 854dade5cbe..0ad4daad390 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb @@ -52,7 +52,7 @@ dependencies = [ ('FFmpeg', '4.3.1'), ('ImageMagick', '7.0.10-35'), ('ACTC', '1.1'), - ('OptiX', '6.5.0', '', True), + ('OptiX', '6.5.0', '', SYSTEM), ('zlib', '1.2.11'), ('libpng', '1.6.37'), ('POV-Ray', '3.7.0.8'), diff --git a/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb index daa2ad6b936..ae2ec85f0ff 100644 --- a/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb @@ -17,9 +17,9 @@ dependencies = [ ('BioPerl', '1.6.924', '-Perl-%(perlver)s'), ('HMMER', '3.1b2'), ('MCL', '14.137'), - ('MetaGeneAnnotator', '20080819', '-x86-64', True), + ('MetaGeneAnnotator', '20080819', '-x86-64', SYSTEM), ('MUSCLE', '3.8.31'), - ('BLAST', '2.2.26', '-Linux_x86_64', True), + ('BLAST', '2.2.26', '-Linux_x86_64', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-GCC-10.3.0.eb b/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-GCC-10.3.0.eb index 6b38503aeb7..01fc5ff1dce 100644 --- a/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-GCC-10.3.0.eb @@ -30,7 +30,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ('libreadline', '8.1'), ] diff --git a/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb index fa730a6cadd..076c0558ad7 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb @@ -13,8 +13,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/hpcugent/vsc-mympirun-scoop/archive/'] dependencies = [ - ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', True), - ('vsc-mympirun', '3.4.2', '', True), + ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', SYSTEM), + ('vsc-mympirun', '3.4.2', '', SYSTEM), ('Python', '2.7.12'), ('SCOOP', '0.6.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/w/WCT/WCT-4.6.0-Java-11.eb b/easybuild/easyconfigs/w/WCT/WCT-4.6.0-Java-11.eb index a889d75fa0b..0b5db53df8a 100644 --- a/easybuild/easyconfigs/w/WCT/WCT-4.6.0-Java-11.eb +++ b/easybuild/easyconfigs/w/WCT/WCT-4.6.0-Java-11.eb @@ -22,7 +22,7 @@ source_urls = ['https://www.ncdc.noaa.gov/wct/app/dist/'] sources = ['%(namelower)s-%(version)s.zip'] checksums = ['951ba0137582d2cd33e18ec61e1bb63c8f775b4ddf23bb21b4784b7ef5d28aad'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb index c6ac6a93321..f9313fcbc6e 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb @@ -26,7 +26,7 @@ dependencies = [ ('PCRE', '8.44'), ('libidn2', '2.3.0'), ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date gnutls for security reasons # ('GnuTLS', '3.7.1'), diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb index 3c7a5559b3a..3e0a4fdaa71 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb @@ -26,7 +26,7 @@ dependencies = [ ('PCRE', '8.45'), ('libidn2', '2.3.2'), ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date gnutls for security reasons # ('GnuTLS', '3.7.1'), diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-GCCcore-5.4.0.eb b/easybuild/easyconfigs/x/X11/X11-20160819-GCCcore-5.4.0.eb index 57e58e0097f..7732b3063a7 100644 --- a/easybuild/easyconfigs/x/X11/X11-20160819-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20160819-GCCcore-5.4.0.eb @@ -20,7 +20,7 @@ source_urls = [ builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ('Autotools', '20150215'), ('Bison', '3.0.4'), ('gettext', '0.19.8'), diff --git a/easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb index f7fe477cb1b..c7c2384daaa 100644 --- a/easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb @@ -26,7 +26,7 @@ dependencies = [ ] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ('Autotools', '20150215'), ('Bison', '3.0.4'), ('gettext', '0.19.8.1'), diff --git a/easybuild/easyconfigs/x/X11/X11-20170129-gimkl-2017a.eb b/easybuild/easyconfigs/x/X11/X11-20170129-gimkl-2017a.eb index cfe2be0316b..f0f68e4c70a 100644 --- a/easybuild/easyconfigs/x/X11/X11-20170129-gimkl-2017a.eb +++ b/easybuild/easyconfigs/x/X11/X11-20170129-gimkl-2017a.eb @@ -23,9 +23,9 @@ dependencies = [ ('zlib', '1.2.11'), ] builddependencies = [ - ('Autotools', '20150215', '', True), + ('Autotools', '20150215', '', SYSTEM), ('Bison', '3.0.4'), - ('gettext', '0.19.8', '', True), + ('gettext', '0.19.8', '', SYSTEM), ('pkg-config', '0.29.1'), ('intltool', '0.51.0', '-Perl-5.24.0') ] diff --git a/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb index e36cb012947..4b11b1d6bfa 100644 --- a/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb @@ -26,7 +26,7 @@ dependencies = [ ] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ('Autotools', '20150215'), ('Bison', '3.0.4'), ('gettext', '0.19.8.1'), diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-20171120-intel-2017b-Java-1.8.0_152.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-20171120-intel-2017b-Java-1.8.0_152.eb index 3fb7c1d49dd..71022a19045 100644 --- a/easybuild/easyconfigs/x/XGBoost/XGBoost-20171120-intel-2017b-Java-1.8.0_152.eb +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-20171120-intel-2017b-Java-1.8.0_152.eb @@ -24,7 +24,7 @@ sources = [{ checksums = [None] builddependencies = [('CMake', '3.9.5')] -dependencies = [('Java', '1.8.0_152', '', True)] +dependencies = [('Java', '1.8.0_152', '', SYSTEM)] buildopts = " && cd jvm-packages && mvn install -Dmaven.repo.local=%(builddir)s/m2" diff --git a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb index 1c770debd8e..dd1c04c7392 100644 --- a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb +++ b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb @@ -20,7 +20,7 @@ builddependencies = [ ('gettext', '0.19.7'), ('intltool', '0.51.0', '-Perl-5.22.1'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb index ce56b41359e..a565c8676f4 100644 --- a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb +++ b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb @@ -20,7 +20,7 @@ builddependencies = [ ('gettext', '0.19.7'), ('intltool', '0.51.0', '-Perl-5.22.1'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb index 0423282a108..3f6ba215d4d 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', True), + ('gettext', '0.19.8', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb index 6c49a4458b9..ec46a64b897 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', True), + ('gettext', '0.19.8', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb index 001a737c6ef..3082194c6b5 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', True), + ('gettext', '0.19.8', '', SYSTEM), ('binutils', '2.25'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb index c9e9efec327..c705099c18c 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb @@ -17,9 +17,9 @@ checksums = [ ] builddependencies = [ - ('gettext', '0.19.8', '', True), + ('gettext', '0.19.8', '', SYSTEM), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb index 08aad5d870e..1ba4448757e 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', True), + ('gettext', '0.19.8', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb index 8b076ecba44..96249ed4220 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb @@ -18,7 +18,7 @@ versionsuffix = '-gettext-%s' % local_gettext_ver builddependencies = [ ('Autotools', '20150215'), - ('gettext', local_gettext_ver, '', True), + ('gettext', local_gettext_ver, '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb index a0c7f313e03..0c774d43908 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.6', '', True), + ('gettext', '0.19.6', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb index e891d5536ae..64b7587aa4a 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', True), + ('gettext', '0.19.8', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb index d8184d70d32..3393bb06e20 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb @@ -18,7 +18,7 @@ versionsuffix = '-gettext-%s' % local_gettext_ver builddependencies = [ ('Autotools', '20150215'), - ('gettext', local_gettext_ver, '', True), + ('gettext', local_gettext_ver, '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb index fdf1453ac4a..243db8e7d90 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.6', '', True), + ('gettext', '0.19.6', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb index 85431b3d6e9..60aeff8c712 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', True), + ('gettext', '0.19.8', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb index 735c3cbe5ba..8ac99515760 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb @@ -14,9 +14,9 @@ source_urls = ['http://tukaani.org/xz/'] patches = ['XZ-5.2.2_compat-libs.patch'] builddependencies = [ - ('gettext', '0.19.8.1', '', True), + ('gettext', '0.19.8.1', '', SYSTEM), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb index c02558f16a4..e6e62af6bf5 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb @@ -18,7 +18,7 @@ checksums = [ builddependencies = [ # use gettext built with dummy as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.19.8.1', '', True), + ('gettext', '0.19.8.1', '', SYSTEM), # use same binutils version that was used when building GCCcore toolchain ('binutils', '2.28'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb index cc9e04a5714..8cc83b07a7f 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb @@ -17,8 +17,8 @@ patches = ['XZ-5.2.2_compat-libs.patch'] # XZ (presumably its executables) depends on gettext, which depends on # xmllib2, which depends (optionally) on XZ builddependencies = [ - ('Autotools', '20150215', '', True), - ('gettext', '0.19.8', '', True), + ('Autotools', '20150215', '', SYSTEM), + ('gettext', '0.19.8', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.2.0.eb index 34d93c09f7b..072decdbb68 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.2.0.eb @@ -18,7 +18,7 @@ checksums = [ builddependencies = [ # use gettext built with dummy as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.19.8.1', '', True), + ('gettext', '0.19.8.1', '', SYSTEM), # use same binutils version that was used when building GCCcore toolchain ('binutils', '2.29'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.3.0.eb index 4807e850e05..90c2e0ed3e8 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.3.0.eb @@ -18,7 +18,7 @@ checksums = [ builddependencies = [ # use gettext built with dummy as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.19.8.1', '', True), + ('gettext', '0.19.8.1', '', SYSTEM), # use same binutils version that was used when building GCCcore toolchain ('binutils', '2.30'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.2.0.eb index e082fd1cfcb..4447786633d 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.2.0.eb @@ -18,7 +18,7 @@ checksums = [ builddependencies = [ # use gettext built with dummy as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.19.8.1', '', True), + ('gettext', '0.19.8.1', '', SYSTEM), # use same binutils version that was used when building GCCcore toolchain ('binutils', '2.31.1'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.3.0.eb index cd9e93e00e0..0d03926cd60 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.3.0.eb @@ -18,7 +18,7 @@ checksums = [ builddependencies = [ # use gettext built with dummy as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.19.8.1', '', True), + ('gettext', '0.19.8.1', '', SYSTEM), # use same binutils version that was used when building GCCcore toolchain ('binutils', '2.32'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-9.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-9.2.0.eb index 368d09a41f9..1622d47af78 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-9.2.0.eb @@ -18,7 +18,7 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.20.1', '', True), + ('gettext', '0.20.1', '', SYSTEM), ('binutils', '2.32'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb index d39dadea0a5..c7d8e9fe1d7 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb @@ -32,7 +32,7 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.20.1', '', True), + ('gettext', '0.20.1', '', SYSTEM), ('binutils', '2.34'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb index e54a2560c6d..2ba344e0acb 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb @@ -32,7 +32,7 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.21', '', True), + ('gettext', '0.21', '', SYSTEM), ('binutils', '2.35'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb index c02c4e17cc9..2f9102b6d69 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb @@ -25,7 +25,7 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.21', '', True), + ('gettext', '0.21', '', SYSTEM), ('binutils', '2.36.1'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb index f6a70e9b211..a482f548042 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb @@ -25,7 +25,7 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.21', '', True), + ('gettext', '0.21', '', SYSTEM), ('binutils', '2.37'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb index 2ee4825b700..c965c1e1efa 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb @@ -25,7 +25,7 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.21', '', True), + ('gettext', '0.21', '', SYSTEM), ('binutils', '2.38'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb index 22e7b6ed6ef..73a74e9e92a 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb @@ -22,7 +22,7 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.20.1', '', True), + ('gettext', '0.20.1', '', SYSTEM), ('binutils', '2.34'), ] diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.19.04-Apollo-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.19.04-Apollo-foss-2019a-Python-2.7.15.eb index 69c5636677f..4923b4db8d7 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.19.04-Apollo-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.19.04-Apollo-foss-2019a-Python-2.7.15.eb @@ -76,7 +76,7 @@ builddependencies = [ dependencies = [ ('Python', '2.7.15'), ('SciPy-bundle', '2019.03'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('OpenCV', '3.4.7', versionsuffix), ('SQLite', '3.27.2'), ('HDF5', '1.10.5'), diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.19.04-Apollo-fosscuda-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.19.04-Apollo-fosscuda-2019a-Python-2.7.15.eb index 771ce085a68..2c960877bb0 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.19.04-Apollo-fosscuda-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.19.04-Apollo-fosscuda-2019a-Python-2.7.15.eb @@ -82,7 +82,7 @@ builddependencies = [ dependencies = [ ('Python', '2.7.15'), ('SciPy-bundle', '2019.03'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('OpenCV', '3.4.7', versionsuffix), ('SQLite', '3.27.2'), ('HDF5', '1.10.5'), diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb index 43b7d9e5a54..7551f83a6ff 100644 --- a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb @@ -12,7 +12,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb index 599b3a7ea3e..823375c47ae 100644 --- a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb @@ -12,7 +12,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb index 6694d3c8d1a..c61c6116cfc 100644 --- a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb index 6d95a13dc49..d6b82b3a951 100644 --- a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb index 20b75e6be45..e7c963b2128 100644 --- a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb @@ -12,7 +12,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb index 2470683fb8a..db62de8e619 100644 --- a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb @@ -12,7 +12,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb index 1c0793e3c1a..738376cb603 100644 --- a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb index c5509644a13..25da228279f 100644 --- a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb index 42b8d1faf07..8cbd9faeae4 100644 --- a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ] diff --git a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb index f862af46cb9..1dfef47a2f7 100644 --- a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ] diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb index 5ffb3e6b974..fe9d080b2b4 100755 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb @@ -24,7 +24,7 @@ checksums = ['0bb70872f45d9973db645123fe9fae9c587d1cc0ad1b3bfa67864c3f99adbd2a'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ('Autotools', '20150215'), ] diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb index 06e2a620f7b..4fdb9b6d636 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ source_urls = [XORG_PROTO_SOURCE] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ('xorg-macros', '1.19.1'), ] diff --git a/easybuild/easyconfigs/y/Yade/Yade-2018.02b-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/y/Yade/Yade-2018.02b-intel-2018a-Python-2.7.14.eb index a81eb292daf..3f708d997cf 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-2018.02b-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-2018.02b-intel-2018a-Python-2.7.14.eb @@ -43,7 +43,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.12.1'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] separate_build_dir = True diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.1.0.eb index a7164e8d8fc..169f8988f8e 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.1.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.34', '', True)] +builddependencies = [('binutils', '2.34', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb index c26c13b8e50..5a346a38f11 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.35', '', True)] +builddependencies = [('binutils', '2.35', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.3.0.eb index e6d6bbf5052..982b3609ed3 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.3.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.36.1', '', True)] +builddependencies = [('binutils', '2.36.1', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.1.0.eb index 38623a5181d..307df551e63 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.1.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.36.1', '', True)] +builddependencies = [('binutils', '2.36.1', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.2.0.eb index a7d80d3c9c2..dfca691dd42 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.2.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.37', '', True)] +builddependencies = [('binutils', '2.37', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb index 8409e2aa5cb..5d1b362aa15 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb @@ -15,7 +15,7 @@ source_urls = ['http://zlib.net/fossils'] sources = [SOURCELOWER_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.5.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.5.0.eb index bb5db1a26d2..734b6bda65c 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.5.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb index a15fb20fe64..520d56351d8 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb @@ -15,7 +15,7 @@ source_urls = ['http://zlib.net/fossils'] sources = [SOURCELOWER_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb index acbff073f4e..4cabf0a2d5d 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb @@ -20,7 +20,7 @@ checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain builddependencies = [ - ('binutils', '2.28', '', True), + ('binutils', '2.28', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb index bec9454ed8e..5ba01e22f5b 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb @@ -15,7 +15,7 @@ source_urls = ['http://zlib.net/fossils'] sources = [SOURCELOWER_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.28', '', True)] +builddependencies = [('binutils', '2.28', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.2.0.eb index 016a24fff22..ee843d04c0c 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.2.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.29', '', True)] +builddependencies = [('binutils', '2.29', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.3.0.eb index 6576f6849f4..9753d8d119d 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.3.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.30', '', True)] +builddependencies = [('binutils', '2.30', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.4.0.eb index b8e35c68d3a..0bb6e2b7da5 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.4.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.31.1', '', True)] +builddependencies = [('binutils', '2.31.1', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.1.0.eb index f97c6752989..3741db1cf3b 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.1.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.30', '', True)] +builddependencies = [('binutils', '2.30', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.2.0.eb index ec3c9d04c8e..20709893f33 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.2.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.31.1', '', True)] +builddependencies = [('binutils', '2.31.1', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.3.0.eb index b1c7a447036..b868b235321 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.3.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.32', '', True)] +builddependencies = [('binutils', '2.32', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.4.0.eb index 6c89bf42f36..a090047e74b 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.4.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.32', '', True)] +builddependencies = [('binutils', '2.32', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb index 25ecfcd4a9e..6649905e484 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.32', '', True)] +builddependencies = [('binutils', '2.32', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.2.0.eb index a5107c7bfea..dda890bf849 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.2.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.32', '', True)] +builddependencies = [('binutils', '2.32', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.3.0.eb index bbc278b1c0e..090662b5e71 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.3.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.34', '', True)] +builddependencies = [('binutils', '2.34', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.4.0.eb index 670d5940075..3a0036514da 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.4.0.eb @@ -17,7 +17,7 @@ checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain builddependencies = [ - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.3.0.eb index 31726b4af9d..0c3148f7ed0 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.3.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.38', '', True)] +builddependencies = [('binutils', '2.38', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.1.0.eb index 7cd1927d036..f31b53b8ff3 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.1.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.38', '', True)] +builddependencies = [('binutils', '2.38', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.2.0.eb index a9717ade39b..f7bcf94b72a 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.2.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.39', '', True)] +builddependencies = [('binutils', '2.39', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-9.5.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-9.5.0.eb index 67c423db857..b350c9f3c4f 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-9.5.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-9.5.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.38', '', True)] +builddependencies = [('binutils', '2.38', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb index 6aa4e52aa9e..8da5a8874c1 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb index 9ab612053c2..1221095c524 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb index 3475aad2a70..53d82c7a9a8 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb index a7b3977bb9a..274d794a4aa 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb index 1353624765d..360c1a11cb8 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb index 1b44bb97802..b5265dc9d78 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb index f4a9aac7763..a8a5212f418 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.4.0.eb index b139c1dc9a6..5117fda9bf4 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.4.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['36658cb768a54c1d4dec43c3116c27ed893e88b02ecfcb44f2166f9c0b7f2a0d'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb index 47a40a40359..55078920d1d 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb index ecd6eff1be1..16c8391ed1e 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb index 5c5b309e903..1b7951ca5cc 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb @@ -16,7 +16,7 @@ source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', # use same binutils version that was used when building GCC toolchain builddependencies = [ - ('binutils', '2.27', '', True) + ('binutils', '2.27', '', SYSTEM) ] sanity_check_paths = { From 9fc3b9b934a7625bed127ed5c20f0be1009623da Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 11 Oct 2022 11:17:15 +0100 Subject: [PATCH 310/793] remove unused import --- test/easyconfigs/easyconfigs.py | 1 - 1 file changed, 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 21c4692ec27..e749c268c42 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -42,7 +42,6 @@ from easybuild.easyblocks.generic.configuremake import ConfigureMake from easybuild.easyblocks.generic.pythonpackage import PythonPackage from easybuild.framework.easyblock import EasyBlock -from easybuild.framework.easyconfig.constants import EASYCONFIG_CONSTANTS from easybuild.framework.easyconfig.default import DEFAULT_CONFIG from easybuild.framework.easyconfig.format.format import DEPENDENCY_PARAMETERS from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, letter_dir_for From 4cb22e752342a1424e6267c1d62b0f355fb7f1cf Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 11 Oct 2022 12:20:06 +0100 Subject: [PATCH 311/793] make sure ModelTest-NG list is a list, not dict --- .../m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb b/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb index 7402e2f2b74..e07ae257936 100644 --- a/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb @@ -24,10 +24,10 @@ checksums = [None] builddependencies = [('CMake', '3.22.1')] -dependencies = { +dependencies = [ ('flex', '2.6.4'), ('Bison', '3.8.2', '', SYSTEM) -} +] files_to_copy = ['bin'] From f4ac9aa0777d7710d1938a8566c95c788e1c260f Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 11 Oct 2022 13:47:12 +0100 Subject: [PATCH 312/793] undo changes to archived easyconfigs --- .../__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb | 2 +- .../__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb | 2 +- .../easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb | 2 +- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb | 2 +- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb | 2 +- .../b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb | 4 ++-- .../b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb | 2 +- .../b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb | 2 +- .../b/beagle-lib/beagle-lib-20141202-intel-2015a.eb | 2 +- .../b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb | 2 +- .../b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb | 2 +- .../__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb | 2 +- .../d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb | 2 +- .../__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb | 2 +- .../__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb | 2 +- .../__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb | 2 +- .../__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb | 2 +- .../easyconfigs/__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb | 2 +- .../__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb | 2 +- .../g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb | 2 +- .../HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb | 4 ++-- .../HPCBIOS_Profilers-20130829-goolf-1.4.10.eb | 6 +++--- .../hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb | 4 ++-- .../hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb | 4 ++-- .../hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb | 4 ++-- .../hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb | 4 ++-- .../hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb | 2 +- .../hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb | 2 +- .../hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb | 2 +- .../hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb | 2 +- .../hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb | 2 +- .../i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb | 2 +- .../i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb | 2 +- .../jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb | 2 +- .../__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb | 4 ++-- ...DSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb | 2 +- .../MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb | 2 +- .../__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb | 4 ++-- .../__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb | 4 ++-- .../__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb | 2 +- .../__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb | 2 +- .../__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb | 2 +- .../__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb | 2 +- .../__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb | 2 +- .../__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb | 2 +- .../p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 2 +- .../p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb | 2 +- .../p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb | 2 +- .../p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb | 2 +- .../__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb | 2 +- .../__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb | 2 +- .../easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb | 2 +- .../__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb | 2 +- .../__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb | 2 +- .../__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.0-foss-2015a-bare.eb | 2 +- .../__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.0-intel-2015a-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b-bare.eb | 2 +- easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb | 2 +- easybuild/easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb | 2 +- .../s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb | 2 +- .../s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb | 2 +- .../s/Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb | 2 +- .../s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb | 2 +- .../s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb | 2 +- .../t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb | 2 +- .../__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb | 4 ++-- .../__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb | 4 ++-- .../__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb | 2 +- .../t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb | 2 +- .../__archive__/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb | 2 +- .../t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb | 2 +- .../vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb | 4 ++-- .../vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb | 4 ++-- .../vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb | 4 ++-- .../easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb | 2 +- .../easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb | 2 +- .../x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb | 2 +- .../x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb | 2 +- .../x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb | 2 +- 108 files changed, 124 insertions(+), 124 deletions(-) diff --git a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb index 539a0958608..f40658d1411 100644 --- a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['ANTLR-%(version)s_cpp-headers.patch'] -dependencies = [('Java', '1.7.0_60', '', SYSTEM)] +dependencies = [('Java', '1.7.0_60', '', True)] configopts = "--disable-examples --disable-csharp" diff --git a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb index 72a027af04f..8ba4070760d 100644 --- a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['ANTLR-%(version)s_cpp-headers.patch'] -dependencies = [('Java', '1.7.0_60', '', SYSTEM)] +dependencies = [('Java', '1.7.0_60', '', True)] configopts = "--disable-examples --disable-csharp" diff --git a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb index 0d8e1343e3d..31ae0ccb152 100644 --- a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb @@ -20,7 +20,7 @@ pythonversion = '2.7.10' versionsuffix = "-Python-%s" % pythonversion dependencies = [ - ('Java', '1.8.0_60', '', SYSTEM), + ('Java', '1.8.0_60', '', True), ('Python', pythonversion), ] diff --git a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb index 8b6c127a237..00631356607 100644 --- a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb @@ -20,7 +20,7 @@ pythonversion = '2.7.10' versionsuffix = "-Python-%s" % pythonversion dependencies = [ - ('Java', '1.8.0_66', '', SYSTEM), + ('Java', '1.8.0_66', '', True), ('Python', pythonversion), ] diff --git a/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb index c99f5de5a6b..41b26e296f8 100644 --- a/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb @@ -19,7 +19,7 @@ patches = [ dependencies = [ ('libpng', '1.6.6'), ('LibTIFF', '4.0.3'), - ('Java', '1.7.0_15', '', SYSTEM), + ('Java', '1.7.0_15', '', True), ('lynx', '2.8.7'), ('makedepend', '1.0.4'), ('imake', '1.0.5'), diff --git a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb index 174260cddaf..938cb4bc7e4 100644 --- a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb @@ -14,7 +14,7 @@ sources = ['%(name)s_%(version)s.tar.gz'] java = 'Java' javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) -dependencies = [(java, javaver, '', SYSTEM)] +dependencies = [(java, javaver, '', True)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb index 01cd8fffd9e..83c91ab617b 100644 --- a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb @@ -14,7 +14,7 @@ sources = ['%(name)s_%(version)s.tar.gz'] java = 'Java' javaver = '1.8.0_74' versionsuffix = '-%s-%s' % (java, javaver) -dependencies = [(java, javaver, '', SYSTEM)] +dependencies = [(java, javaver, '', True)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb index ec0b679c595..eb31afb5518 100644 --- a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb @@ -13,9 +13,9 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['beagle_release_%s.tar.gz' % version.replace('.', '_')] -dependencies = [('Java', '1.7.0_80', '', SYSTEM)] +dependencies = [('Java', '1.7.0_80', '', True)] -builddependencies = [('Autotools', '20150215', '', SYSTEM)] +builddependencies = [('Autotools', '20150215', '', True)] # parallel build does not work (to test) parallel = 1 diff --git a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb index ac6f731032d..eba16d5a4e3 100644 --- a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} # svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib sources = [SOURCE_TGZ] -dependencies = [('Java', '1.7.0_15', '', SYSTEM)] +dependencies = [('Java', '1.7.0_15', '', True)] builddependencies = [('Autotools', '20150215', '', ('GCC', '4.7.2'))] diff --git a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb index 371db8bef3c..6d20b44133f 100644 --- a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} # svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib sources = [SOURCE_TGZ] -dependencies = [('Java', '1.7.0_15', '', SYSTEM)] +dependencies = [('Java', '1.7.0_15', '', True)] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb index 939c36e304f..0349d94e2ac 100644 --- a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb +++ b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} # svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib sources = [SOURCE_TGZ] -dependencies = [('Java', '1.8.0_31', '', SYSTEM)] +dependencies = [('Java', '1.8.0_31', '', True)] builddependencies = [('Autotools', '20150215')] preconfigopts = './autogen.sh && ' diff --git a/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb b/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb index 0cfcc327bdb..847f0357417 100644 --- a/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb +++ b/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb @@ -30,7 +30,7 @@ dependencies = [ ('Boost', '1.51.0', '-Python-2.7.3'), ('SAMtools', '0.1.18'), ('Perl', '5.16.3', '-bare'), - ('Java', '1.7.0_10', '', SYSTEM), + ('Java', '1.7.0_10', '', True), ('libpng', '1.5.13'), ] diff --git a/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb b/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb index 0b3d2f04c2b..3354b93931c 100644 --- a/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb +++ b/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb @@ -30,7 +30,7 @@ dependencies = [ ('Boost', '1.51.0', '-Python-2.7.3'), ('SAMtools', '0.1.18'), ('Perl', '5.16.3', '-bare'), - ('Java', '1.7.0_10', '', SYSTEM), + ('Java', '1.7.0_10', '', True), ('libpng', '1.5.13'), ] diff --git a/easybuild/easyconfigs/__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb b/easybuild/easyconfigs/__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb index 28db135235f..fc4d0275894 100644 --- a/easybuild/easyconfigs/__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb +++ b/easybuild/easyconfigs/__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = ['cplex_studio%s.linux-x86-64.bin' % ''.join(version.split('.'))] dependencies = [ - ('Java', '1.8.0_66', '', SYSTEM), + ('Java', '1.8.0_66', '', True), ] moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb index 5705d1a9f0d..77e43460d5c 100644 --- a/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb @@ -46,7 +46,7 @@ dependencies = [ ('CGAL', '4.0', versionsuffix), ('PETSc', '3.3-p2', versionsuffix), ('SLEPc', '3.3-p1', versionsuffix), - ('MTL4', '4.0.8878', '', SYSTEM), + ('MTL4', '4.0.8878', '', True), ('Trilinos', '10.12.2', versionsuffix), ('Sphinx', '1.1.3', versionsuffix), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb index 851a565e755..f6b89c67c7a 100644 --- a/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb @@ -42,7 +42,7 @@ dependencies = [ ('CGAL', '4.7', versionsuffix), ('PETSc', '3.6.3', versionsuffix), ('SLEPc', '3.6.2', versionsuffix), - ('MTL4', '4.0.9555', '', SYSTEM), + ('MTL4', '4.0.9555', '', True), ('HDF5', '1.8.15-patch1'), ('Trilinos', '12.4.2', versionsuffix), ('Sphinx', '1.3.3', versionsuffix), diff --git a/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb index 4c53065ba15..573a00a1859 100644 --- a/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb @@ -23,7 +23,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.2.0'), - ('Java', '1.7.0_10', '', SYSTEM), + ('Java', '1.7.0_10', '', True), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb index c5f9edb822c..cfcf1c4b41a 100644 --- a/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb @@ -23,7 +23,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.2.0'), - ('Java', '1.7.0_10', '', SYSTEM), + ('Java', '1.7.0_10', '', True), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb b/easybuild/easyconfigs/__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb index 5bb43ab8b18..3968d910aa4 100644 --- a/easybuild/easyconfigs/__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} sources = ['otp_src_%(version)s.tar.gz'] source_urls = ['http://www.erlang.org/download'] -builddependencies = [('Java', '1.7.0_45', '', SYSTEM)] +builddependencies = [('Java', '1.7.0_45', '', True)] configopts = '--with-javac ' diff --git a/easybuild/easyconfigs/__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb index b12f25299be..d05befd06c3 100644 --- a/easybuild/easyconfigs/__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb @@ -18,7 +18,7 @@ dependencies = [ ('cURL', '7.27.0'), ('ncurses', '5.9'), ('libreadline', '6.2'), - ('Java', '1.7.0_10', '', SYSTEM), + ('Java', '1.7.0_10', '', True), ] parallel = 1 diff --git a/easybuild/easyconfigs/__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb index 640ab72c71a..2f7b37d7ff4 100644 --- a/easybuild/easyconfigs/__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb @@ -16,7 +16,7 @@ dependencies = [ ] builddependencies = [ - ('GHC', '6.12.3', '', SYSTEM), + ('GHC', '6.12.3', '', True), ('libxslt', '1.1.28'), ] diff --git a/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb b/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb index 8db9f79f94f..7a5dd73b3c9 100644 --- a/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ftp.gnu.org/gnu/gmp'] builddependencies = [ - ('Autotools', '20150215', '', SYSTEM), + ('Autotools', '20150215', '', True), ] # enable C++ interface diff --git a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb index 3caf8585701..4634a7fb1a9 100644 --- a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb @@ -26,7 +26,7 @@ dependencies = [ ('Ghostscript', '9.14'), ('GLib', '2.40.0'), ('GTS', '0.7.6'), - ('Java', '1.7.0_60', '', SYSTEM), + ('Java', '1.7.0_60', '', True), ('libpng', '1.6.12'), ('Pango', '1.36.7'), ('Perl', '5.20.0'), diff --git a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb index f0c9457cf81..c9fd0d8f277 100644 --- a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb @@ -28,7 +28,7 @@ dependencies = [ ('fontconfig', '2.11.94'), ('Ghostscript', '9.16'), ('GTS', '0.7.6', glibsuff), - ('Java', '1.7.0_80', '', SYSTEM), + ('Java', '1.7.0_80', '', True), ('libpng', '1.6.17'), ('Pango', '1.37.2'), ('Perl', '5.20.0'), diff --git a/easybuild/easyconfigs/__archive__/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb index 936ae21c317..1b8304beca1 100644 --- a/easybuild/easyconfigs/__archive__/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb @@ -25,8 +25,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} dependencies = [ ('GDB', '7.5.1'), - ('TotalView', '8.12.0-0', '-linux-x86-64', SYSTEM), # provides MemoryScape - ('icc', '2013.5.192', '', SYSTEM), # provides IDB in ictce/5.3.0 compatible mode + ('TotalView', '8.12.0-0', '-linux-x86-64', True), # provides MemoryScape + ('icc', '2013.5.192', '', True), # provides IDB in ictce/5.3.0 compatible mode ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb index 6a56ae85cc2..a39dfd95472 100644 --- a/easybuild/easyconfigs/__archive__/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb @@ -21,9 +21,9 @@ description = """Common Set of Profilers""" toolchain = {'name': 'goolf', 'version': '1.4.10'} dependencies = [ - ('VTune', '2013_update10', '', SYSTEM), - ('Inspector', '2013_update6', '', SYSTEM), - ('itac', '8.0.0.011', '', SYSTEM), + ('VTune', '2013_update10', '', True), + ('Inspector', '2013_update6', '', True), + ('itac', '8.0.0.011', '', True), ('PAPI', '5.0.1'), ('Valgrind', '3.8.1'), ('binutils', '2.22'), # this one provides gprof diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb index fac7767346e..9272f98ff58 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb @@ -23,8 +23,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), - ('vsc-mympirun', '3.4.2', '', SYSTEM), - ('vsc-base', '2.1.2', '', SYSTEM), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb index f619e97afdd..a096633f0b1 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb @@ -23,8 +23,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), - ('vsc-mympirun', '3.4.2', '', SYSTEM), - ('vsc-base', '2.1.2', '', SYSTEM), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb index eb3c96bcc41..c0a03ce83e5 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb @@ -23,8 +23,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), - ('vsc-mympirun', '3.4.2', '', SYSTEM), - ('vsc-base', '2.1.2', '', SYSTEM), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb index 90c502a0495..b6761f74452 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb @@ -23,8 +23,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), - ('vsc-mympirun', '3.4.2', '', SYSTEM), - ('vsc-base', '2.1.2', '', SYSTEM), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb index 858b4f06340..f8c93660f1c 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', SYSTEM), + ('setuptools', '1.4.2', '', True), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb index e19609bcd3b..bcf97f426c7 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', SYSTEM), + ('setuptools', '1.4.2', '', True), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb index 050fc9722ee..5a2ff293ea6 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', SYSTEM), + ('setuptools', '1.4.2', '', True), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb index 8cec50e09ab..b4fa5862100 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', SYSTEM), + ('setuptools', '1.4.2', '', True), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb index 92eb557b169..7cd4104ad9f 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', SYSTEM), + ('setuptools', '1.4.2', '', True), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb b/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb index f0bc1aefaff..3f166576635 100644 --- a/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb +++ b/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb @@ -13,7 +13,7 @@ source_urls = ['http://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s sources = ['%(namelower)s-%(version)s-64-bit.tar.gz'] dependencies = [ - ('Java', '1.7.0_80', '', SYSTEM), + ('Java', '1.7.0_80', '', True), ('Perl', '5.20.3'), ('libgd', '2.1.1'), ('Python', '2.7.10'), diff --git a/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb b/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb index ec5a5e2789d..2388f280096 100644 --- a/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb +++ b/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb @@ -23,7 +23,7 @@ checksums = [ ] dependencies = [ - ('Java', '1.7.0_80', '', SYSTEM), + ('Java', '1.7.0_80', '', True), ('Perl', '5.20.3'), ('libgd', '2.1.1'), ('Python', '2.7.10'), diff --git a/easybuild/easyconfigs/__archive__/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/__archive__/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb index a7381adc66f..dafa45afa95 100644 --- a/easybuild/easyconfigs/__archive__/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/__archive__/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb @@ -20,7 +20,7 @@ java = 'Java' javaver = '1.7.0_75' versionsuffix = '-%s-%s' % (java, javaver) -builddependencies = [('ant', '1.9.6', '-Java-1.7.0_75', SYSTEM)] +builddependencies = [('ant', '1.9.6', '-Java-1.7.0_75', True)] dependencies = [('MPJ-Express', '0.44', '%(versionsuffix)s')] diff --git a/easybuild/easyconfigs/__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb b/easybuild/easyconfigs/__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb index d334e3cb6ea..fe336c46e0c 100644 --- a/easybuild/easyconfigs/__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb @@ -26,7 +26,7 @@ unpack_options = '--strip-components=1' builddependencies = [ ('CMake', '3.4.3'), - ('Autotools', '20150215', '', SYSTEM), + ('Autotools', '20150215', '', True), ] dependencies = [ @@ -34,7 +34,7 @@ dependencies = [ ('zlib', '1.2.8'), ('samblaster', '0.1.24'), ('SAMtools', '1.3.1'), - ('Sambamba', '0.6.6', '', SYSTEM), + ('Sambamba', '0.6.6', '', True), ('gawk', '4.0.2'), ] diff --git a/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb index 904997dd1d9..92964498140 100644 --- a/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] sources = ['stable_release-%s.zip' % version.replace('.', '-')] dependencies = [ - ('Java', '1.7.0_79', '', SYSTEM), + ('Java', '1.7.0_79', '', True), ('Python', '2.7.9'), ('HDF5', '1.8.9'), ('libxml2', '2.9.2'), diff --git a/easybuild/easyconfigs/__archive__/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/__archive__/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb index ac36c94964b..e553dd3905a 100644 --- a/easybuild/easyconfigs/__archive__/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/__archive__/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb @@ -24,7 +24,7 @@ versionsuffix = '-%s-%s' % (java, javaver) builddependencies = [('CMake', '2.8.12')] dependencies = [ - (java, javaver, '', SYSTEM), + (java, javaver, '', True), ] # compile JNI wrapper library as described in docs diff --git a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb index 3a1bccbc96e..4231bf81f8c 100644 --- a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb +++ b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb @@ -31,8 +31,8 @@ dependencies = [ ('libpng', '1.6.12'), ('LibTIFF', '4.0.3'), ('JasPer', '1.900.1'), - ('Java', '1.7.0_79', '', SYSTEM), - ('ant', '1.9.3', '-Java-%(javaver)s', SYSTEM), + ('Java', '1.7.0_79', '', True), + ('ant', '1.9.3', '-Java-%(javaver)s', True), ('GLib', '2.40.0') ] diff --git a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb index b495fa3ffb7..bf5ac8dc56d 100644 --- a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb @@ -31,8 +31,8 @@ dependencies = [ ('libpng', '1.6.12'), ('LibTIFF', '4.0.3'), ('JasPer', '1.900.1'), - ('Java', '1.7.0_60', '', SYSTEM), - ('ant', '1.9.3', '-Java-%(javaver)s', SYSTEM), + ('Java', '1.7.0_60', '', True), + ('ant', '1.9.3', '-Java-%(javaver)s', True), ('GLib', '2.40.0') ] diff --git a/easybuild/easyconfigs/__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb index 3599c26e381..8ad72ec52f4 100644 --- a/easybuild/easyconfigs/__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb @@ -16,7 +16,7 @@ dependencies = [ ] builddependencies = [ - ('FCM', '2.3.1', '', SYSTEM), + ('FCM', '2.3.1', '', True), ('Perl', '5.16.3'), ] diff --git a/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb index 41390bba2c2..ba3147aeda1 100644 --- a/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} dependencies = [ ('make', '3.82'), - ('Java', '1.7.0_10', '', SYSTEM), + ('Java', '1.7.0_10', '', True), ('Bash', '4.2'), ('tcsh', '6.18.01'), ('Tcl', '8.5.12'), diff --git a/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb index ea816765bb3..e1d90973574 100644 --- a/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} dependencies = [ ('make', '3.82'), - ('Java', '1.7.0_10', '', SYSTEM), + ('Java', '1.7.0_10', '', True), ('Bash', '4.2'), ('tcsh', '6.18.01'), ('Tcl', '8.5.12'), diff --git a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb index 239d653b543..9948217fd4e 100644 --- a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb @@ -7,7 +7,7 @@ description = "PASHA is a parallel short read assembler for large genomes using toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -dependencies = [('tbb', '4.0.5.339', '', SYSTEM)] +dependencies = [('tbb', '4.0.5.339', '', True)] source_urls = ['http://downloads.sourceforge.net/pasha'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb index c658a85d703..4043dd5630c 100644 --- a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb @@ -8,7 +8,7 @@ description = "PASHA is a parallel short read assembler for large genomes using toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -dependencies = [('tbb', '4.0.5.339', '', SYSTEM)] +dependencies = [('tbb', '4.0.5.339', '', True)] source_urls = ['http://downloads.sourceforge.net/pasha'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb index 7c33ed3c62f..161ca2d3837 100644 --- a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb @@ -8,7 +8,7 @@ description = "PASHA is a parallel short read assembler for large genomes using toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -dependencies = [('tbb', '4.0.5.339', '', SYSTEM)] +dependencies = [('tbb', '4.0.5.339', '', True)] source_urls = ['http://downloads.sourceforge.net/pasha'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index 8391bc11951..8b0668a68f1 100644 --- a/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -19,7 +19,7 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2014b'} dependencies = [ - ('Java', '1.7.0_60', '', SYSTEM), + ('Java', '1.7.0_60', '', True), ('libreadline', '6.3'), ('zlib', '1.2.8'), # OS dependency should be preferred if the os version is more recent then this version, diff --git a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb index 5afdb61e1c4..e8adea5cdda 100644 --- a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb @@ -20,7 +20,7 @@ source_urls = [ mpich_opts = '--enable-static' dependencies = [ - ('pscom', '5.0.48-1', '', SYSTEM), + ('pscom', '5.0.48-1', '', True), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb index 0b59ed106c8..9bf66b57282 100644 --- a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb +++ b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb @@ -20,7 +20,7 @@ mpich_opts = '--enable-static' threaded = True dependencies = [ - ('pscom', '5.0.48-1', '', SYSTEM), + ('pscom', '5.0.48-1', '', True), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb index 9c841513aa2..8251dde430d 100644 --- a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb @@ -17,7 +17,7 @@ source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] mpich_opts = '--enable-static' dependencies = [ - ('pscom', '5.0.48-1', '', SYSTEM), + ('pscom', '5.0.48-1', '', True), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb index 09cc0738ddc..c6290e63183 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.5.13'), # for plotting in R - ('Java', '1.7.0_10', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb index cff665b0ada..b23784df275 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.5.13'), # for plotting in R - ('Java', '1.7.0_10', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb index 7d9a9a6b9be..4bb85edabe4 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.5.13'), # for plotting in R - ('Java', '1.7.0_10', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb index 70a3f64db0d..b5a30ff434c 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.5.13'), # for plotting in R - ('Java', '1.7.0_10', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb index 8fcddd02617..419fa691885 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.2'), # for plotting in R - ('Java', '1.7.0_15', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb index cd8a6bcddf6..2437804b50b 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.2'), # for plotting in R - ('Java', '1.7.0_15', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb index a85fdf5d8fc..c0064ba6a8c 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.2'), # for plotting in R - ('Java', '1.7.0_21', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb index 8939ec6a4eb..3b03bc30042 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.2'), # for plotting in R - ('Java', '1.7.0_21', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb index edd7812782e..7db65a77f3e 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.6'), # for plotting in R - ('Java', '1.7.0_21', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb index 5aa63fa961d..1c63079ab4a 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.6'), # for plotting in R - ('Java', '1.7.0_21', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb index b3be0a49a90..ea1488b7501 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.6'), # for plotting in R - ('Java', '1.7.0_15', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb index bb2cdf29ef3..72798af0c69 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.6'), # for plotting in R - ('Java', '1.7.0_15', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb index cac8a78c01f..7b3d9ff4712 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.9'), # for plotting in R - ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb index faed73f4aef..4125b82ac4e 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.9'), # for plotting in R - ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb index e9736a0d521..0b46e45f459 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb @@ -17,7 +17,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.12'), # for plotting in R ('libjpeg-turbo', '1.3.1'), # for plotting in R - ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb index 8f2c4740b2d..33df27d4460 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb @@ -17,7 +17,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.12'), # for plotting in R ('libjpeg-turbo', '1.3.1'), # for plotting in R - ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb index f55402b39c8..3462ebf3f2c 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.12'), # for plotting in R ('libjpeg-turbo', '1.3.1'), # for plottting in R - ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb index cfb1fdded86..32f9e3876e9 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb index 6e9bb7dd130..8dfe1121a12 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a-bare.eb index c704735c37c..95f4896bccf 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb index a2c3729ee62..20b83d30bca 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb index c96c15e9389..2b252579399 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('NLopt', '2.4.2'), # for nloptr diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb index db6599ad293..1992cbe8043 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('NLopt', '2.4.2'), # for nloptr diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-foss-2015a-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-foss-2015a-bare.eb index 3de945fb60b..83033319bd9 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-foss-2015a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb index 35f77ae5f85..712ca683f37 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb index 034bec8b1d3..fc8747efae8 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.43.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb index 9789a570017..dec3fef7965 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ] diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-intel-2015a-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-intel-2015a-bare.eb index 282eb2bede6..68941ac7809 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-intel-2015a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b-bare.eb index f37ad6d3f33..f4738f44f4b 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb index 77140a3bb18..eb6d134dc02 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.43.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb index 4b3e1115ed6..bf999bcdca7 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.43.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b-bare.eb index 25e622f04e6..ad909a5e62b 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb index b00f07b4b09..28a924627e0 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.43.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb index 986af941152..dba91bd2533 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.45.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb index 8bde637585c..b503f4c6397 100644 --- a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [ ('Boost', '1.55.0', versionsuffix), - ('tbb', '4.0.5.339', '', SYSTEM), + ('tbb', '4.0.5.339', '', True), ('Jellyfish', '2.1.3'), ('g2log', '1.0'), ] diff --git a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb index 93274668b83..c80c41e1d54 100644 --- a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb @@ -27,7 +27,7 @@ builddependencies = [ dependencies = [ ('Boost', '1.59.0', versionsuffix), - ('tbb', '4.3.6.211', '', SYSTEM), + ('tbb', '4.3.6.211', '', True), ('Jellyfish', '2.2.3'), ('g2log', '1.0'), ] diff --git a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb index 37c7bd731e4..b4805f08e04 100644 --- a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb @@ -29,7 +29,7 @@ builddependencies = [ dependencies = [ ('Boost', '1.59.0', versionsuffix), - ('tbb', '4.3.6.211', '', SYSTEM), + ('tbb', '4.3.6.211', '', True), ('Jellyfish', '2.2.4'), ('g2log', '1.0'), ] diff --git a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb index 9317f21af8c..878c68876e0 100644 --- a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb @@ -24,7 +24,7 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ ('Boost', '1.59.0', versionsuffix), - ('tbb', '4.3.6.211', '', SYSTEM), + ('tbb', '4.3.6.211', '', True), ('Jellyfish', '2.2.3'), ] builddependencies = [('CMake', '3.2.3')] diff --git a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb index 0f6804b6b3c..7699ae06d5a 100644 --- a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb @@ -24,7 +24,7 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ ('Boost', '1.59.0', versionsuffix), - ('tbb', '4.3.6.211', '', SYSTEM), + ('tbb', '4.3.6.211', '', True), ('Jellyfish', '2.2.4'), ] builddependencies = [('CMake', '3.2.3')] diff --git a/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb index dffa4ab145e..f895fa63df1 100644 --- a/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb @@ -16,7 +16,7 @@ source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s' install_cmd = "cp -a %(namelower)s_zip/* %(installdir)s && chmod +x %(installdir)s/%(namelower)s" dependencies = [ - ('FastQC', '0.10.1', '-Java-1.7.0_80', SYSTEM), + ('FastQC', '0.10.1', '-Java-1.7.0_80', True), ('cutadapt', '1.5', '-Python-2.7.10'), ] diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb index abd5e0edeaa..821333d6ef7 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb @@ -19,8 +19,8 @@ sources = ['v%(version)s.tar.gz'] patches = ['Trinity-%(version)s_plugins-Makefile.patch'] dependencies = [ - ('Java', '1.7.0_80', '', SYSTEM), - ('ant', '1.9.6', '-Java-%(javaver)s', SYSTEM), + ('Java', '1.7.0_80', '', True), + ('ant', '1.9.6', '-Java-%(javaver)s', True), ('ncurses', '5.9'), ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb index 7fb8a37a67b..014e8ca4110 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb @@ -19,8 +19,8 @@ sources = ['v%(version)s.tar.gz'] patches = ['Trinity-2.0.4_plugins-Makefile.patch'] dependencies = [ - ('Java', '1.7.0_80', '', SYSTEM), - ('ant', '1.9.6', '-Java-%(javaver)s', SYSTEM), + ('Java', '1.7.0_80', '', True), + ('ant', '1.9.6', '-Java-%(javaver)s', True), ('ncurses', '5.9'), ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb index 063da9c3d98..71643e32bd6 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - (java, javaver, '', SYSTEM), + (java, javaver, '', True), ('ant', '1.9.6', '-%s-%s' % (java, javaver), True), ('Bowtie', '1.1.2'), ('Bowtie2', '2.2.6'), diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb index 2092bcc77db..dcb9ea5cadb 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb @@ -24,7 +24,7 @@ java = 'Java' javaver = '1.7.0_10' dependencies = [ - (java, javaver, '', SYSTEM), + (java, javaver, '', True), ('ant', '1.8.4', '-%s-%s' % (java, javaver), True), ('ncurses', '5.9'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb index afb90c64534..7f5d5792225 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb @@ -25,7 +25,7 @@ java = 'Java' javaver = '1.7.0_10' dependencies = [ - (java, javaver, '', SYSTEM), + (java, javaver, '', True), ('ant', '1.8.4', '-%s-%s' % (java, javaver), True), ('ncurses', '5.9'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb index 10bbd992eac..f6e15e437ab 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb @@ -23,7 +23,7 @@ java = 'Java' javaver = '1.7.0_15' dependencies = [ - (java, javaver, '', SYSTEM), + (java, javaver, '', True), ('ant', '1.9.0', '-%s-%s' % (java, javaver), True), ('ncurses', '5.9'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb index 50efb697da2..dfd259613d8 100644 --- a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb @@ -16,8 +16,8 @@ python = 'Python' pyver = '2.7.6' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - ('vsc-processcontrol', '1.0', '', SYSTEM), - ('vsc-mympirun', version, '', SYSTEM), + ('vsc-processcontrol', '1.0', '', True), + ('vsc-mympirun', version, '', True), (python, pyver), ('SCOOP', '0.6.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb index 8afa94b6137..1bbd44502a0 100644 --- a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb @@ -16,8 +16,8 @@ python = 'Python' pyver = '2.7.10' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', SYSTEM), - ('vsc-mympirun', '3.4.2', '', SYSTEM), + ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', True), + ('vsc-mympirun', '3.4.2', '', True), (python, pyver), ('SCOOP', '0.6.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb index f2a99790fa6..24d1ff604f7 100644 --- a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb @@ -16,8 +16,8 @@ python = 'Python' pyver = '2.7.10' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', SYSTEM), - ('vsc-mympirun', '3.4.2', '', SYSTEM), + ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', True), + ('vsc-mympirun', '3.4.2', '', True), (python, pyver), ('SCOOP', '0.6.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb index 99d0531e740..f5d80fe9e55 100644 --- a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb +++ b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.4', '', SYSTEM), + ('gettext', '0.19.4', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb index 9c13936bba0..4c118e934ff 100644 --- a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215', '', ('GCC', '4.7.2')), - ('gettext', '0.18.2', '', SYSTEM), + ('gettext', '0.18.2', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb index df2d19b7d0b..43117900f60 100644 --- a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.18.2', '', SYSTEM), + ('gettext', '0.18.2', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb index 092e66d8068..63e623f082d 100644 --- a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb @@ -20,7 +20,7 @@ pyver = '2.7.9' versionsuffix = '-Python-%s' % pyver dependencies = [ - ('Java', '1.8.0_40', '', SYSTEM), + ('Java', '1.8.0_40', '', True), ('Python', pyver), # should have a working sqlite, and provide numpy/mpi4py ('LibTIFF', '4.0.4beta'), ('HDF5', '1.8.14'), diff --git a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb index 3f34c8c15f5..18d8b11833b 100644 --- a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb +++ b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb @@ -12,6 +12,6 @@ sources = ['Xmipp-%(version)s-src.tar.gz'] toolchain = {'name': 'goolf', 'version': '1.4.10'} # note: all other dependencies are taken care of by Xmipp itself -dependencies = [('Java', '1.7.0_80', '', SYSTEM)] +dependencies = [('Java', '1.7.0_80', '', True)] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb index 294af452fee..d6d8c64ef43 100644 --- a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb @@ -20,7 +20,7 @@ pyver = '2.7.9' versionsuffix = '-Python-%s' % pyver dependencies = [ - ('Java', '1.8.0_40', '', SYSTEM), + ('Java', '1.8.0_40', '', True), ('Python', pyver), # should have a working sqlite, and provide numpy/mpi4py ('LibTIFF', '4.0.4beta'), ('HDF5', '1.8.14'), From 31ea71fd860f2fee1ed1e1fc9adcf48dad29621f Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 11 Oct 2022 14:39:01 +0100 Subject: [PATCH 313/793] undo changes from old easyconfigs failing other CI tests --- .../a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb | 2 +- .../Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb | 2 +- ...16.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb | 2 +- easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb | 2 +- easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb | 2 +- .../easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 2 +- .../b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb | 2 +- .../CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb | 2 +- .../CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb | 2 +- .../c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb | 2 +- .../c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb | 2 +- .../c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb | 2 +- .../c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb | 2 +- .../c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb | 4 ++-- easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb | 2 +- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb | 2 +- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb | 2 +- easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb | 2 +- .../f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb | 4 ++-- .../f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb | 2 +- .../fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb | 2 +- .../f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb | 2 +- .../f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-1.4.0-foss-2018b-Python-3.6.6.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-1.4.0-intel-2018b-Python-3.6.6.eb | 2 +- .../g/GPAW/GPAW-19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-19.8.1-foss-2019a-Python-3.7.2.eb | 2 +- .../g/GPAW/GPAW-19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6.eb | 2 +- .../g/GPAW/GPAW-19.8.1-intel-2019a-Python-3.7.2.eb | 2 +- .../g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb | 2 +- .../g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb | 2 +- .../g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb | 2 +- .../easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb | 2 +- .../easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb | 2 +- easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb | 2 +- .../i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb | 2 +- .../easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb | 2 +- .../easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb | 2 +- .../easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb | 2 +- .../easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb | 2 +- .../easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb | 2 +- .../easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb | 2 +- .../easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb | 2 +- .../l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb | 2 +- easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb | 2 +- .../l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb | 2 +- easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb | 2 +- .../easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb | 2 +- .../l/libXinerama/libXinerama-1.1.3-intel-2016a.eb | 2 +- .../easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb | 2 +- .../easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb | 2 +- .../easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb | 2 +- .../easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb | 2 +- .../easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb | 2 +- .../easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.2.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.3.0.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb | 2 +- .../l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb | 2 +- .../l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb | 2 +- .../l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb | 2 +- .../easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb | 2 +- .../MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb | 2 +- .../MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb | 2 +- .../MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb | 2 +- .../MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb | 2 +- .../m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb | 2 +- .../m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb | 2 +- .../m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb | 2 +- .../m/minieigen/minieigen-0.5.4-intel-2018a-Python-2.7.14.eb | 2 +- .../mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb | 4 ++-- .../mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb | 4 ++-- .../mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb | 4 ++-- .../mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb | 4 ++-- easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb | 2 +- .../easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb | 2 +- .../o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb | 2 +- easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb | 2 +- .../p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb | 2 +- .../p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb | 2 +- .../p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb | 2 +- .../PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb | 2 +- .../p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb | 2 +- .../p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb | 2 +- .../p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb | 2 +- .../PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb | 2 +- .../easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb | 2 +- .../parallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb | 2 +- easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb | 2 +- .../p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb | 2 +- .../p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb | 2 +- easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb | 2 +- .../q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb | 2 +- .../q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb | 2 +- .../q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb | 2 +- .../q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb | 2 +- easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb | 2 +- .../easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb | 2 +- easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb | 2 +- .../r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb | 2 +- .../r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb | 2 +- .../r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb | 2 +- .../s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb | 2 +- .../easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb | 2 +- .../TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb | 4 ++-- easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb | 4 ++-- easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb | 2 +- .../v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb | 4 ++-- .../vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb | 4 ++-- .../x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb | 2 +- .../x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb | 2 +- .../easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb | 2 +- .../easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb | 4 ++-- easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb | 4 ++-- .../x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb | 2 +- .../x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb | 2 +- .../x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb | 2 +- .../x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb | 2 +- .../xcb-util-renderutil-0.3.9-foss-2016a.eb | 2 +- .../xcb-util-renderutil-0.3.9-intel-2016a.eb | 2 +- .../easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb | 2 +- .../x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb | 2 +- easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb | 2 +- .../easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb | 2 +- 212 files changed, 225 insertions(+), 225 deletions(-) diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb index 654825d9ff3..ddbfe7c0922 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_includes.patch'] dependencies = [ - ('Java', '1.8.0_74', '', SYSTEM), + ('Java', '1.8.0_74', '', True), ('Python', '2.7.11'), ] diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb index 123c3e1e968..e00f225a130 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_includes.patch'] dependencies = [ - ('Java', '1.8.0_131', '', SYSTEM), + ('Java', '1.8.0_131', '', True), ('Python', '2.7.13'), ] diff --git a/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb b/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb index 1f73638a1c1..d3c79474bb6 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb @@ -27,7 +27,7 @@ patches = [ ] dependencies = [ - ('CUDA', '7.5.18', '', SYSTEM), + ('CUDA', '7.5.18', '', True), ('netCDF', '4.4.0'), ('netCDF-Fortran', '4.4.4'), ('Python', '2.7.11'), diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb index 5b391327a36..4193c584dca 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb @@ -23,7 +23,7 @@ patches = ['Amber-%(version)s_fix-hardcoding.patch', dependencies = [ - ('CUDA', '7.5.18', '', SYSTEM), + ('CUDA', '7.5.18', '', True), ('netCDF', '4.4.0'), ('netCDF-Fortran', '4.4.4'), ('Python', '2.7.11'), diff --git a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb index ca38ef74542..8b901156428 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb @@ -22,7 +22,7 @@ source_urls = ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(ver sources = ['BEASTv%(version)s.tgz'] dependencies = [ - ('Java', '1.8.0_74', '', SYSTEM), + ('Java', '1.8.0_74', '', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb b/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb index 6210023c8d0..b0ee97e8f9e 100644 --- a/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb +++ b/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['http://download.bpipe.org/versions/'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('Java', '1.8.0_131', '', SYSTEM)] +dependencies = [('Java', '1.8.0_131', '', True)] sanity_check_paths = { 'files': ['bin/bpipe', 'lib/bpipe.jar'], diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb index fa78496309d..76868b55c45 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['beagle_release_%s.tar.gz' % version.replace('.', '_')] -dependencies = [('Java', '1.8.0_74', '', SYSTEM)] +dependencies = [('Java', '1.8.0_74', '', True)] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index dfa2e11582d..08e10d150ca 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb index 7627c686af3..9709696cf5d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index 9be29fca484..d6e68008e5b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb index 0e86573cab6..9ec7a3f3f32 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb @@ -16,7 +16,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb index f331b902250..f411442d121 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb @@ -16,7 +16,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb index e631c72676f..4eee9df8fa2 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb @@ -16,7 +16,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb index ecd95aca019..d7c829040f2 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked instatically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb index c9f35fe7a36..d95c058f0c8 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb @@ -17,7 +17,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb index 847c265d57c..215aaf0cb28 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb index 00cbe46a478..88e16771dff 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb index e56efe34428..9346ceba7e7 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb index 86e013bcdfd..138a0a59d7f 100644 --- a/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'cstd': 'c++03'} builddependencies = [ - ('Eigen', '3.3.7', '', SYSTEM), + ('Eigen', '3.3.7', '', True), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb index 217755142f3..18103c12dc1 100644 --- a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb @@ -14,7 +14,7 @@ dependencies = [ ('TopHat', '2.1.1'), ('Cufflinks', '2.2.1'), ('BEDTools', '2.26.0'), - ('Kent_tools', '20171107', '-linux.x86_64', SYSTEM), + ('Kent_tools', '20171107', '-linux.x86_64', True), ('STAR', '2.5.3a'), ('BWA', '0.7.17'), ('segemehl', '0.2.0'), diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb index 2362960ae99..edff9ff989f 100644 --- a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb @@ -18,7 +18,7 @@ dependencies = [ ('TopHat', '2.1.0', versionsuffix), ('Cufflinks', '2.2.1'), ('BEDTools', '2.27.1'), - ('Kent_tools', '20180716', '-linux.x86_64', SYSTEM), + ('Kent_tools', '20180716', '-linux.x86_64', True), ('STAR', '2.6.0c'), ('BWA', '0.7.17'), ('segemehl', '0.2.0'), diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb index 113d81b7610..6b1b02e8197 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb @@ -22,7 +22,7 @@ dependencies = [ ('scikit-learn', '0.19.1', versionsuffix), ('MEGAHIT', '1.1.3', versionsuffix), ('BEDTools', '2.27.1'), - ('picard', '2.18.27', '-Java-1.8', SYSTEM), + ('picard', '2.18.27', '-Java-1.8', True), ('SAMtools', '1.6'), ('Bowtie2', '2.3.4.1'), ('parallel', '20171122'), diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb index 22128baa385..30bfadb038e 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb @@ -22,7 +22,7 @@ dependencies = [ ('scikit-learn', '0.19.1', versionsuffix), ('MEGAHIT', '1.1.3', versionsuffix), ('BEDTools', '2.27.1'), - ('picard', '2.18.27', '-Java-1.8', SYSTEM), + ('picard', '2.18.27', '-Java-1.8', True), ('SAMtools', '1.6'), ('Bowtie2', '2.3.4.1'), ('parallel', '20171122'), diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb index dc99d2aeb67..b8d52d0019d 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb @@ -23,7 +23,7 @@ dependencies = [ ('scikit-learn', '0.20.2', versionsuffix), ('MEGAHIT', '1.1.4', versionsuffix), ('BEDTools', '2.27.1'), - ('picard', '2.18.27', '-Java-1.8', SYSTEM), + ('picard', '2.18.27', '-Java-1.8', True), ('SAMtools', '1.9'), ('Bowtie2', '2.3.4.2'), ('parallel', '20190222'), diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb index df708ac5e1f..f1334d88a22 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb @@ -27,7 +27,7 @@ dependencies = [ ('scikit-learn', '0.20.3'), ('MEGAHIT', '1.2.8'), ('BEDTools', '2.28.0'), - ('picard', '2.21.1', '-Java-11', SYSTEM), + ('picard', '2.21.1', '-Java-11', True), ('SAMtools', '1.9'), ('Bowtie2', '2.3.5.1'), ('parallel', '20190622'), diff --git a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb index cf48d75ac7f..bcf0c9ef120 100644 --- a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb @@ -29,8 +29,8 @@ dependencies = [ ('glog', '0.3.4'), ('gflags', '2.1.2'), ('OpenCV', '3.1.0'), - ('CUDA', local_cudaversion, '', SYSTEM), - ('cuDNN', '4.0', '', SYSTEM), + ('CUDA', local_cudaversion, '', True), + ('cuDNN', '4.0', '', True), ('LMDB', '0.9.18'), ('LevelDB', '1.18'), ('snappy', '1.1.3'), diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb index 28584d265c3..09811fccdee 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb index 9c8d5222d95..8d7f087e2b7 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb b/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb index d3b3a9cf790..ff486b7b508 100755 --- a/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb +++ b/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb @@ -25,7 +25,7 @@ start_dir = 'src' files_to_copy = ['Linux-amd64/*'] dependencies = [ - ('Java', '1.8.0_112', '', SYSTEM), + ('Java', '1.8.0_112', '', True), ('Perl', '5.24.0'), ('gnuplot', '5.0.5'), ] diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb index 08887154a33..0d6ccf3dc76 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb @@ -29,7 +29,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.3.0'), - ('Java', '1.7.0_80', '', SYSTEM), + ('Java', '1.7.0_80', '', True), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb index 8796b8995a5..d6fa49965ac 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb @@ -29,7 +29,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.3.0'), - ('Java', '1.7.0_80', '', SYSTEM), + ('Java', '1.7.0_80', '', True), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb index fdb59680efe..20703396833 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ - ('NASM', '2.12.02', '', SYSTEM), + ('NASM', '2.12.02', '', True), ('x264', '20170406'), ('X11', '20170129'), # pulls in bzip2 and zlib ] diff --git a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb index 0e1c47bba9b..4cb227e1d23 100644 --- a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb @@ -17,8 +17,8 @@ dependencies = [ ('FSL', '5.0.11', versionsuffix), ('ANTs', '2.3.1', versionsuffix), ('AFNI', '18.3.00', versionsuffix), - ('C3D', '1.0.0', '', SYSTEM), - ('FreeSurfer', '6.0.1', '-centos6_x86_64', SYSTEM), + ('C3D', '1.0.0', '', True), + ('FreeSurfer', '6.0.1', '-centos6_x86_64', True), ('ICA-AROMA', '0.4.4-beta', versionsuffix), ('Seaborn', '0.9.0', versionsuffix), ('PyYAML', '3.13', versionsuffix), diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb index 8f37cf904d2..fc9583cf3bc 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb @@ -20,7 +20,7 @@ dependencies = [ # use same binutils version that was used when building GCCcore toolchain builddependencies = [ - ('binutils', '2.26', '', SYSTEM), + ('binutils', '2.26', '', True), ('pkg-config', '0.29.1'), ] diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb index d9df0e9ca8d..0b86b4b9dbd 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb @@ -20,7 +20,7 @@ dependencies = [ # use same binutils version that was used when building GCCcore toolchain builddependencies = [ - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ('pkg-config', '0.29.2'), ] diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb index 4c6ef6f4dd4..2ff9e6f9623 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb @@ -20,7 +20,7 @@ dependencies = [ # use same binutils version that was used when building GCCcore toolchain builddependencies = [ - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ('pkg-config', '0.29.2'), ] diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb index c1cfebce521..f01c0208b56 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb @@ -18,7 +18,7 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] configopts = '--with-harfbuzz=no' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb index eb85cf2630c..2b17c553f92 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb @@ -20,7 +20,7 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] configopts = '--with-harfbuzz=no' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-foss-2018b-Python-3.6.6.eb index 06af8a8bbb1..d489fda525c 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-foss-2018b-Python-3.6.6.eb @@ -29,7 +29,7 @@ dependencies = [ ('ASE', '3.16.2', versionsuffix), ('libxc', '3.0.1'), ('libvdwxc', '0.3.2'), - ('GPAW-setups', '0.9.20000', '', SYSTEM), + ('GPAW-setups', '0.9.20000', '', True), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-intel-2018b-Python-3.6.6.eb index fa75dd66180..8e5a3d625fa 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-intel-2018b-Python-3.6.6.eb @@ -28,7 +28,7 @@ dependencies = [ ('Python', '3.6.6'), ('ASE', '3.16.2', versionsuffix), ('libxc', '3.0.1'), - ('GPAW-setups', '0.9.20000', '', SYSTEM), + ('GPAW-setups', '0.9.20000', '', True), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6.eb b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6.eb index 660743db68a..6a5eb1c4ce2 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6.eb @@ -28,7 +28,7 @@ dependencies = [ ('ASE', local_aseversion, local_pythonsuffix), ('libxc', '3.0.1'), # Old version to maintain consistency with AtomPAW and ABINIT. ('libvdwxc', '0.3.2'), - ('GPAW-setups', '0.9.20000', '', SYSTEM), + ('GPAW-setups', '0.9.20000', '', True), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2019a-Python-3.7.2.eb index 6c10491a0d2..ed31bbedf0e 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2019a-Python-3.7.2.eb @@ -27,7 +27,7 @@ dependencies = [ ('ASE', '3.18.0', versionsuffix), ('libxc', '4.3.4'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', SYSTEM), + ('GPAW-setups', '0.9.20000', '', True), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6.eb b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6.eb index 3158794bf1a..c06fe0fe7ca 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6.eb @@ -28,7 +28,7 @@ dependencies = [ ('Python', '3.6.6'), ('ASE', local_aseversion, local_pythonsuffix), ('libxc', '3.0.1'), # Old version to maintain consistency with AtomPAW and ABINIT. - ('GPAW-setups', '0.9.20000', '', SYSTEM), + ('GPAW-setups', '0.9.20000', '', True), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2019a-Python-3.7.2.eb index b6da87b17cc..337d63d58b0 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2019a-Python-3.7.2.eb @@ -26,7 +26,7 @@ dependencies = [ ('SciPy-bundle', '2019.03'), ('ASE', '3.18.0', versionsuffix), ('libxc', '4.3.4'), - ('GPAW-setups', '0.9.20000', '', SYSTEM), + ('GPAW-setups', '0.9.20000', '', True), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb index f73039f0fbb..c6e3c5bf573 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb @@ -15,7 +15,7 @@ dependencies = [ ('matplotlib', '2.2.3', versionsuffix), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), - ('pplacer', '1.1.alpha19', '', SYSTEM), + ('pplacer', '1.1.alpha19', '', True), ('FastANI', '1.1'), ('FastTree', '2.1.10'), ] diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb index baa0455e8d4..96d22c898b8 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb @@ -19,7 +19,7 @@ dependencies = [ ('matplotlib', '2.2.4', versionsuffix), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), - ('pplacer', '1.1.alpha19', '', SYSTEM), + ('pplacer', '1.1.alpha19', '', True), ('FastANI', '1.2'), ('FastTree', '2.1.11'), ] diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb index 234c38d3b4a..89a5cfe9651 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb @@ -19,7 +19,7 @@ dependencies = [ ('matplotlib', '2.2.4', versionsuffix), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), - ('pplacer', '1.1.alpha19', '', SYSTEM), + ('pplacer', '1.1.alpha19', '', True), ('FastANI', '1.2'), ('FastTree', '2.1.11'), ] diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb index 5584942b29c..ef9c393d1a7 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb @@ -21,7 +21,7 @@ dependencies = [ ('freetype', '2.6.5'), ('Ghostscript', '9.20'), ('GTS', '0.7.6'), - ('Java', '1.8.0_92', '', SYSTEM), + ('Java', '1.8.0_92', '', True), ('libpng', '1.6.24'), ('Pango', '1.40.3'), ('Perl', '5.24.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb index 2a678bb2b9e..50d0e0b4494 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb @@ -21,7 +21,7 @@ dependencies = [ ('freetype', '2.6.5'), ('Ghostscript', '9.20'), ('GTS', '0.7.6'), - ('Java', '1.8.0_92', '', SYSTEM), + ('Java', '1.8.0_92', '', True), ('libpng', '1.6.24'), ('Pango', '1.40.3'), ('Perl', '5.24.0'), diff --git a/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb index 35dbf494bc9..4f4fa3e2f0c 100644 --- a/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ] -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] configopts = " --enable-error-on-warning=no" diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb index 1257db05441..0d730043fba 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_XZ] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', SYSTEM), + ('binutils', '2.26', '', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb index 3ff4d3ef78f..4931b9f6ce3 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_XZ] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb index 402e97d506e..f487ba55300 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_XZ] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.28', '', SYSTEM), + ('binutils', '2.28', '', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb index 1cdc59d3ecd..56433fb0b9c 100644 --- a/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb @@ -34,7 +34,7 @@ dependencies = [ ('ImageMagick', '6.9.4-8'), ('STAMP', '1.3'), ('Cluster-Buster', '20160106'), - ('Kent_tools', '20130806', '-linux.x86_64', SYSTEM), + ('Kent_tools', '20130806', '-linux.x86_64', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb index f0c3fff870f..29c369131f2 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb @@ -13,7 +13,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb index 7fb4df0019e..52b296562ea 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb @@ -13,7 +13,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb index f0d08dd8dd7..5d0e481e2b0 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb @@ -13,7 +13,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb index d3c68c53159..ecc53857740 100644 --- a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb index 9b673d9b132..8068f14ea72 100644 --- a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb index 2e7d6b7a9f3..b9a8c3b204c 100644 --- a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb @@ -15,7 +15,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('fixesproto', '5.0'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb index 1eb5c2b11e2..bbe2ea95f7e 100644 --- a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb @@ -15,7 +15,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('fixesproto', '5.0'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb index 4d51c3577b5..dcc203e11e3 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb @@ -15,7 +15,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('xextproto', '7.3.0'), ('libpthread-stubs', '0.3'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('kbproto', '1.0.7'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb index 40f48498460..ba7aa8aa456 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb @@ -15,7 +15,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('xextproto', '7.3.0'), ('libpthread-stubs', '0.3'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('kbproto', '1.0.7'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb index 9478bc5d4a6..76dc5940533 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('libpthread-stubs', '0.3'), ('inputproto', '2.3.1'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb index bcc8bb91b85..d0b72a86ea2 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('libpthread-stubs', '0.3'), ('inputproto', '2.3.1'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb index f215f8541e5..5af14da529b 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('libpthread-stubs', '0.3'), ('inputproto', '2.3.1'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb index 50f49048f36..8117c7c96b3 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb @@ -17,7 +17,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb index 7512c727f34..b95d581275b 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb index c06e453df9d..1cc411ee297 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb @@ -17,7 +17,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb index f5d786fdb45..6589aeeb492 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb index e95534157b7..2f7d28f58a9 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('fixesproto', '5.0'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('libpthread-stubs', '0.3'), ('xtrans', '1.3.5'), ] diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb index c23a7491a1f..028286d1610 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('fixesproto', '5.0'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('libpthread-stubs', '0.3'), ('xtrans', '1.3.5'), ] diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb index 787ed0a6b96..7f990b2124d 100644 --- a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('xorg-macros', '1.19.0'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('libpthread-stubs', '0.3'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb index 20acc539c5d..7e2411fa015 100644 --- a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('xorg-macros', '1.19.0'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('libpthread-stubs', '0.3'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb index 1f7e10f14bb..62c62161692 100644 --- a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('libpthread-stubs', '0.3'), ('randrproto', '1.5.0'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb index 66d8e8e7988..d6e4b7406dd 100644 --- a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('libpthread-stubs', '0.3'), ('randrproto', '1.5.0'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb index f3c947b005a..b4c2ef6a53d 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb index c981feacb52..2c473580acb 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb index 61d8f22229f..c7e832fe55b 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('kbproto', '1.0.7'), ('xorg-macros', '1.19.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('libpthread-stubs', '0.3'), ('xextproto', '7.3.0'), ('inputproto', '2.3.1'), diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb index 4401fe752de..e12535727a9 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('kbproto', '1.0.7'), ('xorg-macros', '1.19.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('libpthread-stubs', '0.3'), ('xextproto', '7.3.0'), ('inputproto', '2.3.1'), diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb index 8c219ad876e..fe73b8ae707 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb @@ -18,7 +18,7 @@ sources = ['%(name)s-%(version)s-stable.tar.gz'] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.25', '', SYSTEM), + ('binutils', '2.25', '', True), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb index 0e6381d00bb..c2a203f1b2d 100644 --- a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb @@ -12,7 +12,7 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] sanity_check_paths = { 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb index 33ce05138dc..8fe50e9968e 100644 --- a/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] sanity_check_paths = { 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb index 5679b67d18b..f33c3fbc3e1 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('zlib', '1.2.11')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb index 156f6db5ca5..8c7fd2019e9 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('zlib', '1.2.11')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb index 82f2dfb2315..e8763aba9c4 100644 --- a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] sanity_check_paths = { 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.2.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.2.eb index 5cb32f20da8..fdb971d5a6b 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.2.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.3.0.eb index 11b1fbaf2be..42794e4902b 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.3.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb index 2e615320fc8..e7ade18cd5e 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb index 91409103d4c..09f8321dfd0 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb index 763a4f1aefd..f8debfbbbad 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb index fe4f7047b25..f22547e6446 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb index e97d8ea1348..c1f1541e7ad 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} sources = [SOURCELOWER_TAR_XZ] source_urls = [GNU_SOURCE] -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] parallel = 1 diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb index 965a763a8c8..7a2944d9e46 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('pkg-config', '0.29'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb index 3ec05ecfbde..ab5bcf6b380 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ] diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb index 4f81dd3b454..c69ddcedb6e 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('pkg-config', '0.29'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb index 690edb297f9..54ae8147222 100644 --- a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb @@ -22,7 +22,7 @@ dependencies = [ builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb index 7c8c84e827d..b3bcbc8fa66 100644 --- a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb @@ -22,7 +22,7 @@ dependencies = [ builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb index f5aef73bc13..b71554c4dfa 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb @@ -21,6 +21,6 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb index 6d0bea61d24..d33516e092f 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['ba65236116de8326d83378b2bd929879fa185195bc530b9d1aba72107910b6b3'] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb index 17a1f835e91..7009268301e 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} dependencies = [ ('Python', '2.7.14'), - ('MATLAB', version, '', SYSTEM) + ('MATLAB', version, '', True) ] # Since this setup.py does not provide a separate --build-base for the install diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb index 55b0c6ce81f..d7fcbc99902 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} dependencies = [ ('Python', '3.6.3'), - ('MATLAB', version, '', SYSTEM) + ('MATLAB', version, '', True) ] # Since this setup.py does not provide a separate --build-base for the install diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb index 14e3d088e33..fc816ba2323 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} dependencies = [ ('Python', '2.7.14'), - ('MATLAB', version, '', SYSTEM) + ('MATLAB', version, '', True) ] # Since this setup.py does not provide a separate --build-base for the install diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb index 76000b4dc4a..0c39c8a729c 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} dependencies = [ ('Python', '3.6.3'), - ('MATLAB', version, '', SYSTEM) + ('MATLAB', version, '', True) ] # Since this setup.py does not provide a separate --build-base for the install diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb index 8ac5cb405dc..7ce8669e278 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} multi_deps = {'Python': ['3.7.4', '2.7.16']} dependencies = [ - ('MATLAB', version, '', SYSTEM) + ('MATLAB', version, '', True) ] use_pip = False diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb index fb935602693..b7d5d70c2df 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ source_urls = [XORG_UTIL_SOURCE] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ('xproto', '7.0.31'), ('xorg-macros', '1.19.1'), ] diff --git a/easybuild/easyconfigs/m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb index e87d9e19fd7..388d152019f 100644 --- a/easybuild/easyconfigs/m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb @@ -19,7 +19,7 @@ dependencies = [ ('Bowtie2', '2.3.2'), ('Bowtie', '1.1.2'), ('SAMtools', '1.6'), - ('picard', '2.6.0', '-Java-1.8.0_131', SYSTEM), + ('picard', '2.6.0', '-Java-1.8.0_131', True), ('GSL', '2.3'), ] diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.4-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.4-intel-2018a-Python-2.7.14.eb index fd51cdde93e..4a532cf4fe8 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.4-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.4-intel-2018a-Python-2.7.14.eb @@ -19,7 +19,7 @@ checksums = [ builddependencies = [('Boost.Python', '1.66.0', versionsuffix)] dependencies = [ - ('Eigen', '3.3.4', '', SYSTEM), + ('Eigen', '3.3.4', '', True), ('Python', '2.7.14'), ] diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb index c76c50c23f9..321116d715d 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb @@ -14,8 +14,8 @@ checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] dependencies = [ ('Python', '2.7.15'), - ('vsc-base', '2.8.3', '', SYSTEM), - ('vsc-mympirun', '4.1.8', '', SYSTEM), + ('vsc-base', '2.8.3', '', True), + ('vsc-mympirun', '4.1.8', '', True), ('matplotlib', '2.2.4', versionsuffix), ('h5py', '2.9.0'), ('mpi4py', '3.0.2', '-timed-pingpong'), diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb index 194aa344082..e26533855e6 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb @@ -14,8 +14,8 @@ checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] dependencies = [ ('Python', '2.7.13'), - ('vsc-base', '2.5.8', '', SYSTEM), - ('vsc-mympirun', '4.0.2', '', SYSTEM), + ('vsc-base', '2.5.8', '', True), + ('vsc-mympirun', '4.0.2', '', True), ('matplotlib', '2.0.2', versionsuffix), ('h5py', '2.7.1', versionsuffix), ('mpi4py', '2.0.0', versionsuffix + '-timed-pingpong'), diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb index 9c4144e7c47..7c14b8aa091 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb @@ -14,8 +14,8 @@ checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] dependencies = [ ('Python', '2.7.14'), - ('vsc-base', '2.8.1', '', SYSTEM), - ('vsc-mympirun', '4.1.5', '', SYSTEM), + ('vsc-base', '2.8.1', '', True), + ('vsc-mympirun', '4.1.5', '', True), ('matplotlib', '2.1.2', versionsuffix), ('h5py', '2.7.1', versionsuffix), ('mpi4py', '3.0.0', versionsuffix + '-timed-pingpong'), diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb index 6202bc1f6ce..5c72b2d9539 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb @@ -14,8 +14,8 @@ checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] dependencies = [ ('Python', '2.7.15'), - ('vsc-base', '2.8.3', '', SYSTEM), - ('vsc-mympirun', '4.1.8', '', SYSTEM), + ('vsc-base', '2.8.3', '', True), + ('vsc-mympirun', '4.1.8', '', True), ('matplotlib', '2.2.4', versionsuffix), ('h5py', '2.9.0'), ('mpi4py', '3.0.2', '-timed-pingpong'), diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb index abba6ab7b5b..5ebb8f01ff7 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_92', '', SYSTEM)] +dependencies = [('Java', '1.8.0_92', '', True)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb index 5375c605408..ed0e37836cc 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_77', '', SYSTEM)] +dependencies = [('Java', '1.8.0_77', '', True)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb index e2ec60825f6..8b032e04685 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_92', '', SYSTEM)] +dependencies = [('Java', '1.8.0_92', '', True)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb index fc51bb5ca7f..8d0219a7422 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_121', '', SYSTEM)] +dependencies = [('Java', '1.8.0_121', '', True)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb index 5c5cf246ba1..ff686a0a357 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.58'), ('GL2PS', '1.3.9'), ('gnuplot', '5.0.3'), - ('Java', '1.8.0_72', '', SYSTEM), + ('Java', '1.8.0_72', '', True), ('zlib', '1.2.8'), ('Mesa', '11.1.2'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb index c2c9f653f54..ce3a19f67d0 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.60'), ('GL2PS', '1.3.9'), ('gnuplot', '5.0.5'), - ('Java', '1.8.0_112', '', SYSTEM), + ('Java', '1.8.0_112', '', True), ('zlib', '1.2.8'), ('Mesa', '12.0.2'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb index 20d927dc1fb..ea85cfeafc9 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb @@ -33,7 +33,7 @@ dependencies = [ ('GLPK', '4.60'), ('GL2PS', '1.3.9'), ('gnuplot', '5.0.5'), - ('Java', '1.8.0_121', '', SYSTEM), + ('Java', '1.8.0_121', '', True), ('zlib', '1.2.8'), ('Mesa', '12.0.2'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb index 86f569eb1f8..29256de39d1 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.openssl.org/source/'] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.25', '', SYSTEM), + ('binutils', '2.25', '', True), ] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb index f80a7efa49f..904ddedf279 100644 --- a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb @@ -19,7 +19,7 @@ dependencies = [ ('Perl', '5.24.0'), ('MCL', '%s.%s' % (local_mcl_majver, local_mcl_minver)), ('BioPerl', '1.7.1', versionsuffix), - ('BLAST', '2.2.26', '-Linux_x86_64', SYSTEM), + ('BLAST', '2.2.26', '-Linux_x86_64', True), ] start_dir = 'ORTHOMCLV%(version)s' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb index 484eb213be4..9dc98305542 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb @@ -18,7 +18,7 @@ checksums = [ builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ] configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb index e0de2012bfd..99940a8a08d 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -20,7 +20,7 @@ dependencies = [ ('Perl', '5.22.1'), ('libpsortb', '1.0'), ('BioPerl', '1.6.924', '-Perl-5.22.1'), - ('BLAST', '2.2.26', '-Linux_x86_64', SYSTEM), + ('BLAST', '2.2.26', '-Linux_x86_64', True), ('pftoolsV3', '20160324'), ] diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb index ce30da2a7da..2899a206f1b 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb @@ -15,7 +15,7 @@ checksums = ['a7dbdac7e2f0c0d2ad98f5f281d5a9d29d6673b3c20210e261b96e9a2d0b6e37'] dependencies = [ ('Python', '2.7.12'), - ('CUDA', '8.0.61', '', SYSTEM), + ('CUDA', '8.0.61', '', True), ('Boost', '1.61.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb index 13947e02b8c..e98942047c3 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb @@ -15,7 +15,7 @@ checksums = ['6b5a9384e38c603ee429f8a6bee424532db7b3505027ce22f7e18ad19564b563'] dependencies = [ ('Python', '2.7.14'), - ('CUDA', '9.1.85', '', SYSTEM), + ('CUDA', '9.1.85', '', True), ('Boost.Python', '1.66.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb index 1d9ef9ef9e6..a3f849bd92e 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb @@ -15,7 +15,7 @@ checksums = ['7079f7738e83ee79ae26f0827ada29fe55921fec9760201199cc2bfb69446c92'] dependencies = [ ('Python', '3.6.4'), - ('CUDA', '9.1.85', '', SYSTEM), + ('CUDA', '9.1.85', '', True), ('Boost.Python', '1.66.0', '-Python-%(pyver)s'), ] diff --git a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb index b2c7e5f1d25..134d0b6c5f4 100644 --- a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb @@ -23,7 +23,7 @@ checksums = ['0799e6c3021d6e163ef7250853922fc365c3fb94246c2cb0984381741b83ea98'] dependencies = [ ('Python', '2.7.12'), ('PyCogent', '1.9', versionsuffix), - ('UCLUST', '1.2.22q', '-i86linux64', SYSTEM), + ('UCLUST', '1.2.22q', '-i86linux64', True), ] options = {'modulename': '%(namelower)s'} diff --git a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb index d4fd449da32..3d6d9af5489 100644 --- a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb @@ -24,7 +24,7 @@ checksums = ['0799e6c3021d6e163ef7250853922fc365c3fb94246c2cb0984381741b83ea98'] dependencies = [ ('Python', '2.7.15'), ('PyCogent', '1.9', versionsuffix), - ('UCLUST', '1.2.22q', '-i86linux64', SYSTEM), + ('UCLUST', '1.2.22q', '-i86linux64', True), ] options = {'modulename': '%(namelower)s'} diff --git a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb index dcf058b6b89..651a588075e 100644 --- a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb @@ -19,7 +19,7 @@ sources = ['%(version)s.tar.gz'] dependencies = [ ('Python', '2.7.12'), ('PyCogent', '1.5.3', versionsuffix), - ('UCLUST', '1.2.22q', '-i86linux64', SYSTEM), + ('UCLUST', '1.2.22q', '-i86linux64', True), ] options = {'modulename': 'pynast'} diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb index b6ac75df40b..2a45738b149 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb @@ -72,7 +72,7 @@ builddependencies = [('CMake', '3.10.2')] dependencies = [ ('Python', '3.6.4'), ('PyYAML', '3.12', '-Python-%(pyver)s'), - ('CUDA', local_cuda_ver, '', SYSTEM), + ('CUDA', local_cuda_ver, '', True), ('magma', '2.3.0', '-CUDA-%s' % local_cuda_ver), ('cuDNN', '7.0.5', '-CUDA-%s' % local_cuda_ver, True), ] diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb index fa0cc0df4bd..0e997ce499e 100644 --- a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb @@ -20,7 +20,7 @@ dependencies = [ ('libffi', '3.2.1'), ] -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] sanity_check_paths = { 'files': ['bin/p11-kit', 'bin/trust'] + diff --git a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb index 99145dac6d6..c92a89c0b3d 100644 --- a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb @@ -26,7 +26,7 @@ builddependencies = [('binutils', '2.31.1')] dependencies = [ ('Python', '3.7.2'), - ('SRA-Toolkit', '2.9.6-1', '-centos_linux64', SYSTEM) + ('SRA-Toolkit', '2.9.6-1', '-centos_linux64', True) ] download_dep_fail = True diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb index 6b79129e1de..185ce92b1dc 100644 --- a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ source_urls = ['http://cairographics.org/releases/'] sources = [SOURCE_TAR_GZ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] sanity_check_paths = { 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb index 876023e3f43..dadba07804c 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb @@ -19,7 +19,7 @@ patches = [ builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ] # don't use PAX, it might break. diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb index 60acff26e4a..b75a0d85ea9 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb @@ -16,7 +16,7 @@ source_urls = ['https://pkg-config.freedesktop.org/releases/'] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ] # don't use PAX, it might break. diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb index 4af4cb4cfef..dfba4ffaa84 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb @@ -20,7 +20,7 @@ source_urls = [ mpich_opts = '--enable-static' dependencies = [ - ('pscom', '5.0.48-1', '', SYSTEM), + ('pscom', '5.0.48-1', '', True), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb index 7c6c53dd6bf..1bfdad4fb7a 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb @@ -20,7 +20,7 @@ mpich_opts = '--enable-static' threaded = True dependencies = [ - ('pscom', '5.0.48-1', '', SYSTEM), + ('pscom', '5.0.48-1', '', True), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb index 4937bd9d705..93f76f8af09 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb @@ -17,7 +17,7 @@ source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] mpich_opts = '--enable-static' dependencies = [ - ('pscom', '5.0.48-1', '', SYSTEM), + ('pscom', '5.0.48-1', '', True), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb index 43f185c60fd..341f884f89e 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb @@ -25,7 +25,7 @@ dependencies = [ ('Python', '3.5.2'), ('Perl', '5.24.0'), ('matplotlib', '1.5.3', versionsuffix), - ('Java', '1.8.0_131', '', SYSTEM), + ('Java', '1.8.0_131', '', True), ('Boost', '1.63.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb index 79f2d229658..f0f4d2c5b81 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb @@ -23,7 +23,7 @@ dependencies = [ ('Python', '3.6.4'), ('Perl', '5.26.1'), ('matplotlib', '2.1.2', versionsuffix), - ('Java', '1.8.0_162', '', SYSTEM), + ('Java', '1.8.0_162', '', True), ('Boost', '1.66.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb index da0694b350b..f3b210b0ca5 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '2.7.15'), ('Perl', '5.28.0'), ('matplotlib', '2.2.3', versionsuffix), - ('Java', '1.8', '', SYSTEM), + ('Java', '1.8', '', True), ('Boost', '1.67.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb index aee9ee6a397..cef7ad2f682 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb @@ -20,7 +20,7 @@ dependencies = [ ('Python', '2.7.15'), ('Perl', '5.28.1'), ('matplotlib', '2.2.4', versionsuffix), - ('Java', '11', '', SYSTEM), + ('Java', '11', '', True), ('Boost', '1.70.0'), ] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb index d81dfc2eebd..26cc0e00521 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('pkg-config', '0.29.1'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb index dc3c3684a36..5bc3462602c 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('pkg-config', '0.29.1'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb index 856611cdef4..503529a7dda 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb index 8598fef3f0a..4606a8754dd 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.47.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb index acb8163c2da..10bcf7e69ec 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.23'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb index cf10b5462d5..aa995966ac0 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb index c5c88c181d4..f3ec1cac38c 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb @@ -23,7 +23,7 @@ dependencies = [ ('libjpeg-turbo', '1.4.2'), # for plottting in R ('LibTIFF', '4.0.6'), # for plotting in R ('cairo', '1.14.6'), # for plotting in R - ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', versionsuffix), # for tcltk ('cURL', '7.47.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index 4f6c9a71091..841c073f2b3 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.47.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb index 84e20abc2e2..067c596089e 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb @@ -20,7 +20,7 @@ dependencies = [ ('libpng', '1.6.23'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb index 32c2e7ab309..cd605ba827a 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb @@ -20,7 +20,7 @@ dependencies = [ ('libpng', '1.6.23'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb b/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb index 724a3ceed71..ebe33155b56 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb @@ -20,7 +20,7 @@ dependencies = [ ('libpng', '1.6.23'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb index 2f0044cf886..13ed7e3b872 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb @@ -26,7 +26,7 @@ dependencies = [ ('libpng', '1.6.24'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 8436e30f382..11f7ae9944f 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -26,7 +26,7 @@ dependencies = [ ('libpng', '1.6.29'), # for plotting in R ('libjpeg-turbo', '1.5.1'), # for plottting in R ('LibTIFF', '4.0.7'), - ('Java', '1.8.0_121', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_121', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.6'), # for tcltk ('Tk', '8.6.6'), # for tcltk ('cURL', '7.53.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index c8fa9e81b36..01b9b412a37 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -26,7 +26,7 @@ dependencies = [ ('libpng', '1.6.29'), # for plotting in R ('libjpeg-turbo', '1.5.1'), # for plottting in R ('LibTIFF', '4.0.7'), - ('Java', '1.8.0_121', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_121', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.6'), # for tcltk ('Tk', '8.6.6'), # for tcltk ('cURL', '7.53.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb index e6902b752ee..515080f4f37 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb @@ -32,7 +32,7 @@ dependencies = [ ('libpng', '1.6.24'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_141', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_141', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb b/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb index 25a9ce4249a..93b5974cfca 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.32'), # for plotting in R ('libjpeg-turbo', '1.5.2'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_152', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_152', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.7'), # for tcltk ('Tk', '8.6.7'), # for tcltk ('cURL', '7.55.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb index f09e4a993e8..72a1d8f4d5b 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb @@ -31,7 +31,7 @@ dependencies = [ ('libpng', '1.6.32'), # for plotting in R ('libjpeg-turbo', '1.5.2'), # for plottting in R ('LibTIFF', '4.0.8'), - ('Java', '1.8.0_152', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_152', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.7'), # for tcltk ('Tk', '8.6.7'), # for tcltk ('cURL', '7.56.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb index ea2dd212efd..10a97cc8586 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.32'), # for plotting in R ('libjpeg-turbo', '1.5.2'), # for plottting in R ('LibTIFF', '4.0.8'), - ('Java', '1.8.0_152', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_152', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.7'), # for tcltk ('Tk', '8.6.7'), # for tcltk ('cURL', '7.56.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb index 70cf55f16c3..25d65103609 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '1.5.3'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_162', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_162', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.8'), # for tcltk ('Tk', '8.6.8'), # for tcltk ('cURL', '7.58.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb index 5422e8e8b16..dc9f868dc2b 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '1.5.3'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_162', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_162', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.8'), # for tcltk ('Tk', '8.6.8'), # for tcltk ('cURL', '7.58.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb index df2f0ef39b8..83ac3843168 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '1.5.3'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_162', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_162', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.8'), # for tcltk ('Tk', '8.6.8'), # for tcltk ('cURL', '7.58.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb index 147016a5526..7cc11725a88 100644 --- a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb @@ -18,7 +18,7 @@ dependencies = [ ('Python', '3.6.6'), ('Pysam', '0.15.1', versionsuffix), ('scikit-learn', '0.20.0', versionsuffix), - ('Java', '1.8', '', SYSTEM), + ('Java', '1.8', '', True), ] download_dep_fail = True diff --git a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb index 1a666f6fc94..dc9c93177cf 100644 --- a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb @@ -18,7 +18,7 @@ dependencies = [ ('Python', '3.6.6'), ('Pysam', '0.15.1', versionsuffix), ('scikit-learn', '0.20.0', versionsuffix), - ('Java', '1.8', '', SYSTEM), + ('Java', '1.8', '', True), ] download_dep_fail = True diff --git a/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb index 01f18a9bb75..35d4801c28d 100644 --- a/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb @@ -23,7 +23,7 @@ dependencies = [ ('OrfM', '0.7.1'), ('HMMER', '3.2.1'), ('fxtract', '2.3'), - ('pplacer', '1.1.alpha19', '', SYSTEM), + ('pplacer', '1.1.alpha19', '', True), ('KronaTools', '2.7.1'), ('DIAMOND', '0.9.24'), ] diff --git a/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb index e45a4e372cc..06f3fc97f7e 100644 --- a/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] sanity_check_paths = { 'files': ['bin/shar', 'bin/uudecode', 'bin/uuencode', 'bin/unshar'], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb index ad59ec63441..3bf1060dd25 100755 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb @@ -17,8 +17,8 @@ local_pymajmin = local_pymaj + local_pymin dependencies = [ ('Python', '%s.%s.2' % (local_pymaj, local_pymin)), ('protobuf-python', '3.3.0', local_pythonsuffix), - ('CUDA', '8.0.44', '', SYSTEM), - ('cuDNN', '5.1', '-CUDA-8.0.44', SYSTEM), + ('CUDA', '8.0.44', '', True), + ('cuDNN', '5.1', '-CUDA-8.0.44', True), ] exts_list = [ diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb index 65072fe8b8e..b4e2affc990 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb @@ -26,8 +26,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.8.0_92', '', SYSTEM), - ('ant', '1.9.7', '-Java-%(javaver)s', SYSTEM), + ('Java', '1.8.0_92', '', True), + ('ant', '1.9.7', '-Java-%(javaver)s', True), ('Bowtie', '1.1.2'), ('Bowtie2', '2.2.8'), ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb index 5e8309a25ee..35b020b401a 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb @@ -27,8 +27,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.8.0_162', '', SYSTEM), - ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), + ('Java', '1.8.0_162', '', True), + ('ant', '1.10.1', '-Java-%(javaver)s', True), ('Bowtie', '1.2.2'), ('Bowtie2', '2.3.4.1'), ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb index 843aa1c597d..7522e28d255 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb @@ -29,7 +29,7 @@ source_urls = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] dependencies = [('ncurses', '6.0')] diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb index 0e32b78cf2d..bb013b1619c 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb @@ -15,7 +15,7 @@ source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.25', '', SYSTEM), + ('binutils', '2.25', '', True), ] dependencies = [ diff --git a/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb index ae2ec85f0ff..daa2ad6b936 100644 --- a/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb @@ -17,9 +17,9 @@ dependencies = [ ('BioPerl', '1.6.924', '-Perl-%(perlver)s'), ('HMMER', '3.1b2'), ('MCL', '14.137'), - ('MetaGeneAnnotator', '20080819', '-x86-64', SYSTEM), + ('MetaGeneAnnotator', '20080819', '-x86-64', True), ('MUSCLE', '3.8.31'), - ('BLAST', '2.2.26', '-Linux_x86_64', SYSTEM), + ('BLAST', '2.2.26', '-Linux_x86_64', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb index 076c0558ad7..fa730a6cadd 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb @@ -13,8 +13,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/hpcugent/vsc-mympirun-scoop/archive/'] dependencies = [ - ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', SYSTEM), - ('vsc-mympirun', '3.4.2', '', SYSTEM), + ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', True), + ('vsc-mympirun', '3.4.2', '', True), ('Python', '2.7.12'), ('SCOOP', '0.6.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb index dd1c04c7392..1c770debd8e 100644 --- a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb +++ b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb @@ -20,7 +20,7 @@ builddependencies = [ ('gettext', '0.19.7'), ('intltool', '0.51.0', '-Perl-5.22.1'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb index a565c8676f4..ce56b41359e 100644 --- a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb +++ b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb @@ -20,7 +20,7 @@ builddependencies = [ ('gettext', '0.19.7'), ('intltool', '0.51.0', '-Perl-5.22.1'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb index 3f6ba215d4d..0423282a108 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', SYSTEM), + ('gettext', '0.19.8', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb index ec46a64b897..6c49a4458b9 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', SYSTEM), + ('gettext', '0.19.8', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb index 3082194c6b5..001a737c6ef 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', SYSTEM), + ('gettext', '0.19.8', '', True), ('binutils', '2.25'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb index 1ba4448757e..08aad5d870e 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', SYSTEM), + ('gettext', '0.19.8', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb index 96249ed4220..8b076ecba44 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb @@ -18,7 +18,7 @@ versionsuffix = '-gettext-%s' % local_gettext_ver builddependencies = [ ('Autotools', '20150215'), - ('gettext', local_gettext_ver, '', SYSTEM), + ('gettext', local_gettext_ver, '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb index 0c774d43908..a0c7f313e03 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.6', '', SYSTEM), + ('gettext', '0.19.6', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb index 64b7587aa4a..e891d5536ae 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', SYSTEM), + ('gettext', '0.19.8', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb index 3393bb06e20..d8184d70d32 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb @@ -18,7 +18,7 @@ versionsuffix = '-gettext-%s' % local_gettext_ver builddependencies = [ ('Autotools', '20150215'), - ('gettext', local_gettext_ver, '', SYSTEM), + ('gettext', local_gettext_ver, '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb index 243db8e7d90..fdf1453ac4a 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.6', '', SYSTEM), + ('gettext', '0.19.6', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb index 60aeff8c712..85431b3d6e9 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', SYSTEM), + ('gettext', '0.19.8', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb index 8ac99515760..735c3cbe5ba 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb @@ -14,9 +14,9 @@ source_urls = ['http://tukaani.org/xz/'] patches = ['XZ-5.2.2_compat-libs.patch'] builddependencies = [ - ('gettext', '0.19.8.1', '', SYSTEM), + ('gettext', '0.19.8.1', '', True), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb index 8cc83b07a7f..cc9e04a5714 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb @@ -17,8 +17,8 @@ patches = ['XZ-5.2.2_compat-libs.patch'] # XZ (presumably its executables) depends on gettext, which depends on # xmllib2, which depends (optionally) on XZ builddependencies = [ - ('Autotools', '20150215', '', SYSTEM), - ('gettext', '0.19.8', '', SYSTEM), + ('Autotools', '20150215', '', True), + ('gettext', '0.19.8', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb index 7551f83a6ff..43b7d9e5a54 100644 --- a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb @@ -12,7 +12,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb index 823375c47ae..599b3a7ea3e 100644 --- a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb @@ -12,7 +12,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb index c61c6116cfc..6694d3c8d1a 100644 --- a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb index d6b82b3a951..6d95a13dc49 100644 --- a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb index e7c963b2128..20b75e6be45 100644 --- a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb @@ -12,7 +12,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb index db62de8e619..2470683fb8a 100644 --- a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb @@ -12,7 +12,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb index 738376cb603..1c0793e3c1a 100644 --- a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb index 25da228279f..c5509644a13 100644 --- a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb index 8cbd9faeae4..42b8d1faf07 100644 --- a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ] diff --git a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb index 1dfef47a2f7..f862af46cb9 100644 --- a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ] diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb index 4fdb9b6d636..06e2a620f7b 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ source_urls = [XORG_PROTO_SOURCE] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ('xorg-macros', '1.19.1'), ] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb index 5d1b362aa15..8409e2aa5cb 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb @@ -15,7 +15,7 @@ source_urls = ['http://zlib.net/fossils'] sources = [SOURCELOWER_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb index 520d56351d8..a15fb20fe64 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb @@ -15,7 +15,7 @@ source_urls = ['http://zlib.net/fossils'] sources = [SOURCELOWER_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb index 5ba01e22f5b..bec9454ed8e 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb @@ -15,7 +15,7 @@ source_urls = ['http://zlib.net/fossils'] sources = [SOURCELOWER_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.28', '', SYSTEM)] +builddependencies = [('binutils', '2.28', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb index 8da5a8874c1..6aa4e52aa9e 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb index 1221095c524..9ab612053c2 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb index 53d82c7a9a8..3475aad2a70 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb index 274d794a4aa..a7b3977bb9a 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb index 360c1a11cb8..1353624765d 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb index b5265dc9d78..1b44bb97802 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb index a8a5212f418..f4a9aac7763 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb index 55078920d1d..47a40a40359 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb index 16c8391ed1e..ecd6eff1be1 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb index 1b7951ca5cc..5c5b309e903 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb @@ -16,7 +16,7 @@ source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', # use same binutils version that was used when building GCC toolchain builddependencies = [ - ('binutils', '2.27', '', SYSTEM) + ('binutils', '2.27', '', True) ] sanity_check_paths = { From 0f0d7886acb607803d6cb8d2d8d59900486ef5e7 Mon Sep 17 00:00:00 2001 From: scimerman <80223690+scimerman@users.noreply.github.com> Date: Tue, 11 Oct 2022 16:03:02 +0200 Subject: [PATCH 314/793] Changed to perl minimal --- .../easyconfigs/o/OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb index 25d87d8dddb..1aedc1e69df 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb @@ -16,7 +16,7 @@ checksums = ['d7939ce614029cdff0b6c20f0e2e5703158a489a72b2507b8bd51bf8c8fd10ca'] dependencies = [('zlib', '1.2.11')] builddependencies = [ - ('Perl', '5.32.1'), + ('Perl', '5.32.1', '-minimal'), ('binutils', '2.36.1'), ] From 7672eda7e0ed7e954e15bc0743ee5394f6b20d1f Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 11 Oct 2022 15:17:10 +0100 Subject: [PATCH 315/793] more changes undone from old easyconfigs failing other CI tests --- .../b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb | 2 +- .../d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb | 2 +- .../g/GRNBoost/GRNBoost-20171009-intel-2017b-Java-1.8.0_152.eb | 2 +- .../m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb | 2 +- .../MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 2 +- .../m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb | 2 +- .../easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb | 2 +- .../PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb | 2 +- .../PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb | 2 +- ...-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb | 2 +- .../easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb | 2 +- .../easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb | 2 +- 12 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb index 3d6512a5f33..d90fb13229d 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_112', '', SYSTEM)] +dependencies = [('Java', '1.8.0_112', '', True)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb b/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb index 43608ef12b5..5077e846a5f 100644 --- a/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb @@ -18,7 +18,7 @@ source_urls = ['https://bitbucket.org/nrg/dicombrowser/downloads/'] sources = ['%(name)s-%(version)s-bin-with-dependencies.jar'] dependencies = [ - ('Java', '1.7.0_80', '', SYSTEM), + ('Java', '1.7.0_80', '', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GRNBoost/GRNBoost-20171009-intel-2017b-Java-1.8.0_152.eb b/easybuild/easyconfigs/g/GRNBoost/GRNBoost-20171009-intel-2017b-Java-1.8.0_152.eb index a8e13772a67..633322c56c4 100644 --- a/easybuild/easyconfigs/g/GRNBoost/GRNBoost-20171009-intel-2017b-Java-1.8.0_152.eb +++ b/easybuild/easyconfigs/g/GRNBoost/GRNBoost-20171009-intel-2017b-Java-1.8.0_152.eb @@ -16,7 +16,7 @@ sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_ builddependencies = [('sbt', '1.0.2', versionsuffix, True)] dependencies = [ - ('Java', '1.8.0_152', '', SYSTEM), + ('Java', '1.8.0_152', '', True), ('XGBoost', '20171120', versionsuffix), ('Spark', '2.2.0', '-Hadoop-2.6' + versionsuffix, True), ] diff --git a/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb b/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb index 13a5f06fec5..f41f912592a 100644 --- a/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb @@ -13,7 +13,7 @@ source_urls = ['https://github.com/matsim-org/matsim/releases/download/%(namelow sources = ['%(namelower)s-%(version)s.zip'] dependencies = [ - ('Java', '1.8.0_112', '', SYSTEM), + ('Java', '1.8.0_112', '', True), ('X11', '20160819'), ] diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index 05e8b2e18a0..9b8ad14bb5f 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] sources = ['stable_release-%s.zip' % version.replace('.', '-')] dependencies = [ - ('Java', '1.7.0_79', '', SYSTEM), + ('Java', '1.7.0_79', '', True), ('Python', '2.7.11'), ('HDF5', '1.8.16'), ('libxml2', '2.9.3'), diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb index 97b0d2699a0..d8d121944ac 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb @@ -21,7 +21,7 @@ sources = ['mpj-v%s.tar.gz' % (version.replace('.', '_'))] builddependencies = [('CMake', '3.5.2')] dependencies = [ - ('Java', '1.8.0_92', '', SYSTEM), + ('Java', '1.8.0_92', '', True), ] # compile JNI wrapper library as described in docs diff --git a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb index ece457c65a0..53475269537 100644 --- a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb @@ -18,7 +18,7 @@ source_urls = ['http://cmpg.unibe.ch/software/PGDSpider/'] sources = ['%(name)s_%(version)s.zip'] dependencies = [ - ('Java', '1.7.0_80', '', SYSTEM), + ('Java', '1.7.0_80', '', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb index 83910094da9..a77bf58f492 100644 --- a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.7.0_80', '', SYSTEM), + ('Java', '1.7.0_80', '', True), ('Python', '2.7.11'), ('Perl', '5.22.1'), ('Tcl', '8.6.4'), diff --git a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb index 79bce614bbe..fb25f08bf9e 100644 --- a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.8'), - ('Java', '1.7.0_80', '', SYSTEM), + ('Java', '1.7.0_80', '', True), ('Python', '2.7.12'), ('Perl', '5.24.0'), ('cairo', '1.14.6'), diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb b/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb index 31aafdd2c90..0e81ab6be6c 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb @@ -18,7 +18,7 @@ source_urls = [ checksums = ['86f33f6f4fe545cb848600004144f09b6e8413af47ce02c1203c3ecda075288d'] dependencies = [ - ('Java', '1.8.0_152', '', SYSTEM), + ('Java', '1.8.0_152', '', True), ('Python', '3.6.3'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb index 5a6e085b08a..b6070a5118c 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb @@ -21,7 +21,7 @@ source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s' install_cmd = "cp -a %(namelower)s_zip/* %(installdir)s && chmod +x %(installdir)s/%(namelower)s" dependencies = [ - ('FastQC', '0.11.5', '-Java-1.7.0_80', SYSTEM), + ('FastQC', '0.11.5', '-Java-1.7.0_80', True), ('cutadapt', '1.9.1', '-Python-2.7.12'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb index 132db8b33b2..ed3b6794101 100755 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb @@ -21,7 +21,7 @@ source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s' install_cmd = "cp -a * %(installdir)s && chmod +x %(installdir)s/%(namelower)s" dependencies = [ - ('FastQC', '0.11.5', '-Java-1.7.0_80', SYSTEM), + ('FastQC', '0.11.5', '-Java-1.7.0_80', True), ('cutadapt', '1.9.1', '-Python-2.7.12'), ] From dd57d5e74656e72be224fa5ce3b02ddc8f3eb39e Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 11 Oct 2022 16:29:43 +0200 Subject: [PATCH 316/793] Increase tolerance in the compression test --- .../netcdf4-python-1.6.1-foss-2022a.eb | 7 ++++++- ...n-1.6.1_relax_tolerance_compression_test.patch | 15 +++++++++++++++ 2 files changed, 21 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1_relax_tolerance_compression_test.patch diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb index e4909b8b62d..3073dcfd28b 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb @@ -24,13 +24,18 @@ exts_list = [ 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], }), (name, version, { - 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'patches': [ + 'netcdf4-python-1.1.8-avoid-diskless-test.patch', + 'netcdf4-python-1.6.1_relax_tolerance_compression_test.patch', + ], 'source_tmpl': 'netCDF4-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], 'checksums': [ 'ba8dc5d65293a99f1afb8c2acf588d903fdfdc1963a62545b677fa2734262a78', # netCDF4-1.6.1.tar.gz # netcdf4-python-1.1.8-avoid-diskless-test.patch 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + # netcdf4-python-1.6.1_relax_tolerance_compression_test.patch + '64d192a5d1e3e00af78f053da78f5a35015fa713c7f97b10b622be6a44347166', ], }), ] diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1_relax_tolerance_compression_test.patch b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1_relax_tolerance_compression_test.patch new file mode 100644 index 00000000000..57dda863c8b --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1_relax_tolerance_compression_test.patch @@ -0,0 +1,15 @@ +# Relax tolerance in the compression_szip test to avoid fails on some systems. +# author: maxim-masterov (SURF) +# +diff -Nru netcdf4-python-1.6.1.orig/test/tst_compression_szip.py netcdf4-python-1.6.1/test/tst_compression_szip.py +--- netcdf4-python-1.6.1.orig/test/tst_compression_szip.py 2022-10-11 14:47:31.830359000 +0200 ++++ netcdf4-python-1.6.1/test/tst_compression_szip.py 2022-10-11 14:48:13.300393000 +0200 +@@ -33,7 +33,7 @@ + assert_almost_equal(datarr,f.variables['data'][:]) + assert f.variables['data'].filters() ==\ + {'zlib':False,'szip':False,'zstd':False,'bzip2':False,'blosc':False,'shuffle':False,'complevel':0,'fletcher32':False} +- assert_almost_equal(datarr,f.variables['data_szip'][:]) ++ assert_almost_equal(datarr,f.variables['data_szip'][:], 6) + dtest = {'zlib': False, 'szip': {'coding': 'ec', 'pixels_per_block': 32}, 'zstd': False, 'bzip2': False, 'blosc': False, 'shuffle': False, 'complevel': 0, 'fletcher32': False} + assert f.variables['data_szip'].filters() == dtest + f.close() From 6b0e07573193c0fe87407ed2dcfe5a52e81466f9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 11 Oct 2022 16:41:28 +0200 Subject: [PATCH 317/793] Fix patch description + checksum --- .../easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb | 11 +++++++++++ .../easyconfigs/v/VMD/VMD-1.9.4a57_configure.patch | 2 ++ 2 files changed, 13 insertions(+) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb index c79d12f48f5..33c06f706b8 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb @@ -25,6 +25,17 @@ patches = [ ('VMD-%(version)s_configure.patch', 'vmd-%(version)s'), ('VMD-1.9.4a51_extra_colors.patch', 'vmd-%(version)s'), ] +checksums = [ + 'de278d0c5d969336d89068e0806fb50aaa0cb0f546ba985d840b279357860679', # vmd-1.9.4a57.src.tar.gz + '51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a', # stride.tar.gz + '85760d6ae838e2b09801e34b36b484532383f7aaf2e8634b3ef808002a92baa3', # VMD-1.9.3_plugins.patch + 'd5cfa88064b7cffbc75accd69707d4e45fda974e8127de9ab606fdad501bd68a', # VMD-1.9.3_surf_Makefile.patch + 'f3c2a8c155e38db8e644cee6a01f6beaea5988e72ac74cde26b71670b151cc34', # VMD-1.9.3_surf_bad_printfs.patch + 'eb194ac0d8c086b73f87b29f7d732687f902431b1cdfa139c090401fefdee51e', # VMD-1.9.3_stride_Makefile.patch + 'eff1ca00cec637a6c8a156b2fb038e078d1835ba0eb15a571ed820bca5a866d9', # VMD-1.9.3_stride_MAX_AT_IN_RES.patch + '231b55bcc2e9e71a0934b2693b56170be4d922a9afe98f39b583617533ef1349', # VMD-1.9.4a57_configure.patch + '253eba282b570eb00e4764f46f77fd5ca898d10360d5707dd50ad1f14615af80', # VMD-1.9.4a51_extra_colors.patch +] dependencies = [ ('Tcl', '8.6.12'), diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57_configure.patch b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57_configure.patch index 63b8e014f84..da64877ec97 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57_configure.patch +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57_configure.patch @@ -1,3 +1,5 @@ +Update hardcoded configurations to be compatible with EB +Author: Last updated micketeer@gmail.com --- configure.orig 2022-10-03 21:19:36.313951477 +0000 +++ configure 2022-10-03 21:44:36.664710705 +0000 @@ -498,17 +498,17 @@ From dcc80e2c754d267162097da3d9a4a742f8e3fb78 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 11 Oct 2022 15:45:21 +0100 Subject: [PATCH 318/793] revert old flex easyconfig changes --- .../easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb | 2 +- .../easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb | 2 +- .../easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb | 2 +- 16 files changed, 16 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb index f93575efa78..ac2d9ea1647 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb index 5845a2c4a99..72d2805b5fe 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb index 6dfeb43eb04..facf8e7f13d 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb index 77843fba611..a28470817bb 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb index db2144c50dd..68344b21cb3 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb index 152ebf1d622..f579ff8a965 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb index fd99cc06be2..bf74b3065c0 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb @@ -14,6 +14,6 @@ checksums = ['71dd1b58158c935027104c830c019e48c73250708af5def45ea256c789318948'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.28', '', SYSTEM)] +builddependencies = [('binutils', '2.28', '', True)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb index 92ac3157fe7..b7b82f91973 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.25', '', SYSTEM), + ('binutils', '2.25', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb index 18c962e0803..73279c6d88c 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.25', '', SYSTEM), + ('binutils', '2.25', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb index adf1e7911c6..954dea0d03b 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', SYSTEM), + ('binutils', '2.26', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb index 171d19af2db..ee9b4ed94d3 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', SYSTEM), + ('binutils', '2.26', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb index 1f313caa5a3..51d6c9f7b63 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb index cafaa07872a..43cfdfac42c 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb index 50026211e06..fea26879081 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ('Bison', '3.0.4'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', SYSTEM), + ('binutils', '2.26', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb index b8bb432df65..e7dd6de964c 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ('Bison', '3.0.4'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb index 8f9ab00f288..28c855c205d 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ('Bison', '3.0.4'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.28', '', SYSTEM), + ('binutils', '2.28', '', True), ] moduleclass = 'lang' From e239ae1a429fdfc7641e2d8142d714fa7ad48dcc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Oct 2022 22:50:41 +0200 Subject: [PATCH 319/793] add sanity check command for x13as --- easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb index 0687aee7c0e..efe8235a510 100644 --- a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb @@ -41,11 +41,13 @@ builddependencies = [ build_cmd = 'make -f makefile.gf' -files_to_copy = [(["x13as"], "bin")] +files_to_copy = [(['x13as'], 'bin')] sanity_check_paths = { 'files': ['bin/x13as'], 'dirs': [], } +sanity_check_commands = ["x13as --help"] + moduleclass = 'math' From 257ee5bd5ac65516629326ba112e76d4bb522780 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Oct 2022 23:09:37 +0200 Subject: [PATCH 320/793] add sanity check command for x13as --- easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb index 4359434e6cf..92ba2cefb87 100644 --- a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb @@ -41,11 +41,13 @@ builddependencies = [ build_cmd = 'make -f makefile.gf' -files_to_copy = [(["x13as"], "bin")] +files_to_copy = [(['x13as'], 'bin')] sanity_check_paths = { 'files': ['bin/x13as'], 'dirs': [], } +sanity_check_commands = ["x13as --help"] + moduleclass = 'math' From 84d47b9e40f33867fc246bd2e456fb1021ad987d Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 12 Oct 2022 12:03:33 +0100 Subject: [PATCH 321/793] exclude older toolchain easyconfigs from SYSTEM template constant check --- test/easyconfigs/easyconfigs.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 766b4bad1eb..2d0e06c6ace 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1424,6 +1424,11 @@ def template_easyconfig_test(self, spec): orig_val = resolve_template(ec_dict[key], ec.template_values) dumped_val = resolve_template(dumped_ec[key], ec.template_values) + # skip SYSTEM template constant check for pre-2019b toolchain generation easyconfigs + # since these fail other CI checks when updated + regex = re.compile('(201\d[ab])|(^[1-8]\.\d+\.\d+)') + skip_system_template_check = regex.match(ec['toolchain']['version']) + # take into account that dumped value for *dependencies may include hard-coded subtoolchains # if no easyconfig was found for the dependency with the 'parent' toolchain, # if may get resolved using a subtoolchain, which is then hardcoded in the dumped easyconfig @@ -1452,9 +1457,9 @@ def template_easyconfig_test(self, spec): if len(dumped_dep) >= 4: if len(orig_dep) >= 4: # use of `True` is deprecated in favour of the more intuitive `SYSTEM` template - if orig_dep[3] is True: + if orig_dep[3] is True and not skip_system_template_check: error_msg = "use of `True` to indicate the system toolchain for dependency " - error_msg += "%s is deprecated, use the `SYSTEM` template instead" % dumped_dep[0] + error_msg += "%s is deprecated, use the `SYSTEM` template constant instead" % dumped_dep[0] self.fail(error_msg) else: self.assertEqual(dumped_dep[3], orig_dep[3]) From a9afaa4b990f1c715823056f0fe8dac89354c446 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 12 Oct 2022 12:11:45 +0100 Subject: [PATCH 322/793] linting --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 2d0e06c6ace..741effc1729 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1426,7 +1426,7 @@ def template_easyconfig_test(self, spec): # skip SYSTEM template constant check for pre-2019b toolchain generation easyconfigs # since these fail other CI checks when updated - regex = re.compile('(201\d[ab])|(^[1-8]\.\d+\.\d+)') + regex = re.compile(r'(201\d[ab])|(^[1-8]\.\d+\.\d+)') skip_system_template_check = regex.match(ec['toolchain']['version']) # take into account that dumped value for *dependencies may include hard-coded subtoolchains From f99a9299ab2dfc457792ea53e2d84b33985b12e7 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 12 Oct 2022 12:29:27 +0100 Subject: [PATCH 323/793] fix logic and re-instate original test for easyconfigs excluded from the SYSTEM template constant check --- test/easyconfigs/easyconfigs.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 741effc1729..b4f60e5a0c8 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -42,6 +42,7 @@ from easybuild.easyblocks.generic.configuremake import ConfigureMake from easybuild.easyblocks.generic.pythonpackage import PythonPackage from easybuild.framework.easyblock import EasyBlock +from easybuild.framework.easyconfig.constants import EASYCONFIG_CONSTANTS from easybuild.framework.easyconfig.default import DEFAULT_CONFIG from easybuild.framework.easyconfig.format.format import DEPENDENCY_PARAMETERS from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, letter_dir_for @@ -1457,10 +1458,13 @@ def template_easyconfig_test(self, spec): if len(dumped_dep) >= 4: if len(orig_dep) >= 4: # use of `True` is deprecated in favour of the more intuitive `SYSTEM` template - if orig_dep[3] is True and not skip_system_template_check: - error_msg = "use of `True` to indicate the system toolchain for dependency " - error_msg += "%s is deprecated, use the `SYSTEM` template constant instead" % dumped_dep[0] - self.fail(error_msg) + if orig_dep[3] is True: + if skip_system_template_check: + self.assertEqual(dumped_dep[3], EASYCONFIG_CONSTANTS['SYSTEM'][0]) + else: + error_msg = "use of `True` to indicate the system toolchain for dependency " + error_msg += "%s is deprecated, use the `SYSTEM` template constant instead" % dumped_dep[0] + self.fail(error_msg) else: self.assertEqual(dumped_dep[3], orig_dep[3]) else: From f441f621127d3a6dc74c5eb29272dd215e8e13b4 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 12 Oct 2022 13:41:32 +0100 Subject: [PATCH 324/793] also exempt old toolchains of the form 201X.YZ --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index b4f60e5a0c8..3d18c0cf585 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1425,9 +1425,9 @@ def template_easyconfig_test(self, spec): orig_val = resolve_template(ec_dict[key], ec.template_values) dumped_val = resolve_template(dumped_ec[key], ec.template_values) - # skip SYSTEM template constant check for pre-2019b toolchain generation easyconfigs + # skip SYSTEM template constant check for 2019b and older toolchain generation easyconfigs # since these fail other CI checks when updated - regex = re.compile(r'(201\d[ab])|(^[1-8]\.\d+\.\d+)') + regex = re.compile(r'(201\d([ab]|\.\d+))|(^[1-8]\.\d+\.\d+)') skip_system_template_check = regex.match(ec['toolchain']['version']) # take into account that dumped value for *dependencies may include hard-coded subtoolchains From 9dfd27048cee13c0a6f179123c2924c01ca4d90e Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 12 Oct 2022 13:49:16 +0100 Subject: [PATCH 325/793] switch to SYSTEM template constant in the remaining easyconfigs overlooked in #16386 --- .../a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb | 2 +- .../a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb | 2 +- .../easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb | 2 +- .../f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb | 2 +- .../easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb | 2 +- .../easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb | 2 +- .../easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb | 2 +- .../o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb | 4 ++-- .../t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb | 2 +- .../t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb | 2 +- ...orchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb | 2 +- 14 files changed, 15 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb index 7911a59e768..1a85d18683e 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb @@ -27,7 +27,7 @@ dependencies = [ ('Kalign', '3.3.1'), ('jax', '0.2.24', versionsuffix), # also provides absl-py ('UCX-CUDA', '1.10.0', versionsuffix), - ('cuDNN', '8.2.1.32', versionsuffix, True), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('OpenMM', '7.5.1', '-DeepMind-patch'), ] diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb index 2ab59fb243c..b6993861962 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb @@ -27,7 +27,7 @@ dependencies = [ ('Kalign', '3.3.1'), ('jax', '0.3.9', versionsuffix), # also provides absl-py ('UCX-CUDA', '1.10.0', versionsuffix), - ('cuDNN', '8.2.1.32', versionsuffix, True), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('OpenMM', '7.5.1', '-DeepMind-patch'), ] diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb index 3448b11526f..ff8966f9f92 100644 --- a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb @@ -26,7 +26,7 @@ builddependencies = [ ] dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), - ('cuDNN', '8.2.1.32', versionsuffix, True), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb index 2e329e07f19..0149030d604 100644 --- a/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb @@ -20,7 +20,7 @@ dependencies = [ ('HMMER', '3.3.2'), ('Kalign', '3.3.1'), ('UCX-CUDA', '1.10.0', versionsuffix), - ('cuDNN', '8.2.1.32', versionsuffix, True), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('dm-tree', '0.1.6'), ('einops', '0.4.1'), diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb index d9c4a4c51a4..a50c9db2fc7 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), - ('cuDNN', '8.2.1.32', versionsuffix, True), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb index 387bbe5cc6c..c7812a8bd25 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), - ('cuDNN', '8.4.1.50', versionsuffix, True), + ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM), ('NCCL', '2.12.12', versionsuffix), ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb index 92459f0310c..d77b7c6e666 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), - ('cuDNN', '8.2.1.32', versionsuffix, True), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), diff --git a/easybuild/easyconfigs/l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb index 9e9a544e9f6..91983a9e242 100644 --- a/easybuild/easyconfigs/l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb @@ -17,7 +17,7 @@ builddependencies = [ ('CMake', '3.23.1'), ('Ninja', '1.10.2'), # building LDC from source requires LDC - ('LDC', '1.24.0', '-%(arch)s', True), + ('LDC', '1.24.0', '-%(arch)s', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb index 1d5296cc0d5..52743c921ac 100644 --- a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb @@ -24,7 +24,7 @@ dependencies = [ ('HMMER', '3.3.2'), ('Kalign', '3.3.1'), ('UCX-CUDA', '1.10.0', versionsuffix), - ('cuDNN', '8.2.1.32', versionsuffix, True), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('dm-tree', '0.1.6'), ('einops', '0.4.1'), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb index cf6a5d92445..e6bc2880ce8 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb @@ -51,7 +51,7 @@ builddependencies = [ ('hypothesis', '6.46.7'), ] dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions ('Python', '3.10.4'), ('protobuf', '3.19.4'), @@ -64,7 +64,7 @@ dependencies = [ ('numactl', '2.0.14'), ('FFmpeg', '4.4.2'), ('Pillow', '9.1.1'), - ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.6.2', '-CUDA-%(cudaver)s'), ('NCCL', '2.12.12', '-CUDA-%(cudaver)s'), ('expecttest', '0.1.3'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb index 0ac39221678..32ddf1501b5 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), - ('cuDNN', '8.2.1.32', versionsuffix, True), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.5'), ('h5py', '3.2.1'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb index 8c4c862c922..21750d02e0a 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), - ('cuDNN', '8.2.1.32', versionsuffix, True), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.5'), ('h5py', '3.2.1'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb index 24cafa17438..6f8467a3d68 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ ('CUDA', '11.4.1', '', SYSTEM), - ('cuDNN', '8.2.2.26', versionsuffix, True), + ('cuDNN', '8.2.2.26', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.6'), ('h5py', '3.6.0'), diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb index ca3b8eac2e9..041a172edb9 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb @@ -15,7 +15,7 @@ checksums = ['99e6d3d304184895ff4f6152e2d2ec1cbec89b3e057d9c940ae0125546b04e91'] builddependencies = [('CMake', '3.20.1')] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('Pillow-SIMD', '8.2.0'), ('PyTorch', local_pytorch_version, '-CUDA-%(cudaver)s'), From 681e7267b08ae0801a557f91db5e01665c4aab9f Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 12 Oct 2022 13:53:37 +0100 Subject: [PATCH 326/793] line length --- test/easyconfigs/easyconfigs.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 3d18c0cf585..35b3a60886f 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1462,8 +1462,10 @@ def template_easyconfig_test(self, spec): if skip_system_template_check: self.assertEqual(dumped_dep[3], EASYCONFIG_CONSTANTS['SYSTEM'][0]) else: - error_msg = "use of `True` to indicate the system toolchain for dependency " - error_msg += "%s is deprecated, use the `SYSTEM` template constant instead" % dumped_dep[0] + error_msg = ( + "use of `True` to indicate the system toolchain for dependency " + "%s is deprecated, use the `SYSTEM` template constant instead" % dumped_dep[0] + ) self.fail(error_msg) else: self.assertEqual(dumped_dep[3], orig_dep[3]) From 1937a12077392134a19cea2b599cfb54d0c864a3 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 12 Oct 2022 14:12:56 +0100 Subject: [PATCH 327/793] adding easyconfigs: DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb --- ...epLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..1d6063dbbd9 --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,68 @@ +# Loosely based on PR #7680 +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'DeepLabCut' +version = '2.2.0.6' +versionsuffix = '-CUDA-%(cudaver)s' +local_version = '%(versionsuffix)s-contrib' + +homepage = 'http://www.mousemotorlab.org/deeplabcut' +description = "Markerless tracking of user-defined features with deep learning" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('Python', '3.9.5'), + ('h5py', '3.2.1'), + ('IPython', '7.25.0'), + ('scikit-learn', '0.24.2'), + ('scikit-image', '0.18.3'), + ('TensorFlow', '2.6.0', versionsuffix), + ('PyYAML', '5.4.1'), + ('PyTables', '3.6.1'), + ('wxPython', '4.1.1'), + ('OpenCV', '4.5.3', local_version), + ('numba', '0.53.1'), + ('libyaml', '0.2.5'), + ('imgaug', '0.4.0', versionsuffix), + ('tqdm', '4.61.2'), + ('ruamel.yaml', '0.17.21'), + ('PyYAML', '5.4.1'), + ('statsmodels', '0.12.2'), + ('PyTorch', '1.10.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('filterpy', '1.4.5', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['4f2a4d39e4ea601b9ab42b2db08b5918a9538c168cff1c6895ae26646f3d73b1'], + }), + ('pandas', '1.3.3', { + 'checksums': ['272c8cb14aa9793eada6b1ebe81994616e647b5892a370c7135efb2924b701df'], + }), + ('tensorpack', '0.11', { + 'checksums': ['022b610e416e62e3575424cd08e60af27808a5fb6914294615391caf582cbd4f'], + }), + ('tf_slim', '1.1.0', { + 'source_urls': ['https://github.com/google-research/tf-slim/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['964cde4b7728a408dcd5c841ab6b93d95137ab4b60db28b10400f86286bfeb8b'], + }), + ('msgpack-numpy', '0.4.8', { + 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], + 'sources': ['msgpack-numpy-0.4.8.tar.gz'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84'], + }), +] + +moduleclass = 'lib' From 56f6898350ae23dc0829890e1dc67c6fed6fc371 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 12 Oct 2022 14:46:54 +0100 Subject: [PATCH 328/793] adding easyconfigs: imgaug-0.4.0-foss-2021b-CUDA-11.4.1.eb --- .../imgaug-0.4.0-foss-2021b-CUDA-11.4.1.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021b-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..e724dbda37e --- /dev/null +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,35 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'imgaug' +version = '0.4.0' +versionsuffix = '-CUDA-11.4.1' + +homepage = 'https://imgaug.readthedocs.io/en/latest/' +description = """ This python library helps you with augmenting images for your machine learning projects. + It converts a set of input images into a new, much larger set of slightly altered images. """ + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('Pillow', '8.3.2'), + ('matplotlib', '3.4.3'), + ('scikit-image', '0.19.1'), + ('OpenCV', '4.5.5', versionsuffix + '-contrib'), + ('Shapely', '1.8.2'), + ('imageio', '2.13.5'), +] + +sources = [SOURCE_TAR_GZ] +patches = ['imgaug-0.4.0_openvc_requirement.patch'] +checksums = [ + '46bab63ed38f8980630ff721a09ca2281b7dbd4d8c11258818b6ebcc69ea46c7', # imgaug-0.4.0.tar.gz + '2ff0b66ba38fdcf5f267a3d0ad1dc2710fee3c2f8cd3d086c56ea538a2a9ffc8', # imgaug-0.4.0_openvc_requirement.patch +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'lib' From 017727e76347b0711c241238746e57bd8be6e32c Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 12 Oct 2022 14:55:05 +0100 Subject: [PATCH 329/793] adding easyconfigs: OpenCV-4.5.5-foss-2021b-CUDA-11.4.1-contrib.eb --- ...CV-4.5.5-foss-2021b-CUDA-11.4.1-contrib.eb | 86 +++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-CUDA-11.4.1-contrib.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-CUDA-11.4.1-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-CUDA-11.4.1-contrib.eb new file mode 100644 index 00000000000..935c5f8c301 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-CUDA-11.4.1-contrib.eb @@ -0,0 +1,86 @@ +name = 'OpenCV' +version = '4.5.5' +versionsuffix = '-CUDA-%(cudaver)s-contrib' + +# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake +local_ippicv_hash = 'a56b6ac6f030c312b2dce17430eef13aed9af274' + +homepage = 'https://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products. + Includes extra modules for OpenCV from the contrib repository.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [ + {'source_urls': ['https://github.com/opencv/opencv/archive/'], + 'download_filename': '%(version)s.zip', 'filename': SOURCELOWER_ZIP}, + {'source_urls': ['https://github.com/opencv/opencv_contrib/archive/'], + 'download_filename': '%(version)s.zip', 'filename': '%(namelower)s_contrib-%(version)s.zip'}, + {'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], + 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + 'fb16b734db3a28e5119d513bd7c61ef417edf3756165dc6259519bb9d23d04e2', # opencv-4.5.5.zip + 'f53a0e531b2e284d2d1af013f5d96a86dfc1165d71eb47ddc9e7b834cc803091', # opencv_contrib-4.5.5.zip + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz +] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # for numpy + ('zlib', '1.2.11'), + ('FFmpeg', '4.3.2'), + ('freetype', '2.11.0'), + ('HarfBuzz', '2.8.2'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('libwebp', '1.2.0'), + ('OpenEXR', '3.1.1'), + ('JasPer', '2.0.33'), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.11', '-Java-%(javaver)s', SYSTEM), + ('GLib', '2.69.1'), + ('GTK3', '3.24.31'), + ('HDF5', '1.12.1'), # needed by hdf from contrib + ('CUDA', '11.4.1', '', SYSTEM), + ('cuDNN', '8.2.2.26', '-CUDA-%(cudaver)s', SYSTEM), +] + +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = '-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules ' +configopts += '-DFREETYPE_FOUND=ON ' +configopts += '-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/ ' +configopts += '-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so ' +configopts += '-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so ' +configopts += '-DFREETYPE_LINK_LIBRARIES_XXXXX=ON ' +configopts += '-DHARFBUZZ_FOUND=ON ' +configopts += '-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz ' +configopts += '-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so ' +configopts += '-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so ' +configopts += '-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON ' +configopts += '-DBUILD_opencv_python2=OFF ' + +enhance_sanity_check = True + +local_contrib_libs = [ + 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', + 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', + 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', + 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' +] + +sanity_check_paths = { + 'files': ['lib64/libopencv_%s.%s' % (x, SHLIB_EXT) for x in local_contrib_libs], + 'dirs': [], +} + +moduleclass = 'vis' From 9704a24ceae84106f69fde86ed50258f8d719cf6 Mon Sep 17 00:00:00 2001 From: guacke Date: Wed, 12 Oct 2022 16:24:35 +0200 Subject: [PATCH 330/793] adding easyconfigs: PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb --- .../PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb new file mode 100644 index 00000000000..b597c4a7e59 --- /dev/null +++ b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonPackage' + +name = 'PyMOL' +version = '2.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/schrodinger/pymol-open-source' +description = """ +PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D +visualization of proteins, small molecules, density, surfaces, and trajectories. +It also includes molecular editing, ray tracing, and movies. Open Source PyMOL +is free to everyone! +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ["https://github.com/schrodinger/pymol-open-source/archive/refs/tags/"] +sources = ['v%(version)s.tar.gz'] +checksums = ['aa828bf5719bd9a14510118a93182a6e0cadc03a574ba1e327e1e9780a0e80b3'] + +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('Pmw', '2.0.1', { + 'buildopts': '', + 'installopts': '', + 'modulename': 'Pmw', + 'sources': [{ + 'download_filename': '8bedfc8747e7757c1048bc5e11899d1163717a43.zip', + 'source_urls': ['https://github.com/schrodinger/pmw-patched/archive/'], + 'filename': 'Pmw-patched-2.0.1-20200210-8bedfc8.zip'}], + 'use_pip': True, + 'checksums': ['db1ab4ee1020023ad814bb24c74f6361fb72e1011871911f7d37bb6ecf6c79ed'], + }), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyQt5', '5.15.1'), + ('glew', '2.1.0'), + ('libpng', '1.6.37'), + ('libxml2', '2.9.10'), + ('freetype', '2.10.3'), + ('GLM', '0.9.9.8'), + ('netCDF', '4.7.4'), + ('Tkinter', '%(pyver)s'), +] + +download_dep_fail = True +use_pip = False + +buildopts = '' +buildopts += '--use-msgpackc=no ' +installopts = buildopts + +modextravars = {'PYMOL_PATH': 'lib/python%(pyshortver)s/site-packages/pymol/pymol_path'} + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/pymol'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'vis' From 924191a138166afc6e0e431646fada1e913e0c2a Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Wed, 12 Oct 2022 17:36:30 +0200 Subject: [PATCH 331/793] adding easyconfigs: Delly-1.1.5-GCC-11.3.0.eb --- .../d/Delly/Delly-1.1.5-GCC-11.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/d/Delly/Delly-1.1.5-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/d/Delly/Delly-1.1.5-GCC-11.3.0.eb b/easybuild/easyconfigs/d/Delly/Delly-1.1.5-GCC-11.3.0.eb new file mode 100644 index 00000000000..fdbd1ffc53e --- /dev/null +++ b/easybuild/easyconfigs/d/Delly/Delly-1.1.5-GCC-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'Delly' +version = '1.1.5' + +homepage = 'https://github.com/dellytools/delly/' +description = """Delly is an integrated structural variant (SV) prediction +method that can discover, genotype and visualize deletions, tandem duplications, +inversions and translocations at single-nucleotide resolution in short-read +massively parallel sequencing data. It uses paired-ends, split-reads and +read-depth to sensitively and accurately delineate genomic rearrangements +throughout the genome.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'dellytools' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['aa5d994d4bd973e519931845c27f53a647d21ea6f649c651c0c2836b2bc7e801'] + +dependencies = [ + ('HTSlib', '1.15.1'), + ('Boost', '1.79.0'), +] + +build_cmd = 'make PARALLEL=1 -B src/delly' + +files_to_copy = [ + (['src/delly'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/delly'], + 'dirs': ['bin'] +} + +sanity_check_commands = ['delly'] + +moduleclass = 'bio' From c85aec299ad057cb912231bdc72c0d5ff7a9eff4 Mon Sep 17 00:00:00 2001 From: guacke Date: Wed, 12 Oct 2022 18:04:17 +0200 Subject: [PATCH 332/793] Style fixes. --- .../easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb index b597c4a7e59..ba9045003d0 100644 --- a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb +++ b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb @@ -46,9 +46,6 @@ dependencies = [ ('Tkinter', '%(pyver)s'), ] -download_dep_fail = True -use_pip = False - buildopts = '' buildopts += '--use-msgpackc=no ' installopts = buildopts From 0893308e9988d05dc23a8e9c827639301c0634f5 Mon Sep 17 00:00:00 2001 From: guacke Date: Wed, 12 Oct 2022 18:31:36 +0200 Subject: [PATCH 333/793] Style fixes. --- .../p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb index ba9045003d0..227d4407f08 100644 --- a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb +++ b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb @@ -28,10 +28,16 @@ exts_list = [ 'download_filename': '8bedfc8747e7757c1048bc5e11899d1163717a43.zip', 'source_urls': ['https://github.com/schrodinger/pmw-patched/archive/'], 'filename': 'Pmw-patched-2.0.1-20200210-8bedfc8.zip'}], - 'use_pip': True, 'checksums': ['db1ab4ee1020023ad814bb24c74f6361fb72e1011871911f7d37bb6ecf6c79ed'], }), ] +exts_default_options = { + 'use_pip': True, + 'download_dep_fail': True, +} + +download_dep_fail = True +use_pip = False dependencies = [ ('Python', '3.8.6'), From ddcc55e8ce2893b6a4ed3b0260cfca3b36db3f56 Mon Sep 17 00:00:00 2001 From: guacke Date: Wed, 12 Oct 2022 18:49:19 +0200 Subject: [PATCH 334/793] Style fixes. --- .../p/PyMOL/PyMOL-2.5.0-foss-2020b.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb new file mode 100644 index 00000000000..8173740a5a3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonPackage' + +name = 'PyMOL' +version = '2.5.0' + +homepage = 'https://github.com/schrodinger/pymol-open-source' +description = """ +PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D +visualization of proteins, small molecules, density, surfaces, and trajectories. +It also includes molecular editing, ray tracing, and movies. Open Source PyMOL +is free to everyone! +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ["https://github.com/schrodinger/pymol-open-source/archive/refs/tags/"] +sources = ['v%(version)s.tar.gz'] +checksums = ['aa828bf5719bd9a14510118a93182a6e0cadc03a574ba1e327e1e9780a0e80b3'] + +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('Pmw', '2.0.1', { + 'buildopts': '', + 'installopts': '', + 'modulename': 'Pmw', + 'sources': [{ + 'download_filename': '8bedfc8747e7757c1048bc5e11899d1163717a43.zip', + 'source_urls': ['https://github.com/schrodinger/pmw-patched/archive/'], + 'filename': 'Pmw-patched-2.0.1-20200210-8bedfc8.zip'}], + 'checksums': ['db1ab4ee1020023ad814bb24c74f6361fb72e1011871911f7d37bb6ecf6c79ed'], + }), +] +exts_default_options = { + 'use_pip': True, + 'download_dep_fail': True, +} + +download_dep_fail = True +use_pip = False + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyQt5', '5.15.1'), + ('glew', '2.1.0'), + ('libpng', '1.6.37'), + ('libxml2', '2.9.10'), + ('freetype', '2.10.3'), + ('GLM', '0.9.9.8'), + ('netCDF', '4.7.4'), + ('Tkinter', '%(pyver)s'), +] + +buildopts = '' +buildopts += '--use-msgpackc=no ' +installopts = buildopts + +modextravars = {'PYMOL_PATH': 'lib/python%(pyshortver)s/site-packages/pymol/pymol_path'} + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/pymol'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'vis' From d24202dc9b38f21d2993ad3c02e3fecbc474d1f2 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 12 Oct 2022 18:54:08 +0200 Subject: [PATCH 335/793] fix using system qhull and freetype for matplotlib --- .../easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2022a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2022a.eb index ade6e567845..3a1a017fd44 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2022a.eb @@ -30,7 +30,7 @@ sanity_pip_check = True # avoid that matplotlib downloads and builds its own copies of freetype and qhull _fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " -_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >setup.cfg && " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >mplsetup.cfg && " _include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " From fb26afdc27696923eedf8e713aae6576fbae0014 Mon Sep 17 00:00:00 2001 From: Guillaume Acke Date: Wed, 12 Oct 2022 19:57:37 +0200 Subject: [PATCH 336/793] Delete PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb --- .../PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb | 67 ------------------- 1 file changed, 67 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb deleted file mode 100644 index 227d4407f08..00000000000 --- a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb +++ /dev/null @@ -1,67 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PyMOL' -version = '2.5.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/schrodinger/pymol-open-source' -description = """ -PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D -visualization of proteins, small molecules, density, surfaces, and trajectories. -It also includes molecular editing, ray tracing, and movies. Open Source PyMOL -is free to everyone! -""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = ["https://github.com/schrodinger/pymol-open-source/archive/refs/tags/"] -sources = ['v%(version)s.tar.gz'] -checksums = ['aa828bf5719bd9a14510118a93182a6e0cadc03a574ba1e327e1e9780a0e80b3'] - -exts_defaultclass = 'PythonPackage' -exts_list = [ - ('Pmw', '2.0.1', { - 'buildopts': '', - 'installopts': '', - 'modulename': 'Pmw', - 'sources': [{ - 'download_filename': '8bedfc8747e7757c1048bc5e11899d1163717a43.zip', - 'source_urls': ['https://github.com/schrodinger/pmw-patched/archive/'], - 'filename': 'Pmw-patched-2.0.1-20200210-8bedfc8.zip'}], - 'checksums': ['db1ab4ee1020023ad814bb24c74f6361fb72e1011871911f7d37bb6ecf6c79ed'], - }), -] -exts_default_options = { - 'use_pip': True, - 'download_dep_fail': True, -} - -download_dep_fail = True -use_pip = False - -dependencies = [ - ('Python', '3.8.6'), - ('SciPy-bundle', '2020.11'), - ('PyQt5', '5.15.1'), - ('glew', '2.1.0'), - ('libpng', '1.6.37'), - ('libxml2', '2.9.10'), - ('freetype', '2.10.3'), - ('GLM', '0.9.9.8'), - ('netCDF', '4.7.4'), - ('Tkinter', '%(pyver)s'), -] - -buildopts = '' -buildopts += '--use-msgpackc=no ' -installopts = buildopts - -modextravars = {'PYMOL_PATH': 'lib/python%(pyshortver)s/site-packages/pymol/pymol_path'} - -sanity_pip_check = True -sanity_check_paths = { - 'files': ['bin/pymol'], - 'dirs': ['bin', 'lib'], -} - -moduleclass = 'vis' From 7f3973d12d919b1446fb2313ec7d3555ed3cfaeb Mon Sep 17 00:00:00 2001 From: Randy Pittman Date: Wed, 12 Oct 2022 11:16:38 -0700 Subject: [PATCH 337/793] Fix GitHub download link in libpsl-0.21.1-GCCcore-11.2.0.eb The existing download link in this doesn't work anymore. This file was added by #16087. --- easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb index 18012521272..66143f4a39a 100644 --- a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb @@ -8,7 +8,7 @@ description = "C library for the Public Suffix List" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = ['https://github.com/rockdaboot/libpsl/archive'] +source_urls = ['https://github.com/rockdaboot/libpsl/releases/download/%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['ac6ce1e1fbd4d0254c4ddb9d37f1fa99dec83619c1253328155206b896210d4c'] From 6e3a4e67d11c077851405490dd0c98ea28fb482c Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Wed, 12 Oct 2022 20:54:24 +0200 Subject: [PATCH 338/793] adding easyconfigs: pocl-1.8-GCC-11.3.0.eb --- .../easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb new file mode 100644 index 00000000000..469e6ffef6f --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeNinja' + +name = 'pocl' +version = '1.8' + +homepage = 'https://portablecl.org' +description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['pocl-%(version)s_fix-header-install.patch'] +checksums = [ + '0f63377ae1826e16e90038fc8e7f65029be4ff6f9b059f6907174b5c0d1f8ab2', # v1.8.tar.gz +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Clang', '13.0.1'), + ('hwloc', '2.7.1'), + ('libtool', '2.4.7'), + ('libxml2', '2.9.13'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From a17ed42e18d40031eaf73d225aacc85c7a8e5fb5 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Wed, 12 Oct 2022 21:20:26 +0200 Subject: [PATCH 339/793] Forgot patch checksum --- easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb index 469e6ffef6f..d9dbdf2fa1d 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb @@ -13,6 +13,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['pocl-%(version)s_fix-header-install.patch'] checksums = [ '0f63377ae1826e16e90038fc8e7f65029be4ff6f9b059f6907174b5c0d1f8ab2', # v1.8.tar.gz + '97dc45437ae7464bda9f13088720482804b8a19a4e71067196daa86af487222d', # pocl-1.8_fix-header-install.patch ] builddependencies = [ From fee40ea341c5c36158344b058fe42a18c13b36ec Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 12 Oct 2022 21:15:35 +0100 Subject: [PATCH 340/793] pkgconf added as more modern compared to the suggested pkg-config --- easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb index b78028c24b1..8145961cb31 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb @@ -34,6 +34,7 @@ checksums = [ builddependencies = [ ('binutils', '2.37'), ('GObject-Introspection', '1.68.0'), + ('pkgconf', '1.8.0'), ] dependencies = [ From a660197549c9b5db8d05e16b28b17cde0f555faf Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 13 Oct 2022 11:10:37 +0200 Subject: [PATCH 341/793] also add the intel twin --- .../easyconfigs/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb index 2bf90cc74a0..34b9ef271bb 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb @@ -30,7 +30,7 @@ sanity_pip_check = True # avoid that matplotlib downloads and builds its own copies of freetype and qhull _fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " -_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >setup.cfg && " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >mplsetup.cfg && " _include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " From aef3eeeb5ce80afff447b2cf6fc788f128f0e1fd Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 13 Oct 2022 16:53:03 +0200 Subject: [PATCH 342/793] adding easyconfigs: PyTorch-1.12.0-foss-2022a.eb --- .../p/PyTorch/PyTorch-1.12.0-foss-2022a.eb | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb new file mode 100644 index 00000000000..06f29a6402e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb @@ -0,0 +1,97 @@ +name = 'PyTorch' +version = '1.12.0' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +patches = [ + '%(name)s-1.7.0_avoid-nan-in-test-torch.patch', + '%(name)s-1.7.0_disable-dev-shm-test.patch', + '%(name)s-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + '%(name)s-1.10.0_fix-test-dataloader-fixed-affinity.patch', + '%(name)s-1.10.0_skip_cmake_rpath.patch', + '%(name)s-1.11.0_increase-distributed-test-timeout.patch', + '%(name)s-1.11.0_increase_c10d_gloo_timeout.patch', + '%(name)s-1.11.0_disable_failing_jit_cuda_fuser_tests.patch', +] +checksums = [ + None, # PyTorch-1.12.0.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch + 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', # PyTorch-1.10.0_skip_cmake_rpath.patch + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch + 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('hypothesis', '6.46.7'), +] +dependencies = [ + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.10.4'), + ('protobuf', '3.19.4'), + ('protobuf-python', '3.19.4'), + ('pybind11', '2.9.2'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.4.2'), + ('Pillow', '9.1.1'), + ('expecttest', '0.1.3'), +] + +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] + +excluded_tests = { + '': [ + # Bad tests: https://github.com/pytorch/pytorch/issues/60260 + 'distributed/elastic/utils/distributed_test', + 'distributed/elastic/multiprocessing/api_test', + # These tests fail on A10s at the very least, they time out forever no matter how long the timeout is. + # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html + # 'distributed/test_distributed_fork', + 'distributed/test_distributed_spawn', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + 'test_optim', + # Test from this suite timeout often. The process group backend is deprecated anyway + # 'distributed/rpc/test_process_group_agent', + # This test fails constently when run as part of the test suite, but succeeds when run interactively + 'test_model_dump', + # These tests appear flaky, possibly related to number of GPUs that are used + 'distributed/fsdp/test_fsdp_memory', + 'distributed/fsdp/test_fsdp_overlap', + ] +} + +runtest = "cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s" + +# several tests are known to be flaky, and fail in some contexts (like having multiple GPUs available), +# so we allow up to 400 (out of ~90k) tests to fail before treating the installation to be faulty +max_failed_tests = 400 + +tests = ['%(name)s-check-cpp-extension.py'] + +moduleclass = 'ai' From fce73ff22f18fc49d84d1a7493d29a9d36eb0324 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 13 Oct 2022 16:40:09 +0100 Subject: [PATCH 343/793] True changed to SYSTEM --- .../d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index 1d6063dbbd9..086b4db0913 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -15,8 +15,8 @@ toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'pic': True} dependencies = [ - ('CUDA', '11.3.1', '', True), - ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('CUDA', '11.3.1', '', SYSTEM), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), ('Python', '3.9.5'), ('h5py', '3.2.1'), ('IPython', '7.25.0'), From 64312589a59a183b433d1b46c54d38575758b8fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 13 Oct 2022 17:47:07 +0000 Subject: [PATCH 344/793] use http due to bad ssl cert --- easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb index 33c06f706b8..791a53cb6f9 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} source_urls = [ 'https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.4/files/alpha/', 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', - 'https://webclu.bio.wzw.tum.de/stride/' + 'http://webclu.bio.wzw.tum.de/stride/' # bad SSL cert ] sources = [ 'vmd-%(version)s.src.tar.gz', From 7ab5413e8737afd32254d31a3200c980d3d23e16 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 13 Oct 2022 20:53:48 +0200 Subject: [PATCH 345/793] use source tarball --- .../p/PyTorch/PyTorch-1.12.0-foss-2022a.eb | 39 ++++++++----------- 1 file changed, 16 insertions(+), 23 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb index 06f29a6402e..acaa8d0b12a 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb @@ -7,15 +7,8 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'foss', 'version': '2022a'} -sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/pytorch', - 'repo_name': 'pytorch', - 'tag': 'v%(version)s', - 'recursive': True, - }, -}] +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] patches = [ '%(name)s-1.7.0_avoid-nan-in-test-torch.patch', '%(name)s-1.7.0_disable-dev-shm-test.patch', @@ -27,20 +20,20 @@ patches = [ '%(name)s-1.11.0_disable_failing_jit_cuda_fuser_tests.patch', ] checksums = [ - None, # PyTorch-1.12.0.tar.gz - 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch - '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch - # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch - 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', - # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch - '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', - 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', # PyTorch-1.10.0_skip_cmake_rpath.patch - # PyTorch-1.11.0_increase-distributed-test-timeout.patch - '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', - # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch - '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', - # PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch - 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', + {'pytorch-v1.12.0.tar.gz': '46eff236370b759c427b03ff535c3597099043e8e467b8f81f9cd4b258a7a321'}, + {'PyTorch-1.7.0_avoid-nan-in-test-torch.patch': 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18'}, + {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'}, + {'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch': + 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea'}, + {'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch': + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707'}, + {'PyTorch-1.10.0_skip_cmake_rpath.patch': 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448'}, + {'PyTorch-1.11.0_increase-distributed-test-timeout.patch': + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f'}, + {'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch': + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953'}, + {'PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch': + 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51'}, ] builddependencies = [ From 29645050f50cb0c2b2da344b6ca58d08e4808348 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Oct 2022 09:40:05 +0200 Subject: [PATCH 346/793] stick to http in source URL for stride.tar.gz in VMD 1.9.4a51 easyconfigs due to problems with SSL certificate --- easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb | 2 +- easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb index e2b6645847e..b170a6dc5ff 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = [ 'https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.4/files/alpha/', 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', - 'https://webclu.bio.wzw.tum.de/stride/' + 'http://webclu.bio.wzw.tum.de/stride/' ] sources = [ 'vmd-%(version)s.src.tar.gz', diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb index 0ad4daad390..6a7845eece2 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} source_urls = [ 'https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.4/files/alpha/', 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', - 'https://webclu.bio.wzw.tum.de/stride/' + 'http://webclu.bio.wzw.tum.de/stride/' ] sources = [ 'vmd-%(version)s.src.tar.gz', From 8694579f9d500a5c1489404ef051420086d13f5f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Oct 2022 11:31:39 +0200 Subject: [PATCH 347/793] enable running of LAPACK tests for recent OpenBLAS easyconfigs + set max. number of failing tests due to numerical errors to 150 --- .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 6 ++++++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb | 6 ++++++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 6 ++++++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 6 ++++++ 4 files changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index 35e4b615bf8..d9c5442457e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -5,6 +5,9 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.2.0'} +# disable use -free-vectorize to work around compiler miscompilation bug, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/16380 +toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble @@ -30,6 +33,9 @@ checksums = [ 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111', # OpenBLAS-0.3.17_fix-segfault-ztrsv.patch ] +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb index 18fdbab68f8..8329f09da38 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -5,6 +5,9 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.2.0'} +# disable use -free-vectorize to work around compiler miscompilation bug, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/16380 +toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble @@ -27,6 +30,9 @@ checksums = [ 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111', # OpenBLAS-0.3.17_fix-segfault-ztrsv.patch ] +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index a6bed05840b..8d3d92504a6 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -5,6 +5,9 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.2.0'} +# disable use -free-vectorize to work around compiler miscompilation bug, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/16380 +toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble @@ -25,6 +28,9 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', ] +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index 72e27286e56..95511e2adc0 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -5,6 +5,9 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.3.0'} +# disable use -free-vectorize to work around compiler miscompilation bug, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/16380 +toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble @@ -25,6 +28,9 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', ] +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' From 20b690f55c211bec8d5d5cdb914d9b8724a8ca59 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 14 Oct 2022 11:43:57 +0100 Subject: [PATCH 348/793] detect available cores and remove unneeded deps in Unicycler 0.5.0 --- .../Unicycler/Unicycler-0.5.0-gompi-2021b.eb | 10 ++-- .../Unicycler-0.5.0_available-cpus.patch | 51 +++++++++++++++++++ 2 files changed, 56 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0_available-cpus.patch diff --git a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb index 3fc79ebf2db..68544dec87b 100644 --- a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb @@ -13,16 +13,16 @@ toolchain = {'name': 'gompi', 'version': '2021b'} github_account = 'rrwick' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['84a8709c9f2e624225410af702d779ffb0cb06f7c22c20e1f01b989945e08a47'] +patches = ['%(name)s-%(version)s_available-cpus.patch'] +checksums = [ + {'v0.5.0.tar.gz': '84a8709c9f2e624225410af702d779ffb0cb06f7c22c20e1f01b989945e08a47'}, + {'Unicycler-0.5.0_available-cpus.patch': '4c99e889826924b375e07f264b8a8a875a094d63127d5b39c3ebfaab267ce235'}, +] dependencies = [ ('Python', '3.9.6'), - ('Java', '11', '', SYSTEM), - ('Bowtie2', '2.4.4'), - ('SAMtools', '1.14'), ('SPAdes', '3.15.3'), ('Racon', '1.5.0'), - ('Pilon', '1.23', '-Java-%(javaver)s', SYSTEM), ('BLAST+', '2.12.0'), ] diff --git a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0_available-cpus.patch b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0_available-cpus.patch new file mode 100644 index 00000000000..b8b2c8b49f3 --- /dev/null +++ b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0_available-cpus.patch @@ -0,0 +1,51 @@ +Determine the number of cores available to avoid using all that the system has. +Patch by Simon Branford (University of Birmingham) +--- setup.py.orig 2022-10-14 11:09:52.253946000 +0100 ++++ setup.py 2022-10-14 11:18:10.743520156 +0100 +@@ -104,7 +104,11 @@ + # Build Unicycler's C++ code. + make_cmd = ['make'] + try: +- make_cmd += ['-j', str(min(8, multiprocessing.cpu_count()))] ++ num_cpus = len(os.sched_getaffinity(0)) ++ except AttributeError: ++ num_cpus = multiprocessing.cpu_count() ++ try: ++ make_cmd += ['-j', str(min(8, num_cpus))] + except NotImplementedError: + pass + if self.makeargs: +--- unicycler/unicycler.py.orig 2022-10-14 11:09:58.407681000 +0100 ++++ unicycler/unicycler.py 2022-10-14 11:16:43.446404128 +0100 +@@ -627,9 +627,13 @@ + log.log('Unicycler version: v' + __version__) + log.log('Using ' + str(args.threads) + ' thread' + ('' if args.threads == 1 else 's')) + log.log('') +- if args.threads > 2 * multiprocessing.cpu_count(): +- log.log(red('Warning: you have specified a lot more threads than this machine seems to ' +- 'have! Was this intentional?')) ++ try: ++ num_cpus = len(os.sched_getaffinity(0)) ++ except AttributeError: ++ num_cpus = multiprocessing.cpu_count() ++ if args.threads > 2 * num_cpus: ++ log.log(red('Warning: you have specified a lot more threads than available! ' ++ 'Was this intentional?')) + log.log('') + log.log(out_dir_message) + +--- unicycler/misc.py.orig 2022-10-14 11:10:02.942374000 +0100 ++++ unicycler/misc.py 2022-10-14 11:17:30.093646345 +0100 +@@ -793,7 +793,11 @@ + + + def get_default_thread_count(): +- return min(multiprocessing.cpu_count(), settings.MAX_AUTO_THREAD_COUNT) ++ try: ++ num_cpus = len(os.sched_getaffinity(0)) ++ except AttributeError: ++ num_cpus = multiprocessing.cpu_count() ++ return min(num_cpus, settings.MAX_AUTO_THREAD_COUNT) + + + def spades_path_and_version(spades_path): From 83e4d44f949995fb07a9306f84ef1ebb4ef7b994 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Oct 2022 13:52:18 +0200 Subject: [PATCH 349/793] make requested changes to spaln 2.4.12 easyconfig --- easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb index 364c2101be1..6012bf6434b 100644 --- a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb @@ -16,7 +16,10 @@ source_urls = ['https://github.com/ogotoh/spaln/archive/'] sources = ['ver%(version)s.tar.gz'] checksums = ['0c5f842131409686dbaad01778960f53f1ebba8dd83d55b454ec4bf1b6bde2af'] -dependencies = [('zlib', '1.2.11')] +dependencies = [ + ('zlib', '1.2.11'), + ('Perl', '5.32.0'), +] start_dir = 'src' @@ -26,6 +29,8 @@ prefix_opt = '--exec_prefix=' configopts = "--exec_prefix=%(installdir)s/bin --table_dir=%(installdir)s/table --alndbs_dir=%(installdir)s/seqdb " configopts += "--use_zlib=1" +fix_perl_shebang_for = ['seqdb/*.pl'] + sanity_check_paths = { 'files': ['bin/%s' % x for x in ['makdbs', 'makmdm', 'sortgrcd', 'spaln']], 'dirs': ['seqdb', 'table'], @@ -33,4 +38,6 @@ sanity_check_paths = { sanity_check_commands = ["spaln -h 2>&1 | grep 'SPALN version %(version)s'"] +modextrapaths = {'PATH': 'seqdb'} + moduleclass = 'bio' From cace0a6cae60891fc7840fc9ea0594220b40a986 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 14 Oct 2022 11:56:45 +0000 Subject: [PATCH 350/793] Add OpenEXR to POV-Ray --- .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 31 +++++++++++++++++++ .../p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb | 1 + 2 files changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e81697b1a73 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '3.1.5' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/openexr/openexr/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['93925805c1fc4f8162b35f0ae109c4a75344e6decae5a240afdfce25f8a433ec'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in + ['Iex', 'IlmThread', 'Imath', 'OpenEXR', 'OpenEXRUtil']] + + ['bin/exr%s' % x for x in + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr']], + 'dirs': ['include/OpenEXR', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb index 04c5b90e972..de9f5ed3ce8 100644 --- a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb @@ -44,6 +44,7 @@ dependencies = [ ('X11', '20220504'), ('LibTIFF', '4.3.0'), ('SDL2', '2.0.22'), + ('OpenEXR', '3.1.5'), ] preconfigopts = "cd unix && sed -i 's/^automake/automake --add-missing; automake/g' prebuild.sh && " From db5244f51d0d4ef4305ae6997c9b6891c7916b5c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Oct 2022 13:58:10 +0200 Subject: [PATCH 351/793] also update $PERL5LIB to Perl module required by spaln Perl scripts are found --- easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb index 6012bf6434b..1d2162cf617 100644 --- a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb @@ -38,6 +38,9 @@ sanity_check_paths = { sanity_check_commands = ["spaln -h 2>&1 | grep 'SPALN version %(version)s'"] -modextrapaths = {'PATH': 'seqdb'} +modextrapaths = { + 'PATH': 'seqdb', + 'PERL5LIB': 'seqdb', +} moduleclass = 'bio' From 55822cabf6b4a71d5609ffd9d4132aa5eea6dbd4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Oct 2022 16:20:07 +0200 Subject: [PATCH 352/793] {vis}[foss/2021a] Nipype v1.6.0, RDFlib v6.2.0 w/ Python 3.9.5 --- .../n/Nipype/Nipype-1.6.0-foss-2021a.eb | 58 +++++++++++++++++++ .../r/RDFlib/RDFlib-6.2.0-GCCcore-10.3.0.eb | 29 ++++++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/r/RDFlib/RDFlib-6.2.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb new file mode 100644 index 00000000000..6eb80b477ea --- /dev/null +++ b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'Nipype' +version = '1.6.0' + +homepage = 'https://nipype.readthedocs.io' +description = """Nipype is a Python project that provides a uniform interface to existing neuroimaging software and + facilitates interaction between these packages within a single workflow.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('lxml', '4.6.3'), + ('networkx', '2.6.3'), + ('pydot', '1.4.2'), + ('NiBabel', '3.2.1'), + ('RDFlib', '6.2.0'), + ('pytest-xdist', '2.3.0'), +] + +use_pip = True + +exts_list = [ + ('traits', '6.4.1', { + 'checksums': ['78bb2ccafd60aff606515aac46de64668a0a81cb5c54c650b9877a841aa9e812'], + }), + ('pydotplus', '2.0.2', { + 'checksums': ['91e85e9ee9b85d2391ead7d635e3d9c7f5f44fd60a60e59b13e2403fa66505c4'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('prov', '2.0.0', { + 'checksums': ['b6438f2195ecb9f6e8279b58971e02bc51814599b5d5383366eef91d867422ee'], + }), + ('ci-info', '0.3.0', { + 'checksums': ['1fd50cbd401f29adffeeb18b0489e232d16ac1a7458ac6bc316deab6ae535fb0'], + }), + ('etelemetry', '0.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['78febd59a22eb53d052d731f10f24139eb2854fd237348fba683dd8616fb4a67'], + }), + ('nipype', version, { + 'checksums': ['bc56ce63f74c9a9a23c6edeaf77631377e8ad2bea928c898cc89527a47f101cf'], + }), +] + +sanity_check_paths = { + 'files': ['bin/nipypecli'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import nipype.interfaces'"] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/RDFlib/RDFlib-6.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/RDFlib/RDFlib-6.2.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..17b46ad32a5 --- /dev/null +++ b/easybuild/easyconfigs/r/RDFlib/RDFlib-6.2.0-GCCcore-10.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'RDFlib' +version = '6.2.0' + +homepage = 'https://github.com/RDFLib/rdflib' +description = """RDFLib is a Python library for working with RDF, a simple yet powerful language + for representing information.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '3.9.5')] + +use_pip = True + +exts_list = [ + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('rdflib', version, { + 'checksums': ['62dc3c86d1712db0f55785baf8047f63731fa59b2682be03219cb89262065942'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 0d40c7ea5318cc8a04bafb3c78abceedde953492 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Fri, 14 Oct 2022 16:20:24 +0200 Subject: [PATCH 353/793] Added download link to the tarbal instead of clone. Also, updated the checksums accordingly --- .../i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb index a85a08e980d..36142e01453 100644 --- a/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb @@ -11,15 +11,9 @@ Imath is a C++ and python library of 2D and 3D vector, matrix, and math operatio toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} -sources = [{ - 'filename': '%(name)s_v%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/AcademySoftwareFoundation', - 'repo_name': '%(name)s', - 'tag': 'v%(version)s', - }, -}] -checksums = ['5167b1441e4eaeb0f238faaac02c52ecd89940e7c77a3ed0c7356fb8934db570'] +source_urls = ['https://github.com/AcademySoftwareFoundation/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1e9c7c94797cf7b7e61908aed1f80a331088cc7d8873318f70376e4aed5f25fb'] builddependencies = [ ('binutils', '2.38'), From abe3ca5503ca8621d355b7068bff41cddfaaffcc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Oct 2022 16:24:29 +0200 Subject: [PATCH 354/793] add Python build dependency for OpenBLAS easyconfigs that run LAPACK tests --- .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 5 +++++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb | 5 +++++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 5 +++++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 5 +++++ 4 files changed, 20 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index d9c5442457e..756da27b0e7 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -33,6 +33,11 @@ checksums = [ 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111', # OpenBLAS-0.3.17_fix-segfault-ztrsv.patch ] +builddependencies = [ + # required by LAPACK test suite + ('Python', '3.9.6', '-bare'), +] + run_lapack_tests = True max_failing_lapack_tests_num_errors = 150 diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb index 8329f09da38..971d85d6a77 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -30,6 +30,11 @@ checksums = [ 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111', # OpenBLAS-0.3.17_fix-segfault-ztrsv.patch ] +builddependencies = [ + # required by LAPACK test suite + ('Python', '3.9.6', '-bare'), +] + run_lapack_tests = True max_failing_lapack_tests_num_errors = 150 diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index 8d3d92504a6..b4c9931fbae 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -28,6 +28,11 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', ] +builddependencies = [ + # required by LAPACK test suite + ('Python', '3.9.6', '-bare'), +] + run_lapack_tests = True max_failing_lapack_tests_num_errors = 150 diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index 95511e2adc0..a7ebb133ddc 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -28,6 +28,11 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', ] +builddependencies = [ + # required by LAPACK test suite + ('Python', '3.10.4', '-bare'), +] + run_lapack_tests = True max_failing_lapack_tests_num_errors = 150 From c948ceeb9b7dda1ea626d65a67aa782ea1a50101 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Oct 2022 16:33:57 +0200 Subject: [PATCH 355/793] stick to networkx 2.5.1 as dependency for Nipype 1.6.0 with foss/2021a --- easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb index 6eb80b477ea..9315c346305 100644 --- a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb +++ b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ ('Python', '3.9.5'), ('lxml', '4.6.3'), - ('networkx', '2.6.3'), + ('networkx', '2.5.1'), ('pydot', '1.4.2'), ('NiBabel', '3.2.1'), ('RDFlib', '6.2.0'), From 05bf8888038857818c3f51f55483d77bbf37939a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 14 Oct 2022 14:36:01 +0000 Subject: [PATCH 356/793] Drop openexr easyconfig --- .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb deleted file mode 100644 index e81697b1a73..00000000000 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'OpenEXR' -version = '3.1.5' - -homepage = 'https://www.openexr.com/' -description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic - for use in computer imaging applications""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://github.com/openexr/openexr/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['93925805c1fc4f8162b35f0ae109c4a75344e6decae5a240afdfce25f8a433ec'] - -builddependencies = [ - ('binutils', '2.38'), - ('CMake', '3.23.1'), -] - -configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' - -sanity_check_paths = { - 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in - ['Iex', 'IlmThread', 'Imath', 'OpenEXR', 'OpenEXRUtil']] + - ['bin/exr%s' % x for x in - ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr']], - 'dirs': ['include/OpenEXR', 'share'], -} - -moduleclass = 'vis' From fd422dd641e726a1398f9ae94a0cd8cca5b84569 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Fri, 14 Oct 2022 16:54:50 +0200 Subject: [PATCH 357/793] Replace True by System for the system toolchain --- .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index 3676ebf7da8..4e7764a13b8 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -54,7 +54,7 @@ dependencies = [ ('libwebp', '1.2.4'), ('OpenEXR', '3.1.5'), ('JasPer', '2.0.33'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('ant', '1.10.12', '-Java-%(javaver)s', True), ('GLib', '2.72.1'), ('GTK4', '4.7.0'), From 142a79f971f88cbfc6fd3f72e7f58c786bd17324 Mon Sep 17 00:00:00 2001 From: guacke Date: Fri, 14 Oct 2022 17:00:05 +0200 Subject: [PATCH 358/793] Switch to PythonBundle. --- .../p/PyMOL/PyMOL-2.5.0-foss-2020b.eb | 53 ++++++++----------- 1 file changed, 21 insertions(+), 32 deletions(-) diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb index 8173740a5a3..642fc01b62c 100644 --- a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'PyMOL' version = '2.5.0' @@ -11,33 +11,6 @@ It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone! """ -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = ["https://github.com/schrodinger/pymol-open-source/archive/refs/tags/"] -sources = ['v%(version)s.tar.gz'] -checksums = ['aa828bf5719bd9a14510118a93182a6e0cadc03a574ba1e327e1e9780a0e80b3'] - -exts_defaultclass = 'PythonPackage' -exts_list = [ - ('Pmw', '2.0.1', { - 'buildopts': '', - 'installopts': '', - 'modulename': 'Pmw', - 'sources': [{ - 'download_filename': '8bedfc8747e7757c1048bc5e11899d1163717a43.zip', - 'source_urls': ['https://github.com/schrodinger/pmw-patched/archive/'], - 'filename': 'Pmw-patched-2.0.1-20200210-8bedfc8.zip'}], - 'checksums': ['db1ab4ee1020023ad814bb24c74f6361fb72e1011871911f7d37bb6ecf6c79ed'], - }), -] -exts_default_options = { - 'use_pip': True, - 'download_dep_fail': True, -} - -download_dep_fail = True -use_pip = False - dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), @@ -51,13 +24,29 @@ dependencies = [ ('Tkinter', '%(pyver)s'), ] -buildopts = '' -buildopts += '--use-msgpackc=no ' -installopts = buildopts +toolchain = {'name': 'foss', 'version': '2020b'} + +use_pip = False +sanity_pip_check = True + +exts_list = [ + ('Pmw', '2.0.1', { + 'modulename': 'Pmw', + 'source_tmpl': 'Pmw-patched-%(version)s-20200210-8bedfc8.zip', + 'source_urls': ['https://github.com/schrodinger/pmw-patched/archive/'], + 'checksums': ['db1ab4ee1020023ad814bb24c74f6361fb72e1011871911f7d37bb6ecf6c79ed'], + }), + (name, version, { + 'buildopts': '--use-msgpackc=no', + 'installopts': '--use-msgpackc=no', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ["https://github.com/schrodinger/pymol-open-source/archive/refs/tags/"], + 'checksums': ['aa828bf5719bd9a14510118a93182a6e0cadc03a574ba1e327e1e9780a0e80b3'], + }), +] modextravars = {'PYMOL_PATH': 'lib/python%(pyshortver)s/site-packages/pymol/pymol_path'} -sanity_pip_check = True sanity_check_paths = { 'files': ['bin/pymol'], 'dirs': ['bin', 'lib'], From 8b779b2776025525a295811c7ed013e6cbf0eaa7 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Fri, 14 Oct 2022 17:23:41 +0200 Subject: [PATCH 359/793] Now also change True to SYSTEM for ant... --- .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index 4e7764a13b8..b957c01b7d4 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -55,7 +55,7 @@ dependencies = [ ('OpenEXR', '3.1.5'), ('JasPer', '2.0.33'), ('Java', '11', '', SYSTEM), - ('ant', '1.10.12', '-Java-%(javaver)s', True), + ('ant', '1.10.12', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.72.1'), ('GTK4', '4.7.0'), ('HDF5', '1.12.2'), From 587e56a62c7ba7413c5cc02f0049e070b3e1dd4b Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 14 Oct 2022 17:43:04 +0200 Subject: [PATCH 360/793] adding easyconfigs: libunistring-1.0-GCCcore-10.3.0.eb --- .../libunistring-1.0-GCCcore-10.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..619ae320573 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '1.0' + +homepage = 'https://www.gnu.org/software/libunistring/' + +description = """This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['5bab55b49f75d77ed26b257997e919b693f29fd4a1bc22e0e6e024c246c72741'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' From 1905e9aec20e1c34888567d69f3859065bc01edb Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 14 Oct 2022 17:57:04 +0200 Subject: [PATCH 361/793] Previous libpsl was missing libunistring dependency. On os-es where this dependency was not provided by the system, the configure for libpsl would fail --- .../easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb index 58d836e0aab..6eef44963b1 100644 --- a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb @@ -19,6 +19,10 @@ builddependencies = [ ('CMake', '3.20.1'), ] +dependencies = [ + ('libunistring', '1.0'), +] + sanity_check_paths = { 'files': ['bin/psl', 'lib/libpsl.a'], 'dirs': [] From c786e68f2819aef06318a81316073cd0f52c9c7d Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 14 Oct 2022 18:37:51 +0200 Subject: [PATCH 362/793] There was apparently already a libunistring in this toolchain. Using that version now --- .../l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb | 2 +- .../libunistring-1.0-GCCcore-10.3.0.eb | 31 ------------------- 2 files changed, 1 insertion(+), 32 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb index 6eef44963b1..a7d264de762 100644 --- a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ - ('libunistring', '1.0'), + ('libunistring', '0.9.10'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-10.3.0.eb deleted file mode 100644 index 619ae320573..00000000000 --- a/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-10.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libunistring' -version = '1.0' - -homepage = 'https://www.gnu.org/software/libunistring/' - -description = """This library provides functions for manipulating Unicode strings and for - manipulating C strings according to the Unicode standard.""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -toolchainopts = {'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['5bab55b49f75d77ed26b257997e919b693f29fd4a1bc22e0e6e024c246c72741'] - -builddependencies = [ - ('binutils', '2.36.1'), -] - -parallel = 1 - -sanity_check_paths = { - 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs': ['include/unistring'], -} - -moduleclass = 'lib' From 68eda9133825288f21280833f64260813f18924c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 14 Oct 2022 20:31:04 +0200 Subject: [PATCH 363/793] add typing-extensions dep --- ...-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb | 2 -- .../typing-extensions-4.3.0-GCCcore-11.3.0.eb | 22 +++++++++++++++++++ 2 files changed, 22 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb index ff7163f6c19..07edd99a9cf 100644 --- a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb @@ -18,12 +18,10 @@ dependencies = [ ('typing-extensions', '4.3.0'), ] - exts_list = [ ('fsspec', '2022.8.2', { 'checksums': ['7f12b90964a98a7e921d27fb36be536ea036b73bf3b724ac0b0bd7b8e39c7c18'], }), - ('pyDeprecate', '0.3.2', { 'modulename': 'deprecate', 'checksums': ['d481116cc5d7f6c473e7c4be820efdd9b90a16b594b350276e9e66a6cb5bdd29'], diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ada44caf01a --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '4.3.0' + +homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' +description = 'Typing Extensions – Backported and Experimental Type Hints for Python' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From c75621aa2cffa3765b5dd6d737eceb29f12b10fa Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 14 Oct 2022 20:33:47 +0200 Subject: [PATCH 364/793] use SYSTEM rather than True --- .../PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb index 07edd99a9cf..5acbc803ac9 100644 --- a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb @@ -10,7 +10,7 @@ description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML resea toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('Python', '3.10.4'), ('PyTorch', '1.12.0', versionsuffix), ('tqdm', '4.64.0'), From c5260433af2e7cda65e89a9cbddd33edee5b17f6 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 14 Oct 2022 18:51:35 +0000 Subject: [PATCH 365/793] Add backported GCC fix for vectorizer --- .../easyconfigs/g/GCCcore/GCCcore-11.3.0.eb | 2 + .../GCCcore-11.3.0_fix-vectorizer.patch | 137 ++++++++++++++++++ 2 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0_fix-vectorizer.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb index 5df5d559914..1b248b2368e 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb @@ -36,6 +36,7 @@ patches = [ 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCCcore-11.3.0_fuse-ld-mold.patch', 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', + 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ '98438e6cc7294298b474cf0da7655d9a8c8b796421bb0210531c294a950374ed', # gcc-11.3.0.tar.gz @@ -50,6 +51,7 @@ checksums = [ '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch 'bba64714f8b84ad58b3b43c0d21b4ffc298274ae699f514ed2934f002146d840', # GCCcore-11.3.0_fuse-ld-mold.patch '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60', # GCCcore-11_fix-libsanitzer-glibc-2.36.patch + '7dff25b678e2f65b81d9bf0c8402ad46c25a04b0c0d610db50b763ecc5f9ef98', # GCCcore-11.3.0_fix-vectorizer.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0_fix-vectorizer.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0_fix-vectorizer.patch new file mode 100644 index 00000000000..372397d96fe --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0_fix-vectorizer.patch @@ -0,0 +1,137 @@ +From 9ed4a849afb5b18b462bea311e7eee454c2c9f68 Mon Sep 17 00:00:00 2001 +From: Richard Biener +Date: Fri, 14 Oct 2022 11:14:59 +0200 +Subject: [PATCH] tree-optimization/107254 - check and support live lanes from + permutes + +The following fixes an omission from adding SLP permute nodes which +is live lanes originating from those. We have to check that we +can extract the lane and have to actually code generate them. + + PR tree-optimization/107254 + * tree-vect-slp.cc (vect_slp_analyze_node_operations_1): + For permutes also analyze live lanes. + (vect_schedule_slp_node): For permutes also code generate + live lane extracts. + + * gfortran.dg/vect/pr107254.f90: New testcase. +--- + gcc/testsuite/gfortran.dg/vect/pr107254.f90 | 49 +++++++++++++++++++++ + gcc/tree-vect-slp.cc | 33 +++++++++++--- + 2 files changed, 77 insertions(+), 5 deletions(-) + create mode 100644 gcc/testsuite/gfortran.dg/vect/pr107254.f90 + +diff --git a/gcc/testsuite/gfortran.dg/vect/pr107254.f90 b/gcc/testsuite/gfortran.dg/vect/pr107254.f90 +new file mode 100644 +index 0000000000000..85bcb5f3fa2e3 +--- /dev/null ++++ b/gcc/testsuite/gfortran.dg/vect/pr107254.f90 +@@ -0,0 +1,49 @@ ++! { dg-do run } ++ ++subroutine dlartg( f, g, s, r ) ++ implicit none ++ double precision :: f, g, r, s ++ double precision :: d, p ++ ++ d = sqrt( f*f + g*g ) ++ p = 1.d0 / d ++ if( abs( f ) > 1 ) then ++ s = g*sign( p, f ) ++ r = sign( d, f ) ++ else ++ s = g*sign( p, f ) ++ r = sign( d, f ) ++ end if ++end subroutine ++ ++subroutine dhgeqz( n, h, t ) ++ implicit none ++ integer n ++ double precision h( n, * ), t( n, * ) ++ integer jc ++ double precision c, s, temp, temp2, tempr ++ temp2 = 10d0 ++ call dlartg( 10d0, temp2, s, tempr ) ++ c = 0.9d0 ++ s = 1.d0 ++ do jc = 1, n ++ temp = c*h( 1, jc ) + s*h( 2, jc ) ++ h( 2, jc ) = -s*h( 1, jc ) + c*h( 2, jc ) ++ h( 1, jc ) = temp ++ temp2 = c*t( 1, jc ) + s*t( 2, jc ) ++ t( 2, jc ) = -s*t( 1, jc ) + c*t( 2, jc ) ++ t( 1, jc ) = temp2 ++ enddo ++end subroutine dhgeqz ++ ++program test ++ implicit none ++ double precision h(2,2), t(2,2) ++ h = 0 ++ t(1,1) = 1 ++ t(2,1) = 0 ++ t(1,2) = 0 ++ t(2,2) = 0 ++ call dhgeqz( 2, h, t ) ++ if (t(2,2).ne.0) STOP 1 ++end program test +diff --git a/gcc/tree-vect-slp.c b/gcc/tree-vect-slp.c +index 229f2663ebcc6..af27fd56e0242 100644 +--- a/gcc/tree-vect-slp.c ++++ b/gcc/tree-vect-slp.c +@@ -5930,7 +5930,23 @@ vect_slp_analyze_node_operations_1 (vec_info *vinfo, slp_tree node, + + /* Handle purely internal nodes. */ + if (SLP_TREE_CODE (node) == VEC_PERM_EXPR) +- return vectorizable_slp_permutation (vinfo, NULL, node, cost_vec); ++ { ++ if (!vectorizable_slp_permutation (vinfo, NULL, node, cost_vec)) ++ return false; ++ ++ stmt_vec_info slp_stmt_info; ++ unsigned int i; ++ FOR_EACH_VEC_ELT (SLP_TREE_SCALAR_STMTS (node), i, slp_stmt_info) ++ { ++ if (STMT_VINFO_LIVE_P (slp_stmt_info) ++ && !vectorizable_live_operation (vinfo, ++ slp_stmt_info, NULL, node, ++ node_instance, i, ++ false, cost_vec)) ++ return false; ++ } ++ return true; ++ } + + gcc_assert (STMT_SLP_TYPE (stmt_info) != loop_vect); + +@@ -8897,8 +8913,6 @@ vect_schedule_slp_node (vec_info *vinfo, + } + } + +- bool done_p = false; +- + /* Handle purely internal nodes. */ + if (SLP_TREE_CODE (node) == VEC_PERM_EXPR) + { +@@ -8909,9 +8923,18 @@ vect_schedule_slp_node (vec_info *vinfo, + but open-code it here (partly). */ + bool done = vectorizable_slp_permutation (vinfo, &si, node, NULL); + gcc_assert (done); +- done_p = true; ++ stmt_vec_info slp_stmt_info; ++ unsigned int i; ++ FOR_EACH_VEC_ELT (SLP_TREE_SCALAR_STMTS (node), i, slp_stmt_info) ++ if (STMT_VINFO_LIVE_P (slp_stmt_info)) ++ { ++ done = vectorizable_live_operation (vinfo, ++ slp_stmt_info, &si, node, ++ instance, i, true, NULL); ++ gcc_assert (done); ++ } + } +- if (!done_p) ++ else + vect_transform_stmt (vinfo, stmt_info, &si, node, instance); + } + From fa0336ce6e0cf7e368f4870c6b1eaf84edf9afa0 Mon Sep 17 00:00:00 2001 From: guacke Date: Sat, 15 Oct 2022 13:07:54 +0200 Subject: [PATCH 366/793] Fix download link Pmw. --- easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb index 642fc01b62c..c96cc51c180 100644 --- a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb @@ -32,7 +32,7 @@ sanity_pip_check = True exts_list = [ ('Pmw', '2.0.1', { 'modulename': 'Pmw', - 'source_tmpl': 'Pmw-patched-%(version)s-20200210-8bedfc8.zip', + 'source_tmpl': '8bedfc8747e7757c1048bc5e11899d1163717a43.zip', 'source_urls': ['https://github.com/schrodinger/pmw-patched/archive/'], 'checksums': ['db1ab4ee1020023ad814bb24c74f6361fb72e1011871911f7d37bb6ecf6c79ed'], }), From c24f8e557aad37ae971ec4e9152c56dcf1992fef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Oct 2022 13:48:31 +0200 Subject: [PATCH 367/793] update to Nipype 1.8.5 --- ...1.6.0-foss-2021a.eb => Nipype-1.8.5-foss-2021a.eb} | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/n/Nipype/{Nipype-1.6.0-foss-2021a.eb => Nipype-1.8.5-foss-2021a.eb} (81%) diff --git a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb b/easybuild/easyconfigs/n/Nipype/Nipype-1.8.5-foss-2021a.eb similarity index 81% rename from easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb rename to easybuild/easyconfigs/n/Nipype/Nipype-1.8.5-foss-2021a.eb index 9315c346305..fe53e82f565 100644 --- a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb +++ b/easybuild/easyconfigs/n/Nipype/Nipype-1.8.5-foss-2021a.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'Nipype' -version = '1.6.0' +version = '1.8.5' homepage = 'https://nipype.readthedocs.io' description = """Nipype is a Python project that provides a uniform interface to existing neuroimaging software and @@ -22,8 +22,8 @@ dependencies = [ use_pip = True exts_list = [ - ('traits', '6.4.1', { - 'checksums': ['78bb2ccafd60aff606515aac46de64668a0a81cb5c54c650b9877a841aa9e812'], + ('traits', '6.3.2', { + 'checksums': ['4520ef4a675181f38be4a5bab1b1d5472691597fe2cfe4faf91023e89407e2c6'], }), ('pydotplus', '2.0.2', { 'checksums': ['91e85e9ee9b85d2391ead7d635e3d9c7f5f44fd60a60e59b13e2403fa66505c4'], @@ -41,8 +41,11 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['78febd59a22eb53d052d731f10f24139eb2854fd237348fba683dd8616fb4a67'], }), + ('looseversion', '1.0.2', { + 'checksums': ['8b9f2e649eb81620c4527ba33ba87505eb69d4bb3f66523b34182a0450c294bc'], + }), ('nipype', version, { - 'checksums': ['bc56ce63f74c9a9a23c6edeaf77631377e8ad2bea928c898cc89527a47f101cf'], + 'checksums': ['e3842743fb660464dd29de73dcfc9ef66d273be10bcc64059ff21cd5ef1e9655'], }), ] From 0f74df6cda92500d3578be036898b75085c43b31 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Oct 2022 15:14:46 +0200 Subject: [PATCH 368/793] also apply patch to fix vectorizer bug to GCC 11.1, 11.2, 12.1, 12.2 --- .../easyconfigs/g/GCCcore/GCCcore-11.1.0.eb | 1 + .../easyconfigs/g/GCCcore/GCCcore-11.2.0.eb | 1 + .../easyconfigs/g/GCCcore/GCCcore-12.1.0.eb | 1 + .../easyconfigs/g/GCCcore/GCCcore-12.2.0.eb | 1 + .../GCCcore-12.2.0_fix-vectorizer.patch | 137 ++++++++++++++++++ 5 files changed, 141 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_fix-vectorizer.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb index 0bdb99e8555..42fb74e6c11 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb @@ -35,6 +35,7 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCC-10.x_fix-libsanitizer-cyclades.patch', + 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ 'e7abb1b4cb58aaa67c5eb49d98e89d13363b8e258ac2b5b105c197b441c09f85', # gcc-11.1.0.tar.gz diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb index 3453620e9f0..954772edd58 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb @@ -34,6 +34,7 @@ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', + 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ 'f0837f1bf8244a5cc23bd96ff6366712a791cfae01df8e25b137698aca26efc1', # gcc-11.2.0.tar.gz diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb index 0ef3db46d4d..b8b94b6b2fc 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb @@ -33,6 +33,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-12.2.0_fix-vectorizer.patch', ] checksums = [ 'e88a004a14697bbbaba311f38a938c716d9a652fd151aaaa4cf1b5b99b90e2de', # gcc-12.1.0.tar.gz diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb index 843edfa35ec..f898df53dc8 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb @@ -33,6 +33,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-12.2.0_fix-vectorizer.patch', ] checksums = [ 'ac6b317eb4d25444d87cf29c0d141dedc1323a1833ec9995211b13e1a851261c', # gcc-12.2.0.tar.gz diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_fix-vectorizer.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_fix-vectorizer.patch new file mode 100644 index 00000000000..ba4e65259e4 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_fix-vectorizer.patch @@ -0,0 +1,137 @@ +From 9ed4a849afb5b18b462bea311e7eee454c2c9f68 Mon Sep 17 00:00:00 2001 +From: Richard Biener +Date: Fri, 14 Oct 2022 11:14:59 +0200 +Subject: [PATCH] tree-optimization/107254 - check and support live lanes from + permutes + +The following fixes an omission from adding SLP permute nodes which +is live lanes originating from those. We have to check that we +can extract the lane and have to actually code generate them. + + PR tree-optimization/107254 + * tree-vect-slp.cc (vect_slp_analyze_node_operations_1): + For permutes also analyze live lanes. + (vect_schedule_slp_node): For permutes also code generate + live lane extracts. + + * gfortran.dg/vect/pr107254.f90: New testcase. +--- + gcc/testsuite/gfortran.dg/vect/pr107254.f90 | 49 +++++++++++++++++++++ + gcc/tree-vect-slp.cc | 33 +++++++++++--- + 2 files changed, 77 insertions(+), 5 deletions(-) + create mode 100644 gcc/testsuite/gfortran.dg/vect/pr107254.f90 + +diff --git a/gcc/testsuite/gfortran.dg/vect/pr107254.f90 b/gcc/testsuite/gfortran.dg/vect/pr107254.f90 +new file mode 100644 +index 0000000000000..85bcb5f3fa2e3 +--- /dev/null ++++ b/gcc/testsuite/gfortran.dg/vect/pr107254.f90 +@@ -0,0 +1,49 @@ ++! { dg-do run } ++ ++subroutine dlartg( f, g, s, r ) ++ implicit none ++ double precision :: f, g, r, s ++ double precision :: d, p ++ ++ d = sqrt( f*f + g*g ) ++ p = 1.d0 / d ++ if( abs( f ) > 1 ) then ++ s = g*sign( p, f ) ++ r = sign( d, f ) ++ else ++ s = g*sign( p, f ) ++ r = sign( d, f ) ++ end if ++end subroutine ++ ++subroutine dhgeqz( n, h, t ) ++ implicit none ++ integer n ++ double precision h( n, * ), t( n, * ) ++ integer jc ++ double precision c, s, temp, temp2, tempr ++ temp2 = 10d0 ++ call dlartg( 10d0, temp2, s, tempr ) ++ c = 0.9d0 ++ s = 1.d0 ++ do jc = 1, n ++ temp = c*h( 1, jc ) + s*h( 2, jc ) ++ h( 2, jc ) = -s*h( 1, jc ) + c*h( 2, jc ) ++ h( 1, jc ) = temp ++ temp2 = c*t( 1, jc ) + s*t( 2, jc ) ++ t( 2, jc ) = -s*t( 1, jc ) + c*t( 2, jc ) ++ t( 1, jc ) = temp2 ++ enddo ++end subroutine dhgeqz ++ ++program test ++ implicit none ++ double precision h(2,2), t(2,2) ++ h = 0 ++ t(1,1) = 1 ++ t(2,1) = 0 ++ t(1,2) = 0 ++ t(2,2) = 0 ++ call dhgeqz( 2, h, t ) ++ if (t(2,2).ne.0) STOP 1 ++end program test +diff --git a/gcc/tree-vect-slp.cc b/gcc/tree-vect-slp.cc +index 229f2663ebcc6..af27fd56e0242 100644 +--- a/gcc/tree-vect-slp.cc ++++ b/gcc/tree-vect-slp.cc +@@ -5930,7 +5930,23 @@ vect_slp_analyze_node_operations_1 (vec_info *vinfo, slp_tree node, + + /* Handle purely internal nodes. */ + if (SLP_TREE_CODE (node) == VEC_PERM_EXPR) +- return vectorizable_slp_permutation (vinfo, NULL, node, cost_vec); ++ { ++ if (!vectorizable_slp_permutation (vinfo, NULL, node, cost_vec)) ++ return false; ++ ++ stmt_vec_info slp_stmt_info; ++ unsigned int i; ++ FOR_EACH_VEC_ELT (SLP_TREE_SCALAR_STMTS (node), i, slp_stmt_info) ++ { ++ if (STMT_VINFO_LIVE_P (slp_stmt_info) ++ && !vectorizable_live_operation (vinfo, ++ slp_stmt_info, NULL, node, ++ node_instance, i, ++ false, cost_vec)) ++ return false; ++ } ++ return true; ++ } + + gcc_assert (STMT_SLP_TYPE (stmt_info) != loop_vect); + +@@ -8897,8 +8913,6 @@ vect_schedule_slp_node (vec_info *vinfo, + } + } + +- bool done_p = false; +- + /* Handle purely internal nodes. */ + if (SLP_TREE_CODE (node) == VEC_PERM_EXPR) + { +@@ -8909,9 +8923,18 @@ vect_schedule_slp_node (vec_info *vinfo, + but open-code it here (partly). */ + bool done = vectorizable_slp_permutation (vinfo, &si, node, NULL); + gcc_assert (done); +- done_p = true; ++ stmt_vec_info slp_stmt_info; ++ unsigned int i; ++ FOR_EACH_VEC_ELT (SLP_TREE_SCALAR_STMTS (node), i, slp_stmt_info) ++ if (STMT_VINFO_LIVE_P (slp_stmt_info)) ++ { ++ done = vectorizable_live_operation (vinfo, ++ slp_stmt_info, &si, node, ++ instance, i, true, NULL); ++ gcc_assert (done); ++ } + } +- if (!done_p) ++ else + vect_transform_stmt (vinfo, stmt_info, &si, node, instance); + } + From 3464b7f52649d503e0aece1b64504733e5fafdad Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 15 Oct 2022 16:10:29 +0200 Subject: [PATCH 369/793] adding easyconfigs: PyTorch-Lightning-1.7.7-foss-2022a.eb --- .../PyTorch-Lightning-1.7.7-foss-2022a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a.eb new file mode 100644 index 00000000000..2ad23369cd6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Lightning' +version = '1.7.7' + +homepage = 'https://pytorchlightning.ai' +description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), + ('tqdm', '4.64.0'), + ('tensorboard', '2.10.0'), + ('typing-extensions', '4.3.0'), +] + +exts_list = [ + ('fsspec', '2022.8.2', { + 'checksums': ['7f12b90964a98a7e921d27fb36be536ea036b73bf3b724ac0b0bd7b8e39c7c18'], + }), + ('pyDeprecate', '0.3.2', { + 'modulename': 'deprecate', + 'checksums': ['d481116cc5d7f6c473e7c4be820efdd9b90a16b594b350276e9e66a6cb5bdd29'], + }), + ('torchmetrics', '0.9.3', { + 'checksums': ['4ebfd2466021db26397636966ee1a195d3b340ba5d71bb258e764340dfc2476f'], + }), + ('pytorch-lightning', version, { + 'checksums': ['27c2dd01a18db2415168e3fa3775ccb5a1fa1e2961a50439ad9365507fe9d4ae'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From e30aeac29a712478fdbd0237d18a919f3b09e971 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Oct 2022 16:36:31 +0200 Subject: [PATCH 370/793] add checksum for patch to fix vectorizer bug in GCC v11.x + v12.x --- .../easyconfigs/g/GCCcore/GCCcore-11.1.0.eb | 24 +++++++++-------- .../easyconfigs/g/GCCcore/GCCcore-11.2.0.eb | 22 ++++++++------- .../easyconfigs/g/GCCcore/GCCcore-11.3.0.eb | 27 ++++++++++--------- .../easyconfigs/g/GCCcore/GCCcore-12.1.0.eb | 19 ++++++------- .../easyconfigs/g/GCCcore/GCCcore-12.2.0.eb | 19 ++++++------- 5 files changed, 59 insertions(+), 52 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb index 42fb74e6c11..a5a30163948 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb @@ -38,17 +38,19 @@ patches = [ 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ - 'e7abb1b4cb58aaa67c5eb49d98e89d13363b8e258ac2b5b105c197b441c09f85', # gcc-11.1.0.tar.gz - 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 - 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 - '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz - 'c58922c14ae7d0791a77932f377840890f19bc486b653fa64eba7f1026fb214d', # isl-0.23.tar.bz2 - 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz - '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2', # nvptx-tools-20210115.tar.gz - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch - '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch - 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832', # GCC-10.x_fix-libsanitizer-cyclades.patch + {'gcc-11.1.0.tar.gz': 'e7abb1b4cb58aaa67c5eb49d98e89d13363b8e258ac2b5b105c197b441c09f85'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'}, + {'isl-0.23.tar.bz2': 'c58922c14ae7d0791a77932f377840890f19bc486b653fa64eba7f1026fb214d'}, + {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'}, + {'nvptx-tools-20210115.tar.gz': '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCC-10.x_fix-libsanitizer-cyclades.patch': 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832'}, + {'GCCcore-11.3.0_fix-vectorizer.patch': '7dff25b678e2f65b81d9bf0c8402ad46c25a04b0c0d610db50b763ecc5f9ef98'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb index 954772edd58..5efade9fb39 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb @@ -37,16 +37,18 @@ patches = [ 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ - 'f0837f1bf8244a5cc23bd96ff6366712a791cfae01df8e25b137698aca26efc1', # gcc-11.2.0.tar.gz - 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 - 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 - '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz - 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0', # isl-0.24.tar.bz2 - 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz - '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2', # nvptx-tools-20210115.tar.gz - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch - '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch + {'gcc-11.2.0.tar.gz': 'f0837f1bf8244a5cc23bd96ff6366712a791cfae01df8e25b137698aca26efc1'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'}, + {'isl-0.24.tar.bz2': 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0'}, + {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'}, + {'nvptx-tools-20210115.tar.gz': '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCCcore-11.3.0_fix-vectorizer.patch': '7dff25b678e2f65b81d9bf0c8402ad46c25a04b0c0d610db50b763ecc5f9ef98'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb index 1b248b2368e..479660986dc 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb @@ -39,19 +39,20 @@ patches = [ 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ - '98438e6cc7294298b474cf0da7655d9a8c8b796421bb0210531c294a950374ed', # gcc-11.3.0.tar.gz - 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 - 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 - '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz - 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0', # isl-0.24.tar.bz2 - 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz - '20e3c1eeae7f375c36455b6036c4801de16b854910ff54268bbd3346f3685080', # nvptx-tools-20220412.tar.gz - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch - '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch - 'bba64714f8b84ad58b3b43c0d21b4ffc298274ae699f514ed2934f002146d840', # GCCcore-11.3.0_fuse-ld-mold.patch - '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60', # GCCcore-11_fix-libsanitzer-glibc-2.36.patch - '7dff25b678e2f65b81d9bf0c8402ad46c25a04b0c0d610db50b763ecc5f9ef98', # GCCcore-11.3.0_fix-vectorizer.patch + {'gcc-11.3.0.tar.gz': '98438e6cc7294298b474cf0da7655d9a8c8b796421bb0210531c294a950374ed'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'}, + {'isl-0.24.tar.bz2': 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0'}, + {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'}, + {'nvptx-tools-20220412.tar.gz': '20e3c1eeae7f375c36455b6036c4801de16b854910ff54268bbd3346f3685080'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCCcore-11.3.0_fuse-ld-mold.patch': 'bba64714f8b84ad58b3b43c0d21b4ffc298274ae699f514ed2934f002146d840'}, + {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, + {'GCCcore-11.3.0_fix-vectorizer.patch': '7dff25b678e2f65b81d9bf0c8402ad46c25a04b0c0d610db50b763ecc5f9ef98'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb index b8b94b6b2fc..da98d2ef021 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb @@ -36,15 +36,16 @@ patches = [ 'GCCcore-12.2.0_fix-vectorizer.patch', ] checksums = [ - 'e88a004a14697bbbaba311f38a938c716d9a652fd151aaaa4cf1b5b99b90e2de', # gcc-12.1.0.tar.gz - 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 - 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 - '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz - 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0', # isl-0.24.tar.bz2 - 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz - '20e3c1eeae7f375c36455b6036c4801de16b854910ff54268bbd3346f3685080', # nvptx-tools-20220412.tar.gz - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch + {'gcc-12.1.0.tar.gz': 'e88a004a14697bbbaba311f38a938c716d9a652fd151aaaa4cf1b5b99b90e2de'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'}, + {'isl-0.24.tar.bz2': 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0'}, + {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'}, + {'nvptx-tools-20220412.tar.gz': '20e3c1eeae7f375c36455b6036c4801de16b854910ff54268bbd3346f3685080'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-12.2.0_fix-vectorizer.patch': '0b76fc379308fd189ee39c4a3a49facacf8ede08dbec4280f289341083f1632b'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb index f898df53dc8..623abd95ffe 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb @@ -36,15 +36,16 @@ patches = [ 'GCCcore-12.2.0_fix-vectorizer.patch', ] checksums = [ - 'ac6b317eb4d25444d87cf29c0d141dedc1323a1833ec9995211b13e1a851261c', # gcc-12.2.0.tar.gz - 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 - 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 - '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz - 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0', # isl-0.24.tar.bz2 - 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz - '53e7973af841935490b8a7b9e4d1331f775589b54e21f9921f18589183fb9997', # nvptx-tools-20220610.tar.gz - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch + {'gcc-12.2.0.tar.gz': 'ac6b317eb4d25444d87cf29c0d141dedc1323a1833ec9995211b13e1a851261c'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'}, + {'isl-0.24.tar.bz2': 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0'}, + {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'}, + {'nvptx-tools-20220610.tar.gz': '53e7973af841935490b8a7b9e4d1331f775589b54e21f9921f18589183fb9997'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-12.2.0_fix-vectorizer.patch': '0b76fc379308fd189ee39c4a3a49facacf8ede08dbec4280f289341083f1632b'}, ] builddependencies = [ From c94ee34ced3170f45e67f8851519311c1ef58bc5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Oct 2022 17:42:41 +0200 Subject: [PATCH 371/793] use SYSTEM template constant to indicate that CUDA dependency of torchvision uses system toolchain --- .../t/torchvision/torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb index c2820fcd722..3ab02f0dc56 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb @@ -14,7 +14,7 @@ checksums = ['c32fab734e62c7744dadeb82f7510ff58cc3bca1189d17b16aa99b08afc42249'] builddependencies = [('CMake', '3.23.1')] dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('Python', '3.10.4'), ('Pillow-SIMD', '9.2.0'), ('PyTorch', '1.12.0', '-CUDA-%(cudaver)s'), From bf2fc71d7727c27bd735dc3c8d240b2996a91498 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 17 Oct 2022 09:48:18 +0100 Subject: [PATCH 372/793] pandas removed as already in SciPy-bundle --- .../d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index 086b4db0913..26c7449b3c6 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -44,9 +44,6 @@ exts_list = [ 'sources': ['%(name)s-%(version)s.zip'], 'checksums': ['4f2a4d39e4ea601b9ab42b2db08b5918a9538c168cff1c6895ae26646f3d73b1'], }), - ('pandas', '1.3.3', { - 'checksums': ['272c8cb14aa9793eada6b1ebe81994616e647b5892a370c7135efb2924b701df'], - }), ('tensorpack', '0.11', { 'checksums': ['022b610e416e62e3575424cd08e60af27808a5fb6914294615391caf582cbd4f'], }), From c282fb2ec3b963795ecbc29b12ecfb2e759a60ab Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 25 Jul 2022 09:15:03 +0200 Subject: [PATCH 373/793] Fix PyTorch 1.10.0 build on PPC --- .../PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 53 +++++--- .../p/PyTorch/PyTorch-1.10.0-foss-2021a.eb | 47 ++++--- .../PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 53 +++++--- ...ch-1.10.0_add-dummy-bfloat16-for-ppc.patch | 116 ++++++++++++++++++ ...> PyTorch-1.10.0_fix-faulty-asserts.patch} | 21 +--- ...orch-1.10.0_fix-missing-VSX-dispatch.patch | 26 ++++ ...rch-1.10.0_remove-vec-dump-functions.patch | 114 +++++++++++++++++ 7 files changed, 356 insertions(+), 74 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch rename easybuild/easyconfigs/p/PyTorch/{PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch => PyTorch-1.10.0_fix-faulty-asserts.patch} (88%) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-missing-VSX-dispatch.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_remove-vec-dump-functions.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index 3dedead0354..fbed1049947 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -8,15 +8,9 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'foss', 'version': '2021a'} -sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/pytorch', - 'repo_name': 'pytorch', - 'tag': 'v%(version)s', - 'recursive': True, - }, -}] +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', @@ -24,18 +18,25 @@ patches = [ 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', - 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', - 'PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vnni-detection.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_fix-XNNPACK-tests.patch', 'PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch', + 'PyTorch-1.10.0_remove-vec-dump-functions.patch', + 'PyTorch-1.10.0_skip_cmake_rpath.patch', 'PyTorch-1.10.0_skip_failing_ops_tests.patch', 'PyTorch-1.10.0_skip_nan_tests_openblas.patch', - 'PyTorch-1.10.0_skip_cmake_rpath.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', ] checksums = [ - None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + '1970225700d1f9791eb553855ad3c22e7c9fd69cff2765d532506b33e449831e', # pytorch-v1.10.0.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch @@ -45,24 +46,38 @@ checksums = [ '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', - # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch - '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch + '0c8bf4b284c5c2cb4d175645d44bed674cca5218de741a8ea698cef2884a86da', # PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', - # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch - '67152215e4530a9b1d7349fb20864445fd815288f04ab9e96e45c73b2d87827a', + # PyTorch-1.10.0_fix-faulty-asserts.patch + '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch + '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch '51f83f5d5ef69656ef35b73f17e0671e70113798421be11ea4c7b56ffcc4da03', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', # PyTorch-1.10.0_fix-vnni-detection.patch '1f3664c0febfa2a3fc4c0cd3bae185f289716ac0b6c3d7e8fa1cee19ba62b7cc', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_fix-XNNPACK-tests.patch + 'd3e749a2a42efce463e3b8a1aebb21f0edf2256682c4417297d9a44a6210e5f8', # PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch 'e65afb01786f7f030ccb5faada1eb474bb0c418bcadcf1baaa71a4fa2f3f4240', + # PyTorch-1.10.0_remove-vec-dump-functions.patch + '5e796c83f74e77aa193fef2720a7a41e3e0eb39df726a6f0a2a1c55d37d8fcc8', + # PyTorch-1.10.0_skip_cmake_rpath.patch + 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', # PyTorch-1.10.0_skip_failing_ops_tests.patch '399af94ffcef4a6db5226552c46f11e9b0f0f371b2d7924b9e5764d2281581ab', # PyTorch-1.10.0_skip_nan_tests_openblas.patch '7d3f83e3056d9e47a460790313238f28708beb596cafaa7ae55e374d368bbedf', - # PyTorch-1.10.0_skip_cmake_rpath.patch - 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb index c05632ab43f..27db7713d1d 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb @@ -7,32 +7,33 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'foss', 'version': '2021a'} -sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/pytorch', - 'repo_name': 'pytorch', - 'tag': 'v%(version)s', - 'recursive': True, - }, -}] +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', - 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', - 'PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vnni-detection.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_fix-XNNPACK-tests.patch', 'PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch', + 'PyTorch-1.10.0_remove-vec-dump-functions.patch', 'PyTorch-1.10.0_skip_failing_ops_tests.patch', 'PyTorch-1.10.0_skip_nan_tests_openblas.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', ] checksums = [ - None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + '1970225700d1f9791eb553855ad3c22e7c9fd69cff2765d532506b33e449831e', # pytorch-v1.10.0.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch @@ -41,22 +42,36 @@ checksums = [ '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', - # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch - '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch + '0c8bf4b284c5c2cb4d175645d44bed674cca5218de741a8ea698cef2884a86da', # PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', - # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch - '67152215e4530a9b1d7349fb20864445fd815288f04ab9e96e45c73b2d87827a', + # PyTorch-1.10.0_fix-faulty-asserts.patch + '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch + '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch '51f83f5d5ef69656ef35b73f17e0671e70113798421be11ea4c7b56ffcc4da03', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', # PyTorch-1.10.0_fix-vnni-detection.patch '1f3664c0febfa2a3fc4c0cd3bae185f289716ac0b6c3d7e8fa1cee19ba62b7cc', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_fix-XNNPACK-tests.patch + 'd3e749a2a42efce463e3b8a1aebb21f0edf2256682c4417297d9a44a6210e5f8', # PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch 'e65afb01786f7f030ccb5faada1eb474bb0c418bcadcf1baaa71a4fa2f3f4240', + # PyTorch-1.10.0_remove-vec-dump-functions.patch + '5e796c83f74e77aa193fef2720a7a41e3e0eb39df726a6f0a2a1c55d37d8fcc8', # PyTorch-1.10.0_skip_failing_ops_tests.patch '399af94ffcef4a6db5226552c46f11e9b0f0f371b2d7924b9e5764d2281581ab', # PyTorch-1.10.0_skip_nan_tests_openblas.patch '7d3f83e3056d9e47a460790313238f28708beb596cafaa7ae55e374d368bbedf', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb index 938b94c4f93..450db866c3a 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -7,15 +7,9 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'fosscuda', 'version': '2020b'} -sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/pytorch', - 'repo_name': 'pytorch', - 'tag': 'v%(version)s', - 'recursive': True, - }, -}] +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', @@ -23,18 +17,25 @@ patches = [ 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', - 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', - 'PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vnni-detection.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_fix-XNNPACK-tests.patch', 'PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch', + 'PyTorch-1.10.0_remove-vec-dump-functions.patch', + 'PyTorch-1.10.0_skip_cmake_rpath.patch', 'PyTorch-1.10.0_skip_failing_ops_tests.patch', 'PyTorch-1.10.0_skip_nan_tests_openblas.patch', - 'PyTorch-1.10.0_skip_cmake_rpath.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', ] checksums = [ - None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + '1970225700d1f9791eb553855ad3c22e7c9fd69cff2765d532506b33e449831e', # pytorch-v1.10.0.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch @@ -44,24 +45,38 @@ checksums = [ '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', - # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch - '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch + '0c8bf4b284c5c2cb4d175645d44bed674cca5218de741a8ea698cef2884a86da', # PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', - # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch - '67152215e4530a9b1d7349fb20864445fd815288f04ab9e96e45c73b2d87827a', + # PyTorch-1.10.0_fix-faulty-asserts.patch + '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch + '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch '51f83f5d5ef69656ef35b73f17e0671e70113798421be11ea4c7b56ffcc4da03', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', # PyTorch-1.10.0_fix-vnni-detection.patch '1f3664c0febfa2a3fc4c0cd3bae185f289716ac0b6c3d7e8fa1cee19ba62b7cc', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_fix-XNNPACK-tests.patch + 'd3e749a2a42efce463e3b8a1aebb21f0edf2256682c4417297d9a44a6210e5f8', # PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch 'e65afb01786f7f030ccb5faada1eb474bb0c418bcadcf1baaa71a4fa2f3f4240', + # PyTorch-1.10.0_remove-vec-dump-functions.patch + '5e796c83f74e77aa193fef2720a7a41e3e0eb39df726a6f0a2a1c55d37d8fcc8', + # PyTorch-1.10.0_skip_cmake_rpath.patch + 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', # PyTorch-1.10.0_skip_failing_ops_tests.patch '399af94ffcef4a6db5226552c46f11e9b0f0f371b2d7924b9e5764d2281581ab', # PyTorch-1.10.0_skip_nan_tests_openblas.patch '7d3f83e3056d9e47a460790313238f28708beb596cafaa7ae55e374d368bbedf', - # PyTorch-1.10.0_skip_cmake_rpath.patch - 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch new file mode 100644 index 00000000000..8e74d538e62 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch @@ -0,0 +1,116 @@ +Fix missing `vec_scalar_t` on PPC during compilation. + +From https://github.com/pytorch/pytorch/pull/67331 + +From: Nikita Shulga +Date: Wed, 27 Oct 2021 08:04:08 -0700 +Subject: [PATCH] Add dummy bfloat16 VSX implementation + +Just a copy of DEFAULT bfloat16 implementation and revert restriction +introduced by https://github.com/pytorch/pytorch/pull/61630 + +Fixes https://github.com/pytorch/pytorch/issues/66867 and https://github.com/pytorch/pytorch/issues/62016 +--- + aten/src/ATen/cpu/vec/functional.h | 2 - + .../cpu/vec/vec256/vsx/vec256_bfloat16_vsx.h | 54 +++++++++++++++++++ + .../cpu/vec/vec256/vsx/vec256_common_vsx.h | 6 +++ + 3 files changed, 60 insertions(+), 2 deletions(-) + create mode 100644 aten/src/ATen/cpu/vec/vec256/vsx/vec256_bfloat16_vsx.h + +diff --git a/aten/src/ATen/cpu/vec/functional.h b/aten/src/ATen/cpu/vec/functional.h +index 210ae9e9e883..388b3170d5b5 100644 +--- a/aten/src/ATen/cpu/vec/functional.h ++++ b/aten/src/ATen/cpu/vec/functional.h +@@ -1,6 +1,4 @@ + #pragma once + + #include +-#if !defined(__VSX__) || !defined(CPU_CAPABILITY_VSX) + #include +-#endif +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_bfloat16_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_bfloat16_vsx.h +new file mode 100644 +index 000000000000..ee8ca997a20e +--- /dev/null ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_bfloat16_vsx.h +@@ -0,0 +1,54 @@ ++#pragma once ++ ++#include ++#include ++#include ++namespace at { ++namespace vec { ++// See Note [Acceptable use of anonymous namespace in header] ++namespace { ++ ++inline std::tuple, Vectorized> convert_bfloat16_float( ++ const Vectorized& a) { ++ constexpr int64_t K = Vectorized::size(); ++ __at_align__ float arr[K]; ++ __at_align__ BFloat16 arr2[K]; ++ a.store(arr2); ++ convert(arr2, arr, K); ++ return std::make_tuple( ++ Vectorized::loadu(arr), ++ Vectorized::loadu(arr + Vectorized::size())); ++} ++ ++inline Vectorized convert_float_bfloat16( ++ const Vectorized& a, ++ const Vectorized& b) { ++ constexpr int64_t K = Vectorized::size(); ++ __at_align__ float arr[K]; ++ __at_align__ BFloat16 arr2[K]; ++ a.store(arr); ++ b.store(arr + Vectorized::size()); ++ convert(arr, arr2, K); ++ return Vectorized::loadu(arr2); ++} ++ ++void load_fp32_from_bf16(const c10::BFloat16* data, Vectorized& out) { ++ __at_align__ float values[Vectorized::size()]; ++ for (int k = 0; k < Vectorized::size(); ++k) { ++ values[k] = data[k]; ++ } ++ out = Vectorized::loadu(values); ++} ++ ++C10_UNUSED void load_fp32_from_bf16( ++ const c10::BFloat16* data, ++ Vectorized& out1, ++ Vectorized& out2) { ++ load_fp32_from_bf16(data, out1); ++ data += Vectorized::size(); ++ load_fp32_from_bf16(data, out2); ++} ++ ++} // namespace ++} // namespace vec ++} // namespace at +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_common_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_common_vsx.h +index 3d798a7f6268..b06f6a4bd1b5 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_common_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_common_vsx.h +@@ -3,6 +3,8 @@ + #include + #include + #include ++ ++// Note: header order is important here + #include + #include + #include +@@ -11,8 +13,12 @@ + #include + #include + #include ++ + #include + #include ++ ++#include ++ + namespace at { + namespace vec { + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts.patch similarity index 88% rename from easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch rename to easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts.patch index eab07090d2a..1ba71564df7 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts.patch @@ -1,6 +1,6 @@ From: Alexander Grund Date: Tue, 18 May 2021 15:08:41 +0200 -Subject: [PATCH 1/2] Fix usage of TORCH_INTERNAL_ASSERT with message +Subject: Fix usage of TORCH_INTERNAL_ASSERT with message Using only a string as the argument for TORCH_INTERNAL_ASSERT will never trigger a failure as a string is always a truethy value. @@ -8,11 +8,6 @@ This hides actual bugs and makes users and devs think all worked while it did not. Change to use TORCH_INTERNAL_ASSERT(false, "msg") -Subject: [PATCH 2/2] Add missing skip decorator for -test_preserve_bundled_inputs_methods - -This test uses optimize_for_mobile which requires NNPACK to work - diff --git a/aten/src/ATen/native/BinaryOps.cpp b/aten/src/ATen/native/BinaryOps.cpp index c4edadb03e..e889cd03a8 100644 --- a/aten/src/ATen/native/BinaryOps.cpp @@ -83,20 +78,6 @@ index 6de646acfe..66341c959d 100644 } for (int i = num_output_channels; i < num_output_channels_padded; ++i) { weight_scales_data[i] = 1.f; -diff --git a/test/test_mobile_optimizer.py b/test/test_mobile_optimizer.py -index 11ef019a26..7b5ac1a239 100644 ---- a/test/test_mobile_optimizer.py -+++ b/test/test_mobile_optimizer.py -@@ -269,6 +269,9 @@ class TestOptimizer(TestCase): - bi_module_lint_list = generate_mobile_module_lints(bi_module) - self.assertEqual(len(bi_module_lint_list), 0) - -+ @unittest.skipUnless(torch.backends.xnnpack.enabled, -+ " XNNPACK must be enabled for these tests." -+ " Please build with USE_XNNPACK=1.") - def test_preserve_bundled_inputs_methods(self): - class MyBundledInputModule(torch.nn.Module): - def __init__(self): diff --git a/torch/csrc/jit/api/module.cpp b/torch/csrc/jit/api/module.cpp index 38592b80b9..8f9508321b 100644 --- a/torch/csrc/jit/api/module.cpp diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-missing-VSX-dispatch.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-missing-VSX-dispatch.patch new file mode 100644 index 00000000000..dcc0eac4bf0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-missing-VSX-dispatch.patch @@ -0,0 +1,26 @@ + +Fix for following error on PPC: +> undefined reference to `at::native::DispatchStub, c10::ArrayRef, c10::ArrayRef, void const*, c10::ArrayRef, void*), at::native::fft_fill_with_conjugate_symmetry_stub>::VSX' + +From https://github.com/pytorch/pytorch/pull/68914 + +From: Deepali Chourasia +Date: Thu, 25 Nov 2021 12:29:50 +0000 +Subject: [PATCH] add VSX dispatch for fft_fill_with_conjugate_symmetry_stub + +--- + aten/src/ATen/native/mkl/SpectralOps.cpp | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/aten/src/ATen/native/mkl/SpectralOps.cpp b/aten/src/ATen/native/mkl/SpectralOps.cpp +index 0625110a04ff..2bd05ca19cac 100644 +--- a/aten/src/ATen/native/mkl/SpectralOps.cpp ++++ b/aten/src/ATen/native/mkl/SpectralOps.cpp +@@ -151,6 +151,7 @@ static void _fft_fill_with_conjugate_symmetry_cpu_( + REGISTER_ARCH_DISPATCH(fft_fill_with_conjugate_symmetry_stub, DEFAULT, &_fft_fill_with_conjugate_symmetry_cpu_) + REGISTER_AVX2_DISPATCH(fft_fill_with_conjugate_symmetry_stub, &_fft_fill_with_conjugate_symmetry_cpu_) + REGISTER_AVX512_DISPATCH(fft_fill_with_conjugate_symmetry_stub, &_fft_fill_with_conjugate_symmetry_cpu_) ++REGISTER_VSX_DISPATCH(fft_fill_with_conjugate_symmetry_stub, &_fft_fill_with_conjugate_symmetry_cpu_) + + // _out variants can be shared between PocketFFT and MKL + Tensor& _fft_r2c_mkl_out(const Tensor& self, IntArrayRef dim, int64_t normalization, diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_remove-vec-dump-functions.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_remove-vec-dump-functions.patch new file mode 100644 index 00000000000..b6e2100a178 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_remove-vec-dump-functions.patch @@ -0,0 +1,114 @@ +Fix compilation on PPC due to missing include + +From https://patch-diff.githubusercontent.com/raw/pytorch/pytorch/pull/66085 + +From e0fa15d188986e2a68973e3facf9d794f6cfc5df Mon Sep 17 00:00:00 2001 +From: Nikita Shulga +Date: Mon, 4 Oct 2021 09:26:37 -0700 +Subject: [PATCH] Remove unused `dump` method from VSX vec256 methods + +Follow up after https://github.com/pytorch/pytorch/pull/63533 + +Probably fixes https://github.com/pytorch/pytorch/issues/65956 +--- + .../ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h | 5 ----- + .../ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h | 8 -------- + aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h | 3 --- + aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h | 7 ------- + aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h | 9 --------- + 5 files changed, 32 deletions(-) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h +index 888f2f0b932b..3a3e0daade09 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h +@@ -356,11 +356,6 @@ class Vectorized { + return {vec_sqrt(_vec0), vec_sqrt(_vec1)}; + } + +- void dump() const { +- std::cout << _vec0[0] << "," << _vec0[1] << ","; +- std::cout << _vec1[0] << "," << _vec1[1] << std::endl; +- } +- + Vectorized sqrt() const { + return map(std::sqrt); + } +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +index 0aa726b9bfdd..712de24597dc 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +@@ -144,7 +144,6 @@ class Vectorized { + // convert std::complex index mask to V index mask: xy -> xxyy + auto mask_complex = Vectorized( + vec_mergeh(mask._vec0, mask._vec0), vec_mergeh(mask._vec1, mask._vec1)); +- // mask_complex.dump(); + return { + vec_sel(a._vec0, b._vec0, mask_complex._vec0), + vec_sel(a._vec1, b._vec1, mask_complex._vec1), +@@ -409,13 +408,6 @@ class Vectorized { + return {vec_sqrt(_vec0), vec_sqrt(_vec1)}; + } + +- void dump() const { +- std::cout << _vec0[0] << "," << _vec0[1] << "," << _vec0[2] << "," +- << _vec0[3] << ","; +- std::cout << _vec1[0] << "," << _vec1[1] << "," << _vec1[2] << "," +- << _vec1[3] << std::endl; +- } +- + Vectorized sqrt() const { + return map(std::sqrt); + } +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h +index 29616182fe12..0d5b5cb39384 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h +@@ -188,9 +188,6 @@ class Vectorized { + } + const double& operator[](int idx) const = delete; + double& operator[](int idx) = delete; +- void dump() const { +- std::cout << _vec0[0] << "," << _vec0[1] << "," << _vec1[0] << "," << _vec1[1] << std::endl; +- } + Vectorized map(double (*const f)(double)) const { + Vectorized ret; + for (int i = 0; i < size()/2; i++) { +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +index 2427276bcea2..58d4b057b507 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +@@ -436,13 +436,6 @@ class Vectorized { + return {vec_neg(_vec0), vec_neg(_vec1)}; + } + +- void dump() const { +- std::cout << _vec0[0] << "," << _vec0[1] << "," << _vec0[2] << "," +- << _vec0[3] << ","; +- std::cout << _vec1[0] << "," << _vec1[1] << "," << _vec1[2] << "," +- << _vec1[3] << std::endl; +- } +- + Vectorized C10_ALWAYS_INLINE round() const { + return {vec_round(_vec0), vec_round(_vec1)}; + } +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h +index c335ace0ced6..2482af6ec232 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h +@@ -369,15 +369,6 @@ struct Vectorized { + return {vec0, vec1}; + } + +- void dump() const { +- value_type vals[size()]; +- store((void*)vals); +- for (int i = 0; i < size(); ++i) { +- std::cout << (int)(vals[i]) << " "; +- } +- std::cout << std::endl; +- } +- + DEFINE_MEMBER_OP(operator==, c10::quint8, vec_cmpeq) + DEFINE_MEMBER_OP(operator!=, c10::quint8, vec_cmpne) + DEFINE_MEMBER_OP(operator<, c10::quint8, vec_cmplt) From 642d33b48aae5ea6aef3a5ecebbcafa4e6fc8644 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 9 Sep 2022 16:40:19 +0200 Subject: [PATCH 374/793] Fix FP16 quantization (fixes test_quantization) --- .../PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 3 ++ .../p/PyTorch/PyTorch-1.10.0-foss-2021a.eb | 3 ++ .../PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 3 ++ ...fix-fp16-quantization-without-fbgemm.patch | 43 +++++++++++++++++++ 4 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index fbed1049947..f16073d8956 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -21,6 +21,7 @@ patches = [ 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -52,6 +53,8 @@ checksums = [ '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', # PyTorch-1.10.0_fix-faulty-asserts.patch '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch + 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb index 27db7713d1d..20e9c720a35 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb @@ -19,6 +19,7 @@ patches = [ 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -48,6 +49,8 @@ checksums = [ '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', # PyTorch-1.10.0_fix-faulty-asserts.patch '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch + 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb index 450db866c3a..412066dcf6f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -20,6 +20,7 @@ patches = [ 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -51,6 +52,8 @@ checksums = [ '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', # PyTorch-1.10.0_fix-faulty-asserts.patch '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch + 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch new file mode 100644 index 00000000000..b62f757853f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch @@ -0,0 +1,43 @@ +From https://github.com/pytorch/pytorch/pull/84750 + +From d5480f56374e7612d4400e845b05bc3a4507d87c Mon Sep 17 00:00:00 2001 +From: Alexander Grund +Date: Fri, 9 Sep 2022 14:39:49 +0200 +Subject: [PATCH] Fix Use-after-Free in qembeddingbag_byte_prepack_out + +When FBGEMM is not used (either manually disabled or on platforms such +as POWER where it isn't supported at all) the fallback code requests a +`data_ptr` on a `Tensor` object returned by +`to(ScalarType::Float)` in the same line. This object will be destroyed +at the end of the line leading to a dangling pointer. + +On some platforms this manifests in wrong results being returned as the +memory gets overwritten. + +Fix this by binding the temporary object (or initial object) to a const +value reference which extents its lifetime and getting the `data_ptr` +from that. + +Fixes #84748 +--- + .../ATen/native/quantized/cpu/qembeddingbag_prepack.cpp | 7 ++++--- + 1 file changed, 4 insertions(+), 3 deletions(-) + +diff --git a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +index 614e274b54..6c04d0ae12 100644 +--- a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp ++++ b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +@@ -242,9 +242,10 @@ Tensor& qembeddingbag_byte_prepack_out(Tensor& output, const Tensor& weight) { + } + + #else +- const auto weight_data = weight_contig->scalar_type() == at::ScalarType::Half +- ? weight_contig->to(at::ScalarType::Float).data_ptr() +- : weight_contig->data_ptr(); ++ const Tensor& float_weight = weight_contig->scalar_type() == at::ScalarType::Half ++ ? weight_contig->to(at::ScalarType::Float) ++ : *weight_contig; ++ const auto weight_data = float_weight.data_ptr(); + constexpr float kEpsilon = 1e-8f; + for (auto row: c10::irange(embedding_rows)) { + const float* input_row = weight_data + row * embedding_cols; From c1f6e508906b9a59d2ce250b896d5b46474bd1c9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 22 Sep 2022 11:04:57 +0200 Subject: [PATCH 375/793] Add PyTorch-1.10.0_fix-kineto-crash.patch --- .../p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 3 +++ easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb | 3 +++ .../easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 3 +++ 3 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index f16073d8956..33304aa7d22 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -22,6 +22,7 @@ patches = [ 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -55,6 +56,8 @@ checksums = [ '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb index 20e9c720a35..208a35c065a 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb @@ -20,6 +20,7 @@ patches = [ 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -51,6 +52,8 @@ checksums = [ '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb index 412066dcf6f..ffbf98f586c 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -21,6 +21,7 @@ patches = [ 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -54,6 +55,8 @@ checksums = [ '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch From 28080783312808a6655707e2e179679577067b9a Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 17 Oct 2022 10:22:14 +0100 Subject: [PATCH 376/793] Duplicated PyYAML removed --- .../d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index 26c7449b3c6..b210c0f9419 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -32,7 +32,6 @@ dependencies = [ ('imgaug', '0.4.0', versionsuffix), ('tqdm', '4.61.2'), ('ruamel.yaml', '0.17.21'), - ('PyYAML', '5.4.1'), ('statsmodels', '0.12.2'), ('PyTorch', '1.10.0', versionsuffix), ] From bb0269a6931a99cf6ae3b1f2bf7cc65a6d7232cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Oct 2022 12:04:16 +0200 Subject: [PATCH 377/793] add patch to fix failing LAPACK tests due to -ftree-vectorize + lower max. number of failing LAPACK tests due to numerical errors to 10 + don't disable vectorize toolchain option --- .../o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 24 +++++------ .../o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb | 20 ++++----- .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 18 ++++---- .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 18 ++++---- ...nBLAS-0.3.21_fix-order-vectorization.patch | 43 +++++++++++++++++++ 5 files changed, 83 insertions(+), 40 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_fix-order-vectorization.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index 756da27b0e7..63c99b77086 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -5,9 +5,6 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.2.0'} -# disable use -free-vectorize to work around compiler miscompilation bug, -# see https://github.com/easybuilders/easybuild-easyconfigs/issues/16380 -toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble @@ -21,16 +18,19 @@ patches = [ 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-%(version)s_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch', 'OpenBLAS-%(version)s_fix-segfault-ztrsv.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', ] checksums = [ - 'df2934fa33d04fd84d839ca698280df55c690c86a5a1133b3f7266fce1de279f', # v0.3.17.tar.gz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch - 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', - # OpenBLAS-0.3.17_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch - 'ea76320bc047eff1bf2a2f50c1c19acb4fd6d2b8a5bf81a4dce73145a2a5cfcb', - 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111', # OpenBLAS-0.3.17_fix-segfault-ztrsv.patch + {'v0.3.17.tar.gz': 'df2934fa33d04fd84d839ca698280df55c690c86a5a1133b3f7266fce1de279f'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.17_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch': + 'ea76320bc047eff1bf2a2f50c1c19acb4fd6d2b8a5bf81a4dce73145a2a5cfcb'}, + {'OpenBLAS-0.3.17_fix-segfault-ztrsv.patch': 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, ] builddependencies = [ @@ -39,7 +39,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 150 +max_failing_lapack_tests_num_errors = 10 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb index 971d85d6a77..3a587ae6e7d 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -5,9 +5,6 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.2.0'} -# disable use -free-vectorize to work around compiler miscompilation bug, -# see https://github.com/easybuilders/easybuild-easyconfigs/issues/16380 -toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble @@ -20,14 +17,17 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.17_fix-segfault-ztrsv.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', ] checksums = [ - '1632c1e8cca62d8bed064b37747e331a1796fc46f688626337362bf0d16aeadb', # v0.3.18.tar.gz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch - 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', - 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111', # OpenBLAS-0.3.17_fix-segfault-ztrsv.patch + {'v0.3.18.tar.gz': '1632c1e8cca62d8bed064b37747e331a1796fc46f688626337362bf0d16aeadb'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.17_fix-segfault-ztrsv.patch': 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, ] builddependencies = [ @@ -36,7 +36,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 150 +max_failing_lapack_tests_num_errors = 10 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index b4c9931fbae..8d3080bf8fd 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -5,9 +5,6 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.2.0'} -# disable use -free-vectorize to work around compiler miscompilation bug, -# see https://github.com/easybuilders/easybuild-easyconfigs/issues/16380 -toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble @@ -19,13 +16,16 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', ] checksums = [ - '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c', # v0.3.20.tar.gz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch - 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', + {'v0.3.20.tar.gz': '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, ] builddependencies = [ @@ -34,7 +34,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 150 +max_failing_lapack_tests_num_errors = 10 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index a7ebb133ddc..2e1cdaca17e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -5,9 +5,6 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.3.0'} -# disable use -free-vectorize to work around compiler miscompilation bug, -# see https://github.com/easybuilders/easybuild-easyconfigs/issues/16380 -toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble @@ -19,13 +16,16 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', ] checksums = [ - '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c', # v0.3.20.tar.gz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch - 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', + {'v0.3.20.tar.gz': '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, ] builddependencies = [ @@ -34,7 +34,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 150 +max_failing_lapack_tests_num_errors = 10 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_fix-order-vectorization.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_fix-order-vectorization.patch new file mode 100644 index 00000000000..846ffbe1c84 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_fix-order-vectorization.patch @@ -0,0 +1,43 @@ +add parentheses to force a certain order that is compatible with non-FMA instructions; +fixes failing LAPACK tests when -ftree-vectorize is used +author: Bart Oldeman (Digital Research Alliance of Canada) +--- OpenBLAS-0.3.21/lapack-netlib/SRC/clahqr.f.orig 2022-08-07 20:36:26.000000000 +0000 ++++ OpenBLAS-0.3.21/lapack-netlib/SRC/clahqr.f 2022-10-15 02:56:05.646906448 +0000 +@@ -484,7 +484,7 @@ + * in columns K to I2. + * + DO 80 J = K, I2 +- SUM = CONJG( T1 )*H( K, J ) + T2*H( K+1, J ) ++ SUM = CONJG( T1 )*H( K, J ) + ( T2*H( K+1, J ) ) + H( K, J ) = H( K, J ) - SUM + H( K+1, J ) = H( K+1, J ) - SUM*V2 + 80 CONTINUE +@@ -493,7 +493,7 @@ + * matrix in rows I1 to min(K+2,I). + * + DO 90 J = I1, MIN( K+2, I ) +- SUM = T1*H( J, K ) + T2*H( J, K+1 ) ++ SUM = T1*H( J, K ) + ( T2*H( J, K+1 ) ) + H( J, K ) = H( J, K ) - SUM + H( J, K+1 ) = H( J, K+1 ) - SUM*CONJG( V2 ) + 90 CONTINUE +--- OpenBLAS-0.3.21/lapack-netlib/SRC/zlahqr.f.orig 2022-08-07 20:36:26.000000000 +0000 ++++ OpenBLAS-0.3.21/lapack-netlib/SRC/zlahqr.f 2022-10-15 02:11:54.111966029 +0000 +@@ -484,7 +484,7 @@ + * in columns K to I2. + * + DO 80 J = K, I2 +- SUM = DCONJG( T1 )*H( K, J ) + T2*H( K+1, J ) ++ SUM = DCONJG( T1 )*H( K, J ) + ( T2*H( K+1, J ) ) + H( K, J ) = H( K, J ) - SUM + H( K+1, J ) = H( K+1, J ) - SUM*V2 + 80 CONTINUE +@@ -493,7 +493,7 @@ + * matrix in rows I1 to min(K+2,I). + * + DO 90 J = I1, MIN( K+2, I ) +- SUM = T1*H( J, K ) + T2*H( J, K+1 ) ++ SUM = T1*H( J, K ) + ( T2*H( J, K+1 ) ) + H( J, K ) = H( J, K ) - SUM + H( J, K+1 ) = H( J, K+1 ) - SUM*DCONJG( V2 ) + 90 CONTINUE From 6506f62a95d89a03b51d048c05931f2eba66fc32 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 17 Oct 2022 11:14:56 +0100 Subject: [PATCH 378/793] pip_sanity_check added --- .../d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index b210c0f9419..3349b849e4f 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -36,6 +36,8 @@ dependencies = [ ('PyTorch', '1.10.0', versionsuffix), ] +download_dep_fail = True +sanity_pip_check = True use_pip = True exts_list = [ From 3b822c4244353022b1da082f570d12e30f2b3398 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 17 Oct 2022 11:44:21 +0100 Subject: [PATCH 379/793] download_dep removed as PythonBundle being used --- .../d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index 3349b849e4f..9416f4eee39 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -36,7 +36,6 @@ dependencies = [ ('PyTorch', '1.10.0', versionsuffix), ] -download_dep_fail = True sanity_pip_check = True use_pip = True From 394461632696f6a991511352b7f3ae19d858ebae Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 17 Oct 2022 13:41:19 +0200 Subject: [PATCH 380/793] Added ICU dependency --- easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb index a7d264de762..51cd88b1aaa 100644 --- a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb @@ -20,6 +20,7 @@ builddependencies = [ ] dependencies = [ + ('ICU', '69.1'), ('libunistring', '0.9.10'), ] From 35cf91b72ca9ff877866ada47660b6383c0dc954 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Mon, 17 Oct 2022 13:54:33 +0200 Subject: [PATCH 381/793] adding easyconfigs: TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb --- ...w-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..38e8358f882 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow-Datasets' +version = '4.7.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.tensorflow.org/datasets' +description = """ +TensorFlow Datasets is a collection of datasets ready to use, with TensorFlow or other Python ML frameworks, such as +Jax. All datasets are exposed as tf.data.Datasets , enabling easy-to-use and high-performance input pipelines. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('Python', '3.9.5'), + ('tqdm', '4.61.2'), + ('TensorFlow', '2.6.0', '-CUDA-%(cudaver)s'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('promise', '2.3', { + 'checksums': ['dfd18337c523ba4b6a58801c164c1904a9d4d1b1747c7d5dbf45b693a49d93d0'], + }), + ('googleapis-common-protos', '1.56.4', { + 'modulename': 'google', + 'checksums': ['c25873c47279387cfdcbdafa36149887901d36202cb645a0e4f29686bf6e4417'], + }), + ('tensorflow-metadata', '1.10.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_urls': [ + 'https://files.pythonhosted.org/packages/3a/86/' + + '2b3251bb560068f31817d9b678588098e28f396c1f6b88c57cf5d28670af/' + + 'tensorflow_metadata-1.10.0-py3-none-any.whl' + + '#sha256=e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3', + ], + 'checksums': ['e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3'], + }), + ('etils', '0.8.0', { + 'checksums': ['d1d5af7bd9c784a273c4e1eccfaa8feaca5e0481a08717b5313fa231da22a903'], + }), + (name, version, { + 'download_filename': 'v(%version)s.tar.gz', + 'filename': '%(name)s-v(%version)s.tar.gz', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/datasets/archive'], + 'checksums': ['ed7c3b959d10ba762137e18b93631ab42f4ed0915bc3d9ce98ee66eef9c61418'], + }), +] + +moduleclass = 'lib' From bf17187f91939a0e298c9e4550cd63af4759e062 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 17 Oct 2022 14:03:52 +0200 Subject: [PATCH 382/793] Add GITHUB_(LOWER_)RELEASE to known constants --- setup.cfg | 2 ++ 1 file changed, 2 insertions(+) diff --git a/setup.cfg b/setup.cfg index 1209f2f4ea8..c1167840f91 100644 --- a/setup.cfg +++ b/setup.cfg @@ -28,6 +28,8 @@ builtins = FTPGNOME_SOURCE, GITHUB_SOURCE, GITHUB_LOWER_SOURCE, + GITHUB_RELEASE, + GITHUB_LOWER_RELEASE, GNU_SAVANNAH_SOURCE, GNU_SOURCE, GOOGLECODE_SOURCE, From 299c6dc7bfae327daddc8a22dd6158b915da995e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 22 Jul 2022 13:34:21 +0200 Subject: [PATCH 383/793] adding easyconfigs: CUDAcompat-11.6.eb, CUDAcompat-11.7.eb --- .../c/CUDAcompat/CUDAcompat-11.6.eb | 38 ++++++++++++++++++ .../c/CUDAcompat/CUDAcompat-11.7.eb | 39 +++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6.eb create mode 100644 easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7.eb diff --git a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6.eb b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6.eb new file mode 100644 index 00000000000..ec72ddcd2eb --- /dev/null +++ b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6.eb @@ -0,0 +1,38 @@ +name = 'CUDAcompat' +version = '11.6' +nv_version = '510.73.08' + +# Compatible driver versions: +# 418.40.04+ (CUDA 10.1) +# 450.36.06+ (CUDA 11.0) +# 470.57.02+ (CUDA 11.4) + +homepage = 'https://docs.nvidia.com/deploy/cuda-compatibility/index.html' +description = """Using the CUDA Forward Compatibility package, + system administrators can run applications built using a newer toolkit + even when an older driver that does not satisfy the minimum required driver version + is installed on the system. + This forward compatibility allows the CUDA deployments in data centers and enterprises + to benefit from the faster release cadence and the latest features and performance of CUDA Toolkit. +""" + +toolchain = SYSTEM + +# The full driver runfile installers are downloaded but we will only use a small portion of them +# (see https://docs.nvidia.com/deploy/cuda-compatibility/index.html#manually-installing-from-runfile) +# By downloading, you accept the "License For Customer Use of NVIDIA Software for use of the driver +# (https://www.nvidia.com/content/DriverDownload-March2009/licence.php?lang=us) + +# accept_eula = True +source_urls = ['https://us.download.nvidia.com/tesla/' + nv_version] +sources = ['NVIDIA-Linux-%%(arch)s-%s.run' % nv_version] +checksums = [{ + 'NVIDIA-Linux-aarch64-%s.run' % nv_version: + '99fbb188e69513c970bb20c530323ea1205a93245fd0316723ad7308dde8d362', + 'NVIDIA-Linux-ppc64le-%s.run' % nv_version: + 'f9b77f8d6a12a499a146ca6ac1b4fba26268956e308f7272753d53f92cd5b830', + 'NVIDIA-Linux-x86_64-%s.run' % nv_version: + 'c854bb2dc3368c0127dc08a85bd902f8558a5149085af13d061c612cf06c2913', +}] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7.eb b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7.eb new file mode 100644 index 00000000000..4ca891db19f --- /dev/null +++ b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7.eb @@ -0,0 +1,39 @@ +name = 'CUDAcompat' +version = '11.7' +nv_version = '515.48.07' + +# Compatible driver versions: +# 450.36.06+ (CUDA 11.0) +# 470.57.02+ (CUDA 11.4) +# 510.39.01+ (CUDA 11.6) + +homepage = 'https://docs.nvidia.com/deploy/cuda-compatibility/index.html' +description = """Using the CUDA Forward Compatibility package, + system administrators can run applications built using a newer toolkit + even when an older driver that does not satisfy the minimum required driver version + is installed on the system. + This forward compatibility allows the CUDA deployments in data centers and enterprises + to benefit from the faster release cadence and the latest features and performance of CUDA Toolkit. +""" + +toolchain = SYSTEM + +# The full driver runfile installers are downloaded but we will only use a small portion of them +# (see https://docs.nvidia.com/deploy/cuda-compatibility/index.html#manually-installing-from-runfile) +# By downloading, you accept the "License For Customer Use of NVIDIA Software for use of the driver +# (https://www.nvidia.com/content/DriverDownload-March2009/licence.php?lang=us) + +# accept_eula = True + +source_urls = ['https://us.download.nvidia.com/tesla/' + nv_version] +sources = ['NVIDIA-Linux-%%(arch)s-%s.run' % nv_version] +checksums = [{ + 'NVIDIA-Linux-aarch64-%s.run' % nv_version: + 'a4e071055a5f6c110fd49264d76c57a07f3fbd37b8ee2f9eb90c25f51fa59ef5', + 'NVIDIA-Linux-ppc64le-%s.run' % nv_version: + '476466e768ca3cd4e5d01b2467bed61623728e637efbe7f81ac976bb2dd96aa8', + 'NVIDIA-Linux-x86_64-%s.run' % nv_version: + 'e28764cc5b13c32e76370513daeafc05c289b77ee0511552450f1a00e31ae1e3', +}] + +moduleclass = 'system' From f2e6b052039b34bb0d37702552d5a6602face865 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 22 Jul 2022 14:15:21 +0200 Subject: [PATCH 384/793] Add alias modules and the compatible driver versions a list --- .../c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb | 45 +++++++++++++++++++ .../c/CUDAcompat/CUDAcompat-11.6.eb | 25 ++--------- .../c/CUDAcompat/CUDAcompat-11.7-515.65.01.eb | 45 +++++++++++++++++++ .../c/CUDAcompat/CUDAcompat-11.7.eb | 26 ++--------- .../easyconfigs/c/CUDAcompat/CUDAcompat-11.eb | 19 ++++++++ 5 files changed, 115 insertions(+), 45 deletions(-) create mode 100644 easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb create mode 100644 easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7-515.65.01.eb create mode 100644 easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.eb diff --git a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb new file mode 100644 index 00000000000..7bc5e5a3d2d --- /dev/null +++ b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb @@ -0,0 +1,45 @@ +name = 'CUDAcompat' +version = '11.6' +nv_version = '510.85.02' +versionsuffix = "-" + nv_version + +# Minimal driver requirements for each production branch / major version as found on +# https://docs.nvidia.com/deploy/cuda-compatibility/index.html#use-the-right-compat-package +# Compatibility test can be skipped with --skip-test-step/--ignore-test-failure +# but then tests running actual CUDA applications should be used to verify compatibility +compatible_driver_versions = [ + '418.40.04', # (CUDA 10.1) + '450.36.06', # (CUDA 11.0) + '470.57.02', # (CUDA 11.4) +] + +homepage = 'https://docs.nvidia.com/deploy/cuda-compatibility/index.html' +description = """Using the CUDA Forward Compatibility package, + system administrators can run applications built using a newer toolkit + even when an older driver that does not satisfy the minimum required driver version + is installed on the system. + This forward compatibility allows the CUDA deployments in data centers and enterprises + to benefit from the faster release cadence and the latest features and performance of CUDA Toolkit. +""" + +toolchain = SYSTEM + +# The full driver runfile installers are downloaded but we will only use a small portion of them +# (see https://docs.nvidia.com/deploy/cuda-compatibility/index.html#manually-installing-from-runfile) +# By downloading, you accept the "License For Customer Use of NVIDIA Software for use of the driver +# (https://www.nvidia.com/content/DriverDownload-March2009/licence.php?lang=us) + +# accept_eula = True + +source_urls = ['https://us.download.nvidia.com/tesla/' + nv_version] +sources = ['NVIDIA-Linux-%%(arch)s-%s.run' % nv_version] +checksums = [{ + 'NVIDIA-Linux-aarch64-%s.run' % nv_version: + 'bb5e844a69bc05dade9148438a71f2bb7dea1864278d37864f1a303e437e40c3', + 'NVIDIA-Linux-ppc64le-%s.run' % nv_version: + '46626294cf18ead6eeb53a6614f7b340e66c57ea50f95d4dc670e90b4650c335', + 'NVIDIA-Linux-x86_64-%s.run' % nv_version: + '372427e633f32cff6dd76020e8ed471ef825d38878bd9655308b6efea1051090', +}] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6.eb b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6.eb index ec72ddcd2eb..f931186e517 100644 --- a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6.eb +++ b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6.eb @@ -1,11 +1,7 @@ +easyblock = 'ModuleRC' + name = 'CUDAcompat' version = '11.6' -nv_version = '510.73.08' - -# Compatible driver versions: -# 418.40.04+ (CUDA 10.1) -# 450.36.06+ (CUDA 11.0) -# 470.57.02+ (CUDA 11.4) homepage = 'https://docs.nvidia.com/deploy/cuda-compatibility/index.html' description = """Using the CUDA Forward Compatibility package, @@ -18,21 +14,6 @@ description = """Using the CUDA Forward Compatibility package, toolchain = SYSTEM -# The full driver runfile installers are downloaded but we will only use a small portion of them -# (see https://docs.nvidia.com/deploy/cuda-compatibility/index.html#manually-installing-from-runfile) -# By downloading, you accept the "License For Customer Use of NVIDIA Software for use of the driver -# (https://www.nvidia.com/content/DriverDownload-March2009/licence.php?lang=us) - -# accept_eula = True -source_urls = ['https://us.download.nvidia.com/tesla/' + nv_version] -sources = ['NVIDIA-Linux-%%(arch)s-%s.run' % nv_version] -checksums = [{ - 'NVIDIA-Linux-aarch64-%s.run' % nv_version: - '99fbb188e69513c970bb20c530323ea1205a93245fd0316723ad7308dde8d362', - 'NVIDIA-Linux-ppc64le-%s.run' % nv_version: - 'f9b77f8d6a12a499a146ca6ac1b4fba26268956e308f7272753d53f92cd5b830', - 'NVIDIA-Linux-x86_64-%s.run' % nv_version: - 'c854bb2dc3368c0127dc08a85bd902f8558a5149085af13d061c612cf06c2913', -}] +dependencies = [(name, version, "-510.85.02")] moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7-515.65.01.eb b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7-515.65.01.eb new file mode 100644 index 00000000000..eba7e2ca957 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7-515.65.01.eb @@ -0,0 +1,45 @@ +name = 'CUDAcompat' +version = '11.7' +nv_version = '515.65.01' +versionsuffix = "-" + nv_version + +# Minimal driver requirements for each production branch / major version as found on +# https://docs.nvidia.com/deploy/cuda-compatibility/index.html#use-the-right-compat-package +# Compatibility test can be skipped with --skip-test-step/--ignore-test-failure +# but then tests running actual CUDA applications should be used to verify compatibility +compatible_driver_versions = [ + '450.36.06', # (CUDA 11.0) + '470.57.02', # (CUDA 11.4) + '510.39.01', # (CUDA 11.6) +] + +homepage = 'https://docs.nvidia.com/deploy/cuda-compatibility/index.html' +description = """Using the CUDA Forward Compatibility package, + system administrators can run applications built using a newer toolkit + even when an older driver that does not satisfy the minimum required driver version + is installed on the system. + This forward compatibility allows the CUDA deployments in data centers and enterprises + to benefit from the faster release cadence and the latest features and performance of CUDA Toolkit. +""" + +toolchain = SYSTEM + +# The full driver runfile installers are downloaded but we will only use a small portion of them +# (see https://docs.nvidia.com/deploy/cuda-compatibility/index.html#manually-installing-from-runfile) +# By downloading, you accept the "License For Customer Use of NVIDIA Software for use of the driver +# (https://www.nvidia.com/content/DriverDownload-March2009/licence.php?lang=us) + +# accept_eula = True + +source_urls = ['https://us.download.nvidia.com/tesla/' + nv_version] +sources = ['NVIDIA-Linux-%%(arch)s-%s.run' % nv_version] +checksums = [{ + 'NVIDIA-Linux-aarch64-%s.run' % nv_version: + '0d2ac6c6ca144c8c7bbf1a62034998463b21f2660a793607d88c031650d93e93', + 'NVIDIA-Linux-ppc64le-%s.run' % nv_version: + 'd217c7539d049ab1b7a889815d14d1655116616e7e9943387a1b190aec816063', + 'NVIDIA-Linux-x86_64-%s.run' % nv_version: + '0492ddc5b5e65aa00cbc762e8d6680205c8d08e103b7131087a15126aee495e9', +}] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7.eb b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7.eb index 4ca891db19f..c3a7b3b2e0e 100644 --- a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7.eb +++ b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7.eb @@ -1,11 +1,7 @@ +easyblock = 'ModuleRC' + name = 'CUDAcompat' version = '11.7' -nv_version = '515.48.07' - -# Compatible driver versions: -# 450.36.06+ (CUDA 11.0) -# 470.57.02+ (CUDA 11.4) -# 510.39.01+ (CUDA 11.6) homepage = 'https://docs.nvidia.com/deploy/cuda-compatibility/index.html' description = """Using the CUDA Forward Compatibility package, @@ -18,22 +14,6 @@ description = """Using the CUDA Forward Compatibility package, toolchain = SYSTEM -# The full driver runfile installers are downloaded but we will only use a small portion of them -# (see https://docs.nvidia.com/deploy/cuda-compatibility/index.html#manually-installing-from-runfile) -# By downloading, you accept the "License For Customer Use of NVIDIA Software for use of the driver -# (https://www.nvidia.com/content/DriverDownload-March2009/licence.php?lang=us) - -# accept_eula = True - -source_urls = ['https://us.download.nvidia.com/tesla/' + nv_version] -sources = ['NVIDIA-Linux-%%(arch)s-%s.run' % nv_version] -checksums = [{ - 'NVIDIA-Linux-aarch64-%s.run' % nv_version: - 'a4e071055a5f6c110fd49264d76c57a07f3fbd37b8ee2f9eb90c25f51fa59ef5', - 'NVIDIA-Linux-ppc64le-%s.run' % nv_version: - '476466e768ca3cd4e5d01b2467bed61623728e637efbe7f81ac976bb2dd96aa8', - 'NVIDIA-Linux-x86_64-%s.run' % nv_version: - 'e28764cc5b13c32e76370513daeafc05c289b77ee0511552450f1a00e31ae1e3', -}] +dependencies = [(name, version, '-515.65.01')] moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.eb b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.eb new file mode 100644 index 00000000000..17159182bc1 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.eb @@ -0,0 +1,19 @@ +easyblock = 'ModuleRC' + +name = 'CUDAcompat' +version = '11' + +homepage = 'https://docs.nvidia.com/deploy/cuda-compatibility/index.html' +description = """Using the CUDA Forward Compatibility package, + system administrators can run applications built using a newer toolkit + even when an older driver that does not satisfy the minimum required driver version + is installed on the system. + This forward compatibility allows the CUDA deployments in data centers and enterprises + to benefit from the faster release cadence and the latest features and performance of CUDA Toolkit. +""" + +toolchain = SYSTEM + +dependencies = [(name, '11.7')] + +moduleclass = 'system' From 352b6273fb575bb9ec7299b039850a0d5ca2921b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 19 Sep 2022 14:00:57 +0200 Subject: [PATCH 385/793] Mark 11.6 as compatible to R440 and R460 As tested by @Flamefire and @ocaisa --- easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb index 7bc5e5a3d2d..721f22cf426 100644 --- a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb +++ b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb @@ -9,7 +9,9 @@ versionsuffix = "-" + nv_version # but then tests running actual CUDA applications should be used to verify compatibility compatible_driver_versions = [ '418.40.04', # (CUDA 10.1) + '440.33.00', # (CUDA 10.2, actually EoL but works) '450.36.06', # (CUDA 11.0) + '460.73.01', # (CUDA 11.2, actually EoL but works) '470.57.02', # (CUDA 11.4) ] From c65bed37af572d6a2bfd13266c2ad88021b33687 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Oct 2022 14:38:32 +0200 Subject: [PATCH 386/793] fix checksum for GULP 6.1 (fixes #15984) --- easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb b/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb index c26d7a70c8c..4a48ff9555c 100644 --- a/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb @@ -20,7 +20,7 @@ patches = [ 'GULP-6.1_fftw-blas-linking-gcc-11.patch', ] checksums = [ - '503dff253f4686c570adfd3ff75a657e29151b4255dec726daa50eda5a7ac3f4', # gulp-6.1.tgz + '1b52fe2928ccf2cea5d2c3466162764d0de6b4d06e86fe292ab37859d6a0e6d6', # gulp-6.1.tgz '156449c96a97ff24f6add83c10fd383f07c43c79420eebe3290387b65b34549b', # gulp-6.1_fftw-blas-linking-gcc-11.patch ] From 4fcf6ec98a14756f8b9b327f178df5b1833edb43 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Mon, 17 Oct 2022 15:42:03 +0200 Subject: [PATCH 387/793] Add missing parenthesis --- .../TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb index 38e8358f882..667bb710d9e 100644 --- a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb @@ -32,12 +32,12 @@ exts_list = [ }), ('tensorflow-metadata', '1.10.0', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'source_urls': [ + 'source_urls': [( 'https://files.pythonhosted.org/packages/3a/86/' + '2b3251bb560068f31817d9b678588098e28f396c1f6b88c57cf5d28670af/' + 'tensorflow_metadata-1.10.0-py3-none-any.whl' - + '#sha256=e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3', - ], + + '#sha256=e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3' + )], 'checksums': ['e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3'], }), ('etils', '0.8.0', { From c474ce7cb330ff51fe7aa6c548f5e6e40d570f56 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Oct 2022 18:18:37 +0200 Subject: [PATCH 388/793] increase max. number of failing LAPACK tests with numerical error to 100 for recent OpenBLAS easyconfigs, due to eigenvalue test being a bit too strict --- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index 63c99b77086..545706a97b2 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -39,7 +39,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 10 +max_failing_lapack_tests_num_errors = 100 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb index 3a587ae6e7d..e60362e973a 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -36,7 +36,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 10 +max_failing_lapack_tests_num_errors = 100 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index 8d3080bf8fd..1bcda13c08c 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -34,7 +34,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 10 +max_failing_lapack_tests_num_errors = 100 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index 2e1cdaca17e..29dff20315a 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -34,7 +34,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 10 +max_failing_lapack_tests_num_errors = 100 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' From 3f8a3ed2c5682ded3f1e804ea0ccc11534bcc906 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Oct 2022 22:31:10 +0200 Subject: [PATCH 389/793] increase max. number of failing LAPACK tests with numerical error a bit more to 150 for recent OpenBLAS easyconfigs --- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index 545706a97b2..93e65aa9221 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -39,7 +39,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 100 +max_failing_lapack_tests_num_errors = 150 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb index e60362e973a..866cd7de515 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -36,7 +36,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 100 +max_failing_lapack_tests_num_errors = 150 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index 1bcda13c08c..c654f92e700 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -34,7 +34,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 100 +max_failing_lapack_tests_num_errors = 150 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index 29dff20315a..bb82984319e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -34,7 +34,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 100 +max_failing_lapack_tests_num_errors = 150 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' From 14e91fc4df7d2d9dc7f286b1c514492b8a3b9032 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Tue, 18 Oct 2022 09:41:25 +0200 Subject: [PATCH 390/793] tfds to pypi version Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb index 667bb710d9e..60233e3f9ff 100644 --- a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb @@ -44,11 +44,8 @@ exts_list = [ 'checksums': ['d1d5af7bd9c784a273c4e1eccfaa8feaca5e0481a08717b5313fa231da22a903'], }), (name, version, { - 'download_filename': 'v(%version)s.tar.gz', - 'filename': '%(name)s-v(%version)s.tar.gz', - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/datasets/archive'], - 'checksums': ['ed7c3b959d10ba762137e18b93631ab42f4ed0915bc3d9ce98ee66eef9c61418'], + 'source_tmpl': SOURCELOWER_TAR_GZ, + 'checksums': ['590faf3763bc14757906b36c718389eeded533ee8ae4d030ede140db86aca4cd'], }), ] From 367f739096267f6f81fee2e1ab0fac847d124aae Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Tue, 18 Oct 2022 09:41:53 +0200 Subject: [PATCH 391/793] Update easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb index 60233e3f9ff..08ec6bcebe1 100644 --- a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb @@ -16,7 +16,7 @@ dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('tqdm', '4.61.2'), - ('TensorFlow', '2.6.0', '-CUDA-%(cudaver)s'), + ('TensorFlow', '2.6.0', versionsuffix), ] sanity_pip_check = True From a80dadb4d8639b292ac7ce2c8759b1f7733432c0 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Tue, 18 Oct 2022 10:27:03 +0200 Subject: [PATCH 392/793] Remove url specification for tf metadata Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb | 6 ------ 1 file changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb index 08ec6bcebe1..4242b5cd1ae 100644 --- a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb @@ -32,12 +32,6 @@ exts_list = [ }), ('tensorflow-metadata', '1.10.0', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'source_urls': [( - 'https://files.pythonhosted.org/packages/3a/86/' - + '2b3251bb560068f31817d9b678588098e28f396c1f6b88c57cf5d28670af/' - + 'tensorflow_metadata-1.10.0-py3-none-any.whl' - + '#sha256=e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3' - )], 'checksums': ['e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3'], }), ('etils', '0.8.0', { From d69075a34a59a510476dd9429101e80c73691c67 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Tue, 18 Oct 2022 10:28:04 +0200 Subject: [PATCH 393/793] adding easyconfigs: ruffus-2.8.4-foss-2021b.eb --- .../r/ruffus/ruffus-2.8.4-foss-2021b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb diff --git a/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb new file mode 100644 index 00000000000..f2046029233 --- /dev/null +++ b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'ruffus' +version = '2.8.4' + +homepage = 'http://www.ruffus.org.uk/' +description = "Ruffus is a Computation Pipeline library for python. It is open-sourced, powerful and user-friendly, and widely used in science and bioinformatics." + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['6cd3d96e459a1aedcc10341f14fddedfdc13664551757fcd429a241de63826aa'] + +dependencies = [ + ('Python', '3.9.6'), + ('Graphviz', '2.50.0'), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = [ + "python -c 'import ruffus'", + "python -c 'import ruffus.graph'", +] + +moduleclass = 'vis' From 4a164a0cac6a93664677ef3ebfbca0f0630eb2a1 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 18 Oct 2022 11:33:16 +0100 Subject: [PATCH 394/793] update libxml2, libxslt sources to use gnome.org (#16419) --- .../l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb | 9 +++------ .../l/libxml2/libxml2-2.9.10-GCCcore-10.3.0.eb | 9 +++------ .../l/libxml2/libxml2-2.9.10-GCCcore-11.2.0.eb | 9 +++------ .../l/libxml2/libxml2-2.9.10-GCCcore-9.2.0.eb | 9 +++------ .../l/libxml2/libxml2-2.9.10-GCCcore-9.3.0.eb | 9 +++------ .../easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.2.0.eb | 9 +++------ .../easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.3.0.eb | 9 +++------ .../easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-8.2.0.eb | 9 +++------ .../easyconfigs/l/libxml2/libxml2-2.9.9-GCCcore-8.3.0.eb | 9 +++------ .../l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb | 9 +++------ .../l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb | 9 +++------ .../l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb | 9 +++------ .../l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb | 9 +++------ .../l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb | 9 +++------ .../l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb | 9 +++------ .../l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb | 9 +++------ .../l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb | 9 +++------ 17 files changed, 51 insertions(+), 102 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb index 38a25e4b1a7..aeed9cfa941 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb @@ -11,12 +11,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['aafee193ffb8fe0c82d4afef6ef91972cbaf5feea100edc2f262750611b4be1f'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['593b7b751dd18c2d6abcd0c4bcb29efc203d0b4373a6df98e3a455ea74ae2813'] builddependencies = [('binutils', '2.35')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.3.0.eb index 8b050c1144f..d8f7f588096 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.3.0.eb @@ -14,12 +14,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['aafee193ffb8fe0c82d4afef6ef91972cbaf5feea100edc2f262750611b4be1f'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['593b7b751dd18c2d6abcd0c4bcb29efc203d0b4373a6df98e3a455ea74ae2813'] builddependencies = [('binutils', '2.36.1')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-11.2.0.eb index c0fa3931030..4e4b321a783 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-11.2.0.eb @@ -11,12 +11,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['aafee193ffb8fe0c82d4afef6ef91972cbaf5feea100edc2f262750611b4be1f'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['593b7b751dd18c2d6abcd0c4bcb29efc203d0b4373a6df98e3a455ea74ae2813'] builddependencies = [('binutils', '2.37')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.2.0.eb index 5e7273f67e7..d256f11c658 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.2.0.eb @@ -11,12 +11,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '9.2.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['aafee193ffb8fe0c82d4afef6ef91972cbaf5feea100edc2f262750611b4be1f'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['593b7b751dd18c2d6abcd0c4bcb29efc203d0b4373a6df98e3a455ea74ae2813'] builddependencies = [('binutils', '2.32')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.3.0.eb index 53b484f969b..3669c4c6bca 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.3.0.eb @@ -11,12 +11,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['aafee193ffb8fe0c82d4afef6ef91972cbaf5feea100edc2f262750611b4be1f'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['593b7b751dd18c2d6abcd0c4bcb29efc203d0b4373a6df98e3a455ea74ae2813'] builddependencies = [('binutils', '2.34')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.2.0.eb index 8f28af864fe..a9f2c2e2125 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.2.0.eb @@ -11,12 +11,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.2.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['0b74e51595654f958148759cfef0993114ddccccbb6f31aee018f3558e8e2732'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['dcca21d624bbbe094fcc104e1f15f2eacfb65aecd0e38ed220aeca56b62c81e2'] builddependencies = [('binutils', '2.29')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.3.0.eb index d85ba7444da..417881a12ed 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.3.0.eb @@ -11,12 +11,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['0b74e51595654f958148759cfef0993114ddccccbb6f31aee018f3558e8e2732'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['dcca21d624bbbe094fcc104e1f15f2eacfb65aecd0e38ed220aeca56b62c81e2'] builddependencies = [('binutils', '2.30')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-8.2.0.eb index 9a02ed10f47..fc27adc85d2 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-8.2.0.eb @@ -11,12 +11,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['0b74e51595654f958148759cfef0993114ddccccbb6f31aee018f3558e8e2732'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['dcca21d624bbbe094fcc104e1f15f2eacfb65aecd0e38ed220aeca56b62c81e2'] builddependencies = [('binutils', '2.31.1')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.9-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.9-GCCcore-8.3.0.eb index 7f8f41a3902..e427981571a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.9-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.9-GCCcore-8.3.0.eb @@ -11,12 +11,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['94fb70890143e3c6549f265cee93ec064c80a84c42ad0f23e85ee1fd6540a871'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['58a5c05a2951f8b47656b676ce1017921a29f6b1419c45e3baed0d6435ba03f5'] builddependencies = [('binutils', '2.32')] diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb index 9f2ba0ca1be..140e353a598 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb @@ -9,12 +9,9 @@ description = """Libxslt is the XSLT C library developed for the GNOME project toolchain = {'name': 'GCCcore', 'version': '7.3.0'} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['526ecd0abaf4a7789041622c3950c0e7f2c4c8835471515fd77eec684a355460'] +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['b7da90eaa6b0dae9e9a3769e29a757342eef0edb9a7b431424814375414422af'] builddependencies = [('binutils', '2.30')] diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb index 0df6959430a..07d27c99af2 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb @@ -9,12 +9,9 @@ description = """Libxslt is the XSLT C library developed for the GNOME project toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['8e36605144409df979cab43d835002f63988f3dc94d5d3537c12796db90e38c8'] +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['3944d3a74b4ca6b40f59967e2a587abc6994f6935d697d9fa1b8edd722513e90'] builddependencies = [('binutils', '2.31.1')] diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb index d17aa440dc4..fc7feb6f53a 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb @@ -9,12 +9,9 @@ description = """Libxslt is the XSLT C library developed for the GNOME project toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['98b1bd46d6792925ad2dfe9a87452ea2adebf69dcb9919ffd55bf926a7f93f7f'] +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] builddependencies = [('binutils', '2.35')] diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb index 121392cf7dc..304d2938dcd 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb @@ -9,12 +9,9 @@ description = """Libxslt is the XSLT C library developed for the GNOME project toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['98b1bd46d6792925ad2dfe9a87452ea2adebf69dcb9919ffd55bf926a7f93f7f'] +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] builddependencies = [('binutils', '2.36.1')] diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb index 705654d4093..5cc9afc5c7f 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb @@ -9,12 +9,9 @@ description = """Libxslt is the XSLT C library developed for the GNOME project toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['98b1bd46d6792925ad2dfe9a87452ea2adebf69dcb9919ffd55bf926a7f93f7f'] +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] builddependencies = [('binutils', '2.37')] diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb index 49e57192bf3..14d3083a7bc 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb @@ -9,12 +9,9 @@ description = """Libxslt is the XSLT C library developed for the GNOME project toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['98b1bd46d6792925ad2dfe9a87452ea2adebf69dcb9919ffd55bf926a7f93f7f'] +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] builddependencies = [('binutils', '2.38')] diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb index 6097396bc50..edec6edc2cb 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb @@ -9,12 +9,9 @@ description = """Libxslt is the XSLT C library developed for the GNOME project toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['98b1bd46d6792925ad2dfe9a87452ea2adebf69dcb9919ffd55bf926a7f93f7f'] +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] builddependencies = [('binutils', '2.32')] diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb index f414649f8fe..33d3ef1c1a8 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb @@ -9,12 +9,9 @@ description = """Libxslt is the XSLT C library developed for the GNOME project toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['98b1bd46d6792925ad2dfe9a87452ea2adebf69dcb9919ffd55bf926a7f93f7f'] +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] builddependencies = [('binutils', '2.34')] From 8bc993e53c3199e287655db2cc92b1d773582762 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 18 Oct 2022 12:40:30 +0200 Subject: [PATCH 395/793] adding easyconfigs: MIGRATE-N-5.0.4-foss-2021b.eb and patches: migrate-5.0.4_install.patch, migrate-5.0.4_locale.patch --- .../m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb | 41 +++++++++++++++++++ .../m/MIGRATE-N/migrate-5.0.4_install.patch | 14 +++++++ .../m/MIGRATE-N/migrate-5.0.4_locale.patch | 15 +++++++ 3 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb create mode 100644 easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_install.patch create mode 100644 easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_locale.patch diff --git a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb new file mode 100644 index 00000000000..5abedc1fb58 --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'MIGRATE-N' +version = '5.0.4' + +homepage = 'https://peterbeerli.com/migrate-html5/index.html' +description = """ +Migrate estimates population parameters, effective population sizes +and migration rates of n populations, using genetic data. It +uses a coalescent theory approach taking into account history of +mutations and uncertainty of the genealogy. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ["https://peterbeerli.com/migrate-html5/download_version4"] +sources = ['migrate-%(version)s.src.tar.gz'] +patches = [ + 'migrate-%(version)s_install.patch', + 'migrate-%(version)s_locale.patch', +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-A4 "CC=$CC" STDCPLUS=-lstdc++' +prebuildopts = 'make mpis && make clean &&' +installopts = "&& make clean && make installmpi" + +parallel = 1 + +start_dir = 'src' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['migrate-n', 'migrate-n-mpi']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_install.patch b/easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_install.patch new file mode 100644 index 00000000000..ba33af1af0a --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_install.patch @@ -0,0 +1,14 @@ +Create parent directories during install +Author: B. Hajgato +Updated: Orient Kružík (INUITS) +--- migrate-5.0.3_orig/src/configure 2021-11-08 22:48:21.000000000 +0100 ++++ migrate-5.0.3/src/configure 2022-05-09 17:15:29.368752420 +0200 +@@ -4104,7 +4104,7 @@ + test -s conftest.dir/conftest.one && + test -s conftest.dir/conftest.two + then +- ac_cv_path_install="$as_dir$ac_prog$ac_exec_ext -c" ++ ac_cv_path_install="$as_dir$ac_prog$ac_exec_ext -c -D" + break 3 + fi + fi \ No newline at end of file diff --git a/easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_locale.patch b/easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_locale.patch new file mode 100644 index 00000000000..29cd65e5d99 --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_locale.patch @@ -0,0 +1,15 @@ +Don't use the xlocale.h header since it is an OS package and not always provided. +Author: R. van Dijk, 2018-03-07 +Updated by: Orient Kružík (INUITS) +--- migrate-5.0.3_orig/src/src/data.c 2022-04-03 00:11:20.000000000 +0200 ++++ migrate-5.0.3/src/src/data.c 2022-05-09 17:17:46.836503576 +0200 +@@ -53,9 +53,6 @@ + + #include + #include +-#ifndef WIN32 +-#include +-#endif + #include "migration.h" + #include "sighandler.h" + #include "tools.h" \ No newline at end of file From 330da15302a5eeb245d5e9617af746e8740f1c93 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Tue, 18 Oct 2022 13:02:23 +0200 Subject: [PATCH 396/793] Fixed style error --- .../easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb index 5abedc1fb58..624706433b6 100644 --- a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb +++ b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb @@ -17,8 +17,8 @@ toolchainopts = {'usempi': True} source_urls = ["https://peterbeerli.com/migrate-html5/download_version4"] sources = ['migrate-%(version)s.src.tar.gz'] patches = [ - 'migrate-%(version)s_install.patch', - 'migrate-%(version)s_locale.patch', + 'migrate-%(version)s_install.patch', + 'migrate-%(version)s_locale.patch', ] dependencies = [ From aa1bea027d51f4571b2e7fa42e690e479c8686d8 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 18 Oct 2022 12:05:06 +0100 Subject: [PATCH 397/793] add sanity_check_paths to older libxslt easyconfigs --- .../easyconfigs/l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb | 5 +++++ .../easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb index 140e353a598..7d24e0af0d1 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb @@ -20,4 +20,9 @@ dependencies = [ ('libxml2', '2.9.8'), ] +sanity_check_paths = { + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb index 07d27c99af2..e1b9d08e742 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb @@ -20,4 +20,9 @@ dependencies = [ ('libxml2', '2.9.8'), ] +sanity_check_paths = { + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + moduleclass = 'lib' From a8843f563495686c1edd706450e7e8f6e81b5821 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 14:30:20 +0200 Subject: [PATCH 398/793] fix patch for latest revision of source tarball of GULP 6.1 --- .../easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb | 4 ++-- .../GULP-6.1_fftw-blas-linking-gcc-11.patch | 23 +++++-------------- 2 files changed, 8 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb b/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb index 4a48ff9555c..707e2eb1bb0 100644 --- a/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb @@ -20,8 +20,8 @@ patches = [ 'GULP-6.1_fftw-blas-linking-gcc-11.patch', ] checksums = [ - '1b52fe2928ccf2cea5d2c3466162764d0de6b4d06e86fe292ab37859d6a0e6d6', # gulp-6.1.tgz - '156449c96a97ff24f6add83c10fd383f07c43c79420eebe3290387b65b34549b', # gulp-6.1_fftw-blas-linking-gcc-11.patch + {'gulp-6.1.tgz': '1b52fe2928ccf2cea5d2c3466162764d0de6b4d06e86fe292ab37859d6a0e6d6'}, + {'GULP-6.1_fftw-blas-linking-gcc-11.patch': 'd32babd56e859a9378548981a00b876a88b66e392cb532d33193b6e3362f7940'}, ] download_instructions = """Download requires registration, please see diff --git a/easybuild/easyconfigs/g/GULP/GULP-6.1_fftw-blas-linking-gcc-11.patch b/easybuild/easyconfigs/g/GULP/GULP-6.1_fftw-blas-linking-gcc-11.patch index 89f6cc6151d..a43f7ed0e14 100644 --- a/easybuild/easyconfigs/g/GULP/GULP-6.1_fftw-blas-linking-gcc-11.patch +++ b/easybuild/easyconfigs/g/GULP/GULP-6.1_fftw-blas-linking-gcc-11.patch @@ -1,11 +1,9 @@ Removing hard-coded paths in the mkgulp file, which is creating the makefile Using the suggested compiler flags for gfortran-10 author: J. Sassmannshausen (Imperial College London/UK) -diff --git a/gulp-6.1.orig/Src/mkgulp b/gulp-6.1/Src/mkgulp -index 5a6ca20..a1fdb42 100755 ---- a/gulp-6.1.orig/Src/mkgulp -+++ b/gulp-6.1/Src/mkgulp -@@ -196,7 +196,7 @@ fi +--- gulp-6.1.orig/Src/mkgulp.orig 2022-10-14 05:14:21.541000000 +0200 ++++ gulp-6.1/Src/mkgulp 2022-10-18 13:18:12.812436767 +0200 +@@ -196,7 +196,7 @@ # Include file directories # #--USER--Start @@ -14,16 +12,7 @@ index 5a6ca20..a1fdb42 100755 #--USER--End # If using Macports then use the following instead #--USER--Start -@@ -230,7 +230,7 @@ case $compiler in - # On the Mac the following is sufficient when using Macports: - # echo 'MLIBS=-L/opt/local/lib/lapack/ -llapack -lblas ' >> makefile - # If using the accelerate framework then leave blank: -- echo 'MLIBS=' >> makefile -+ echo 'MLIBS=-L'${EBROOTFLEXIBLAS}'/lib -lflexiblas' >> makefile - # Or if optimised maths libraries are not available then: - # echo 'MLIBS=lapack.o blas.o' >> makefile - #--USER--End -@@ -238,7 +238,7 @@ case $compiler in +@@ -242,7 +242,7 @@ else # NB: For gfortran v10 then use these lines echo 'RUNF90=mpif90 -fallow-argument-mismatch ' >> makefile @@ -32,7 +21,7 @@ index 5a6ca20..a1fdb42 100755 # echo 'RUNF90=mpif90 ' >> makefile # echo 'RUNCC=mpif90 ' >> makefile # -@@ -247,14 +247,14 @@ case $compiler in +@@ -251,14 +251,14 @@ # On the Mac the following is sufficient when using Macports: # echo 'MLIBS=-L/opt/local/lib/lapack/ -llapack -lblas ' >> makefile # If using the accelerate framework then leave blank: @@ -49,7 +38,7 @@ index 5a6ca20..a1fdb42 100755 # echo 'SLIBS=-L/opt/local/lib -lscalapack ' >> makefile #--USER--End fi -@@ -363,11 +363,11 @@ else +@@ -371,11 +371,11 @@ echo 'FDEFS=-DFFTW3 ' >> makefile if [ "$parallel" = "" ] #--USER--Start From ad4dc970f99b7f12134b8ce2ddf5ba67e5cafaf0 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Tue, 18 Oct 2022 14:31:37 +0200 Subject: [PATCH 399/793] fixed sanity check, multi-line description and moduleclass --- .../easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb index f2046029233..122b155d477 100644 --- a/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb +++ b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb @@ -4,7 +4,8 @@ name = 'ruffus' version = '2.8.4' homepage = 'http://www.ruffus.org.uk/' -description = "Ruffus is a Computation Pipeline library for python. It is open-sourced, powerful and user-friendly, and widely used in science and bioinformatics." +description = """Ruffus is a Computation Pipeline library for python. It is open-sourced, powerful and user-friendly, + and widely used in science and bioinformatics.""" toolchain = {'name': 'foss', 'version': '2021b'} @@ -17,11 +18,7 @@ dependencies = [ ] use_pip = True -sanity_pip_check = True -sanity_check_commands = [ - "python -c 'import ruffus'", - "python -c 'import ruffus.graph'", -] +sanity_check_commands = ["python -c 'import ruffus.graph'"] -moduleclass = 'vis' +moduleclass = 'lib' From 42c98d8ed8c1f8943b455ef704ca5a4bad0bfd48 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 14:43:34 +0200 Subject: [PATCH 400/793] add --with-versioned-syms configure option for ncurses 6.3 with GCCcore/12.2 Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb index 7fed097a62f..6e0cca39d81 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb @@ -20,7 +20,7 @@ checksums = ['97fc51ac2b085d4cde31ef4d2c3122c21abc217e9090a43a30fc5ec21684e059'] builddependencies = [('binutils', '2.39')] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, From 40ba6f2468269d23a348c2a5c47624fa1e793550 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 14:49:06 +0200 Subject: [PATCH 401/793] update to expat 2.4.9 + libreadline 8.2 as dependencies for Perl 5.36.0 with GCCcore/12.2.0 --- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb | 2 +- ....4.8-GCCcore-12.2.0.eb => expat-2.4.9-GCCcore-12.2.0.eb} | 5 +++-- ...-GCCcore-12.2.0.eb => libreadline-8.2-GCCcore-12.2.0.eb} | 4 ++-- easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 6 +++--- 4 files changed, 9 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/e/expat/{expat-2.4.8-GCCcore-12.2.0.eb => expat-2.4.9-GCCcore-12.2.0.eb} (90%) rename easybuild/easyconfigs/l/libreadline/{libreadline-8.1.2-GCCcore-12.2.0.eb => libreadline-8.2-GCCcore-12.2.0.eb} (92%) diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb index 7bc947e2ae0..83b4de99325 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [('binutils', '2.39')] -dependencies = [('OpenSSL', '1.1', '', True)] +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', diff --git a/easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/e/expat/expat-2.4.9-GCCcore-12.2.0.eb similarity index 90% rename from easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/e/expat/expat-2.4.9-GCCcore-12.2.0.eb index df978cec524..2adfd581f7c 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.4.9-GCCcore-12.2.0.eb @@ -1,6 +1,7 @@ easyblock = 'ConfigureMake' + name = 'expat' -version = '2.4.8' +version = '2.4.9' homepage = 'https://libexpat.github.io' @@ -13,7 +14,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')] sources = [SOURCE_TAR_BZ2] -checksums = ['a247a7f6bbb21cf2ca81ea4cbb916bfb9717ca523631675f99b3d4a5678dcd16'] +checksums = ['7f44d1469b110773a94b0d5abeeeffaef79f8bd6406b07e52394bcf48126437a'] builddependencies = [('binutils', '2.39')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-12.2.0.eb similarity index 92% rename from easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-12.2.0.eb index b164af87b06..569af9fc736 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-12.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libreadline' -version = '8.1.2' +version = '8.2' homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' description = """ @@ -18,7 +18,7 @@ toolchainopts = {'pic': True} source_urls = ['https://ftp.gnu.org/gnu/readline'] sources = ['readline-%(version)s.tar.gz'] -checksums = ['7589a2381a8419e68654a47623ce7dfcb756815c8fee726b98f90bf668af7bc6'] +checksums = ['3feb7171f16a84ee82ca18a36d7b9be109a52c04f492a053331d7d1095007c35'] builddependencies = [ ('binutils', '2.39'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb index 5e960b5fcac..168f7b94b45 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -18,11 +18,11 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.12'), # for Net::SSLeay - ('expat', '2.4.8'), # for XML::Parser + ('expat', '2.4.9'), # for XML::Parser ('ncurses', '6.3'), # for Term::ReadLine::Gnu - ('libreadline', '8.1.2'), # for Term::ReadLine::Gnu + ('libreadline', '8.2'), # for Term::ReadLine::Gnu ('DB', '18.1.40'), # for DB_File - ('OpenSSL', '1.1', '', True), # required for Net::SSLeay + ('OpenSSL', '1.1', '', SYSTEM), # required for Net::SSLeay ] # !! order of extensions is important !! From dd6aec8b72adb7a7fea50e3c35bfe7bf165098ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 15:03:25 +0200 Subject: [PATCH 402/793] fix comment in Perl 5.36.0 using GCCcore/12.2.0 toolchain w.r.t. when list of extensions was updated --- easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb index 168f7b94b45..df8c81ece83 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -26,7 +26,7 @@ dependencies = [ ] # !! order of extensions is important !! -# extensions updated on Apr 28th 2022 +# extensions updated on 8 Sept 2022 exts_list = [ ('Config::General', '2.65', { 'source_tmpl': 'Config-General-%(version)s.tar.gz', From f515ed8e185f92018515c7ee74819452f882ba5b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 15:12:30 +0200 Subject: [PATCH 403/793] {devel}[GCCcore/12.2.0] Autotools v20220317: Autoconf v2.71, Automake v1.16.5, libtool v2.4.7 --- .../Autoconf/Autoconf-2.71-GCCcore-12.2.0.eb | 48 +++++++++++++++++++ .../Automake-1.16.5-GCCcore-12.2.0.eb | 39 +++++++++++++++ .../Autotools-20220317-GCCcore-12.2.0.eb | 24 ++++++++++ .../l/libtool/libtool-2.4.7-GCCcore-12.2.0.eb | 32 +++++++++++++ 4 files changed, 143 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..4e315d3a24c --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.71' + +homepage = 'https://www.gnu.org/software/autoconf/' + +description = """ + Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can + adapt the packages to many kinds of UNIX-like systems without manual user + intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can + use, in the form of M4 macro calls. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('M4', '1.4.19'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.36.0'), +] + +preconfigopts = "export PERL='/usr/bin/env perl' && " + +sanity_check_paths = { + 'files': ["bin/%s" % x + for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +sanity_check_commands = [ + "autoconf --help", + "autom4te --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..ff89d29e31a --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Automake' +version = '1.16.5' + +homepage = 'https://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['07bd24ad08a64bc17250ce09ec56e921d6343903943e99ccf63bbf0705e34605'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Autoconf', '2.71'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.36.0'), +] + +preconfigopts = "export PERL='/usr/bin/env perl' && " + +sanity_check_paths = { + 'files': ['bin/aclocal', 'bin/automake'], + 'dirs': [] +} + +sanity_check_commands = [ + "aclocal --help", + "automake --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..80a6cff18b1 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-12.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20220317' # date of the most recent change + +homepage = 'https://autotools.io' + +description = """ + This bundle collect the standard GNU build tools: Autoconf, Automake + and libtool +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +dependencies = [ + ('Autoconf', '2.71'), # 20210128 + ('Automake', '1.16.5'), # 20211003 + ('libtool', '2.4.7'), # 20220317 +] + +# Pure bundle -- no need to specify 'binutils' used when building GCCcore +# toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..249e1aff8db --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.7' + +homepage = 'https://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['04e96c2404ea70c590c546eba4202a4e12722c640016c12b9b2f1ce3d481e9a8'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +sanity_check_paths = { + 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], + 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], +} + +moduleclass = 'lib' From 6dfe21e8c53184fc8f11ee47aee273b7e410ed06 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 18 Oct 2022 15:35:42 +0200 Subject: [PATCH 404/793] adding easyconfigs: Mamba-4.14.0-0.eb --- .../easyconfigs/m/Mamba/Mamba-4.14.0-0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb diff --git a/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb b/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb new file mode 100644 index 00000000000..65373fbe5fb --- /dev/null +++ b/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb @@ -0,0 +1,29 @@ +# author: Caspar van Leeuwen +easyblock = 'EB_Mamba' + +name = 'Mamba' +version = '4.14.0-0' + +homepage = 'https://mamba.readthedocs.io/' +description = """Mamba is a fast, robust, and cross-platform package manager. It runs on Windows, OS X and Linux +(ARM64 and PPC64LE included) and is fully compatible with conda packages and supports most of conda's commands. +""" + +toolchain = SYSTEM + +# Note: Using Mambaforge is the recommended way of installing mamba, +# according to https://mamba.readthedocs.io/en/latest/installation.html +local_name = 'Mambaforge' +source_urls = ['https://github.com/conda-forge/miniforge/releases/download/%(version)s'] +sources = ['{local_name}-%(version)s-Linux-%(arch)s.sh'.format(local_name = local_name)] + +checksums = [ + { + '{local_name}-%(version)s-Linux-x86_64.sh'.format(local_name = local_name): + 'd47b78b593e3cf5513bafbfa6a51eafcd9f0e164c41c79c790061bb583c82859', + '{local_name}-%(version)s-Linux-ppc64le.sh'.format(local_name = local_name): + '607bbd38aa21af4c79a663f2a183a06cca054efdd8d617c17370522504c7be1e', + } +] + +moduleclass = 'lang' From 03ff8e1ea1283f49e94b700ff91fe0701efbbc15 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 18 Oct 2022 16:38:19 +0200 Subject: [PATCH 405/793] Fixed formatting errors --- easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb b/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb index 65373fbe5fb..4abc47f1660 100644 --- a/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb +++ b/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb @@ -15,13 +15,13 @@ toolchain = SYSTEM # according to https://mamba.readthedocs.io/en/latest/installation.html local_name = 'Mambaforge' source_urls = ['https://github.com/conda-forge/miniforge/releases/download/%(version)s'] -sources = ['{local_name}-%(version)s-Linux-%(arch)s.sh'.format(local_name = local_name)] +sources = ['{local_name}-%(version)s-Linux-%(arch)s.sh'.format(local_name=local_name)] checksums = [ { - '{local_name}-%(version)s-Linux-x86_64.sh'.format(local_name = local_name): + '{local_name}-%(version)s-Linux-x86_64.sh'.format(local_name=local_name): 'd47b78b593e3cf5513bafbfa6a51eafcd9f0e164c41c79c790061bb583c82859', - '{local_name}-%(version)s-Linux-ppc64le.sh'.format(local_name = local_name): + '{local_name}-%(version)s-Linux-ppc64le.sh'.format(local_name=local_name): '607bbd38aa21af4c79a663f2a183a06cca054efdd8d617c17370522504c7be1e', } ] From 8297a3a702a631ab1cb0ea68b3146df5ae0a718d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 17:41:45 +0200 Subject: [PATCH 406/793] adding easyconfigs: pkgconf-1.9.3-GCCcore-12.2.0.eb --- .../p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..bd5895c7aa0 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'pkgconf' +version = '1.9.3' + +homepage = 'https://github.com/pkgconf/pkgconf' + +description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries. + It is similar to pkg-config from freedesktop.org.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://distfiles.dereferenced.org/pkgconf/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6d73ac21a9410f5cc636acf730f3a5bf46b28d1e18a239c89efc4b2c5548792f'] + +builddependencies = [('binutils', '2.39')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"] + +sanity_check_paths = { + 'files': ['bin/pkg-config', 'bin/pkgconf'], + 'dirs': [], +} + +sanity_check_commands = [ + "pkg-config --help", + "pkgconf --help", +] + +moduleclass = 'devel' From a0e4239c307dc7b55269558b3b27a7265af51b19 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 17:45:56 +0200 Subject: [PATCH 407/793] {lib}[GCCcore/12.2.0] UCX v1.13.1, numactl v2.0.16 --- .../numactl/numactl-2.0.16-GCCcore-12.2.0.eb | 34 ++++++++++++ .../u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb | 54 +++++++++++++++++++ .../u/UCX/UCX-1.13.1-dynamic_modules.patch | 29 ++++++++++ .../u/UCX/UCX-1.13.1_fix-undeclared-PTR.patch | 27 ++++++++++ 4 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.13.1-dynamic_modules.patch create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.13.1_fix-undeclared-PTR.patch diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d9344685b43 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.16' + +homepage = 'https://github.com/numactl/numactl' + +description = """ + The numactl program allows you to run your application program on specific + cpu's and memory nodes. It does this by supplying a NUMA memory policy to + the operating system before running your program. The libnuma library provides + convenient ways for you to add NUMA memory policies into your own program. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/numactl/numactl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a35c3bdb3efab5c65927e0de5703227760b1101f5e27ab741d8f32b3d5f0a44c'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..bdc002c20df --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.13.1' + +homepage = 'https://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = [ + 'UCX-1.13.1-dynamic_modules.patch', + 'UCX-1.13.1_fix-undeclared-PTR.patch', +] +checksums = [ + {'ucx-1.13.1.tar.gz': 'efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828'}, + {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, + {'UCX-1.13.1_fix-undeclared-PTR.patch': 'ef22c29604552ad3223f2a6bac352f30023cc5cf68f786abfdc4ad7c04189a76'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.3'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('zlib', '1.2.12'), + ('numactl', '2.0.16'), +] + +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --without-go --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.13.1-dynamic_modules.patch b/easybuild/easyconfigs/u/UCX/UCX-1.13.1-dynamic_modules.patch new file mode 100644 index 00000000000..bf0e5564853 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.13.1-dynamic_modules.patch @@ -0,0 +1,29 @@ +# UCX is hardcoded to only load the modules it is compiled with. +# This patch adds an optional EB_UCX_xxx_MODULES that can override this list, allowing new modules to be loaded later. +# Author: micketeer@gmail.com - updated for UCX 1.13.1 by Kenneth Hoste (HPC-UGent) +--- ucx-1.13.1.orig/src/ucs/sys/module.c 2022-09-07 09:16:18.000000000 +0200 ++++ ucx-1.13.1/src/ucs/sys/module.c 2022-10-18 16:29:29.318490689 +0200 +@@ -271,6 +271,8 @@ + char *modules_str; + char *saveptr; + char *module_name; ++ char *env_modules; ++ char buf[64]; + + ucs_module_loader_init_paths(); + +@@ -278,7 +280,13 @@ + ucs_assert(ucs_sys_is_dynamic_lib()); + + ucs_module_debug("loading modules for %s", framework); +- modules_str = ucs_strdup(modules, "modules_list"); ++ ucs_snprintf_safe(buf, sizeof(buf), "EB_UCX_%s_MODULES", framework); ++ env_modules = getenv(buf); ++ if (env_modules != NULL) { ++ modules_str = ucs_strdup(env_modules, "modules_list"); ++ } else { ++ modules_str = ucs_strdup(modules, "modules_list"); ++ } + if (modules_str != NULL) { + saveptr = NULL; + module_name = strtok_r(modules_str, ":", &saveptr); diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.13.1_fix-undeclared-PTR.patch b/easybuild/easyconfigs/u/UCX/UCX-1.13.1_fix-undeclared-PTR.patch new file mode 100644 index 00000000000..4551b62371b --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.13.1_fix-undeclared-PTR.patch @@ -0,0 +1,27 @@ +From 6b6128efd416831cec3a1820f7d1c8e648b79448 Mon Sep 17 00:00:00 2001 +From: Hui Zhou +Date: Sun, 14 Aug 2022 23:29:09 -0500 +Subject: [PATCH] UCS/DEBUG: replace PTR with void * + +The PTR macro is missing on the latest Arch linux. +--- + src/ucs/debug/debug.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/src/ucs/debug/debug.c b/src/ucs/debug/debug.c +index 4ab9a9b7a2a..c51c99ba2b1 100644 +--- a/src/ucs/debug/debug.c ++++ b/src/ucs/debug/debug.c +@@ -272,10 +272,10 @@ static int load_file(struct backtrace_file *file) + goto err_close; + } + +- symcount = bfd_read_minisymbols(file->abfd, 0, (PTR)&file->syms, &size); ++ symcount = bfd_read_minisymbols(file->abfd, 0, (void *)&file->syms, &size); + if (symcount == 0) { + free(file->syms); +- symcount = bfd_read_minisymbols(file->abfd, 1, (PTR)&file->syms, &size); ++ symcount = bfd_read_minisymbols(file->abfd, 1, (void *)&file->syms, &size); + } + if (symcount < 0) { + goto err_close; From 31b2da0662c986d394ce0ec507675f0ec8aeb150 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 17:52:12 +0200 Subject: [PATCH 408/793] {toolchain} intel/2022.09 --- .../h/HPL/HPL-2.3-intel-2022.09.eb | 21 ++++++++++++ .../easyconfigs/i/iimpi/iimpi-2022.09.eb | 18 ++++++++++ .../imkl-FFTW-2022.2.0-iimpi-2022.09.eb | 11 +++++++ easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb | 18 ++++++++++ .../impi-2021.7.0-intel-compilers-2022.2.0.eb | 16 +++++++++ .../intel-compilers-2022.2.0.eb | 33 +++++++++++++++++++ .../easyconfigs/i/intel/intel-2022.09.eb | 22 +++++++++++++ 7 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.09.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2022.09.eb create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.0-iimpi-2022.09.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2022.09.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.09.eb new file mode 100644 index 00000000000..fb7197f51a4 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.09.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2022.09'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2022.09.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2022.09.eb new file mode 100644 index 00000000000..f29ac7e5524 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2022.09.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2022.09' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2022.2.0' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', '2021.7.0', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.0-iimpi-2022.09.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.0-iimpi-2022.09.eb new file mode 100644 index 00000000000..ed5487ee565 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.0-iimpi-2022.09.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2022.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2022.09'} + +dependencies = [('imkl', version, '', SYSTEM)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb new file mode 100644 index 00000000000..82776023871 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb @@ -0,0 +1,18 @@ +name = 'imkl' +version = '2022.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18898/'] +sources = ['l_onemkl_p_%(version)s.8748_offline.sh'] +checksums = ['07d7caedd4b9f025c6fd439a0d2c2f279b18ecbbb63cadb864f6c63c1ed942db'] + +interfaces = False + +installopts = "--download-cache=%(builddir)s/cache --download-dir=%(builddir)s/download --log-dir=%(builddir)s/log" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb new file mode 100644 index 00000000000..8f400fabac4 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb @@ -0,0 +1,16 @@ +name = 'impi' +version = '2021.7.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.0'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18926/'] +sources = ['l_mpi_oneapi_p_%(version)s.8711_offline.sh'] +checksums = ['4eb1e1487b67b98857bc9b7b37bcac4998e0aa6d1b892b2c87b003bf84fb38e9'] + +dependencies = [('UCX', '1.13.1')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb new file mode 100644 index 00000000000..17262278b13 --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb @@ -0,0 +1,33 @@ +name = 'intel-compilers' +version = '2022.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18849/'], + 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.8772_offline.sh', + }, + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18909/'], + 'filename': 'l_fortran-compiler_p_%(version)s.8773_offline.sh', + }, +] +checksums = [ + {'l_dpcpp-cpp-compiler_p_2022.2.0.8772_offline.sh': + '8ca97f7ea8abf7876df6e10ce2789ea8cbc310c100ad7bf0b5ffccc4f3c7f2c9'}, + {'l_fortran-compiler_p_2022.2.0.8773_offline.sh': + '4054e4bf5146d55638d21612396a19ea623d22cbb8ac63c0a7150773541e0311'}, +] + +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/intel/intel-2022.09.eb b/easybuild/easyconfigs/i/intel/intel-2022.09.eb new file mode 100644 index 00000000000..8e5967bdb58 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2022.09.eb @@ -0,0 +1,22 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2022.09' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2022.2.0' +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', '2021.7.0', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', SYSTEM), + ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From e2c9ce8d712e1ea47b837298d4d047b921dbabb3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 18:27:44 +0200 Subject: [PATCH 409/793] adding easyconfigs: CDBtools-0.99-GCC-10.2.0.eb --- .../c/CDBtools/CDBtools-0.99-GCC-10.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-10.2.0.eb new file mode 100644 index 00000000000..11fc1a9fd9c --- /dev/null +++ b/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'CDBtools' +version = '0.99' + +homepage = 'http://compbio.dfci.harvard.edu/tgi' +description = "CDB (Constant DataBase) indexing and retrieval tools for FASTA files" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/cdbfasta'] +sources = [{'download_filename': 'cdbfasta.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c'] + +buildopts = 'CC="$CXX" DBGFLAGS="$CXXFLAGS"' + +files_to_copy = [(['cdbfasta', 'cdbyank'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/cdbfasta', 'bin/cdbyank'], + 'dirs': [], +} + +sanity_check_commands = [ + "cdbfasta -v", + "cdbyank -v", +] + +moduleclass = 'bio' From adb81d77b0d1f6606407cdbf5d16c71228326ae8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Oct 2022 08:52:14 +0200 Subject: [PATCH 410/793] adding easyconfigs: AMAPVox-1.9.4-Java-11.eb --- .../a/AMAPVox/AMAPVox-1.9.4-Java-11.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMAPVox/AMAPVox-1.9.4-Java-11.eb diff --git a/easybuild/easyconfigs/a/AMAPVox/AMAPVox-1.9.4-Java-11.eb b/easybuild/easyconfigs/a/AMAPVox/AMAPVox-1.9.4-Java-11.eb new file mode 100644 index 00000000000..af51c0503ca --- /dev/null +++ b/easybuild/easyconfigs/a/AMAPVox/AMAPVox-1.9.4-Java-11.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'AMAPVox' +version = '1.9.4' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://amap-dev.cirad.fr/projects/amapvox' +description = "LiDAR data voxelisation software" + +toolchain = SYSTEM + +source_urls = ['http://amap-dev.cirad.fr/attachments/download/1916/'] +sources = ['AMAPVox-%(version)s.zip'] +checksums = ['6d3e65fbd17a8e3a45962f5d1ce60a58ad0bfd899fa704dc172f2819fc309b74'] + +dependencies = [('Java', '11')] + +postinstallcmds = ["chmod a+x %(installdir)s/AMAPVox.sh"] + +sanity_check_paths = { + 'files': ['AMAPVox.sh', 'AMAPVox-1.9.4.jar'], + 'dirs': ['lib'], +} + +sanity_check_commands = ["AMAPVox.sh -h"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'data' From edf648109147b06ac9c55135c3ec21bb89cb3f25 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Oct 2022 08:57:02 +0200 Subject: [PATCH 411/793] drop explicit easyblock specification in Mamba easyconfig (derived from name by default) + add checksum for aarch64 installer --- easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb b/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb index 4abc47f1660..aad49d0ae6b 100644 --- a/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb +++ b/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb @@ -1,6 +1,4 @@ # author: Caspar van Leeuwen -easyblock = 'EB_Mamba' - name = 'Mamba' version = '4.14.0-0' @@ -16,13 +14,14 @@ toolchain = SYSTEM local_name = 'Mambaforge' source_urls = ['https://github.com/conda-forge/miniforge/releases/download/%(version)s'] sources = ['{local_name}-%(version)s-Linux-%(arch)s.sh'.format(local_name=local_name)] - checksums = [ { - '{local_name}-%(version)s-Linux-x86_64.sh'.format(local_name=local_name): - 'd47b78b593e3cf5513bafbfa6a51eafcd9f0e164c41c79c790061bb583c82859', + '{local_name}-%(version)s-Linux-aarch64.sh'.format(local_name=local_name): + '37221b8d818951fab125c0bfb6cc6e83dac059f66892d2544a83192828d8e2c4', '{local_name}-%(version)s-Linux-ppc64le.sh'.format(local_name=local_name): '607bbd38aa21af4c79a663f2a183a06cca054efdd8d617c17370522504c7be1e', + '{local_name}-%(version)s-Linux-x86_64.sh'.format(local_name=local_name): + 'd47b78b593e3cf5513bafbfa6a51eafcd9f0e164c41c79c790061bb583c82859', } ] From f85a4f85f84eeead0789f46416df0c627c57f132 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Oct 2022 08:59:18 +0200 Subject: [PATCH 412/793] add AMAPVox extension to R v4.2.1 --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index b97f484e225..49b9a97d1a0 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3355,6 +3355,9 @@ exts_list = [ ('rtdists', '0.11-5', { 'checksums': ['97cf2ea758aa02b1dfaeef5032c6e50570777552aa771ed9a86df048b7871eed'], }), + ('AMAPVox', '0.12.0', { + 'checksums': ['b30fefef8661e27ffe3883665204b623eda2143dbcd3084a1d5810f8ea834c85'], + }), ] moduleclass = 'lang' From de9e295548ff7663079328caae55e70ba02cdd51 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Wed, 19 Oct 2022 09:16:31 +0200 Subject: [PATCH 413/793] added sanity_pip_check and download_dep_fail --- easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb index 122b155d477..1d9f666570f 100644 --- a/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb +++ b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb @@ -17,7 +17,11 @@ dependencies = [ ('Graphviz', '2.50.0'), ] +download_dep_fail = True + use_pip = True +sanity_pip_check = True + sanity_check_commands = ["python -c 'import ruffus.graph'"] From 72425460ca636b8f1f71f2c30319937e95651d2f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 19 Oct 2022 11:34:56 +0200 Subject: [PATCH 414/793] adding easyconfigs: jq-1.6-GCCcore-11.2.0.eb, jq-1.6-GCCcore-11.3.0.eb, jq-1.6-GCCcore-12.2.0.eb --- .../easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb | 31 +++++++++++++++++++ .../easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb | 31 +++++++++++++++++++ .../easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb | 31 +++++++++++++++++++ 3 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..e02bc430983 --- /dev/null +++ b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'jq' +version = '1.6' + +homepage = 'https://stedolan.github.io/jq/' +description = """jq is a lightweight and flexible command-line JSON processor.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/stedolan/jq/releases/download/jq-%(version)s'] +sources = ['jq-%(version)s.tar.gz'] +checksums = ['5de8c8e29aaa3fb9cc6b47bb27299f271354ebb72514e3accadc7d38b5bbaa72'] + +builddependencies = [ + ('binutils', '2.37'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), + ('Autotools', '20210726'), +] + +preconfigopts = "autoreconf -fi && " + +configopts = '--with-oniguruma=builtin' + +sanity_check_paths = { + 'files': ['bin/jq'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e70d4d8080f --- /dev/null +++ b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'jq' +version = '1.6' + +homepage = 'https://stedolan.github.io/jq/' +description = """jq is a lightweight and flexible command-line JSON processor.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/stedolan/jq/releases/download/jq-%(version)s'] +sources = ['jq-%(version)s.tar.gz'] +checksums = ['5de8c8e29aaa3fb9cc6b47bb27299f271354ebb72514e3accadc7d38b5bbaa72'] + +builddependencies = [ + ('binutils', '2.38'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Autotools', '20220317'), +] + +preconfigopts = "autoreconf -fi && " + +configopts = '--with-oniguruma=builtin' + +sanity_check_paths = { + 'files': ['bin/jq'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..6fd2d201102 --- /dev/null +++ b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'jq' +version = '1.6' + +homepage = 'https://stedolan.github.io/jq/' +description = """jq is a lightweight and flexible command-line JSON processor.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/stedolan/jq/releases/download/jq-%(version)s'] +sources = ['jq-%(version)s.tar.gz'] +checksums = ['5de8c8e29aaa3fb9cc6b47bb27299f271354ebb72514e3accadc7d38b5bbaa72'] + +builddependencies = [ + ('binutils', '2.39'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Autotools', '20220317'), +] + +preconfigopts = "autoreconf -fi && " + +configopts = '--with-oniguruma=builtin' + +sanity_check_paths = { + 'files': ['bin/jq'], + 'dirs': [], +} + +moduleclass = 'tools' From 047f5028ebb35ea4a7ee64ce5ebe0ec81ee09873 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Oct 2022 13:13:58 +0200 Subject: [PATCH 415/793] adding easyconfigs: Nextflow-22.10.0.eb --- .../n/Nextflow/Nextflow-22.10.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.0.eb diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.0.eb new file mode 100644 index 00000000000..70231eabec8 --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CmdCp' + +name = 'Nextflow' +version = '22.10.0' + +homepage = 'https://www.nextflow.io' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/%(namelower)s-io/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7eceff3e32bd1bcd09744890501456e0a2b5448916fb25f3e6a8f338a239af8b'] + +# specify dependency on Java/11 "wrapper", rather than a specific Java version +dependencies = [('Java', '11', '', SYSTEM)] + +skipsteps = ['configure', 'build'] + +_exe_files = ['%(namelower)s', 'gradlew'] + +files_to_copy = [ + (_exe_files, '%(installdir)s/bin'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [ + "%(namelower)s -v", + "%(namelower)s help", +] + +moduleclass = 'tools' From c0c71387faa66ba04eaefc506d0ff61ef80d16ce Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 19 Oct 2022 16:04:05 +0200 Subject: [PATCH 416/793] Update easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb index e02bc430983..4f44b8686e1 100644 --- a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb @@ -28,4 +28,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['jq --help', 'jq --version'] + moduleclass = 'tools' From 91865347b77ae3dc2b7041bd2c674bb1c8820a09 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 19 Oct 2022 16:04:12 +0200 Subject: [PATCH 417/793] Update easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb index e70d4d8080f..06922fad5b8 100644 --- a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb @@ -28,4 +28,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['jq --help', 'jq --version'] + moduleclass = 'tools' From 3afe1287da9feda33d1c288ff24f9b26269a44b7 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 19 Oct 2022 16:04:18 +0200 Subject: [PATCH 418/793] Update easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb index 6fd2d201102..8ffe5702c24 100644 --- a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb @@ -28,4 +28,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['jq --help', 'jq --version'] + moduleclass = 'tools' From 0cd66fd8614e50df8389ad31436706564b755021 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Wed, 19 Oct 2022 16:39:37 +0200 Subject: [PATCH 419/793] adding easyconfigs: python-telegram-bot-20.0a0-GCCcore-10.2.0.eb --- ...thon-telegram-bot-20.0a0-GCCcore-10.2.0.eb | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..925a1086d5a --- /dev/null +++ b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb @@ -0,0 +1,97 @@ +easyblock = 'PythonBundle' + +name = 'python-telegram-bot' +version = '20.0a0' + +homepage = 'https://python-telegram-bot.org/' +description = """This library provides a pure Python, asynchronous interface for the Telegram Bot API. + It's compatible with Python versions 3.7+.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('APScheduler', '3.9.1', { + 'checksums': ['65e6574b6395498d371d045f2a8a7e4f7d50c6ad21ef7313d15b1c7cf20df1e3'], + }), + ('anyio', '3.6.2', { + 'checksums': ['25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421'], + }), + ('backports.zoneinfo', '0.2.1', { + 'checksums': ['fadbfe37f74051d024037f223b8e001611eac868b5c5b06144ef4d8b799862f2'], + }), + ('cachetools', '5.0.0', { + 'checksums': ['486471dfa8799eb7ec503a8059e263db000cdda20075ce5e48903087f79d5fd6'], + }), + ('certifi', '2022.9.24', { + 'checksums': ['0d9c601124e5a6ba9712dbc60d9c53c21e34f5f641fe83002317394311bdce14'], + }), + ('charset-normalizer', '2.1.1', { + 'checksums': ['5a3d016c7c547f69d6f81fb0db9449ce888b418b5b9952cc5e6e66843e9dd845'], + }), + ('flit_core', '3.7.1', { + 'checksums': ['14955af340c43035dbfa96b5ee47407e377ee337f69e70f73064940d27d0a44f'], + }), + ('h11', '0.12.0', { + 'checksums': ['47222cb6067e4a307d535814917cd98fd0a57b6788ce715755fa2b6c28b56042'], + }), + ('httpcore', '0.14.7', { + 'checksums': ['7503ec1c0f559066e7e39bc4003fd2ce023d01cf51793e3c173b864eb456ead1'], + }), + ('httpx', '0.22.0', { + 'checksums': ['d8e778f76d9bbd46af49e7f062467e3157a5a3d2ae4876a4bbfd8a51ed9c9cb4'], + }), + ('idna', '3.4', { + 'checksums': ['814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4'], + }), + ('pytz_deprecation_shim', '0.1.0.post0', { + 'checksums': ['af097bae1b616dde5c5744441e2ddc69e74dfdcb0c263129610d85b87445a59d'], + }), + ('pytz', '2022.4', { + 'checksums': ['48ce799d83b6f8aab2020e369b627446696619e79645419610b9facd909b3174'], + }), + ('requests', '2.28.1', { + 'checksums': ['7c5599b102feddaa661c826c56ab4fee28bfd17f5abca1ebbe3e7f19d7c97983'], + }), + ('rfc3986', '1.5.0', { + 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], + }), + ('ruffus', '2.8.4', { + 'checksums': ['6cd3d96e459a1aedcc10341f14fddedfdc13664551757fcd429a241de63826aa'], + }), + ('setuptools', '65.5.0', { + 'checksums': ['512e5536220e38146176efb833d4a62aa726b7bbff82cfbc8ba9eaa3996e0b17'], + }), + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + ('tzdata', '2022.5', { + 'checksums': ['e15b2b3005e2546108af42a0eb4ccab4d9e225e2dfbf4f77aad50c70a4b1f3ab'], + }), + ('tzlocal', '4.2', { + 'checksums': ['ee5842fa3a795f023514ac2d801c4a81d1743bbe642e3940143326b3a00addd7'], + }), + (name, version, { + 'modulename': 'telegram', + 'checksums': ['a182a3d081071f1ea34833bc68ed7d0843c1fe0d6dca1d260a0e2d253b150f71'], + }), +] + +sanity_check_commands = [ + "python -c 'from telegram import Update'", + "python -c 'from telegram.ext import ApplicationBuilder, CommandHandler, ContextTypes'", +] + +moduleclass = 'lib' From af51ab97117abc587762627c3af87e1b4a72b4b7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 19 Oct 2022 16:47:08 +0200 Subject: [PATCH 420/793] adding easyconfigs: LIBSVM-3.30-GCCcore-11.3.0.eb and patches: LIBSVM-3.30_add_namespace_for_benefit_of_Xmipp.patch --- .../l/LIBSVM/LIBSVM-3.30-GCCcore-11.3.0.eb | 43 ++++++++++ ...0_add_namespace_for_benefit_of_Xmipp.patch | 83 +++++++++++++++++++ 2 files changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30_add_namespace_for_benefit_of_Xmipp.patch diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d58a61173b8 --- /dev/null +++ b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MakeCp' + +name = 'LIBSVM' +version = '3.30' + +homepage = 'https://www.csie.ntu.edu.tw/~cjlin/libsvm/' +description = """LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression + (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'cjlin1' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%s.tar.gz' % version.replace('.', '')] +patches = [ + 'LIBSVM-3.23_shared_lib.patch', + 'LIBSVM-3.30_add_namespace_for_benefit_of_Xmipp.patch', +] +checksums = [ + {'v330.tar.gz': 'e4fe41308c87cc210aec73e4f5f0fb4da14234d90e7a131763fbad3788ca2d80'}, + {'LIBSVM-3.23_shared_lib.patch': 'c0ede89365949644f5d7f11382a3f176fd76317c7f5ae5769226ff7c3a801fe6'}, + {'LIBSVM-3.30_add_namespace_for_benefit_of_Xmipp.patch': + 'f51e4d0b6899041799f43a09aad1e3711a93615a8cc453243042ed8357cabb28'}, +] + +dependencies = [('binutils', '2.38')] + +local_bins = ['svm-%s' % x for x in ['predict', 'scale', 'train']] + +files_to_copy = [ + (local_bins, 'bin'), + (['svm.o'], 'lib'), + (['libsvm*'], 'lib'), + (['svm.h'], 'include/libsvm'), + 'tools' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins] + ['lib/libsvm.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30_add_namespace_for_benefit_of_Xmipp.patch b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30_add_namespace_for_benefit_of_Xmipp.patch new file mode 100644 index 00000000000..d79d00d78a0 --- /dev/null +++ b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30_add_namespace_for_benefit_of_Xmipp.patch @@ -0,0 +1,83 @@ +Taken from https://github.com/cossorzano/libsvm which Xmipp uses. + +Also added "using namespace libsvm" to svm-train.c and svm-predict.c + +Åke Sandgren 2022-10-19 + +commit 2a0db2ec1330db8cd45bf5ba7d55d850ce5c8318 +Author: Carlos Oscar Sorzano +Date: Fri Nov 5 13:37:31 2021 +0100 + + Namespace added + +diff --git a/svm.cpp b/svm.cpp +index fa44818..814b1b6 100644 +--- a/svm.cpp ++++ b/svm.cpp +@@ -1,3 +1,7 @@ ++/* This file has been taken from LibSVM 3.25 */ ++/* Authors: Chih-Chung Chang and Chih-Jen Lin, LIBSVM :*/ ++/* Software available at http://www.csie.ntu.edu.tw/~cjlin/libsvm */ ++ + #include + #include + #include +@@ -8,6 +12,8 @@ + #include + #include + #include "svm.h" ++using namespace libsvm; ++ + int libsvm_version = LIBSVM_VERSION; + typedef float Qfloat; + typedef signed char schar; +diff --git a/svm.h b/svm.h +index 5dfc1f7..ba47063 100644 +--- a/svm.h ++++ b/svm.h +@@ -1,3 +1,7 @@ ++/* This file has been taken from LibSVM 3.25 */ ++/* Authors: Chih-Chung Chang and Chih-Jen Lin, LIBSVM : */ ++/* Software available at http://www.csie.ntu.edu.tw/~cjlin/libsvm */ ++ + #ifndef _LIBSVM_H + #define _LIBSVM_H + +@@ -22,8 +26,10 @@ struct svm_problem + struct svm_node **x; + }; + +-enum { C_SVC, NU_SVC, ONE_CLASS, EPSILON_SVR, NU_SVR }; /* svm_type */ +-enum { LINEAR, POLY, RBF, SIGMOID, PRECOMPUTED }; /* kernel_type */ ++namespace libsvm { ++ enum { C_SVC, NU_SVC, ONE_CLASS, EPSILON_SVR, NU_SVR }; /* svm_type */ ++ enum { LINEAR, POLY, RBF, SIGMOID, PRECOMPUTED }; /* kernel_type */ ++} + + struct svm_parameter + { +diff --git a/svm-train.c b/svm-train.c +index b6ce987..064c29b 100644 +--- a/svm-train.c ++++ b/svm-train.c +@@ -4,6 +4,8 @@ + #include + #include + #include "svm.h" ++using namespace libsvm; ++ + #define Malloc(type,n) (type *)malloc((n)*sizeof(type)) + + void print_null(const char *s) {} +diff --git a/svm-predict.c b/svm-predict.c +index 7a0fa15..328f815 100644 +--- a/svm-predict.c ++++ b/svm-predict.c +@@ -4,6 +4,7 @@ + #include + #include + #include "svm.h" ++using namespace libsvm; + + int print_null(const char *s,...) {return 0;} + From 13b10372e9ce58d1d5abf4cc937c6bd79e7ee0b1 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Wed, 19 Oct 2022 16:55:57 +0200 Subject: [PATCH 421/793] added binutils as builddependency --- .../python-telegram-bot-20.0a0-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb index 925a1086d5a..f98289dd3bc 100644 --- a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb @@ -13,6 +13,8 @@ dependencies = [ ('Python', '3.8.6'), ] +builddependencies = [('binutils', '2.35')] + use_pip = True sanity_pip_check = True From 8ace4ccbeb4496bec7f411ee8ac74d4f8700abb2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Oct 2022 20:23:10 +0200 Subject: [PATCH 422/793] Apply suggestions from code review don't hardcode version in sanity_check_paths for AMAPVox + use SOURCE_ZIP template in sources Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/a/AMAPVox/AMAPVox-1.9.4-Java-11.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AMAPVox/AMAPVox-1.9.4-Java-11.eb b/easybuild/easyconfigs/a/AMAPVox/AMAPVox-1.9.4-Java-11.eb index af51c0503ca..d0d5c54fd5e 100644 --- a/easybuild/easyconfigs/a/AMAPVox/AMAPVox-1.9.4-Java-11.eb +++ b/easybuild/easyconfigs/a/AMAPVox/AMAPVox-1.9.4-Java-11.eb @@ -10,7 +10,7 @@ description = "LiDAR data voxelisation software" toolchain = SYSTEM source_urls = ['http://amap-dev.cirad.fr/attachments/download/1916/'] -sources = ['AMAPVox-%(version)s.zip'] +sources = [SOURCE_ZIP] checksums = ['6d3e65fbd17a8e3a45962f5d1ce60a58ad0bfd899fa704dc172f2819fc309b74'] dependencies = [('Java', '11')] @@ -18,7 +18,7 @@ dependencies = [('Java', '11')] postinstallcmds = ["chmod a+x %(installdir)s/AMAPVox.sh"] sanity_check_paths = { - 'files': ['AMAPVox.sh', 'AMAPVox-1.9.4.jar'], + 'files': ['AMAPVox.sh', 'AMAPVox-%(version)s.jar'], 'dirs': ['lib'], } From dca1c0e2cbc9fcb628ec070b71c6e48f3b0731fa Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 19 Oct 2022 21:34:44 +0200 Subject: [PATCH 423/793] adding easyconfigs: archspec-0.1.4-GCCcore-11.3.0.eb --- .../archspec/archspec-0.1.4-GCCcore-11.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/archspec/archspec-0.1.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.1.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.1.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..710f53f822e --- /dev/null +++ b/easybuild/easyconfigs/a/archspec/archspec-0.1.4-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'archspec' +version = '0.1.4' + +homepage = 'https://github.com/archspec/archspec' +description = "A library for detecting, labeling, and reasoning about microarchitectures" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b8d5eeb4caf892790ff1aa8ccef442a84187986aeab4da29417c9fe35532d94c'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] + +moduleclass = 'tools' From 314650e894a8b06fab1448e9b54fb31a5f600db8 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Thu, 20 Oct 2022 07:06:39 +0200 Subject: [PATCH 424/793] removed ruffus as dependency --- .../python-telegram-bot-20.0a0-GCCcore-10.2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb index f98289dd3bc..34c1581e97c 100644 --- a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb @@ -64,9 +64,6 @@ exts_list = [ ('rfc3986', '1.5.0', { 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], }), - ('ruffus', '2.8.4', { - 'checksums': ['6cd3d96e459a1aedcc10341f14fddedfdc13664551757fcd429a241de63826aa'], - }), ('setuptools', '65.5.0', { 'checksums': ['512e5536220e38146176efb833d4a62aa726b7bbff82cfbc8ba9eaa3996e0b17'], }), From 47ac220bd54bdf003b4e7530393d8f3d5203bc98 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Thu, 20 Oct 2022 09:55:25 +0200 Subject: [PATCH 425/793] removed unnecessary dependencies --- .../python-telegram-bot-20.0a0-GCCcore-10.2.0.eb | 13 +------------ 1 file changed, 1 insertion(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb index 34c1581e97c..dfb7a16b6ba 100644 --- a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb @@ -31,9 +31,6 @@ exts_list = [ ('cachetools', '5.0.0', { 'checksums': ['486471dfa8799eb7ec503a8059e263db000cdda20075ce5e48903087f79d5fd6'], }), - ('certifi', '2022.9.24', { - 'checksums': ['0d9c601124e5a6ba9712dbc60d9c53c21e34f5f641fe83002317394311bdce14'], - }), ('charset-normalizer', '2.1.1', { 'checksums': ['5a3d016c7c547f69d6f81fb0db9449ce888b418b5b9952cc5e6e66843e9dd845'], }), @@ -55,21 +52,13 @@ exts_list = [ ('pytz_deprecation_shim', '0.1.0.post0', { 'checksums': ['af097bae1b616dde5c5744441e2ddc69e74dfdcb0c263129610d85b87445a59d'], }), - ('pytz', '2022.4', { - 'checksums': ['48ce799d83b6f8aab2020e369b627446696619e79645419610b9facd909b3174'], - }), + # to overwrite Python's requests requirement which requires older version of idna ('requests', '2.28.1', { 'checksums': ['7c5599b102feddaa661c826c56ab4fee28bfd17f5abca1ebbe3e7f19d7c97983'], }), ('rfc3986', '1.5.0', { 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], }), - ('setuptools', '65.5.0', { - 'checksums': ['512e5536220e38146176efb833d4a62aa726b7bbff82cfbc8ba9eaa3996e0b17'], - }), - ('six', '1.16.0', { - 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], - }), ('sniffio', '1.3.0', { 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], }), From 37d77d518b1a4dc9e2d40d894900a1198d8c8f54 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 10:35:49 +0200 Subject: [PATCH 426/793] adding easyconfigs: pyWannier90-2021-12-07-foss-2021a.eb --- .../pyWannier90-2021-12-07-foss-2021a.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb new file mode 100644 index 00000000000..ec32ef804a9 --- /dev/null +++ b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb @@ -0,0 +1,76 @@ +easyblock = 'MakeCp' + +name = 'pyWannier90' +local_commit = '8354e91' +version = '2021-12-07' + +homepage = 'https://github.com/hungpham2017/pyWannier90' +description = "A Wannier90 Python interface for VASP and PySCF" + +toolchain = {'name': 'foss', 'version': '2021a'} + +local_wannier90_version = '3.1.0' + +sources = [ + { + 'source_urls': ['https://github.com/hungpham2017/pyWannier90/archive/'], + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ + }, + { + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'], + 'download_filename': 'v%s.tar.gz' % local_wannier90_version, + 'filename': 'Wannier90-%s.tar.gz' % local_wannier90_version, + }, +] +checksums = [ + {'pyWannier90-2021-12-07.tar.gz': '27233891fe39e0f45914dfa756b28319ebd4c3b5ec2124f4c9d1d3816fc0887e'}, + {'Wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'}, +] + +builddependencies = [ + ('pybind11', '2.6.2'), +] + +local_pymaj = '3' +local_pymin = '9' +local_pymajmin = local_pymaj + local_pymin + +dependencies = [ + ('Python', '%s.%s.5' % (local_pymaj, local_pymin)), + ('SciPy-bundle', '2021.05'), + ('PySCF', '1.7.6'), +] + +local_wannier90_make = 'make -j %(parallel)s F90="$F90" FCOPTS="$FFLAGS -fPIC" LDOPTS="$FFLAGS" ' +local_wannier90_make += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK"' + +prebuildopts = "cd %%(builddir)s/wannier90-%s && touch make.inc && " % local_wannier90_version +prebuildopts += "cp %(builddir)s/pyWannier90-*/src/wannier_lib.F90 src/wannier_lib.F90 && " +prebuildopts += local_wannier90_make + " && " +prebuildopts += local_wannier90_make + " lib && " +prebuildopts += "cd %(builddir)s/pyWannier90-*/src && pwd && " + +buildopts = 'CPP="$CXX" LIBS="-L%%(builddir)s/wannier90-%s $LIBLAPACK -lwannier" ' % local_wannier90_version +# with Intel compilers, use libwannier90_intel as make target +# with GCC compilers, use libwannier90_gf as make target +buildopts += "libwannier90_gf && " +buildopts += """sed -i "s@W90LIB = .*@W90LIB = '%(installdir)s'@g" pywannier90.py""" + +files_to_copy = [ + (['src/pywannier90.py', 'src/libwannier90.*.%s' % SHLIB_EXT], 'lib/python%(pyshortver)s/site-packages'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import libwannier90'", + "python -c 'import pywannier90'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' From 85dbd36904fe1f0ee5709fdd5df2292c27c42c73 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 10:40:38 +0200 Subject: [PATCH 427/793] adding easyconfigs: SciPy-bundle-2021.05-gomkl-2021a.eb --- .../SciPy-bundle-2021.05-gomkl-2021a.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb new file mode 100644 index 00000000000..89b95c194e8 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2021.05' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'gomkl', 'version': '2021a'} +toolchainopts = {'pic': True, 'lowopt': True, 'strict': True} + +builddependencies = [('hypothesis', '6.13.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('pybind11', '2.6.2'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.20.3', { + 'patches': [ + 'numpy-1.18.2-mkl.patch', + 'numpy-1.20.3_disable-broken-override-test.patch', + 'numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch', + 'numpy-1.20.3_fix-target-test-ccompiler-opt.patch', + 'numpy-1.20.3_disable_fortran_callback_test.patch', + ], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': [ + 'e55185e51b18d788e49fe8305fd73ef4470596b33fc2c1ceb304566b99c71a69', # numpy-1.20.3.zip + 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch + # numpy-1.20.3_disable-broken-override-test.patch + '43cc2e675c52db1776efcc6c84ebd5fc008b48e6355c81087420d5e790e4af9b', + # numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch + '4c0b194c9d2e2c6b9798ebc271d4517f4c3cdbf2b3cbd68de16c7d4b068bb046', + # numpy-1.20.3_fix-target-test-ccompiler-opt.patch + '3d84e8b7d48387778974a5f6ae342a690ab5989547206b6add9d9667f8d7572a', + # numpy-1.20.3_disable_fortran_callback_test.patch + '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + ], + }), + ('scipy', '1.6.3', { + 'checksums': ['a75b014d3294fce26852a9d04ea27b5671d86736beb34acdfc05859246260707'], + }), + ('mpi4py', '3.0.3', { + 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], + }), + ('numexpr', '2.7.3', { + 'checksums': ['43616529f9b7d1afc83386f943dc66c4da5e052f00217ba7e3ad8dd1b5f3a825'], + }), + ('Bottleneck', '1.3.2', { + 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], + }), + ('pandas', '1.2.4', { + 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'checksums': ['649ecab692fade3cbfcf967ff936496b0cfba0af00a55dfaacd82bdda5cb2279'], + }), + ('mpmath', '1.2.1', { + 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' From 67f9f8c3fdd341ecc78eb28dfe00497a08271dc7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 11:14:45 +0200 Subject: [PATCH 428/793] {chem}[gomkl/2021a] pyWannier90 v2021-12-07, PySCF v1.7.6, h5py v3.2.1, libcint v4.4.0 w/ Python 3.9.5 --- .../h/h5py/h5py-3.2.1-gomkl-2021a.eb | 34 +++++++++ .../l/libcint/libcint-4.4.0-gomkl-2021a.eb | 39 ++++++++++ .../p/PySCF/PySCF-1.7.6-gomkl-2021a.eb | 45 +++++++++++ .../pyWannier90-2021-12-07-gomkl-2021a.eb | 76 +++++++++++++++++++ 4 files changed, 194 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-3.2.1-gomkl-2021a.eb create mode 100644 easybuild/easyconfigs/l/libcint/libcint-4.4.0-gomkl-2021a.eb create mode 100644 easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-gomkl-2021a.eb create mode 100644 easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.2.1-gomkl-2021a.eb b/easybuild/easyconfigs/h/h5py/h5py-3.2.1-gomkl-2021a.eb new file mode 100644 index 00000000000..a21aff6972d --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-3.2.1-gomkl-2021a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '3.2.1' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'gomkl', 'version': '2021a'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['89474be911bfcdb34cbf0d98b8ec48b578c27a89fdb1ae4ee7513f1ef8d9249e'] + +builddependencies = [('pkgconfig', '1.5.4', '-python')] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('HDF5', '1.10.7'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libcint/libcint-4.4.0-gomkl-2021a.eb b/easybuild/easyconfigs/l/libcint/libcint-4.4.0-gomkl-2021a.eb new file mode 100644 index 00000000000..8dc84fd9e8f --- /dev/null +++ b/easybuild/easyconfigs/l/libcint/libcint-4.4.0-gomkl-2021a.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'libcint' +version = '4.4.0' + +homepage = 'https://github.com/sunqm/libcint' +description = """libcint is an open source library for analytical Gaussian integrals.""" + +toolchain = {'name': 'gomkl', 'version': '2021a'} + +source_urls = ['https://github.com/sunqm/libcint/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_remove_pyscftest.patch'] +checksums = [ + '39a831e9131395e7ac312608981495aed3e44d0511b0700b2a1fb163b32c89c1', # v4.4.0.tar.gz + '6449297a6aee30fef3d6a268aa892dea8dd5c3ca9669a50ae694ab9bcf17842d', # libcint-4.4.0_remove_pyscftest.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + # Python with numpy only required for 'make test' + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +separate_build_dir = False # Must use the same directory for tests + +configopts = '-DWITH_RANGE_COULOMB=on -DWITH_COULOMB_ERF=on -DWITH_F12=on -DENABLE_TEST=on' + +buildopts = "VERBOSE=1" + +runtest = 'test ' + +sanity_check_paths = { + 'files': ['include/cint.h', 'lib/libcint.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-gomkl-2021a.eb b/easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-gomkl-2021a.eb new file mode 100644 index 00000000000..cf0c6a26ccc --- /dev/null +++ b/easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-gomkl-2021a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMakeCp' + +name = 'PySCF' +version = '1.7.6' + +homepage = 'http://www.pyscf.org' +description = "PySCF is an open-source collection of electronic structure modules powered by Python." + +toolchain = {'name': 'gomkl', 'version': '2021a'} + +source_urls = ['https://github.com/pyscf/pyscf/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1805819557cf78fb5938a2141a429c74dabb3ba664b60420032584d7a876c2ab'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # for numpy, scipy + ('h5py', '3.2.1'), + ('libcint', '4.4.0'), + ('libxc', '5.1.5'), + ('XCFun', '2.1.1'), +] + +start_dir = 'pyscf/lib' + +separate_build_dir = True + +configopts = "-DBUILD_LIBCINT=OFF -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF" + +prebuildopts = "export PYSCF_INC_DIR=$EBROOTQCINT/include:$EBROOTLIBXC/lib && " + +files_to_copy = ['pyscf'] + +sanity_check_paths = { + 'files': ['pyscf/__init__.py'], + 'dirs': ['pyscf/data', 'pyscf/lib'], +} + +sanity_check_commands = ["python -c 'import pyscf'"] + +modextrapaths = {'PYTHONPATH': ''} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb new file mode 100644 index 00000000000..2a045c216cc --- /dev/null +++ b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb @@ -0,0 +1,76 @@ +easyblock = 'MakeCp' + +name = 'pyWannier90' +local_commit = '8354e91' +version = '2021-12-07' + +homepage = 'https://github.com/hungpham2017/pyWannier90' +description = "A Wannier90 Python interface for VASP and PySCF" + +toolchain = {'name': 'gomkl', 'version': '2021a'} + +local_wannier90_version = '3.1.0' + +sources = [ + { + 'source_urls': ['https://github.com/hungpham2017/pyWannier90/archive/'], + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ + }, + { + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'], + 'download_filename': 'v%s.tar.gz' % local_wannier90_version, + 'filename': 'Wannier90-%s.tar.gz' % local_wannier90_version, + }, +] +checksums = [ + {'pyWannier90-2021-12-07.tar.gz': '27233891fe39e0f45914dfa756b28319ebd4c3b5ec2124f4c9d1d3816fc0887e'}, + {'Wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'}, +] + +builddependencies = [ + ('pybind11', '2.6.2'), +] + +local_pymaj = '3' +local_pymin = '9' +local_pymajmin = local_pymaj + local_pymin + +dependencies = [ + ('Python', '%s.%s.5' % (local_pymaj, local_pymin)), + ('SciPy-bundle', '2021.05'), + ('PySCF', '1.7.6'), +] + +local_wannier90_make = 'make -j %(parallel)s F90="$F90" FCOPTS="$FFLAGS -fPIC" LDOPTS="$FFLAGS" ' +local_wannier90_make += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK"' + +prebuildopts = "cd %%(builddir)s/wannier90-%s && touch make.inc && " % local_wannier90_version +prebuildopts += "cp %(builddir)s/pyWannier90-*/src/wannier_lib.F90 src/wannier_lib.F90 && " +prebuildopts += local_wannier90_make + " && " +prebuildopts += local_wannier90_make + " lib && " +prebuildopts += "cd %(builddir)s/pyWannier90-*/src && pwd && " + +buildopts = 'CPP="$CXX" LIBS="-L%%(builddir)s/wannier90-%s $LIBLAPACK -lwannier" ' % local_wannier90_version +# with Intel compilers, use libwannier90_intel as make target +# with GCC compilers, use libwannier90_gf as make target +buildopts += "libwannier90_gf && " +buildopts += """sed -i "s@W90LIB = .*@W90LIB = '%(installdir)s'@g" pywannier90.py""" + +files_to_copy = [ + (['src/pywannier90.py', 'src/libwannier90.*.%s' % SHLIB_EXT], 'lib/python%(pyshortver)s/site-packages'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import libwannier90'", + "python -c 'import pywannier90'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' From 3f74f3b08f830eb6b2d472b8194d13eb0a0281e0 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 20 Oct 2022 10:17:37 +0100 Subject: [PATCH 429/793] add bzip2 and libxml2 as deps to netCDF 4.9.0 --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb index f79aa51ab54..6aad7ec4860 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb @@ -34,6 +34,8 @@ dependencies = [ ('cURL', '7.83.0'), ('Szip', '2.1.1'), ('zstd', '1.5.2'), + ('bzip2', '1.0.8'), + ('libxml2', '2.9.13'), ] # make sure both static and shared libs are built From 93dfe13c78ed24d585aafb31724d0003b5b7f4c8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 20 Oct 2022 13:12:00 +0200 Subject: [PATCH 430/793] adding easyconfigs: Boost.Python-1.79.0-GCC-11.3.0.eb --- .../Boost.Python-1.79.0-GCC-11.3.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.79.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.79.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.79.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..8f02a65562d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.79.0-GCC-11.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'EB_Boost' + +name = 'Boost.Python' +version = '1.79.0' + +homepage = 'https://boostorg.github.io/python' +description = """Boost.Python is a C++ library which enables seamless interoperability between C++ + and the Python programming language.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('Boost', version), + ('Python', '3.10.4'), +] + +only_python_bindings = True + +moduleclass = 'lib' From 8370597d0dc21f229d096f02b69becc8b970fa57 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 20 Oct 2022 13:24:00 +0200 Subject: [PATCH 431/793] adding easyconfigs: FTGL-2.1.3-rc5-GCCcore-11.3.0.eb --- .../f/FTGL/FTGL-2.1.3-rc5-GCCcore-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..5f44a321631 --- /dev/null +++ b/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FTGL' +version = '2.1.3-rc5' + +homepage = 'http://ftgl.sourceforge.net/docs/html/' +description = """ FTGL is a free open source library to enable developers to use arbitrary +fonts in their OpenGL (www.opengl.org) applications. """ + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5458d62122454869572d39f8aa85745fc05d5518001bcefa63bd6cbb8d26565b'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('freetype', '2.12.1'), + ('libGLU', '9.0.2'), + ('Mesa', '22.0.3'), +] + +sanity_check_paths = { + 'files': ['lib/pkgconfig/ftgl.pc', 'lib/libftgl.a', 'lib/libftgl.la', 'lib/libftgl.%s' % SHLIB_EXT], + 'dirs': ['include/FTGL', 'share'] +} + +moduleclass = 'lib' From 4c2da2454182b30ea9e3c1a713c2e4add46d69a3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 20 Oct 2022 13:38:57 +0200 Subject: [PATCH 432/793] Add missing checksum --- .../easyconfigs/b/Boost.Python/Boost.Python-1.79.0-GCC-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.79.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.79.0-GCC-11.3.0.eb index 8f02a65562d..edd662ea181 100644 --- a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.79.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.79.0-GCC-11.3.0.eb @@ -12,6 +12,7 @@ toolchainopts = {'pic': True} source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['273f1be93238a068aba4f9735a4a2b003019af067b9c183ed227780b8f36062c'] dependencies = [ ('Boost', version), From 3382c5fb798c3db9f6eb7427be6125dfc17dffff Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 20 Oct 2022 16:42:17 +0200 Subject: [PATCH 433/793] use FTGL 2.4.0 instead --- ...e-11.3.0.eb => FTGL-2.4.0-GCCcore-11.3.0.eb} | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/f/FTGL/{FTGL-2.1.3-rc5-GCCcore-11.3.0.eb => FTGL-2.4.0-GCCcore-11.3.0.eb} (65%) diff --git a/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FTGL/FTGL-2.4.0-GCCcore-11.3.0.eb similarity index 65% rename from easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-11.3.0.eb rename to easybuild/easyconfigs/f/FTGL/FTGL-2.4.0-GCCcore-11.3.0.eb index 5f44a321631..343402f780d 100644 --- a/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FTGL/FTGL-2.4.0-GCCcore-11.3.0.eb @@ -1,20 +1,23 @@ easyblock = 'ConfigureMake' name = 'FTGL' -version = '2.1.3-rc5' +version = '2.4.0' -homepage = 'http://ftgl.sourceforge.net/docs/html/' +homepage = 'https://github.com/frankheckenbach/ftgl' description = """ FTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL (www.opengl.org) applications. """ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['5458d62122454869572d39f8aa85745fc05d5518001bcefa63bd6cbb8d26565b'] +github_account = 'frankheckenbach' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] -builddependencies = [('binutils', '2.38')] +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] dependencies = [ ('freetype', '2.12.1'), @@ -22,6 +25,8 @@ dependencies = [ ('Mesa', '22.0.3'), ] +preconfigopts = './autogen.sh && ' + sanity_check_paths = { 'files': ['lib/pkgconfig/ftgl.pc', 'lib/libftgl.a', 'lib/libftgl.la', 'lib/libftgl.%s' % SHLIB_EXT], 'dirs': ['include/FTGL', 'share'] From 84f4715a19987a7f36e7c8b59f7dc0b37e2407da Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 20 Oct 2022 17:00:56 +0200 Subject: [PATCH 434/793] Add missing checksum --- easybuild/easyconfigs/f/FTGL/FTGL-2.4.0-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/FTGL/FTGL-2.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FTGL/FTGL-2.4.0-GCCcore-11.3.0.eb index 343402f780d..87757d797fb 100644 --- a/easybuild/easyconfigs/f/FTGL/FTGL-2.4.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FTGL/FTGL-2.4.0-GCCcore-11.3.0.eb @@ -13,6 +13,7 @@ toolchainopts = {'pic': True} github_account = 'frankheckenbach' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] +checksums = ['aa97da1c3442a8fd3941037655df18016d70b5266381c81d81e8b5335f196ea8'] builddependencies = [ ('binutils', '2.38'), From 54770a0d7116397f9b4e09cb94fa36193bccc97f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 17:13:02 +0200 Subject: [PATCH 435/793] adding easyconfigs: jax-0.3.23-foss-2022a.eb --- .../j/jax/jax-0.3.23-foss-2022a.eb | 109 ++++++++++++++++++ 1 file changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb new file mode 100644 index 00000000000..23d90b71f8b --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb @@ -0,0 +1,109 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.3.23' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('Bazel', '5.1.1'), + ('pytest-xdist', '2.5.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.36.0', '-nodocs'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('flatbuffers-python', '2.0'), +] + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in WORKSPACE +local_tf_commit = 'cb946f223b9b3fa04efdbb7a0e6a9dabb22a7057' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +# replace remote TensorFlow repository with the local one from EB +local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " +local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '1.3.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['463c38a08d2e4cef6c498b76ba5bd4858e4c6ef51da1a5a1f27139a022e20248'], + }), + ('jaxlib', '0.3.22', { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib_local-tensorflow-repo.sed', '.'), + ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir), + ], + 'checksums': [ + # jaxlib-v0.3.22.tar.gz + '680a6f5265ba26d5515617a95ae47244005366f879a5c321782fde60f34e6d0d', + # tensorflow-cb946f223b9b3fa04efdbb7a0e6a9dabb22a7057.tar.gz + '9a7a7a87356bdeef5874fae135de380466482b593469035be3609a9cd2c153c4', + # jaxlib_local-tensorflow-repo.sed + 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5', + # TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch + '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('etils', '0.8.0', { + 'checksums': ['d1d5af7bd9c784a273c4e1eccfaa8feaca5e0481a08717b5313fa231da22a903'], + }), + (name, version, { + 'patches': [ + 'jax-0.3.9_relax-test-tolerance.patch', + ], + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'checksums': [ + {'jax-v0.3.23.tar.gz': 'fa8c68a82fa2fcf3d272bf239c77e7028bb6077466a53349ce85f6e85ed623db'}, + {'jax-0.3.9_relax-test-tolerance.patch': + '3da3c8b4d9ff3449b51a4f39d6bbadd348ea3bd4ca493a6f1292743f86fa7b3d'}, + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 934e5be97e2f87044b863f3c682192d40b984c2f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 18:14:21 +0200 Subject: [PATCH 436/793] adding easyconfigs: Fiji-2.9.0-Java-1.8.eb --- .../easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb b/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb new file mode 100644 index 00000000000..c655cd16540 --- /dev/null +++ b/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb @@ -0,0 +1,49 @@ +easyblock = 'PackedBinary' + +name = 'Fiji' +version = '2.9.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://fiji.sc' +description = """Fiji is an image processing package—a 'batteries-included' distribution of + ImageJ, bundling a lot of plugins which facilitate scientific image analysis. +This release is based on ImageJ-2.1.0 and Fiji-2.1.1""" + +toolchain = SYSTEM + +source_urls = ['https://downloads.imagej.net/fiji/releases/%(version)s/'] +sources = ['fiji-%(version)s-nojre.zip'] +checksums = ['970fb80cf2a4fe8bfcecc2cc9a8617b9ab28f19fbe229ea6ae2f7f42674c8a42'] + +dependencies = [('Java', '1.8', '', SYSTEM)] + +postinstallcmds = [ + # Remove binaries for other platforms + 'rm %(installdir)s/{ImageJ-win32.exe,ImageJ-win64.exe}', + # Enable any update site (edit existing site with same parameters to enable it) + # Full list at https://imagej.github.io/list-of-update-sites/ + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ImageScience"' + ' https://sites.imagej.net/ImageScience/', + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "3D ImageJ Suite"' + ' https://sites.imagej.net/Tboudier/', + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ilastik"' + ' https://sites.imagej.net/Ilastik/', + # Add a new update site + # '%(installdir)s/ImageJ-linux64 --headless --update add-update-site "New Name"' + # ' https://site.url/NewName/', + # Update the installation + '%(installdir)s/ImageJ-linux64 --headless --update update', +] + +sanity_check_paths = { + 'files': ['ImageJ-linux64'], + 'dirs': [], +} + +modloadmsg = """ +Additional plugins can be installed in your $HOME/.plugins folder or requested to user support +Use ImageJ/Fiji in headless mode in your scripts with the command `ImageJ-linux64 --headless` +More information at https://imagej.net/Headless +""" + +moduleclass = 'vis' From d184b5d302a432d653c4e1709e1d87d6469fa689 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 18:24:45 +0200 Subject: [PATCH 437/793] add exception for egl dependency variant of glew --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 518f5594e1d..4eb56e770a7 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -473,6 +473,8 @@ def check_dep_vars(self, gen, dep, dep_vars): 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], + # egl variant of glew is required by libwpe + 'glew': [('2.2.0; versionsuffix: -egl', [r'libwpe-1\.13\.3-GCCcore-11\.2\.0'])], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], From 7b731cbcbd5f437aa69d5bd389e3d7d001f1289e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 19:57:26 +0200 Subject: [PATCH 438/793] clean up TELEMAC-MASCARET easyconfig based on suggestions by @jfgrimm --- .../TELEMAC-MASCARET-8p3r1-foss-2021b.eb | 63 ++++++++++--------- 1 file changed, 32 insertions(+), 31 deletions(-) diff --git a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb index 5b6623b4774..a28af36eaef 100644 --- a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb @@ -29,37 +29,38 @@ unpack_options = '--strip-components=1' buildininstalldir = True -install_cmd = "export HOMETEL=$PWD && " -# add Python scripts to $PATH and $PYTHONPATH -install_cmd += "export PATH=$HOMETEL/scripts/python3/:$PATH && " -install_cmd += "export PYTHONPATH=$HOMETEL/scripts/python3:$PYTHONPATH && " -# force python to flush its output -install_cmd += "export PYTHONUNBUFFERED=1 && " - -# export LD_LIBRARY_PATH=$HOMETEL/builds/$USETELCFG/wrap_api/lib:$LD_LIBRARY_PATH -# export PYTHONPATH=$HOMETEL/builds/$USETELCFG/wrap_api/lib:$PYTHONPATH - -install_cmd += "cp $HOMETEL/configs/systel.edf.cfg $HOMETEL/configs/systel.easybuild.cfg && " -install_cmd += "sed -i 's/S9.gfortran/easybuild/g' $HOMETEL/configs/systel.easybuild.cfg && " -# strip out use of AED, GOTM, MED (optional dependencies) -install_cmd += "sed -i 's/\(^[a-z]*_aed:\).*/\\1/g' $HOMETEL/configs/systel.easybuild.cfg && " -install_cmd += "sed -i 's/\(^[a-z]*_gotm:\).*/\\1/g' $HOMETEL/configs/systel.easybuild.cfg && " -install_cmd += "sed -i 's/\(^[a-z]*_med:\).*/\\1/g' $HOMETEL/configs/systel.easybuild.cfg && " -# replace -O2 with desired compiler options -install_cmd += 'sed -i "s/-O2/$F90FLAGS/g" $HOMETEL/configs/systel.easybuild.cfg && ' -# fix linker option for BLAS -install_cmd += 'sed -i "s/ -lblas/ $LIBBLAS/g" $HOMETEL/configs/systel.easybuild.cfg && ' -# downgrade Fortran compiler error to warning -install_cmd += "sed -i 's/^fflags_gfo:/fflags_gfo: -fallow-invalid-boz/g' $HOMETEL/configs/systel.easybuild.cfg && " -install_cmd += "export SYSTELCFG=$HOMETEL/configs/systel.easybuild.cfg && " -install_cmd += "export USETELCFG=easybuild && " - -install_cmd += "export SCALAPACKHOME=$EBROOTSCALAPACK && " -install_cmd += "export METISHOME=$EBROOTMETIS && " -install_cmd += "export SCOTCHHOME=$EBROOTSCOTCH && " -install_cmd += "export MUMPSHOME=$EBROOTMUMPS && " -install_cmd += "export HDF5HOME=$EBROOTHDF5 && " -install_cmd += "config.py && compile_telemac.py -j %(parallel)s" +local_tweak_cfg_cmd = ' '.join([ + "sed -i -e 's/S9.gfortran/easybuild/g'", + # strip out use of AED, GOTM, MED (optional dependencies) + "-e 's/\(^[a-z]*_aed:\).*/\\1/g' -e 's/\(^[a-z]*_gotm:\).*/\\1/g' -e 's/\(^[a-z]*_med:\).*/\\1/g'", + # replace -O2 with desired compiler options + '-e "s/-O2/$F90FLAGS/g"', + # fix linker option for BLAS + '-e "s/ -lblas/ $LIBBLAS/g"', + # downgrade Fortran compiler error to warning + "-e 's/^fflags_gfo:/fflags_gfo: -fallow-invalid-boz/g'", + "$HOMETEL/configs/systel.easybuild.cfg", +]) + +install_cmd = ' && '.join([ + "export HOMETEL=$PWD", + # add Python scripts to $PATH and $PYTHONPATH + "export PATH=$HOMETEL/scripts/python3/:$PATH", + "export PYTHONPATH=$HOMETEL/scripts/python3:$PYTHONPATH", + # force python to flush its output + "export PYTHONUNBUFFERED=1", + "cp $HOMETEL/configs/systel.edf.cfg $HOMETEL/configs/systel.easybuild.cfg", + local_tweak_cfg_cmd, + "export SYSTELCFG=$HOMETEL/configs/systel.easybuild.cfg", + "export USETELCFG=easybuild", + "export SCALAPACKHOME=$EBROOTSCALAPACK", + "export METISHOME=$EBROOTMETIS", + "export SCOTCHHOME=$EBROOTSCOTCH", + "export MUMPSHOME=$EBROOTMUMPS", + "export HDF5HOME=$EBROOTHDF5", + "config.py", + "compile_telemac.py -j %(parallel)s", +]) sanity_check_paths = { 'files': ['builds/easybuild/bin/telemac2d', 'builds/easybuild/bin/telemac3d', From 67912caf99d976e37dbc601db97a9d382c2c8fe7 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 21 Oct 2022 13:17:34 +0800 Subject: [PATCH 439/793] prepare release notes for EasyBuild v4.6.2 + bump version to 4.6.2 --- RELEASE_NOTES | 49 ++++++++++++++++++++++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 49 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 698ecd7803e..2abf240dc2b 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,10 +3,57 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 15,332 easyconfig files, for 2,773 different software packages, +The latest version of easybuild-easyconfig provides 15,535 easyconfig files, for 2,798 different software packages, incl. 37 different (compiler) toolchains. +4.6.2 (October 21st 2022) +------------------------- + +update/bugfix release + +- added example easyconfig files for 25 new software packages: + - AGAT (#16261), AMAPVox (#16438), Avogadro2 (#16257), buildingspy (#16308), CDBtools (#16436), + Compress-Raw-Zlib (#16307), CUDAcompat (#15892), CWIPI (#16342), enchant-2 (#16319), f90wrap (#16346), + Imath (#16276), Mamba (#16432), Miller (#16221), nghttp2 (#16096), ngtcp2 (#16098), NVSHMEM (#16254), + pairsnp (#16331), paladin (#16320), PyMOL (#16394), python-irodsclient (#16328), ruffus (#16428), + TELEMAC-MASCARET (#16274), torchdata (#16344), Waylandpp (#16092), x13as (#16163) +- added additional easyconfigs for various supported software packages, including: + - ABAQUS 2022, ACTC 1.1, AGAT 0.9.2, AMAPVox 1.9.4, Amber 22.0, AMS 2022.102, Archive Zip, ASE 3.22.1, ASE 3.22.1, ASE 3.22.1, atools 1.5.1, Autoconf 2.71, AutoDock Vina, Automake 1.16.5, Automake 1.16.5.eb, Autotools 20220317, Avogadro2 1.97.0, beagle lib, Beast 2.6.7, Bio DB, biogeme 3.2.10, BioPerl 1.7.8, Boost.Python 1.79.0, buildingspy 4.0.0, ccache 4.6.3.eb, CDBtools 0.99, Clang Python, Compress Raw, CUDAcompat 11.6, CUDAcompat 11.6.eb, CUDAcompat 11.7, CUDAcompat 11.7.eb, CUDAcompat 11.eb, CWIPI 0.12.0, DB 18.1.40, DBD mysql, DB_File 1.858, dbus glib, deal.II 9.1.1, Delly 1.1.5, EasyBuild 4.6.1.eb, enchant 2, ESMF 8.3.0, expat 2.4.9, expecttest 0.1.3, f90wrap 0.2.8, FDS 6.7.9, FFTW 3.3.10, file 5.43, FLTK 1.3.8, FTGL 2.4.0, gawk 5.1.1, gc 8.2.2, GConf 3.2.6, GitPython 3.1.27, gmpy2 2.1.2, Go 1.18.3.eb, GPAW 22.8.0, GPAW 22.8.0, GPAW 22.8.0, GPAW 22.8.0, groff 1.22.4, Guile 3.0.8, hiredis 1.0.2, HPL 2.3, htop 3.2.1.eb, hunspell 1.7.1, iimpi 2022.09.eb, Imath 3.1.5, imgaug 0.4.0, imgaug 0.4.0, imkl 2022.2.0.eb, imkl FFTW, impi 2021.7.0, intel 2022.09.eb, intel compilers, IPython 8.5.0, jq 1.6, jq 1.6, jq 1.6, Judy 1.0.5, Julia 1.6.7, Julia 1.8.0, Julia 1.8.2, LDC 1.24.0, LDC 1.30.0, libaio 0.3.112, libcint 5.1.6, libconfig 1.7.3, libreadline 8.2, libsodium 1.0.18, LibSoup 3.0.7, LIBSVM 3.30, libtool 2.4.7, libtool 2.4.7.eb, libunistring 1.0, libvdwxc 0.4.0, libwebp 1.2.4, likwid 5.2.2, LMfit 1.0.3, LMfit 1.0.3, LZO 2.10, magma 2.6.2, Mamba 4.14.0, MariaDB 10.9.3, matplotlib 3.5.2, MDTraj 1.9.7, MDTraj 1.9.7, MDTraj 1.9.7, Miller 6.4.0.eb, Mmg 5.6.0, MMseqs2 13, ncdu 1.17, ncurses 6.3, netcdf4 python, Nextflow 22.10.0.eb, NFFT 3.5.3, nghttp2 1.48.0, ngtcp2 0.7.0, Nipype 1.8.5, numactl 2.0.16, NVSHMEM 2.5.0, onedrive 2.4.21, OpenCV 4.5.5, OpenCV 4.6.0, OpenEXR 3.1.5, OpenJPEG 2.5.0, OpenMM 7.7.0, OpenMM 7.7.0, OpenMM 7.7.0, OpenPGM 5.2.122, OpenSSL 1.1.1q, p4est 2.2, pairsnp 0.0.7, paladin 1.4.6, paladin 1.4.6, Perl 5.36.0, Pillow SIMD, pkgconf 1.9.3, pocl 1.8, pocl 1.8, PostgreSQL 14.4, POV Ray, PRISMS PF, PyCharm 2022.2.2.eb, PyMOL 2.5.0, pyqstem 1.0.3, pyqstem 1.0.3, python irodsclient, python irodsclient, PyTorch 1.12.0, PyTorch 1.12.0, PyTorch Lightning, PyTorch Lightning, RDFlib 6.2.0, ruamel.yaml 0.17.21, ruffus 2.8.4, SAMtools 1.16.1, SAMtools 1.16.1, scikit learn, Score P, SDL2 2.0.22, spaln 2.4.12, spglib python, spglib python, spglib python, SRA Toolkit, SuiteSparse 5.13.0, SUNDIALS 6.3.0, SUNDIALS 6.3.0, SuperLU 5.3.0, SuperLU 5.3.0, SuperLU 5.3.0, SuperLU 5.3.0, sympy 1.10.1, sympy 1.11.1, TELEMAC MASCARET, tensorboard 2.10.0, torchdata 0.3.0, torchvision 0.12.0, torchvision 0.13.1, TRIQS 3.1.1, TRIQS cthyb, TRIQS dft_tools, TRIQS tprf, TRUST4 1.0.7, TurboVNC 3.0.1, typing extensions, UCX 1.13.1, umap learn, VEP 107, VMD 1.9.4a57, Wannier90 3.1.0, Wayland 1.21.0, Waylandpp 1.0.0, wxWidgets 3.2.1, x13as 1, x13as 1, XML LibXML, xprop 1.2.5, xproto 7.0.31, xtrans 1.3.5, ZeroMQ 4.3.4 +- minor enhancements, including: + - configure recent pocl versions to -DLLC_HOST_CPU=native to avoid CPU auto-detection (#16246) + - add multidep exception for ncbi-vdb-3.0.0 which requires HDF5 1.10.x (#16316) + - deprecate use of True in favour of SYSTEM for system-toolchain dependencies in easyconfigs using a recent toolchain version (>2019b) (#16384) + - enable running of LAPACK tests for recent OpenBLAS easyconfigs + add patch to fix failing LAPACK tests due to use of -ftree-vectorize (#16406) + - add GITHUB_(LOWER_)RELEASE to known constants in setup.cfg (#16422) + - add AMAPVox extension to R v4.2.1 (#16439) + - add OpenEXR depenency to POV-Ray 3.7.0.10 (#16408) +- various bug fixes, including: + - add patch for OpenBLAS 0.3.7-0.3.12 to fix miscomputation on POWER (#16199) + - skip flaky test in PyTorch 1.9.0 (#16258) + - add --with-versioned-syms to ncurses 6.2 and 6.3 (#16270) + - add missing pkg-config builddep to Guile (#16317) + - add missing build dep pkg-config to enchant-2 (#16319) + - add patches to fix incompatibilites between ASE and other packages in 2022a toolchain (#16332) + - add patches to fix PyTorch 1.11 on POWER (#16339) + - add patches for Ambertools 21 to Amber 20.11 to work with new easyblock (#16343) + - use Intel MPI from EasyBuild toolchain in AMS (#16363) + - fix execution permissions for bin/ngm* for NextGenMap v0.5.5 (#16383) + - fix using provided qhull and freetype dependencies for matplotlib 3.5.2 by creating mplsetup.cfg rather than setup.cfg (#16396) + - fix GitHub download link in for libpsl 0.21.1 (#16397) + - stick to http in source URL for stride.tar.gz in VMD 1.9.4a51 easyconfigs due to problems with SSL certificate (#16403) + - add patch to detect available cores and remove unneeded deps for Unicycler 0.5.0 (#16407) + - add missing ICU + libunistring dependencies for libpsl 0.21.1 w/ GCCcore/10.3.0 (#16410) + - add patch to GCC 11.x + 12.x to fix vectorizer bug (#16411) + - use SYSTEM template constant to indicate that CUDA dependency of torchvision uses system toolchain (#16418) + - fix checksum for GULP 6.1 (#16423) + - add bzip2 and libxml2 as dependencies for netCDF 4.9.0 (#16450) +- other changes: + - drop Java dep from ABAQUS 2022 (#16314) + - update easyconfigs to use `SYSTEM` template constant instead of `True` in dependencies (#16386) + - update libxml2 + libxslt easyconfigs to use gnome.org source URL (#16429) + + v4.6.1 (September 12th 2022) ---------------------------- diff --git a/setup.py b/setup.py index 24b137e9759..0528da1ca3f 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.6.2.dev0' +VERSION = '4.6.2' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From bee15c936201b7ed0610c4f634dca86d437428e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Oct 2022 09:37:01 +0200 Subject: [PATCH 440/793] minor tweaks for release notes for v4.6.2 --- RELEASE_NOTES | 32 +++++++++++++++++++++----------- 1 file changed, 21 insertions(+), 11 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 2abf240dc2b..693825cf873 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -12,18 +12,29 @@ incl. 37 different (compiler) toolchains. update/bugfix release +- add easyconfig for intel/2022.09 toolchain (#16435) - added example easyconfig files for 25 new software packages: - AGAT (#16261), AMAPVox (#16438), Avogadro2 (#16257), buildingspy (#16308), CDBtools (#16436), - Compress-Raw-Zlib (#16307), CUDAcompat (#15892), CWIPI (#16342), enchant-2 (#16319), f90wrap (#16346), + Compress-Raw-Zlib (#16307), CUDAcompat (#15892), CWIPI (#16342), enchant-2 (#16082, #16319), f90wrap (#16346), Imath (#16276), Mamba (#16432), Miller (#16221), nghttp2 (#16096), ngtcp2 (#16098), NVSHMEM (#16254), pairsnp (#16331), paladin (#16320), PyMOL (#16394), python-irodsclient (#16328), ruffus (#16428), TELEMAC-MASCARET (#16274), torchdata (#16344), Waylandpp (#16092), x13as (#16163) - added additional easyconfigs for various supported software packages, including: - - ABAQUS 2022, ACTC 1.1, AGAT 0.9.2, AMAPVox 1.9.4, Amber 22.0, AMS 2022.102, Archive Zip, ASE 3.22.1, ASE 3.22.1, ASE 3.22.1, atools 1.5.1, Autoconf 2.71, AutoDock Vina, Automake 1.16.5, Automake 1.16.5.eb, Autotools 20220317, Avogadro2 1.97.0, beagle lib, Beast 2.6.7, Bio DB, biogeme 3.2.10, BioPerl 1.7.8, Boost.Python 1.79.0, buildingspy 4.0.0, ccache 4.6.3.eb, CDBtools 0.99, Clang Python, Compress Raw, CUDAcompat 11.6, CUDAcompat 11.6.eb, CUDAcompat 11.7, CUDAcompat 11.7.eb, CUDAcompat 11.eb, CWIPI 0.12.0, DB 18.1.40, DBD mysql, DB_File 1.858, dbus glib, deal.II 9.1.1, Delly 1.1.5, EasyBuild 4.6.1.eb, enchant 2, ESMF 8.3.0, expat 2.4.9, expecttest 0.1.3, f90wrap 0.2.8, FDS 6.7.9, FFTW 3.3.10, file 5.43, FLTK 1.3.8, FTGL 2.4.0, gawk 5.1.1, gc 8.2.2, GConf 3.2.6, GitPython 3.1.27, gmpy2 2.1.2, Go 1.18.3.eb, GPAW 22.8.0, GPAW 22.8.0, GPAW 22.8.0, GPAW 22.8.0, groff 1.22.4, Guile 3.0.8, hiredis 1.0.2, HPL 2.3, htop 3.2.1.eb, hunspell 1.7.1, iimpi 2022.09.eb, Imath 3.1.5, imgaug 0.4.0, imgaug 0.4.0, imkl 2022.2.0.eb, imkl FFTW, impi 2021.7.0, intel 2022.09.eb, intel compilers, IPython 8.5.0, jq 1.6, jq 1.6, jq 1.6, Judy 1.0.5, Julia 1.6.7, Julia 1.8.0, Julia 1.8.2, LDC 1.24.0, LDC 1.30.0, libaio 0.3.112, libcint 5.1.6, libconfig 1.7.3, libreadline 8.2, libsodium 1.0.18, LibSoup 3.0.7, LIBSVM 3.30, libtool 2.4.7, libtool 2.4.7.eb, libunistring 1.0, libvdwxc 0.4.0, libwebp 1.2.4, likwid 5.2.2, LMfit 1.0.3, LMfit 1.0.3, LZO 2.10, magma 2.6.2, Mamba 4.14.0, MariaDB 10.9.3, matplotlib 3.5.2, MDTraj 1.9.7, MDTraj 1.9.7, MDTraj 1.9.7, Miller 6.4.0.eb, Mmg 5.6.0, MMseqs2 13, ncdu 1.17, ncurses 6.3, netcdf4 python, Nextflow 22.10.0.eb, NFFT 3.5.3, nghttp2 1.48.0, ngtcp2 0.7.0, Nipype 1.8.5, numactl 2.0.16, NVSHMEM 2.5.0, onedrive 2.4.21, OpenCV 4.5.5, OpenCV 4.6.0, OpenEXR 3.1.5, OpenJPEG 2.5.0, OpenMM 7.7.0, OpenMM 7.7.0, OpenMM 7.7.0, OpenPGM 5.2.122, OpenSSL 1.1.1q, p4est 2.2, pairsnp 0.0.7, paladin 1.4.6, paladin 1.4.6, Perl 5.36.0, Pillow SIMD, pkgconf 1.9.3, pocl 1.8, pocl 1.8, PostgreSQL 14.4, POV Ray, PRISMS PF, PyCharm 2022.2.2.eb, PyMOL 2.5.0, pyqstem 1.0.3, pyqstem 1.0.3, python irodsclient, python irodsclient, PyTorch 1.12.0, PyTorch 1.12.0, PyTorch Lightning, PyTorch Lightning, RDFlib 6.2.0, ruamel.yaml 0.17.21, ruffus 2.8.4, SAMtools 1.16.1, SAMtools 1.16.1, scikit learn, Score P, SDL2 2.0.22, spaln 2.4.12, spglib python, spglib python, spglib python, SRA Toolkit, SuiteSparse 5.13.0, SUNDIALS 6.3.0, SUNDIALS 6.3.0, SuperLU 5.3.0, SuperLU 5.3.0, SuperLU 5.3.0, SuperLU 5.3.0, sympy 1.10.1, sympy 1.11.1, TELEMAC MASCARET, tensorboard 2.10.0, torchdata 0.3.0, torchvision 0.12.0, torchvision 0.13.1, TRIQS 3.1.1, TRIQS cthyb, TRIQS dft_tools, TRIQS tprf, TRUST4 1.0.7, TurboVNC 3.0.1, typing extensions, UCX 1.13.1, umap learn, VEP 107, VMD 1.9.4a57, Wannier90 3.1.0, Wayland 1.21.0, Waylandpp 1.0.0, wxWidgets 3.2.1, x13as 1, x13as 1, XML LibXML, xprop 1.2.5, xproto 7.0.31, xtrans 1.3.5, ZeroMQ 4.3.4 + - Amber 22.0, AMS 2022.102, ASE 3.22.1, atools 1.5.1, Beast 2.6.7, biogeme 3.2.10, Boost.Python 1.79.0, ccache 4.6.3, + dbus-glib 0.112, Delly 1.1.5, ESMF 8.3.0, expat 2.4.9, FDS 6.7.9, file 5.43, FLTK 1.3.8, FTGL 2.4.0, gc 8.2.2, + GitPython 3.1.27, Go 1.18.3, GPAW 22.8.0, Guile 3.0.8, htop 3.2.1, hunspell 1.7.1, IPython 8.5.0, jq 1.6, + Julia 1.8.2, LDC 1.30.0, libcint 5.1.6, libconfig 1.7.3, libreadline 8.2, LibSoup 3.0.7, LIBSVM 3.30, + libwebp 1.2.4, likwid 5.2.2, MariaDB 10.9.3, matplotlib 3.5.2, ncdu 1.17, netcdf4-python 1.6.1, Nextflow 22.10.0, + NFFT 3.5.3, Nipype 1.8.5, numactl 2.0.16, onedrive 2.4.21, OpenCV 4.6.0, OpenEXR 3.1.5, OpenJPEG 2.5.0, + OpenMM 7.7.0, OpenPGM 5.2.122, OpenSSL 1.1.1q, Perl 5.36.0, Pillow-SIMD 9.2.0, pkgconf 1.9.3, PostgreSQL 14.4, + PyCharm 2022.2.2, PyTorch 1.12.0, PyTorch 1.12.0, PyTorch-Lightning 1.7.7, RDFlib 6.2.0, SAMtools 1.16.1, + scikit-learn 1.1.2, Score-P 7.1, SDL2 2.0.22, spaln 2.4.12, spglib-python 2.0.0, SuiteSparse 5.13.0, SUNDIALS 6.3.0, + sympy 1.11.1, tensorboard 2.10.0, torchvision 0.13.1, TRIQS 3.1.1, TRIQS-cthyb 3.1.0, TRIQS-dft_tools 3.1.0, + TRIQS-tprf 3.1.1, TRUST4 1.0.7, TurboVNC 3.0.1, typing-extensions 4.3.0, UCX 1.13.1, umap-learn 0.5.3, VEP 107, + VMD 1.9.4a57, Wayland 1.21.0, wxWidgets 3.2.1, xprop 1.2.5 - minor enhancements, including: - - configure recent pocl versions to -DLLC_HOST_CPU=native to avoid CPU auto-detection (#16246) - - add multidep exception for ncbi-vdb-3.0.0 which requires HDF5 1.10.x (#16316) - - deprecate use of True in favour of SYSTEM for system-toolchain dependencies in easyconfigs using a recent toolchain version (>2019b) (#16384) + - configure recent pocl versions with -DLLC_HOST_CPU=native to avoid CPU auto-detection (#16246) + - add multi-dep exception to easyconfigs test suite for ncbi-vdb-3.0.0 which requires HDF5 1.10.x (#16316) - enable running of LAPACK tests for recent OpenBLAS easyconfigs + add patch to fix failing LAPACK tests due to use of -ftree-vectorize (#16406) - add GITHUB_(LOWER_)RELEASE to known constants in setup.cfg (#16422) - add AMAPVox extension to R v4.2.1 (#16439) @@ -32,25 +43,24 @@ update/bugfix release - add patch for OpenBLAS 0.3.7-0.3.12 to fix miscomputation on POWER (#16199) - skip flaky test in PyTorch 1.9.0 (#16258) - add --with-versioned-syms to ncurses 6.2 and 6.3 (#16270) - - add missing pkg-config builddep to Guile (#16317) - - add missing build dep pkg-config to enchant-2 (#16319) + - add missing pkg-config build dependency to Guile (#16317) - add patches to fix incompatibilites between ASE and other packages in 2022a toolchain (#16332) - add patches to fix PyTorch 1.11 on POWER (#16339) - - add patches for Ambertools 21 to Amber 20.11 to work with new easyblock (#16343) + - add patches for Ambertools 21 to Amber 20.11 to work with updated Amber easyblock (#16343) - use Intel MPI from EasyBuild toolchain in AMS (#16363) - fix execution permissions for bin/ngm* for NextGenMap v0.5.5 (#16383) - - fix using provided qhull and freetype dependencies for matplotlib 3.5.2 by creating mplsetup.cfg rather than setup.cfg (#16396) + - fix using provided Qhull and freetype dependencies for matplotlib 3.5.2 by creating mplsetup.cfg rather than setup.cfg (#16396) - fix GitHub download link in for libpsl 0.21.1 (#16397) - stick to http in source URL for stride.tar.gz in VMD 1.9.4a51 easyconfigs due to problems with SSL certificate (#16403) - add patch to detect available cores and remove unneeded deps for Unicycler 0.5.0 (#16407) - add missing ICU + libunistring dependencies for libpsl 0.21.1 w/ GCCcore/10.3.0 (#16410) - add patch to GCC 11.x + 12.x to fix vectorizer bug (#16411) - - use SYSTEM template constant to indicate that CUDA dependency of torchvision uses system toolchain (#16418) - fix checksum for GULP 6.1 (#16423) - add bzip2 and libxml2 as dependencies for netCDF 4.9.0 (#16450) - other changes: - drop Java dep from ABAQUS 2022 (#16314) - - update easyconfigs to use `SYSTEM` template constant instead of `True` in dependencies (#16386) + - deprecate use of True in favour of SYSTEM for system-toolchain dependencies in easyconfigs using a recent toolchain version (>2019b) (#16384) + - update easyconfigs to use `SYSTEM` template constant instead of `True` in dependencies (#16386, #16418) - update libxml2 + libxslt easyconfigs to use gnome.org source URL (#16429) From f11d34b8b40d453c80eaff9bbfdee60c9fd69eb0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Oct 2022 10:58:59 +0200 Subject: [PATCH 441/793] bump version to 4.6.3dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 0528da1ca3f..75d8dacffe3 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.6.2' +VERSION = '4.6.3.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From acd1e0442d09ab4cc9f01210f6f84313776a1260 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 21 Oct 2022 11:48:47 +0200 Subject: [PATCH 442/793] adding easyconfigs: torchsampler-0.1.2-foss-2022a.eb, torchsampler-0.1.2-foss-2022a-CUDA-11.7.0.eb --- ...rchsampler-0.1.2-foss-2022a-CUDA-11.7.0.eb | 30 +++++++++++++++++++ .../torchsampler-0.1.2-foss-2022a.eb | 28 +++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..30864489390 --- /dev/null +++ b/easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'torchsampler' +version = '0.1.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/ufoym/imbalanced-dataset-sampler' +description = """ +A (PyTorch) imbalanced dataset sampler for oversampling low classes and +undersampling high frequent ones.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('PyTorch', '1.12.0', versionsuffix), + ('torchvision', '0.13.1', versionsuffix), +] + +exts_list = [ + (name, version, { + 'checksums': ['6503acf0ff76888905595006a45c2a2fa017f7a13fffbfcddb3827ef8226ea78'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a.eb b/easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a.eb new file mode 100644 index 00000000000..3b4a760bfbc --- /dev/null +++ b/easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'torchsampler' +version = '0.1.2' + +homepage = 'https://github.com/ufoym/imbalanced-dataset-sampler' +description = """ +A (PyTorch) imbalanced dataset sampler for oversampling low classes and +undersampling high frequent ones.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), + ('torchvision', '0.13.1'), +] + +exts_list = [ + (name, version, { + 'checksums': ['6503acf0ff76888905595006a45c2a2fa017f7a13fffbfcddb3827ef8226ea78'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'devel' From d15b1ead95141beae65f0c396f9c9d1a59062081 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 21 Oct 2022 11:20:46 +0100 Subject: [PATCH 443/793] Add patch for correctly skipping a test and add matplotlib builddep --- .../easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb | 5 +++++ ...-0.3.23_correctly-skip-from_dlpack-tests.patch | 15 +++++++++++++++ 2 files changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.23_correctly-skip-from_dlpack-tests.patch diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb index 23d90b71f8b..54a86884e76 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb @@ -17,6 +17,7 @@ builddependencies = [ ('pytest-xdist', '2.5.0'), # git 2.x required to fetch repository 'io_bazel_rules_docker' ('git', '2.36.0', '-nodocs'), + ('matplotlib', '3.5.2'), # required for tests/lobpcg_test.py ] dependencies = [ @@ -93,6 +94,7 @@ exts_list = [ (name, version, { 'patches': [ 'jax-0.3.9_relax-test-tolerance.patch', + 'jax-0.3.23_correctly-skip-from_dlpack-tests.patch', ], 'source_tmpl': '%(name)s-v%(version)s.tar.gz', 'source_urls': ['https://github.com/google/jax/archive/'], @@ -100,7 +102,10 @@ exts_list = [ {'jax-v0.3.23.tar.gz': 'fa8c68a82fa2fcf3d272bf239c77e7028bb6077466a53349ce85f6e85ed623db'}, {'jax-0.3.9_relax-test-tolerance.patch': '3da3c8b4d9ff3449b51a4f39d6bbadd348ea3bd4ca493a6f1292743f86fa7b3d'}, + {'jax-0.3.23_correctly-skip-from_dlpack-tests.patch': + 'a69ce7280ca8bb42e671217f00d9147f8c64b4b7ba65dea7f05f2c6de757b279'}, ], + 'runtest': "pytest -n %(parallel)s tests", }), ] diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23_correctly-skip-from_dlpack-tests.patch b/easybuild/easyconfigs/j/jax/jax-0.3.23_correctly-skip-from_dlpack-tests.patch new file mode 100644 index 00000000000..7354e39c8e3 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23_correctly-skip-from_dlpack-tests.patch @@ -0,0 +1,15 @@ +np.from_dlpack was not added until numpy 1.23 +Patch based off https://github.com/google/jax/pull/12900 and added by Simon Branford (University of Birmingham) +diff --git a/tests/array_interoperability_test.py b/tests/array_interoperability_test.py +index cc2f3a6c08d..ac04ee637c8 100644 +--- a/tests/array_interoperability_test.py ++++ b/tests/array_interoperability_test.py +@@ -200,7 +200,7 @@ def testNumpyToJax(self, shape, dtype): + "shape": shape, "dtype": dtype} + for shape in all_shapes + for dtype in torch_dtypes)) +- @unittest.skipIf(numpy_version < (1, 22, 0), "Requires numpy 1.22 or newer") ++ @unittest.skipIf(numpy_version < (1, 23, 0), "Requires numpy 1.23 or newer") + @jtu.skip_on_devices("gpu") + def testJaxToNumpy(self, shape, dtype): + rng = jtu.rand_default(self.rng()) From 430735ccd8c455694dcca5aa2f6e18e4756f3d91 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 21 Oct 2022 18:24:29 +0800 Subject: [PATCH 444/793] adding easyconfigs: EasyBuild-4.6.2.eb --- .../e/EasyBuild/EasyBuild-4.6.2.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.2.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.2.eb new file mode 100644 index 00000000000..6168661c256 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.2.eb @@ -0,0 +1,45 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.6.2' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/88/7f/67dd44ae3204cba36c66578b14e284ce5210d8217fb383eb24c1691a1bfd/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/fe/52/2609eb0d2b9e9678670c2faec23b14c9c180b4a1d2494fd91c29df2a9a5e/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/5c/6b/1ead89a64a19717e5b0a0c8453458e7186928a36280e9592092ee6d58273/', + +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + '136a49ed40b4d7fed1b3d3d47f0f2804cb7744fd886eb9887672e85f7e820499', # easybuild-framework-4.6.2.tar.gz + 'b88059feeb2a97c944f6a71dc88cec683fef650ac081f8563b3f312cf8fe2794', # easybuild-easyblocks-4.6.2.tar.gz + 'b9a305200c8874852cfa3d07d72ed7295481c1b532f7579dcf1212deebcd393b', # easybuild-easyconfigs-4.6.2.tar.gz +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From 116bd8f61120841cc0809ad734c9d3c682e8890c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 21 Oct 2022 12:25:38 +0200 Subject: [PATCH 445/793] add torchvision dep easyconfig --- .../torchvision-0.13.1-foss-2022a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a.eb new file mode 100644 index 00000000000..26cf963f6da --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a.eb @@ -0,0 +1,21 @@ +name = 'torchvision' +version = '0.13.1' + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c32fab734e62c7744dadeb82f7510ff58cc3bca1189d17b16aa99b08afc42249'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('Pillow-SIMD', '9.2.0'), + ('PyTorch', '1.12.0'), +] + +moduleclass = 'vis' From 0335eb886702eb91e125f6513bea4a2f863097aa Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 12:32:28 +0200 Subject: [PATCH 446/793] adding easyconfigs: sfftk-0.7.4-foss-2021a.eb --- .../s/sfftk/sfftk-0.7.4-foss-2021a.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/s/sfftk/sfftk-0.7.4-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/sfftk/sfftk-0.7.4-foss-2021a.eb b/easybuild/easyconfigs/s/sfftk/sfftk-0.7.4-foss-2021a.eb new file mode 100644 index 00000000000..b2736681544 --- /dev/null +++ b/easybuild/easyconfigs/s/sfftk/sfftk-0.7.4-foss-2021a.eb @@ -0,0 +1,70 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/10 +easyblock = 'PythonBundle' + +name = 'sfftk' +version = '0.7.4' + +homepage = 'https://emdb-empiar.github.io/EMDB-SFF/' +description = """ +sfftk is a set of utilities that facilitate creation, conversion and +modification of Electron Microscopy Data Bank - Segmentation File Format +(EMDB-SFF) files. EMDB-SFF is an open, community-driven file format to handle +annotated segmentations and subtomogram averages that facilitates segmentation +file interchange. It is written in Python and provides both a command-line suite +of commands and a Python API.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('mrcfile', '1.3.0'), + ('lxml', '4.6.3'), + ('h5py', '3.2.1'), + ('scikit-image', '0.18.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('bitarray', '2.6.0', { + 'checksums': ['56d3f16dd807b1c56732a244ce071c135ee973d3edc9929418c1b24c5439a0fd'], + }), + ('ahds', '0.2.4', { + 'checksums': ['3356115351f7f6089f44c6f6503daa4985f158b7dfb730ef88ab3c6a7f8cc1a6'], + }), + ('styled', '0.2.0', { + 'checksums': ['91ab8022913de87fe1a614d3caeebafe046fd20cdd7d821a61738c1ce86e7276'], + }), + ('numpy-stl', '2.17.1', { + 'modulename': 'stl', + 'checksums': ['36c920192f445dd57f091a63629bdda5a9274d47513a33ac2efad12737394b7a'], + }), + ('python-utils', '3.3.3', { + 'checksums': ['3b1c8b706e40e91280eec5fa72ea730880a166cee99afa5555b863d55664478d'], + }), + ('RandomWords', '0.4.0', { + 'modulename': 'random_words', + 'checksums': ['0bb64dc14f7f5d96597e9a08e185b874a3ea20955a1acce632b87122d66d3d6b'], + }), + ('SimpleParse', '2.2.3', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['2c1b130017e708a2c87b3a6119b5844f08a0d53b9e4c9d48da5e6c409798e979'], + }), + ('sfftk-rw', '0.7.2', { + 'modulename': 'sfftkrw', + 'source_urls': ['https://github.com/emdb-empiar/sfftk-rw/archive/refs/tags/'], + 'sources': [{'filename': '%(name)s-%(version)s.tar.gz', 'download_filename': 'v%(version)s.tar.gz'}], + 'checksums': ['c858377d987090aa08984e8ae8dd09d5553eabc3bbea5c0ecc9994c06d474500'], + }), + (name, version, { + 'checksums': ['f165d377d4b7d42bc800a08f220169b7baf5e2faafe337beb77ee0754d52e038'], + }), +] + +sanity_check_commands = [ + "sff -h", +] + +moduleclass = 'tools' From 46c3331eb2937e72122b4dac931e73b9132d0f35 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 12:48:45 +0200 Subject: [PATCH 447/793] add mrcfile-1.3.0-foss-2021a.eb --- .../m/mrcfile/mrcfile-1.3.0-foss-2021a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb new file mode 100644 index 00000000000..4597b91cf82 --- /dev/null +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb @@ -0,0 +1,22 @@ +#Thomas Hoffmann, EMBL Heidelberg, 2022/10 +easyblock = 'PythonPackage' +name = 'mrcfile' +version = '1.3.0' +homepage = 'https://github.com/ccpem/mrcfile' +description = """ mrcfile is a Python implementation of the MRC2014 file format, which is used in structural biology to store image and volume data. + +It allows MRC files to be created and opened easily using a very simple API, which exposes the file’s header and data as numpy arrays. The code runs in Python 2 and 3 and is fully unit-tested. + +This library aims to allow users and developers to read and write standard-compliant MRC files in Python as easily as possible, and with no dependencies on any compiled libraries except numpy. You can use it interactively to inspect files, correct headers and so on, or in scripts and larger software packages to provide basic MRC file I/O functions. """ + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +dependencies = [ + ('Python','3.9.5'), + ('SciPy-bundle','2021.05'), + ] + +use_pip=True +moduleclass = 'bio' From bc45390a1d7bad6fe4260be2c3c97b149edca089 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 13:25:25 +0200 Subject: [PATCH 448/793] mrcfile-1.3.0-foss-2021a.eb: fixed style --- .../m/mrcfile/mrcfile-1.3.0-foss-2021a.eb | 25 +++++++++++++------ 1 file changed, 17 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb index 4597b91cf82..6222f530615 100644 --- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb @@ -1,22 +1,31 @@ -#Thomas Hoffmann, EMBL Heidelberg, 2022/10 +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/10 easyblock = 'PythonPackage' name = 'mrcfile' version = '1.3.0' homepage = 'https://github.com/ccpem/mrcfile' -description = """ mrcfile is a Python implementation of the MRC2014 file format, which is used in structural biology to store image and volume data. +description = """mrcfile is a Python implementation of the MRC2014 file format, which is used in +structural biology to store image and volume data. -It allows MRC files to be created and opened easily using a very simple API, which exposes the file’s header and data as numpy arrays. The code runs in Python 2 and 3 and is fully unit-tested. +It allows MRC files to be created and opened easily using a very simple API, +which exposes the file’s header and data as numpy arrays. The code runs in +Python 2 and 3 and is fully unit-tested. -This library aims to allow users and developers to read and write standard-compliant MRC files in Python as easily as possible, and with no dependencies on any compiled libraries except numpy. You can use it interactively to inspect files, correct headers and so on, or in scripts and larger software packages to provide basic MRC file I/O functions. """ +This library aims to allow users and developers to read and write standard- +compliant MRC files in Python as easily as possible, and with no dependencies on +any compiled libraries except numpy. You can use it interactively to inspect +files, correct headers and so on, or in scripts and larger software packages to +provide basic MRC file I/O functions. """ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['3a113042d24820b9dfc6902cb9d93bcbebdee22beb40552f2c35303ace4b0547'] + dependencies = [ - ('Python','3.9.5'), - ('SciPy-bundle','2021.05'), - ] + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] -use_pip=True +use_pip = True moduleclass = 'bio' From 9bf9b3af85b2b2e4def1ac14c68105585482e10f Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 13:31:45 +0200 Subject: [PATCH 449/793] adding easyconfigs: napari-0.4.15-foss-2021a.eb --- .../n/napari/napari-0.4.15-foss-2021a.eb | 161 ++++++++++++++++++ 1 file changed, 161 insertions(+) create mode 100644 easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb new file mode 100644 index 00000000000..2eb76e76f3e --- /dev/null +++ b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb @@ -0,0 +1,161 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@emblde, 2022/06 +easyblock = 'PythonBundle' + +name = 'napari' +version = '0.4.15' + +homepage = 'https://napari.org/' +description = """napari is a fast, interactive, multi-dimensional image viewer for Python. It's +designed for browsing, annotating, and analyzing large multi-dimensional images. +It's built on top of Qt (for the GUI), vispy (for performant GPU-based +rendering), and the scientific Python stack (numpy, scipy).""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('PyQt5', '5.15.4', '-tools'), + ('SciPy-bundle', '2021.05'), + ('PyYAML', '5.4.1'), + ('dask', '2021.9.1'), + ('PyOpenGL', '3.1.5'), + ('imageio', '2.10.5'), # ext + ('tqdm', '4.61.1'), + ('IPython', '7.25.0'), + # ('VisPy', '0.6.6'), + # ('Qtconsole', '5.0.2'), + ('typing-extensions', '3.10.0.0'), + # ('scikit-image', '0.19.1') # ext . + ('networkx', '2.5.1'), # req. for scikit-image ext + ('matplotlib', '3.4.2'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True +exts_list = [ + ('pytomlpp', '1.0.10', { + 'checksums': ['6de110c8fe43f46c52b2041d5fbaa0522677a712234832ffd8cbb51cff50804e'], + }), + ('freetype_py', '2.3.0', { + 'modulename': 'freetype', + 'sources': ['freetype-py-%(version)s.zip'], + 'checksums': ['f9b64ce3272a5c358dcee824800a32d70997fb872a0965a557adca20fce7a5d0'], + }), + ('hsluv', '5.0.3', { + 'checksums': ['2586bcb61d29d76e89e563a6836df24d86939961c9657f129a59f7617de45377'], + }), + ('vispy', '0.10.0', { + 'checksums': ['b76ad6f3eacadbfc4944cfb8211eadb6ea8417a590993ece5aa7caac082cffc2'], + }), + ('qtconsole', '5.3.1', { + 'checksums': ['b73723fac43938b684dcb237a88510dc7721c43a726cea8ade179a2927c0a2f3'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('cachey', '0.2.1', { + 'checksums': ['0310ba8afe52729fa7626325c8d8356a8421c434bf887ac851e58dcf7cf056a6'], + }), + ('docstring-parser', '0.14.1', { + 'sources': 'docstring_parser-%(version)s.tar.gz', + 'checksums': ['2c77522e31b7c88b1ab457a1f3c9ae38947ad719732260ba77ee8a3deb58622a'], + }), + ('pep517', '0.12.0', { + 'checksums': ['931378d93d11b298cf511dd634cf5ea4cb249a28ef84160b3247ee9afb4e8ab0'], + }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('magicgui', '0.5.1', { + 'checksums': ['dcd05c4c9bbd55bdeb72d41069b2d4304952dabe04c2aac7bdd43f5a4e3a8a94'], + }), + ('napari-console', '0.0.4', { + 'modulename': 'napari_console', + 'checksums': ['ea0e30fbfdd76542adda44be457f1306a65146fe7578f95838e28d62874f4c45'], + }), + ('napari-plugin-engine', '0.2.0', { + 'checksums': ['fa926f869d70e0d652c005661948cd0c7fee5508ae17d437937f34f5287590b3'], + }), + ('napari-svg', '0.1.6', { + 'checksums': ['12fa5c64995fc7179349969a39316355496b463858c3b0815e3b3e7ffcdced34'], + }), + ('Pint', '0.19.2', { + 'checksums': ['e1d4989ff510b378dad64f91711e7bdabe5ca78d75b06a18569ac454678c4baf'], + }), + ('build', '0.8.0', { + 'checksums': ['887a6d471c901b1a6e6574ebaeeebb45e5269a79d095fe9a8f88d6614ed2e5f0'], + }), + ('psygnal', '0.3.5', { + 'patches': ['http://two.embl.de/psygnal-0.3.5_python3.8.patch'], + 'checksums': [ + '5abf84f0da9f487be68299854c4eb39de0765236407736d201f97ef39913a548', # psygnal-0.3.5.tar.gz + 'c55cc07c646cb66e8c5d2ea227249216dbd1a1a9405acbd330d70105a3fd8890', # psygnal-0.3.5_python3.8.patch + ], + }), + ('pydantic', '1.9.1', { + 'checksums': ['1ed987c3ff29fff7fd8c3ea3a3ea877ad310aae2ef9889a119e22d3f2db0691a'], + }), + ('typer', '0.4.1', { + 'checksums': ['5646aef0d936b2c761a10393f0384ee6b5c7fe0bb3e5cd710b17134ca1d99cff'], + }), + ('npe2', '0.5.0', { + 'checksums': ['3d3d43b99bbd3b189fedd7313589c89642a4af0f14b24b9763eb134ba6a5548c'], + }), + ('numpydoc', '1.4.0', { + 'checksums': ['9494daf1c7612f59905fa09e65c9b8a90bbacb3804d91f7a94e778831e6fcfa5'], + }), + ('QtPy', '2.1.0', { + 'checksums': ['ca8cd4217175186344299ee4c0f7e7adcf362c70852ba35b255a534077025c06'], + }), + ('superqt', '0.3.2', { + 'checksums': ['a37df244a2d6e4387e865cdedabe925798b3352ab9cdc52f60701eb12d907960'], + }), + ('tifffile', '2022.5.4', { + 'checksums': ['b03147a15862b7c1d90d47435197f149bef7a52c25ad67cf1f9b465faa71b8d2'], + }), + ('pandas', '1.3.0', { + 'checksums': ['c554e6c9cf2d5ea1aba5979cc837b3649539ced0e18ece186f055450c86622e2'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.3', { + 'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'], + }), + ('pythran', '0.10.0', { + 'checksums': ['9dac8e1d50f33d4676003e350b1f0c878ce113e6f907920e92dc103352cac5bf'], + }), + ('PyWavelets', '1.2.0', { + 'modulename': 'pywt', + 'checksums': ['6cbd69b047bb4e00873097472133425f5f08a4e6bc8b3f0ae709274d4d5e9a8d'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.5.2', { + 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], + }), + ('scikit-image', '0.19.1', { + 'modulename': 'skimage', + 'checksums': ['48f00ee1e8ec2818ae6a152c72df15f4db7f566e839f5c34e1a0c3c9e5210138'], + }), + (name, version, { + 'checksums': ['0d4cf6067d2112c78a705917aa5e74371463982d80147a898c6b5d2f0b514baa'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = [ + '%(name)s --help', + 'pyrcc5 -version 2>&1 |grep pyrcc5' # make sure PyQt5 module was not built with --no-tools +] + +moduleclass = 'vis' From 8bdd165cf0f944d2c3f96df5da2bd117789ad1b9 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 21 Oct 2022 13:34:21 +0200 Subject: [PATCH 450/793] add psygnal-0.3.5_python3.8.patch --- .../n/napari/psygnal-0.3.5_python3.8.patch | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch diff --git a/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch b/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch new file mode 100644 index 00000000000..9ef096a19a4 --- /dev/null +++ b/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch @@ -0,0 +1,12 @@ +#Thomas Hoffmann, EMLB Heidelberg, structures-it@embl.de +#python > 3.7: prevent comple error future feature annotations is not defined +diff -ru psygnal-0.3.5/psygnal/_evented_model.py psygnal-0.3.5_python3.8/psygnal/_evented_model.py +--- psygnal-0.3.5/psygnal/_evented_model.py 2022-05-26 02:03:19.000000000 +0200 ++++ psygnal-0.3.5_python3.8/psygnal/_evented_model.py 2022-06-23 10:41:46.536586585 +0200 +@@ -1,5 +1,4 @@ +-from __future__ import annotations +- ++import annotations + import operator + import sys + import warnings From 0c145a2e2ae761c89ff06b8ecb15cc7b20d450e4 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 13:46:04 +0200 Subject: [PATCH 451/793] add PyQt5-5.15.4-GCCcore-10.3.0-tools.eb --- .../PyQt5-5.15.4-GCCcore-10.3.0-tools.eb | 104 ++++++++++++++++++ 1 file changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb new file mode 100644 index 00000000000..12f9c77e512 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb @@ -0,0 +1,104 @@ +easyblock = 'Bundle' + +name = 'PyQt5' +version = '5.15.4' +versionsuffix = '-tools' +homepage = 'https://www.riverbankcomputing.com/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. +This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'cstd': 'c++11'} + +builddependencies = [('binutils', '2.36.1')] +dependencies = [ + ('Python', '3.9.5'), + ('Qt5', '5.15.2'), +] + +default_easyblock = 'PythonPackage' + +local_sipdir = '%(installdir)s/share/sip' + +local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' + +local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " + +local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--no-stubs --no-dist-info" + +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir + +local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " +local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_sipver = '5.5.0' +components = [ + ('SIP', local_sipver, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['5d024c419b30fea8a6de8c71a560c7ab0bc3c221fbfb14d55a5b865bd58eaac5'], + 'start_dir': 'sip-%s' % local_sipver, + 'use_pip': True, + 'options': {'modulename': 'PyQt5.sip'}, + }), + ('PyQt-builder', '1.10.1', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['967b0c7bac0331597e9f8c5b336660f173a9896830b721d6d025e14bde647e17'], + 'start_dir': 'PyQt-builder-%(version)s', + 'use_pip': True, + }), + ('PyQt5_sip', '12.9.0', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['d3e4489d7c2b0ece9d203ae66e573939f7f60d4d29e089c9f11daa17cfeaae32'], + 'start_dir': 'PyQt5_sip-%(version)s', + 'use_pip': True, + }), + (name, version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + # run python configure.py in order to set bindir, which is no possible with sip-install: + 'configopts': local_pyqt_configopts, + }), + ('PyQtWebEngine', version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['cedc28f54165f4b8067652145aec7f732a17eadf6736835852868cf76119cc19'], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + 'configopts': local_pyqtweb_configopts, + 'options': {'modulename': 'PyQt5.QtWebEngine'}, + }), +] + +sanity_check_paths = { + 'files': ['bin/pyrcc5', 'bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import PyQt5.QtCore'", + "sip5 --help", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'QT_INSTALL_DATA': 'qsci', +} + +moduleclass = 'vis' From 3f22cdee665855a679086f6f28e6daa97af3798a Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 13:49:45 +0200 Subject: [PATCH 452/793] fix mrcfile-1.3.0-foss-2021a.eb --- easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb index 6222f530615..aff2c2636c7 100644 --- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb @@ -18,7 +18,6 @@ provide basic MRC file I/O functions. """ toolchain = {'name': 'foss', 'version': '2021a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['3a113042d24820b9dfc6902cb9d93bcbebdee22beb40552f2c35303ace4b0547'] @@ -27,5 +26,8 @@ dependencies = [ ('SciPy-bundle', '2021.05'), ] +download_dep_fail = True +sanity_pip_check = True + use_pip = True moduleclass = 'bio' From 128ef1d53bdeafdb44043b28a1545c2b60b725e6 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 21 Oct 2022 14:15:37 +0200 Subject: [PATCH 453/793] fix patch url --- easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb index 2eb76e76f3e..3f04fc5590d 100644 --- a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb +++ b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb @@ -87,7 +87,7 @@ exts_list = [ 'checksums': ['887a6d471c901b1a6e6574ebaeeebb45e5269a79d095fe9a8f88d6614ed2e5f0'], }), ('psygnal', '0.3.5', { - 'patches': ['http://two.embl.de/psygnal-0.3.5_python3.8.patch'], + 'patches': ['psygnal-0.3.5_python3.8.patch'], 'checksums': [ '5abf84f0da9f487be68299854c4eb39de0765236407736d201f97ef39913a548', # psygnal-0.3.5.tar.gz 'c55cc07c646cb66e8c5d2ea227249216dbd1a1a9405acbd330d70105a3fd8890', # psygnal-0.3.5_python3.8.patch From a4b320225ccaf553e112b3088604ca69f156aab0 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 14:27:20 +0200 Subject: [PATCH 454/793] mrcfile-1.3.0-foss-2021a.eb: fix style --- easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb index aff2c2636c7..c6e040ded1b 100644 --- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb @@ -27,7 +27,7 @@ dependencies = [ ] download_dep_fail = True -sanity_pip_check = True +sanity_pip_check = True use_pip = True moduleclass = 'bio' From 81d20f68a5a96294b2d1c0db2b034dec7172278a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 21 Oct 2022 13:37:49 +0100 Subject: [PATCH 455/793] relax tolerance of testPoly5 --- .../easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb | 3 +++ .../jax/jax-0.3.23_relax-testPoly5-tolerance.patch | 14 ++++++++++++++ 2 files changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb index 54a86884e76..d5c28009d97 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb @@ -95,6 +95,7 @@ exts_list = [ 'patches': [ 'jax-0.3.9_relax-test-tolerance.patch', 'jax-0.3.23_correctly-skip-from_dlpack-tests.patch', + 'jax-0.3.23_relax-testPoly5-tolerance.patch', ], 'source_tmpl': '%(name)s-v%(version)s.tar.gz', 'source_urls': ['https://github.com/google/jax/archive/'], @@ -104,6 +105,8 @@ exts_list = [ '3da3c8b4d9ff3449b51a4f39d6bbadd348ea3bd4ca493a6f1292743f86fa7b3d'}, {'jax-0.3.23_correctly-skip-from_dlpack-tests.patch': 'a69ce7280ca8bb42e671217f00d9147f8c64b4b7ba65dea7f05f2c6de757b279'}, + {'jax-0.3.23_relax-testPoly5-tolerance.patch': + '47e74771049364e8db9743f8c5f3d0d784e1e4d21595bdd07da94d5b9b42b83d'}, ], 'runtest': "pytest -n %(parallel)s tests", }), diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch b/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch new file mode 100644 index 00000000000..7df1c1dfe7f --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch @@ -0,0 +1,14 @@ +Relax the tolerance for the testPoly5 test +Patch by Simon Branford (University of Birmingham) +--- tmp/jax-jax-v0.3.23/tests/lax_numpy_test.py 2022-10-12 16:23:43.000000000 +0100 ++++ lax_numpy_test.py 2022-10-21 13:33:59.871417000 +0100 +@@ -1277,6 +1277,9 @@ + if jtu.device_under_test() == "tpu": + tol[np.int32] = tol[np.float32] = 1e-1 + tol = jtu.tolerance(dtype, tol) ++ if rank == 2 and dtype == np.int8 and a_shape == (12,): ++ # relax tolerance (from 1e-3) for testPoly5 ++ tol = 2e-3 + args_maker = lambda: [rng(a_shape * rank, dtype)] + self._CheckAgainstNumpy(np.poly, jnp.poly, args_maker, check_dtypes=False, tol=tol) + self._CompileAndCheck(jnp.poly, args_maker, check_dtypes=True, rtol=tol, atol=tol) From bcf403138bd737fdfabae7cd10805a8efaf3fe83 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 21 Oct 2022 13:43:55 +0100 Subject: [PATCH 456/793] correctly generate the patch --- easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb | 2 +- .../j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb index d5c28009d97..769a042f02f 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb @@ -106,7 +106,7 @@ exts_list = [ {'jax-0.3.23_correctly-skip-from_dlpack-tests.patch': 'a69ce7280ca8bb42e671217f00d9147f8c64b4b7ba65dea7f05f2c6de757b279'}, {'jax-0.3.23_relax-testPoly5-tolerance.patch': - '47e74771049364e8db9743f8c5f3d0d784e1e4d21595bdd07da94d5b9b42b83d'}, + 'be64bf36dde4884a97b6c8bb22c6b14ab5b24033cd40bfe7ce18363c55c30e87'}, ], 'runtest': "pytest -n %(parallel)s tests", }), diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch b/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch index 7df1c1dfe7f..38729edac87 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch @@ -1,7 +1,7 @@ Relax the tolerance for the testPoly5 test Patch by Simon Branford (University of Birmingham) ---- tmp/jax-jax-v0.3.23/tests/lax_numpy_test.py 2022-10-12 16:23:43.000000000 +0100 -+++ lax_numpy_test.py 2022-10-21 13:33:59.871417000 +0100 +--- tests/lax_numpy_test.py 2022-10-12 16:23:43.000000000 +0100 ++++ tests/lax_numpy_test.py 2022-10-21 13:33:59.871417000 +0100 @@ -1277,6 +1277,9 @@ if jtu.device_under_test() == "tpu": tol[np.int32] = tol[np.float32] = 1e-1 From 8360dbde5376958b38cd69763d93758860ec5014 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 17:09:10 +0200 Subject: [PATCH 457/793] build missing tool pyrcc5 --- .../p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb | 23 ++++++++++++++----- 1 file changed, 17 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb index 18614197333..e21ab740946 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb @@ -18,15 +18,26 @@ dependencies = [ default_easyblock = 'PythonPackage' +local_sipdir = '%(installdir)s/share/sip' + local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir local_pyqtweb_configopts += "--no-stubs --no-dist-info" +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir + local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_sipver = '5.5.0' @@ -57,10 +68,10 @@ components = [ 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], - 'easyblock': 'Binary', + 'easyblock': 'ConfigureMakePythonPackage', 'start_dir': '%(name)s-%(version)s', - 'skipsteps': ['configure', 'build'], - 'install_cmd': local_setup_env + local_pyqt5_sip_install, + 'preconfigopts': local_setup_env, + 'configopts': local_pyqt_configopts }), ('PyQtWebEngine', version, { 'source_urls': [PYPI_SOURCE], @@ -75,7 +86,7 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'files': ['bin/pyrcc5', 'bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From 8cac0b4b373bf6eb09bcc8dcd47de39ff9927d6a Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 17:17:52 +0200 Subject: [PATCH 458/793] adding easyconfigs: QtPy-2.2.1-GCCcore-11.2.0.eb --- .../q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..deb1b3231ed --- /dev/null +++ b/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'QtPy' +version = '2.2.1' + +homepage = "https://github.com/spyder-ide/qtpy" +description = """QtPy is a small abstraction layer that lets you write applications using a +single API call to either PyQt or PySide. +It provides support for PyQt5, PyQt4, PySide2 and PySide.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['7d5231133b772e40b4ee514b6673aca558331e4b88ca038b26c9e16c5c95524f'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('PyQt5', '5.15.4') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From 6687320ff6d271c5b89489d0fea56c9493ab4fe6 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 17:20:19 +0200 Subject: [PATCH 459/793] adding easyconfigs: Qtconsole-5.3.2-GCCcore-11.2.0.eb --- .../Qtconsole-5.3.2-GCCcore-11.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..cd750a04be5 --- /dev/null +++ b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Qtconsole' +version = '5.3.2' + +homepage = 'https://jupyter.org/' +description = """A rich Qt-based console for working with Jupyter kernels, supporting rich media +output, session export, and more. +The Qtconsole is a very lightweight application that largely feels like a +terminal, but provides a number of enhancements only possible in a GUI, such as +inline figures, proper multiline editing with syntax highlighting, graphical +calltips, and more.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8eadf012e83ab018295803c247c6ab7eacd3d5ab1e1d88a0f37fdcfdab9295a3'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('IPython', '7.26.0'), + ('QtPy', '2.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From 4e648e638a1d845d6361bbb0c0b628f8f00c9f3c Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 17:24:23 +0200 Subject: [PATCH 460/793] bump to foss/2021b --- .../n/napari/napari-0.4.15-foss-2021b.eb | 136 ++++++++++++++++++ .../n/napari/psygnal-0.3.5_python3.8.patch | 2 +- 2 files changed, 137 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb new file mode 100644 index 00000000000..1326a9f443b --- /dev/null +++ b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb @@ -0,0 +1,136 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@emblde, 2022/10 +easyblock = 'PythonBundle' + +name = 'napari' +version = '0.4.15' + +homepage = 'https://napari.org/' +description = """napari is a fast, interactive, multi-dimensional image viewer for Python. It's +designed for browsing, annotating, and analyzing large multi-dimensional images. +It's built on top of Qt (for the GUI), vispy (for performant GPU-based +rendering), and the scientific Python stack (numpy, scipy).""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('PyQt5', '5.15.4'), + ('SciPy-bundle', '2021.10'), + ('PyYAML', '5.4.1'), + ('dask', '2022.1.0'), + ('PyOpenGL', '3.1.6'), + ('imageio', '2.13.5'), + ('tqdm', '4.62.3'), + ('IPython', '7.26.0'), + ('Qtconsole', '5.3.2'), + ('typing-extensions', '3.10.0.2'), + ('scikit-image', '0.19.1'), + ('matplotlib', '3.4.3'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True +exts_list = [ + ('pytomlpp', '1.0.10', { + 'checksums': ['6de110c8fe43f46c52b2041d5fbaa0522677a712234832ffd8cbb51cff50804e'], + }), + ('freetype_py', '2.3.0', { + 'modulename': 'freetype', + 'sources': ['freetype-py-%(version)s.zip'], + 'checksums': ['f9b64ce3272a5c358dcee824800a32d70997fb872a0965a557adca20fce7a5d0'], + }), + ('hsluv', '5.0.3', { + 'checksums': ['2586bcb61d29d76e89e563a6836df24d86939961c9657f129a59f7617de45377'], + }), + ('vispy', '0.10.0', { + 'checksums': ['b76ad6f3eacadbfc4944cfb8211eadb6ea8417a590993ece5aa7caac082cffc2'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('cachey', '0.2.1', { + 'checksums': ['0310ba8afe52729fa7626325c8d8356a8421c434bf887ac851e58dcf7cf056a6'], + }), + ('docstring-parser', '0.14.1', { + 'sources': 'docstring_parser-%(version)s.tar.gz', + 'checksums': ['2c77522e31b7c88b1ab457a1f3c9ae38947ad719732260ba77ee8a3deb58622a'], + }), + ('pep517', '0.12.0', { + 'checksums': ['931378d93d11b298cf511dd634cf5ea4cb249a28ef84160b3247ee9afb4e8ab0'], + }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('magicgui', '0.5.1', { + 'checksums': ['dcd05c4c9bbd55bdeb72d41069b2d4304952dabe04c2aac7bdd43f5a4e3a8a94'], + }), + ('napari-console', '0.0.4', { + 'modulename': 'napari_console', + 'checksums': ['ea0e30fbfdd76542adda44be457f1306a65146fe7578f95838e28d62874f4c45'], + }), + ('napari-plugin-engine', '0.2.0', { + 'checksums': ['fa926f869d70e0d652c005661948cd0c7fee5508ae17d437937f34f5287590b3'], + }), + ('napari-svg', '0.1.6', { + 'checksums': ['12fa5c64995fc7179349969a39316355496b463858c3b0815e3b3e7ffcdced34'], + }), + ('Pint', '0.19.2', { + 'checksums': ['e1d4989ff510b378dad64f91711e7bdabe5ca78d75b06a18569ac454678c4baf'], + }), + ('build', '0.8.0', { + 'checksums': ['887a6d471c901b1a6e6574ebaeeebb45e5269a79d095fe9a8f88d6614ed2e5f0'], + }), + ('psygnal', '0.3.5', { + 'patches': ['psygnal-0.3.5_python3.8.patch'], + 'checksums': [ + '5abf84f0da9f487be68299854c4eb39de0765236407736d201f97ef39913a548', # psygnal-0.3.5.tar.gz + '34c36af20b555c7201da1c4cd26180aa446d9670f55a6e89a27152e4f50e0e29', # psygnal-0.3.5_python3.8.patch + ], + }), + ('pydantic', '1.9.1', { + 'checksums': ['1ed987c3ff29fff7fd8c3ea3a3ea877ad310aae2ef9889a119e22d3f2db0691a'], + }), + ('typer', '0.4.1', { + 'checksums': ['5646aef0d936b2c761a10393f0384ee6b5c7fe0bb3e5cd710b17134ca1d99cff'], + }), + ('npe2', '0.5.0', { + 'checksums': ['3d3d43b99bbd3b189fedd7313589c89642a4af0f14b24b9763eb134ba6a5548c'], + }), + ('numpydoc', '1.4.0', { + 'checksums': ['9494daf1c7612f59905fa09e65c9b8a90bbacb3804d91f7a94e778831e6fcfa5'], + }), + ('superqt', '0.3.2', { + 'checksums': ['a37df244a2d6e4387e865cdedabe925798b3352ab9cdc52f60701eb12d907960'], + }), + ('tifffile', '2022.5.4', { + 'checksums': ['b03147a15862b7c1d90d47435197f149bef7a52c25ad67cf1f9b465faa71b8d2'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.3', { + 'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'], + }), + ('pythran', '0.10.0', { + 'checksums': ['9dac8e1d50f33d4676003e350b1f0c878ce113e6f907920e92dc103352cac5bf'], + }), + (name, version, { + 'checksums': ['0d4cf6067d2112c78a705917aa5e74371463982d80147a898c6b5d2f0b514baa'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = [ + '%(name)s --help', + 'pyrcc5 -version 2>&1 |grep pyrcc5' # make sure PyQt5 module was not built with --no-tools +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch b/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch index 9ef096a19a4..b8f4bace8b2 100644 --- a/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch +++ b/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch @@ -1,4 +1,4 @@ -#Thomas Hoffmann, EMLB Heidelberg, structures-it@embl.de +#Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/10 #python > 3.7: prevent comple error future feature annotations is not defined diff -ru psygnal-0.3.5/psygnal/_evented_model.py psygnal-0.3.5_python3.8/psygnal/_evented_model.py --- psygnal-0.3.5/psygnal/_evented_model.py 2022-05-26 02:03:19.000000000 +0200 From 07e39d076f350b7b76461fbcc5d205bc73539b2f Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 21 Oct 2022 17:28:42 +0200 Subject: [PATCH 461/793] Delete PyQt5-5.15.4-GCCcore-10.3.0-tools.eb see #16469 --- .../PyQt5-5.15.4-GCCcore-10.3.0-tools.eb | 104 ------------------ 1 file changed, 104 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb deleted file mode 100644 index 12f9c77e512..00000000000 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb +++ /dev/null @@ -1,104 +0,0 @@ -easyblock = 'Bundle' - -name = 'PyQt5' -version = '5.15.4' -versionsuffix = '-tools' -homepage = 'https://www.riverbankcomputing.com/software/pyqt' -description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. -This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -toolchainopts = {'cstd': 'c++11'} - -builddependencies = [('binutils', '2.36.1')] -dependencies = [ - ('Python', '3.9.5'), - ('Qt5', '5.15.2'), -] - -default_easyblock = 'PythonPackage' - -local_sipdir = '%(installdir)s/share/sip' - -local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' - -local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " - -local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " -local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir -local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir -local_pyqtweb_configopts += "--no-stubs --no-dist-info" - -local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir -local_pyqt_configopts += "--no-stubs " -local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " -# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: -local_pyqt_configopts += "--bindir=%(installdir)s/bin " -local_pyqt_configopts += "--sipdir=%s " % local_sipdir - -local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " -local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " -local_sipver = '5.5.0' -components = [ - ('SIP', local_sipver, { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCELOWER_TAR_GZ], - 'checksums': ['5d024c419b30fea8a6de8c71a560c7ab0bc3c221fbfb14d55a5b865bd58eaac5'], - 'start_dir': 'sip-%s' % local_sipver, - 'use_pip': True, - 'options': {'modulename': 'PyQt5.sip'}, - }), - ('PyQt-builder', '1.10.1', { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['967b0c7bac0331597e9f8c5b336660f173a9896830b721d6d025e14bde647e17'], - 'start_dir': 'PyQt-builder-%(version)s', - 'use_pip': True, - }), - ('PyQt5_sip', '12.9.0', { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['d3e4489d7c2b0ece9d203ae66e573939f7f60d4d29e089c9f11daa17cfeaae32'], - 'start_dir': 'PyQt5_sip-%(version)s', - 'use_pip': True, - }), - (name, version, { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], - 'easyblock': 'ConfigureMakePythonPackage', - 'start_dir': '%(name)s-%(version)s', - 'preconfigopts': local_setup_env, - # run python configure.py in order to set bindir, which is no possible with sip-install: - 'configopts': local_pyqt_configopts, - }), - ('PyQtWebEngine', version, { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['cedc28f54165f4b8067652145aec7f732a17eadf6736835852868cf76119cc19'], - 'easyblock': 'ConfigureMakePythonPackage', - 'start_dir': '%(name)s-%(version)s', - 'preconfigopts': local_setup_env, - 'configopts': local_pyqtweb_configopts, - 'options': {'modulename': 'PyQt5.QtWebEngine'}, - }), -] - -sanity_check_paths = { - 'files': ['bin/pyrcc5', 'bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - "python -c 'import PyQt5.QtCore'", - "sip5 --help", -] - -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', - 'QT_INSTALL_DATA': 'qsci', -} - -moduleclass = 'vis' From 46ba80c925e0af2188ce63c74612d4a3fb718cff Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 21 Oct 2022 17:44:13 +0200 Subject: [PATCH 462/793] Delete napari-0.4.15-foss-2021a.eb --- .../n/napari/napari-0.4.15-foss-2021a.eb | 161 ------------------ 1 file changed, 161 deletions(-) delete mode 100644 easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb deleted file mode 100644 index 3f04fc5590d..00000000000 --- a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb +++ /dev/null @@ -1,161 +0,0 @@ -# Thomas Hoffmann, EMBL Heidelberg, structures-it@emblde, 2022/06 -easyblock = 'PythonBundle' - -name = 'napari' -version = '0.4.15' - -homepage = 'https://napari.org/' -description = """napari is a fast, interactive, multi-dimensional image viewer for Python. It's -designed for browsing, annotating, and analyzing large multi-dimensional images. -It's built on top of Qt (for the GUI), vispy (for performant GPU-based -rendering), and the scientific Python stack (numpy, scipy).""" - -toolchain = {'name': 'foss', 'version': '2021a'} - -dependencies = [ - ('Python', '3.9.5'), - ('PyQt5', '5.15.4', '-tools'), - ('SciPy-bundle', '2021.05'), - ('PyYAML', '5.4.1'), - ('dask', '2021.9.1'), - ('PyOpenGL', '3.1.5'), - ('imageio', '2.10.5'), # ext - ('tqdm', '4.61.1'), - ('IPython', '7.25.0'), - # ('VisPy', '0.6.6'), - # ('Qtconsole', '5.0.2'), - ('typing-extensions', '3.10.0.0'), - # ('scikit-image', '0.19.1') # ext . - ('networkx', '2.5.1'), # req. for scikit-image ext - ('matplotlib', '3.4.2'), -] - -use_pip = True -sanity_pip_check = True -download_dep_fail = True -exts_list = [ - ('pytomlpp', '1.0.10', { - 'checksums': ['6de110c8fe43f46c52b2041d5fbaa0522677a712234832ffd8cbb51cff50804e'], - }), - ('freetype_py', '2.3.0', { - 'modulename': 'freetype', - 'sources': ['freetype-py-%(version)s.zip'], - 'checksums': ['f9b64ce3272a5c358dcee824800a32d70997fb872a0965a557adca20fce7a5d0'], - }), - ('hsluv', '5.0.3', { - 'checksums': ['2586bcb61d29d76e89e563a6836df24d86939961c9657f129a59f7617de45377'], - }), - ('vispy', '0.10.0', { - 'checksums': ['b76ad6f3eacadbfc4944cfb8211eadb6ea8417a590993ece5aa7caac082cffc2'], - }), - ('qtconsole', '5.3.1', { - 'checksums': ['b73723fac43938b684dcb237a88510dc7721c43a726cea8ade179a2927c0a2f3'], - }), - ('wrapt', '1.12.1', { - 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], - }), - ('cachey', '0.2.1', { - 'checksums': ['0310ba8afe52729fa7626325c8d8356a8421c434bf887ac851e58dcf7cf056a6'], - }), - ('docstring-parser', '0.14.1', { - 'sources': 'docstring_parser-%(version)s.tar.gz', - 'checksums': ['2c77522e31b7c88b1ab457a1f3c9ae38947ad719732260ba77ee8a3deb58622a'], - }), - ('pep517', '0.12.0', { - 'checksums': ['931378d93d11b298cf511dd634cf5ea4cb249a28ef84160b3247ee9afb4e8ab0'], - }), - ('tomli', '2.0.1', { - 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], - }), - ('magicgui', '0.5.1', { - 'checksums': ['dcd05c4c9bbd55bdeb72d41069b2d4304952dabe04c2aac7bdd43f5a4e3a8a94'], - }), - ('napari-console', '0.0.4', { - 'modulename': 'napari_console', - 'checksums': ['ea0e30fbfdd76542adda44be457f1306a65146fe7578f95838e28d62874f4c45'], - }), - ('napari-plugin-engine', '0.2.0', { - 'checksums': ['fa926f869d70e0d652c005661948cd0c7fee5508ae17d437937f34f5287590b3'], - }), - ('napari-svg', '0.1.6', { - 'checksums': ['12fa5c64995fc7179349969a39316355496b463858c3b0815e3b3e7ffcdced34'], - }), - ('Pint', '0.19.2', { - 'checksums': ['e1d4989ff510b378dad64f91711e7bdabe5ca78d75b06a18569ac454678c4baf'], - }), - ('build', '0.8.0', { - 'checksums': ['887a6d471c901b1a6e6574ebaeeebb45e5269a79d095fe9a8f88d6614ed2e5f0'], - }), - ('psygnal', '0.3.5', { - 'patches': ['psygnal-0.3.5_python3.8.patch'], - 'checksums': [ - '5abf84f0da9f487be68299854c4eb39de0765236407736d201f97ef39913a548', # psygnal-0.3.5.tar.gz - 'c55cc07c646cb66e8c5d2ea227249216dbd1a1a9405acbd330d70105a3fd8890', # psygnal-0.3.5_python3.8.patch - ], - }), - ('pydantic', '1.9.1', { - 'checksums': ['1ed987c3ff29fff7fd8c3ea3a3ea877ad310aae2ef9889a119e22d3f2db0691a'], - }), - ('typer', '0.4.1', { - 'checksums': ['5646aef0d936b2c761a10393f0384ee6b5c7fe0bb3e5cd710b17134ca1d99cff'], - }), - ('npe2', '0.5.0', { - 'checksums': ['3d3d43b99bbd3b189fedd7313589c89642a4af0f14b24b9763eb134ba6a5548c'], - }), - ('numpydoc', '1.4.0', { - 'checksums': ['9494daf1c7612f59905fa09e65c9b8a90bbacb3804d91f7a94e778831e6fcfa5'], - }), - ('QtPy', '2.1.0', { - 'checksums': ['ca8cd4217175186344299ee4c0f7e7adcf362c70852ba35b255a534077025c06'], - }), - ('superqt', '0.3.2', { - 'checksums': ['a37df244a2d6e4387e865cdedabe925798b3352ab9cdc52f60701eb12d907960'], - }), - ('tifffile', '2022.5.4', { - 'checksums': ['b03147a15862b7c1d90d47435197f149bef7a52c25ad67cf1f9b465faa71b8d2'], - }), - ('pandas', '1.3.0', { - 'checksums': ['c554e6c9cf2d5ea1aba5979cc837b3649539ced0e18ece186f055450c86622e2'], - }), - ('beniget', '0.4.1', { - 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], - }), - ('ply', '3.11', { - 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], - }), - ('gast', '0.5.3', { - 'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'], - }), - ('pythran', '0.10.0', { - 'checksums': ['9dac8e1d50f33d4676003e350b1f0c878ce113e6f907920e92dc103352cac5bf'], - }), - ('PyWavelets', '1.2.0', { - 'modulename': 'pywt', - 'checksums': ['6cbd69b047bb4e00873097472133425f5f08a4e6bc8b3f0ae709274d4d5e9a8d'], - }), - ('imread', '0.7.4', { - 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], - }), - ('pooch', '1.5.2', { - 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], - }), - ('scikit-image', '0.19.1', { - 'modulename': 'skimage', - 'checksums': ['48f00ee1e8ec2818ae6a152c72df15f4db7f566e839f5c34e1a0c3c9e5210138'], - }), - (name, version, { - 'checksums': ['0d4cf6067d2112c78a705917aa5e74371463982d80147a898c6b5d2f0b514baa'], - }), -] - -sanity_check_paths = { - 'files': ['bin/%(name)s'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], -} - -sanity_check_commands = [ - '%(name)s --help', - 'pyrcc5 -version 2>&1 |grep pyrcc5' # make sure PyQt5 module was not built with --no-tools -] - -moduleclass = 'vis' From b5fb3cea9f0d353188d0430cb139a6f61641a707 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 18:46:08 +0100 Subject: [PATCH 463/793] adding easyconfigs: HTSeq-2.0.2-foss-2022a.eb --- .../h/HTSeq/HTSeq-2.0.2-foss-2022a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb new file mode 100644 index 00000000000..912a8595037 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb @@ -0,0 +1,42 @@ +# Updated to PythonBundle and latest version from Pypi +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'HTSeq' +version = '2.0.2' + +homepage = 'https://github.com/simon-anders/htseq' +description = """HTSeq is a Python library to facilitate processing and analysis + of data from high-throughput sequencing (HTS) experiments.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [('SWIG', '4.0.2')] + +dependencies = [ + ('Python', '3.10.4'), + ('Pysam', '0.19.1'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['e2c7442d6ff3f97293cfa0da276576f0996eae0a66eb3c2006332ef198f7ea09'], + 'modulename': '%(name)s', + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-count', 'bin/%(namelower)s-qa'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s/scripts'], +} + +sanity_check_commands = ['%(namelower)s-count --help'] + +moduleclass = 'bio' From 390bd6fef6998dc0f5701e8617ce384600f55aef Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 18:50:10 +0100 Subject: [PATCH 464/793] adding easyconfigs: psutil-5.9.3-GCCcore-11.3.0.eb --- .../p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c8b8ea559e1 --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'psutil' +version = '5.9.3' + +homepage = 'https://github.com/giampaolo/psutil' +description = """A cross-platform process and system utilities module for Python""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +use_pip = True +download_dep_fail = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/giampaolo/psutil/archive'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['7ccfcdfea4fc4b0a02ca2c31de7fcd186beb9cff8207800e14ab66f79c773af6'], + }), +] + +moduleclass = 'lib' From f9de54bbd6b5cff81931c993c093cf37f0bb15c1 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 18:52:27 +0100 Subject: [PATCH 465/793] adding easyconfigs: pybedtools-0.9.0-GCC-11.3.0.eb --- .../pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..80c02fc63c7 --- /dev/null +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'pybedtools' +version = '0.9.0' + +homepage = 'https://daler.github.io/pybedtools' +description = "pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +dependencies = [ + ('Python', '3.10.4'), + ('BEDTools', '2.30.0'), + ('Pysam', '0.19.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://daler.github.io/pybedtools/archive'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['9267c92cd764173449d9c31baedac0659b4eccc3d7c05e22ec378f86c0fc30a3'], + }), +] + +moduleclass = 'bio' From 756cca0dc2ae8128d92391352646f9e80bf1f14b Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 22:31:04 +0100 Subject: [PATCH 466/793] download_dep_fail removed as PythonBundle --- easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb index 912a8595037..241a26b0ee6 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb @@ -22,7 +22,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True exts_list = [ From fb21f3d920704c4fa21a24cbba474254ecf5e83c Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 22:33:45 +0100 Subject: [PATCH 467/793] download_dep_fail removed, sanity_pip_check added --- easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb index c8b8ea559e1..062ec65ec9a 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb @@ -13,7 +13,7 @@ builddependencies = [('binutils', '2.38')] dependencies = [('Python', '3.10.4')] use_pip = True -download_dep_fail = True +sanity_pip_check = True exts_list = [ (name, version, { From 6986e0ef3950f7ff15acd1a0deb46ccb414f16a3 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 22:36:39 +0100 Subject: [PATCH 468/793] download_dep_fail removed as PythonBundle --- .../easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb index 80c02fc63c7..4b4c5f40023 100644 --- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb @@ -14,7 +14,6 @@ dependencies = [ ('Pysam', '0.19.1'), ] -download_dep_fail = True use_pip = True sanity_pip_check = True From 5954dcafb701f24464d162c15db74a06b7cc8006 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 22 Oct 2022 10:27:25 +0200 Subject: [PATCH 469/793] adding easyconfigs: captum-0.5.0-foss-2022a-CUDA-11.7.0.eb, captum-0.5.0-foss-2022a.eb --- .../captum-0.5.0-foss-2022a-CUDA-11.7.0.eb | 33 +++++++++++++++++++ .../c/captum/captum-0.5.0-foss-2022a.eb | 31 +++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..cb2d2bdffbe --- /dev/null +++ b/easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'captum' +version = '0.5.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://captum.ai/' +description = """ +Captum is a model interpretability and understanding library for PyTorch. +Captum means comprehension in Latin and contains general purpose +implementations of integrated gradients, saliency maps, smoothgrad, vargrad and +others for PyTorch models. It has quick integration for models built with +domain-specific libraries such as torchvision, torchtext, and others.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', '-CUDA-%(cudaver)s'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['84af2c8793d34c440a351793b5ca705b8542745e2dc8bc24afb1d9b86f3bf6ec'], + }), +] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a.eb new file mode 100644 index 00000000000..7836096aaf7 --- /dev/null +++ b/easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'captum' +version = '0.5.0' + +homepage = 'https://captum.ai/' +description = """ +Captum is a model interpretability and understanding library for PyTorch. +Captum means comprehension in Latin and contains general purpose +implementations of integrated gradients, saliency maps, smoothgrad, vargrad and +others for PyTorch models. It has quick integration for models built with +domain-specific libraries such as torchvision, torchtext, and others.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['84af2c8793d34c440a351793b5ca705b8542745e2dc8bc24afb1d9b86f3bf6ec'], + }), +] + +moduleclass = 'ai' From ba3741e917188f3b0e2573509f515d35a63282d2 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Sat, 22 Oct 2022 11:09:12 +0200 Subject: [PATCH 470/793] Update napari-0.4.15-foss-2021b.eb remove download_dep_fail --- easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb index 1326a9f443b..914242860a4 100644 --- a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb +++ b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb @@ -30,7 +30,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = True exts_list = [ ('pytomlpp', '1.0.10', { 'checksums': ['6de110c8fe43f46c52b2041d5fbaa0522677a712234832ffd8cbb51cff50804e'], From ed4dd1f420b4222632beb2dd1b06aa94272ae6ef Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 24 Oct 2022 10:29:52 +0200 Subject: [PATCH 471/793] adding easyconfigs: RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb and patches: RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch, RStudio-Server-2022.07.1+554_fix-libsoci-search.patch, RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch --- ...2022.07.1+554_allow-disabling-quarto.patch | 46 ++++++++ ...ver-2022.07.1+554_fix-libsoci-search.patch | 27 +++++ ...ver-2022.07.1+554_use-XDG_CACHE_HOME.patch | 71 +++++++++++ ...022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb | 111 ++++++++++++++++++ 4 files changed, 255 insertions(+) create mode 100644 easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch create mode 100644 easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_fix-libsoci-search.patch create mode 100644 easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch create mode 100644 easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch new file mode 100644 index 00000000000..f57b688b6a5 --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch @@ -0,0 +1,46 @@ +From 9b7ac4b2952a47568d23f6cbfed4a797798ee161 Mon Sep 17 00:00:00 2001 +From: Kevin Ushey +Date: Fri, 19 Aug 2022 10:01:14 -0700 +Subject: [PATCH] make it possible to control QUARTO_ENABLED from command line + +--- + CMakeGlobals.txt | 26 ++++++++++++++------------ + 1 file changed, 14 insertions(+), 12 deletions(-) + +diff --git a/CMakeGlobals.txt b/CMakeGlobals.txt +index 6dfe1017a9a..cbd8e865672 100644 +--- a/CMakeGlobals.txt ++++ b/CMakeGlobals.txt +@@ -244,18 +244,20 @@ if(LINUX AND EXISTS "/etc/centos-release") + endif() + + # quarto support +-if(LINUX AND UNAME_M STREQUAL aarch64) +- # disabled on linux aarch64 +- message(STATUS "quarto does not yet support aarch64 builds of Linux; disabling quarto") +- set(QUARTO_ENABLED FALSE CACHE INTERNAL "") +-elseif(IS_CENTOS7) +- # disable quarto on Centos 7 +- message(STATUS "quarto is not supported on Centos7; disabling quarto") +- set(QUARTO_ENABLED FALSE CACHE INTERNAL "") +-else() +- # enable by default +- set(QUARTO_ENABLED TRUE CACHE INTERNAL "") +- add_definitions(-DQUARTO_ENABLED) ++if(NOT DEFINED QUARTO_ENABLED) ++ if(LINUX AND UNAME_M STREQUAL aarch64) ++ # disabled on linux aarch64 ++ message(STATUS "quarto does not yet support aarch64 builds of Linux; disabling quarto") ++ set(QUARTO_ENABLED FALSE CACHE INTERNAL "") ++ elseif(IS_CENTOS7) ++ # disable quarto on Centos 7 ++ message(STATUS "quarto is not supported on Centos7; disabling quarto") ++ set(QUARTO_ENABLED FALSE CACHE INTERNAL "") ++ else() ++ # enable by default ++ set(QUARTO_ENABLED TRUE CACHE INTERNAL "") ++ add_definitions(-DQUARTO_ENABLED) ++ endif() + endif() + + # install freedesktop integration files if we are installing into /usr diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_fix-libsoci-search.patch b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_fix-libsoci-search.patch new file mode 100644 index 00000000000..25cae4ea6db --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_fix-libsoci-search.patch @@ -0,0 +1,27 @@ +Allow to find system SOCI_* libraries + +Add a second `find_library` call which will find the SOCI libraries in default locations if it hasn't been found already in `SOCI_LIBRARY_DIR` +See https://github.com/rstudio/rstudio/pull/11691 + +Author: Alexander Grund (TU Dresden) + +diff --git a/src/cpp/CMakeLists.txt b/src/cpp/CMakeLists.txt +index d2be417b40..6a42b4614d 100644 +--- a/src/cpp/CMakeLists.txt ++++ b/src/cpp/CMakeLists.txt +@@ -467,12 +467,12 @@ endif() + # find SOCI libraries + if(UNIX) + set(SOCI_LIBRARY_DIR "${RSTUDIO_TOOLS_SOCI}/build/lib") +- if(NOT APPLE AND RSTUDIO_USE_SYSTEM_SOCI) +- set(SOCI_LIBRARY_DIR "/usr/lib") +- endif() + find_library(SOCI_CORE_LIB NAMES "libsoci_core.a" "soci_core" PATHS "${SOCI_LIBRARY_DIR}" NO_DEFAULT_PATH) ++ find_library(SOCI_CORE_LIB NAMES "libsoci_core.a" "soci_core") + find_library(SOCI_SQLITE_LIB NAMES "libsoci_sqlite3.a" "soci_sqlite3" PATHS "${SOCI_LIBRARY_DIR}" NO_DEFAULT_PATH) ++ find_library(SOCI_SQLITE_LIB NAMES "libsoci_sqlite3.a" "soci_sqlite3") + find_library(SOCI_POSTGRESQL_LIB NAMES "libsoci_postgresql.a" "soci_postgresql" PATHS "${SOCI_LIBRARY_DIR}" NO_DEFAULT_PATH) ++ find_library(SOCI_POSTGRESQL_LIB NAMES "libsoci_postgresql.a" "soci_postgresql") + find_library(DL_LIB "dl") + find_library(SQLITE_LIB "sqlite3") + get_filename_component(SQLITE_LIB "${SQLITE_LIB}" REALPATH) diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch new file mode 100644 index 00000000000..9df3a006a82 --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch @@ -0,0 +1,71 @@ +From https://github.com/rstudio/rstudio/pull/11976 + +From c131989e8ecb19733fe274fe7ad8a18d490fdcf9 Mon Sep 17 00:00:00 2001 +From: Jonathan McPherson +Date: Mon, 19 Sep 2022 14:34:18 -0700 +Subject: [PATCH] use XDG_CACHE_HOME for secure cookie key in low privilege + mode + +--- + src/cpp/core/include/core/system/Xdg.hpp | 7 +++++++ + src/cpp/core/system/Xdg.cpp | 15 +++++++++++++++ + src/cpp/server_core/SecureKeyFile.cpp | 2 +- + 3 files changed, 23 insertions(+), 1 deletion(-) + +diff --git a/src/cpp/core/include/core/system/Xdg.hpp b/src/cpp/core/include/core/system/Xdg.hpp +index 71cb2a8d50f..ed848ca2476 100644 +--- a/src/cpp/core/include/core/system/Xdg.hpp ++++ b/src/cpp/core/include/core/system/Xdg.hpp +@@ -66,6 +66,13 @@ FilePath userDataDir(const boost::optional& user = boost::none, + // Returns the user-specific logging directory underneath the userDataDir + FilePath userLogDir(); + ++// Returns the RStudio XDG user cache directory. ++// ++// On Unix-alikes, this is ~/.cache, or XDG_CACHE_HOME. ++// On Windows, this is 'FOLDERID_InternetCache' (typically 'AppData/Local/Microsoft/Windows/Temporary Files') ++FilePath userCacheDir(const boost::optional& user = boost::none, ++ const boost::optional& homeDir = boost::none); ++ + // This function verifies that the userConfigDir() and userDataDir() exist and are owned by the running user. + // + // It should be invoked once. Any issues with these directories will be emitted to the session log. +diff --git a/src/cpp/core/system/Xdg.cpp b/src/cpp/core/system/Xdg.cpp +index 3866f286437..ca1e7923ac5 100644 +--- a/src/cpp/core/system/Xdg.cpp ++++ b/src/cpp/core/system/Xdg.cpp +@@ -218,6 +218,21 @@ FilePath userDataDir( + ); + } + ++FilePath userCacheDir( ++ const boost::optional& user, ++ const boost::optional& homeDir) ++{ ++ return resolveXdgDir("RSTUDIO_CACHE_HOME", ++ "XDG_CACHE_HOME", ++#ifdef _WIN32 ++ FOLDERID_InternetCache, ++#endif ++ "~/.cache", ++ user, ++ homeDir ++ ); ++} ++ + FilePath userLogDir() + { + return userDataDir().completePath("log"); +diff --git a/src/cpp/server_core/SecureKeyFile.cpp b/src/cpp/server_core/SecureKeyFile.cpp +index d3a5e37c1bd..cbc3a91a44c 100644 +--- a/src/cpp/server_core/SecureKeyFile.cpp ++++ b/src/cpp/server_core/SecureKeyFile.cpp +@@ -113,7 +113,7 @@ core::Error readSecureKeyFile(const std::string& filename, + } + else + { +- secureKeyPath = core::FilePath("/tmp/rstudio-server").completePath(filename); ++ secureKeyPath = core::system::xdg::userCacheDir().completePath(filename); + if (secureKeyPath.exists()) + { + LOG_INFO_MESSAGE("Running without privilege; using secure key at " + secureKeyPath.getAbsolutePath()); diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb new file mode 100644 index 00000000000..1f49f98c15c --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb @@ -0,0 +1,111 @@ +easyblock = 'CMakeNinja' + +name = 'RStudio-Server' +version = '2022.07.2+576' +versionsuffix = '-Java-%(javaver)s-R-%(rver)s' +local_git_rev = '7872775ebddc40635780ca1ed238934c3345c5de' + +homepage = 'https://www.rstudio.com/' +description = """This is the RStudio Server version. +RStudio is a set of integrated tools designed to help you be more productive with R. + +The server can be started with: + rserver --server-daemonize=0 --www-port 8787 --rsession-which-r=$(which R) + +If you need a database config one can be created with: + MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" +and then used with: + rserver ... --database-config-file "${MYTMP}/db.conf" +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/rstudio/rstudio/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-2022.07.1+554_allow-disabling-quarto.patch', + '%(name)s-2022.07.1+554_fix-libsoci-search.patch', + '%(name)s-2022.07.1+554_use-XDG_CACHE_HOME.patch', +] +checksums = [ + '55705c36a9b826064b4d9aa87b58c40bb9f7cd2f149b16d554e20136306ce301', + # RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch + '165306d976c7b851e1e6a2d1f0c2967984b0cd203006aa834a1a6ff17894cf81', + # RStudio-Server-2022.07.1+554_fix-libsoci-search.patch + '0dafd9fa45d745d350c0c852fe03e3e1e77558d94baae2b5c595d97765002cd5', + # RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch + 'd033a383c8518a85dcdf45baf14d0a9d6283d03a28576a6eb03bbfb3682d2b00', +] + +builddependencies = [ + ('ant', '1.10.11', '-Java-%(javaver)s', SYSTEM), + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Boost', '1.79.0'), + ('Java', '11', '', SYSTEM), + ('R', '4.2.1'), + ('SOCI', '4.0.3'), + ('yaml-cpp', '0.7.0'), +] + +osdependencies = [ + ('pam-devel', 'libpam0g-dev') +] + +# Required until https://github.com/easybuilders/easybuild-framework/pull/4035 +local_start_dir = "%(builddir)s/rstudio-" + version.replace("+", "-") + +preconfigopts = " && ".join([ + # Install dependencies via scripts. Done in subshell to preserve PWD + "(export RSTUDIO_TOOLS_ROOT='%(builddir)s'", + "cd '%s/dependencies/common'" % local_start_dir, + "./install-cef", + "./install-dictionaries", + "./install-mathjax", + "./install-pandoc", + "./install-packages", + "./install-npm-dependencies)", + "" +]) + +configopts = " ".join([ + "-DRSTUDIO_TOOLS_ROOT='%(builddir)s'", + "-DRSTUDIO_TARGET=Server", + "-DRSTUDIO_USE_SYSTEM_BOOST=ON", + "-DRSTUDIO_USE_SYSTEM_SOCI=ON", + "-DRSTUDIO_USE_SYSTEM_YAML_CPP=ON", + "-DQUARTO_ENABLED=OFF", # Not available on all archs, use pandoc fallback + "-DRSTUDIO_GIT_REVISION_HASH=" + local_git_rev +]) + +sanity_check_commands = [ + # RSession requires environment variables R_HOME and R_DOC_DIR + 'R_HOME="$EBROOTR/lib64/R" R_DOC_DIR="$R_HOME/doc" rsession --verify-installation=1', + # RServer requires a db conf (this may also be needed for live use) + # Also create and set a soem dirs so it doesn't try to use $HOME + 'MYTMP=`mktemp -d`' + ' && export RSTUDIO_CONFIG_DIR="$MYTMP"' + ' && export XDG_DATA_HOME="$MYTMP/.data"' + ' && export XDG_CACHE_HOME="$MYTMP/.cache"' + ' && mkdir "$XDG_DATA_HOME" "$XDG_CACHE_HOME"' + ' && export RS_LOG_DIR="$MYTMP/log"' + ' && echo -e "provider=sqlite\\ndirectory=$MYTMP/db" >> "$MYTMP/db.conf"' + ' && rserver ' + ' '.join([ + '--verify-installation=1', + '--server-user="$USER"', + '--database-config-file="$MYTMP/db.conf"', + '--server-data-dir="$MYTMP/sdd"', + '--secure-cookie-key-file="$MYTMP/secure-cookie-key"', + ]), +] + +sanity_check_paths = { + 'files': ['bin/rstudio-server'], + 'dirs': ['bin', 'extras', 'resources', 'www', 'www-symbolmaps', 'R'], +} + +moduleclass = 'lang' From d46d46113fd3c6840f138d95449051eac2ffa601 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Mon, 24 Oct 2022 12:03:25 +0200 Subject: [PATCH 472/793] Typo dependency name "-" -> "_" Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb index 4242b5cd1ae..f6ed3b365e2 100644 --- a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb @@ -30,7 +30,7 @@ exts_list = [ 'modulename': 'google', 'checksums': ['c25873c47279387cfdcbdafa36149887901d36202cb645a0e4f29686bf6e4417'], }), - ('tensorflow-metadata', '1.10.0', { + ('tensorflow_metadata', '1.10.0', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3'], }), From 1e50f35c8b4072935096f4275f9e9f7dfae5aa64 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 11:13:29 +0100 Subject: [PATCH 473/793] adding easyconfigs: MoviePy-1.0.3-foss-2021a.eb and patches: moviepy-1.0.3-setup.py.patch --- .../m/MoviePy/MoviePy-1.0.3-foss-2021a.eb | 42 +++++++++++++++++++ .../m/MoviePy/moviepy-1.0.3-setup.py.patch | 16 +++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021a.eb create mode 100644 easybuild/easyconfigs/m/MoviePy/moviepy-1.0.3-setup.py.patch diff --git a/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021a.eb b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021a.eb new file mode 100644 index 00000000000..a5a67866969 --- /dev/null +++ b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021a.eb @@ -0,0 +1,42 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +# Updated to foss 2021a: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'MoviePy' +version = '1.0.3' + +homepage = "https://zulko.github.io/moviepy/" +description = """MoviePy (full documentation) is a Python library for video editing: cutting, concatenations, + title insertions, video compositing (a.k.a. non-linear editing), video processing, and creation of custom effects.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('FFmpeg', '4.3.2'), + ('Python', '3.9.5'), + ('Pillow', '8.2.0'), + ('SciPy-bundle', '2021.05'), + ('tqdm', '4.61.2'), + ('imageio', '2.10.5'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('imageio-ffmpeg', '0.4.7', { + 'checksums': ['7a08838f97f363e37ca41821b864fd3fdc99ab1fe2421040c78eb5f56a9e723e'], + }), + ('proglog', '0.1.10', { + 'checksums': ['658c28c9c82e4caeb2f25f488fff9ceace22f8d69b15d0c1c86d64275e4ddab4'], + }), + (name, version, { + 'source_tmpl': 'moviepy-%(version)s.tar.gz', + 'patches': ['moviepy-1.0.3-setup.py.patch'], + 'checksums': [('2884e35d1788077db3ff89e763c5ba7bfddbd7ae9108c9bc809e7ba58fa433f5'), + ('beca82ff8dfbc9cd0b97296f310de3ddfc43e2e49344a32375d4438485c3f3df')], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/MoviePy/moviepy-1.0.3-setup.py.patch b/easybuild/easyconfigs/m/MoviePy/moviepy-1.0.3-setup.py.patch new file mode 100644 index 00000000000..ce24edbfaea --- /dev/null +++ b/easybuild/easyconfigs/m/MoviePy/moviepy-1.0.3-setup.py.patch @@ -0,0 +1,16 @@ +Changed the max. version of decorator to <6.0 +https://github.com/Zulko/moviepy/blob/master/setup.py +Author: J. Sassmannshausen +diff --git a/moviepy-1.0.3.orig/setup.py b/moviepy-1.0.3/setup.py +index f8088bb..feb7da7 100644 +--- a/moviepy-1.0.3.orig/setup.py ++++ b/moviepy-1.0.3/setup.py +@@ -62,7 +62,7 @@ exec(open('moviepy/version.py').read()) # loads __version__ + + # Define the requirements for specific execution needs. + requires = [ +- 'decorator>=4.0.2,<5.0', ++ 'decorator>=4.0.2,<6.0', + "imageio>=2.5,<3.0; python_version>='3.4'", + "imageio>=2.0,<2.5; python_version<'3.4'", + "imageio_ffmpeg>=0.2.0; python_version>='3.4'", From a00e25f72c3e369e977d91da33be44b6deb3b8da Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 12:13:47 +0100 Subject: [PATCH 474/793] GCCcore-10.2.0 EasyConfig file added --- .../p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..9bae7e1c2ba --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'psutil' +version = '5.9.3' + +homepage = 'https://github.com/giampaolo/psutil' +description = """A cross-platform process and system utilities module for Python""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/giampaolo/psutil/archive'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['7ccfcdfea4fc4b0a02ca2c31de7fcd186beb9cff8207800e14ab66f79c773af6'], + }), +] + +moduleclass = 'lib' From 09b501df5ed25a2b5a89c9d1e0e6a8603c753e87 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 12:36:28 +0100 Subject: [PATCH 475/793] MoviePi added, scikit-image downgraded --- ...epLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 34 +++++++++++++++++-- 1 file changed, 31 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index 9416f4eee39..0a0782a73af 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -1,4 +1,6 @@ # Loosely based on PR #7680 +# Scikit-image is added as an extension to avoid problems with imageio, +# which comes in from MoviePy # J. Sassmannshausen (Imperial College London/UK) easyblock = 'PythonBundle' @@ -15,13 +17,12 @@ toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'pic': True} dependencies = [ - ('CUDA', '11.3.1', '', SYSTEM), - ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), + ('CUDA', '11.3.1', '', True), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), ('Python', '3.9.5'), ('h5py', '3.2.1'), ('IPython', '7.25.0'), ('scikit-learn', '0.24.2'), - ('scikit-image', '0.18.3'), ('TensorFlow', '2.6.0', versionsuffix), ('PyYAML', '5.4.1'), ('PyTables', '3.6.1'), @@ -34,6 +35,7 @@ dependencies = [ ('ruamel.yaml', '0.17.21'), ('statsmodels', '0.12.2'), ('PyTorch', '1.10.0', versionsuffix), + ('MoviePy', '1.0.3'), ] sanity_pip_check = True @@ -56,6 +58,32 @@ exts_list = [ 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], 'sources': ['msgpack-numpy-0.4.8.tar.gz'], }), + + # this is for scikit-image + ('PyWavelets', '1.1.1', { + 'modulename': 'pywt', + 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.5.2', { + 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], + }), + ('tifffile', '2021.10.12', { + 'checksums': ['0a78268a2d844af94929512d28b39bd1ea6fe46de4124103840b5fe4e1c555cd'], + }), + ('scikit-image', '0.18.1', { + 'modulename': 'skimage', + 'patches': ['scikit-image-0.18.1_fix-README-cache-perms.patch'], + 'checksums': [ + 'fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171', # scikit-image-0.18.1.tar.gz + # scikit-image-0.18.1_fix-README-cache-perms.patch + '3a941401231403808963d488aaf498a712c428c3b19a1752652be9972d82b7b8', + ], + }), + # end of scikit-image + (name, version, { 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84'], From 03c6a0b337b37f16a536474ef3f62640e119bd6c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 24 Oct 2022 13:58:39 +0200 Subject: [PATCH 476/793] Remove superflous example parameter --- ...RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb index 1f49f98c15c..b63011c23f4 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb @@ -10,12 +10,12 @@ description = """This is the RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R. The server can be started with: - rserver --server-daemonize=0 --www-port 8787 --rsession-which-r=$(which R) + rserver --server-daemonize=0 --www-port=8787 If you need a database config one can be created with: MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" and then used with: - rserver ... --database-config-file "${MYTMP}/db.conf" + rserver ... --database-config-file="${MYTMP}/db.conf" """ toolchain = {'name': 'foss', 'version': '2022a'} From 3fcbcc9a601c1fe03a7f05e0b0724dc85d0a8b6e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 24 Oct 2022 14:00:56 +0200 Subject: [PATCH 477/793] Add dependencies --- .../s/SOCI/SOCI-4.0.3-GCC-11.3.0.eb | 52 +++++++ .../yaml-cpp/yaml-cpp-0.7.0-GCCcore-11.3.0.eb | 30 ++++ .../yaml-cpp-0.7.0_fix-cmake-export.patch | 143 ++++++++++++++++++ 3 files changed, 225 insertions(+) create mode 100644 easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0_fix-cmake-export.patch diff --git a/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.3.0.eb new file mode 100644 index 00000000000..63024d01cc2 --- /dev/null +++ b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'SOCI' +version = '4.0.3' + +homepage = 'http://soci.sourceforge.net/' +description = """SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the + regular C++ code, staying entirely within the Standard C++.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/SOCI/soci/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4b1ff9c8545c5d802fbe06ee6cd2886630e5c03bf740e269bb625b45cf934928'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Boost', '1.79.0'), + ('SQLite', '3.38.3'), + ('PostgreSQL', '14.4'), +] + +# Matches RStudio (1.4.1717) install options +# https://github.com/rstudio/rstudio/blob/ddcd7191ec89c4da00e77afae7e9f27e61e87c36/dependencies/common/install-soci +configopts = "-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true " +configopts += "-DSOCI_TESTS=OFF " +configopts += "-DSOCI_CXX11=ON " +configopts += "-DSOCI_EMPTY=OFF " +configopts += '-DCMAKE_INCLUDE_PATH="$EBROOTBOOST/include" ' +configopts += "-DBoost_USE_STATIC_LIBS=ON " +configopts += '-DCMAKE_LIBRARY_PATH="$EBROOTBOOST/lib" ' +configopts += "-DWITH_BOOST=ON " +configopts += "-DWITH_POSTGRESQL=ON " +configopts += "-DWITH_SQLITE3=ON " +configopts += "-DWITH_DB2=OFF " +configopts += "-DWITH_MYSQL=OFF " +configopts += "-DWITH_ORACLE=OFF " +configopts += "-DWITH_FIREBIRD=OFF " +configopts += "-DWITH_ODBC=OFF " +configopts += "-DBoost_DEBUG=1 " + +local_dbs = ['postgresql', 'sqlite3'] + +sanity_check_paths = { + 'files': ['lib/libsoci_%s.%s' % (x, SHLIB_EXT) for x in local_dbs + ['core']], + 'dirs': ['include/soci/%s' % x for x in local_dbs], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c218e476fb7 --- /dev/null +++ b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'CMakeMake' +name = 'yaml-cpp' +version = '0.7.0' + +homepage = "https://github.com/jbeder/yaml-cpp" +description = """yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/jbeder/%(name)s/archive/'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-cmake-export.patch'] +checksums = [ + '43e6a9fcb146ad871515f0d0873947e5d497a1c9c60c58cb102a97b47208b7c3', + 'c562a575bbb161af478795e43bfd9073e3f874bea07134a321c1063cd7098c1c', # yaml-cpp-0.7.0_fix-cmake-export.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1') +] + +sanity_check_paths = { + 'files': ['lib/libyaml-cpp.a', 'include/yaml-cpp/yaml.h'], + 'dirs': ['lib', 'include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0_fix-cmake-export.patch b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0_fix-cmake-export.patch new file mode 100644 index 00000000000..45933bb6962 --- /dev/null +++ b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0_fix-cmake-export.patch @@ -0,0 +1,143 @@ +Fix installed CMake config files. +From https://patch-diff.githubusercontent.com/raw/jbeder/yaml-cpp/pull/1077 + +From a339bea6bb7bd461a41e874f78b46a5af98277ff Mon Sep 17 00:00:00 2001 +From: Felix +Date: Thu, 30 Dec 2021 12:53:31 +0100 +Subject: [PATCH 1/2] untabify CMakeLists.txt in some places + +This is to align with the other code parts in this file. +--- + CMakeLists.txt | 16 ++++++++-------- + 1 file changed, 8 insertions(+), 8 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index f65efefa..6adbf45a 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -141,30 +141,30 @@ write_basic_package_version_file( + configure_file(yaml-cpp.pc.in yaml-cpp.pc @ONLY) + + if (YAML_CPP_INSTALL) +- install(TARGETS yaml-cpp ++ install(TARGETS yaml-cpp + EXPORT yaml-cpp-targets + RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} + LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} + ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) +- install(DIRECTORY ${PROJECT_SOURCE_DIR}/include/ ++ install(DIRECTORY ${PROJECT_SOURCE_DIR}/include/ + DESTINATION ${CMAKE_INSTALL_INCLUDEDIR} +- FILES_MATCHING PATTERN "*.h") ++ FILES_MATCHING PATTERN "*.h") + install(EXPORT yaml-cpp-targets + DESTINATION "${CMAKE_INSTALL_DATADIR}/cmake/yaml-cpp") +- install(FILES +- "${PROJECT_BINARY_DIR}/yaml-cpp-config.cmake" +- "${PROJECT_BINARY_DIR}/yaml-cpp-config-version.cmake" ++ install(FILES ++ "${PROJECT_BINARY_DIR}/yaml-cpp-config.cmake" ++ "${PROJECT_BINARY_DIR}/yaml-cpp-config-version.cmake" + DESTINATION "${CMAKE_INSTALL_DATADIR}/cmake/yaml-cpp") + install(FILES "${PROJECT_BINARY_DIR}/yaml-cpp.pc" + DESTINATION ${CMAKE_INSTALL_DATADIR}/pkgconfig) + endif() + + if(YAML_CPP_BUILD_TESTS) +- add_subdirectory(test) ++ add_subdirectory(test) + endif() + + if(YAML_CPP_BUILD_TOOLS) +- add_subdirectory(util) ++ add_subdirectory(util) + endif() + + if (YAML_CPP_CLANG_FORMAT_EXE) + +From c1f987850a6282435f499bee76b12e32d7472f12 Mon Sep 17 00:00:00 2001 +From: Felix +Date: Thu, 30 Dec 2021 15:35:54 +0100 +Subject: [PATCH 2/2] fix cmake export + +After configure the file `yaml-cpp-config.cmake.in` the result ends up with +empty variables. (see also the discussion in #774). + +Rework this file and the call to `configure_package_config_file` according the +cmake documentation +(https://cmake.org/cmake/help/v3.22/module/CMakePackageConfigHelpers.html?highlight=configure_package_config#command:configure_package_config_file) +to overcome this issue and allow a simple `find_package` after install. + +As there was some discussion about the place where to install the +`yaml-cpp-config.cmake` file, e.g. #1055, factor out the install location into +an extra variable to make it easier changing this location in the future. +--- + CMakeLists.txt | 17 ++++++++++++----- + yaml-cpp-config.cmake.in | 10 ++++++---- + 2 files changed, 18 insertions(+), 9 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 6adbf45a..e9310792 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -129,10 +129,16 @@ set_target_properties(yaml-cpp PROPERTIES + PROJECT_LABEL "yaml-cpp ${yaml-cpp-label-postfix}" + DEBUG_POSTFIX "${CMAKE_DEBUG_POSTFIX}") + ++# FIXME(felix2012): A more common place for the cmake export would be ++# `CMAKE_INSTALL_LIBDIR`, as e.g. done in ubuntu or in this project for GTest ++set(CONFIG_EXPORT_DIR "${CMAKE_INSTALL_DATADIR}/cmake/yaml-cpp") ++set(EXPORT_TARGETS yaml-cpp) + configure_package_config_file( + "${PROJECT_SOURCE_DIR}/yaml-cpp-config.cmake.in" + "${PROJECT_BINARY_DIR}/yaml-cpp-config.cmake" +- INSTALL_DESTINATION "${CMAKE_INSTALL_DATADIR}/cmake/yaml-cpp") ++ INSTALL_DESTINATION "${CONFIG_EXPORT_DIR}" ++ PATH_VARS CMAKE_INSTALL_INCLUDEDIR CONFIG_EXPORT_DIR) ++unset(EXPORT_TARGETS) + + write_basic_package_version_file( + "${PROJECT_BINARY_DIR}/yaml-cpp-config-version.cmake" +@@ -150,14 +156,15 @@ if (YAML_CPP_INSTALL) + DESTINATION ${CMAKE_INSTALL_INCLUDEDIR} + FILES_MATCHING PATTERN "*.h") + install(EXPORT yaml-cpp-targets +- DESTINATION "${CMAKE_INSTALL_DATADIR}/cmake/yaml-cpp") ++ DESTINATION "${CONFIG_EXPORT_DIR}") + install(FILES +- "${PROJECT_BINARY_DIR}/yaml-cpp-config.cmake" +- "${PROJECT_BINARY_DIR}/yaml-cpp-config-version.cmake" +- DESTINATION "${CMAKE_INSTALL_DATADIR}/cmake/yaml-cpp") ++ "${PROJECT_BINARY_DIR}/yaml-cpp-config.cmake" ++ "${PROJECT_BINARY_DIR}/yaml-cpp-config-version.cmake" ++ DESTINATION "${CONFIG_EXPORT_DIR}") + install(FILES "${PROJECT_BINARY_DIR}/yaml-cpp.pc" + DESTINATION ${CMAKE_INSTALL_DATADIR}/pkgconfig) + endif() ++unset(CONFIG_EXPORT_DIR) + + if(YAML_CPP_BUILD_TESTS) + add_subdirectory(test) +diff --git a/yaml-cpp-config.cmake.in b/yaml-cpp-config.cmake.in +index 7b41e3f3..a7ace3dc 100644 +--- a/yaml-cpp-config.cmake.in ++++ b/yaml-cpp-config.cmake.in +@@ -3,12 +3,14 @@ + # YAML_CPP_INCLUDE_DIR - include directory + # YAML_CPP_LIBRARIES - libraries to link against + +-# Compute paths +-get_filename_component(YAML_CPP_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) +-set(YAML_CPP_INCLUDE_DIR "@CONFIG_INCLUDE_DIRS@") ++@PACKAGE_INIT@ ++ ++set_and_check(YAML_CPP_INCLUDE_DIR "@PACKAGE_CMAKE_INSTALL_INCLUDEDIR@") + + # Our library dependencies (contains definitions for IMPORTED targets) +-include("${YAML_CPP_CMAKE_DIR}/yaml-cpp-targets.cmake") ++include(@PACKAGE_CONFIG_EXPORT_DIR@/yaml-cpp-targets.cmake) + + # These are IMPORTED targets created by yaml-cpp-targets.cmake + set(YAML_CPP_LIBRARIES "@EXPORT_TARGETS@") ++ ++check_required_components(@EXPORT_TARGETS@) From 7211d86c16354a8e7c0e084c94e148ddd2911ffc Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 24 Oct 2022 15:18:55 +0200 Subject: [PATCH 478/793] Update napari-0.4.15-foss-2021b.eb typo --- easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb index 914242860a4..f439e3019c2 100644 --- a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb +++ b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb @@ -1,4 +1,4 @@ -# Thomas Hoffmann, EMBL Heidelberg, structures-it@emblde, 2022/10 +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/10 easyblock = 'PythonBundle' name = 'napari' From 9102b2e16bb86cd14d65df2ab77d435b79bb83ba Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 14:32:09 +0100 Subject: [PATCH 479/793] True reverted to system, scikit-image readded and setup.py patched to newer version of scikit-image --- ...epLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 37 ++++--------------- 1 file changed, 7 insertions(+), 30 deletions(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index 0a0782a73af..ce1fb1bf8a9 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -1,6 +1,4 @@ # Loosely based on PR #7680 -# Scikit-image is added as an extension to avoid problems with imageio, -# which comes in from MoviePy # J. Sassmannshausen (Imperial College London/UK) easyblock = 'PythonBundle' @@ -17,12 +15,13 @@ toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'pic': True} dependencies = [ - ('CUDA', '11.3.1', '', True), - ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('CUDA', '11.3.1', '', SYSTEM), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), ('Python', '3.9.5'), ('h5py', '3.2.1'), ('IPython', '7.25.0'), ('scikit-learn', '0.24.2'), + ('scikit-image', '0.18.3'), ('TensorFlow', '2.6.0', versionsuffix), ('PyYAML', '5.4.1'), ('PyTables', '3.6.1'), @@ -59,34 +58,12 @@ exts_list = [ 'sources': ['msgpack-numpy-0.4.8.tar.gz'], }), - # this is for scikit-image - ('PyWavelets', '1.1.1', { - 'modulename': 'pywt', - 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], - }), - ('imread', '0.7.4', { - 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], - }), - ('pooch', '1.5.2', { - 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], - }), - ('tifffile', '2021.10.12', { - 'checksums': ['0a78268a2d844af94929512d28b39bd1ea6fe46de4124103840b5fe4e1c555cd'], - }), - ('scikit-image', '0.18.1', { - 'modulename': 'skimage', - 'patches': ['scikit-image-0.18.1_fix-README-cache-perms.patch'], - 'checksums': [ - 'fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171', # scikit-image-0.18.1.tar.gz - # scikit-image-0.18.1_fix-README-cache-perms.patch - '3a941401231403808963d488aaf498a712c428c3b19a1752652be9972d82b7b8', - ], - }), - # end of scikit-image - (name, version, { 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84'], + 'patches': ['deeplabcut-2.2.0.6-setup.py.patch'], + 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84', + # deeplabcut-2.2.0.6-setup.py.patch: + '1dbef23575b105a6b2fa39f28d67bf926701d4c0b4f48bed7a6b179b7e5df2b0'], }), ] From 6edee6bab09760d21ddd8c6e7f6d3fe89767571c Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 14:35:40 +0100 Subject: [PATCH 480/793] patchfile added --- .../DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch diff --git a/easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch b/easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch new file mode 100644 index 00000000000..9bef2d46b0c --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch @@ -0,0 +1,15 @@ +scikit-imiage version bumped to 0.18.3 to use the one in EasyBuild +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/deeplabcut-2.2.0.6.orig/setup.py b/deeplabcut-2.2.0.6/setup.py +index 3bff4f2..2e0926b 100644 +--- a/deeplabcut-2.2.0.6.orig/setup.py ++++ b/deeplabcut-2.2.0.6/setup.py +@@ -33,7 +33,7 @@ setuptools.setup( + "networkx", + "numpy", + "pandas>=1.0.1", +- "scikit-image>=0.17,<=0.18.1", ++ "scikit-image>=0.17,<=0.18.3", + "scikit-learn", + "scipy>=1.4", + "statsmodels>=0.11", From 4bf1cbefb5f7888caddb40fa7a3d9f64f168e403 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 24 Oct 2022 16:13:09 +0200 Subject: [PATCH 481/793] adding easyconfigs: Seurat-4.2.0-foss-2022a-R-4.2.1.eb --- .../Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..af03c570285 --- /dev/null +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,51 @@ +easyblock = 'Bundle' + +name = 'Seurat' +version = '4.2.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://satijalab.org/seurat' +description = "Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data." + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} + +exts_list = [ + ('Matrix', '1.5-1', { + 'checksums': ['557dba0358172d67dc63eb5db90841915bb5ce1528f941a8005ae808d635575d'], + }), + ('SeuratObject', '4.1.2', { + 'checksums': ['6a5945f501b573dbe44a15e7d969e63fd5be0c4f8e9d716b71ca29f695236d0d'], + }), + ('sctransform', '0.3.5', { + 'checksums': ['c08e56df05d64ed04ee53eb9e1d4d321da8aff945e36d56db1d5ceb1cd7e6e0b'], + }), + ('uwot', '0.1.14', { + 'checksums': ['8016e8192b7e72604ca71840cbe43fa1d2caed8a8ad7cbf20e85cd3b384a9fe0'], + }), + (name, version, { + 'checksums': ['22a3d22a9ba255c4db5b37339b183fdfb91e2d37a8b8d58a9ff45b1bc414ebef'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From 9042e641ac937d534e88989b4ff4f67f9c79b9c0 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 24 Oct 2022 16:31:52 +0200 Subject: [PATCH 482/793] Update PyQt5-5.15.4-GCCcore-11.2.0.eb add sanity check commands for pyuic5, pylupdate5, and pyrcc5 --- easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb index e21ab740946..97b56cff0b2 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb @@ -93,6 +93,9 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import PyQt5.QtCore'", "sip5 --help", + "pyuic5 --help", + "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", + "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", ] modextrapaths = { From bbd4bb4620ef1ee9029a862ee85207370aa1f06b Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 15:58:10 +0100 Subject: [PATCH 483/793] download_dep_fail removed sanity_pip_check added --- easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb index 9bae7e1c2ba..6cb55d20405 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb @@ -13,7 +13,7 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] use_pip = True -download_dep_fail = True +sanity_pip_check = True exts_list = [ (name, version, { From 29b3e49e44732deeb4ce465b77061370a363b6f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Oct 2022 10:06:01 +0200 Subject: [PATCH 484/793] extend acceptance of -egl dependency variant of glew to wpebackend-fdo and WebKitGTK+ --- test/easyconfigs/easyconfigs.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f9a7d053f83..374e82ddb0c 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -493,8 +493,12 @@ def check_dep_vars(self, gen, dep, dep_vars): 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], - # egl variant of glew is required by libwpe - 'glew': [('2.2.0; versionsuffix: -egl', [r'libwpe-1\.13\.3-GCCcore-11\.2\.0'])], + # egl variant of glew is required by libwpe, wpebackend-fdo + WebKitGTK+ depend on libwpe + 'glew': [ + ('2.2.0; versionsuffix: -egl', [r'libwpe-1\.13\.3-GCCcore-11\.2\.0', + r'wpebackend-fdo-1\.13\.1-GCCcore-11\.2\.0', + r'WebKitGTK\+-2\.37\.1-GCC-11\.2\.0']), + ], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], # ncbi-vdb v2.x and v3.0.0 require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) 'HDF5': [ From 4aa4c45da8ac56279c7ac80143398e9e61fcd963 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 25 Oct 2022 14:27:15 +0200 Subject: [PATCH 485/793] Fixed style issues --- .../p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb index c171baaaab1..d507f7f7f30 100644 --- a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb @@ -25,11 +25,11 @@ configopts = " ".join([ sanity_check_paths = { 'files': [ - 'include/pugiconfig.hpp', - 'include/pugixml.hpp', - 'lib/libpugixml.a', + 'include/pugiconfig.hpp', + 'include/pugixml.hpp', + 'lib/libpugixml.a', 'lib/libpugixml.%s' % SHLIB_EXT, - 'lib/pkgconfig/pugixml.pc' + 'lib/pkgconfig/pugixml.pc' ], 'dirs': ['lib/cmake/pugixml'], } From d2341f47d675a5576b6774dff5b616606dc485fa Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 25 Oct 2022 15:37:31 +0200 Subject: [PATCH 486/793] @jfgrimm added sanity check commands for tools pyuic5, pylupdate5, and pyrcc5; port changes to recent-ish easyconfigs. --- ...PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb | 19 ++++++++++-- .../p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb | 29 ++++++++++++++----- .../p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb | 27 +++++++++++++---- .../p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb | 3 +- 4 files changed, 60 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb index 2122c835fca..400130674cd 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb @@ -19,15 +19,24 @@ dependencies = [ default_easyblock = 'PythonPackage' +local_sipdir = '%(installdir)s/share/sip' local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir local_pyqtweb_configopts += "--no-stubs --no-dist-info" +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_sipver = '5.4.0' @@ -76,13 +85,17 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'files': ['bin/%s' % x for x in [ + 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ "python -c 'import PyQt5.QtCore'", "sip5 --help", + "pyuic5 --help", + "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", + "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", ] modextrapaths = { diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb index b04ed87846e..775d1c1a6e6 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb @@ -19,20 +19,28 @@ dependencies = [ default_easyblock = 'PythonPackage' +local_sipdir = '%(installdir)s/share/sip' local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir local_pyqtweb_configopts += "--no-stubs --no-dist-info" +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir + local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " - local_sipver = '5.5.0' - components = [ ('SIP', local_sipver, { 'source_urls': [PYPI_SOURCE], @@ -63,10 +71,10 @@ components = [ 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], - 'easyblock': 'Binary', + 'easyblock': 'ConfigureMakePythonPackage', 'start_dir': '%(name)s-%(version)s', - 'skipsteps': ['configure', 'build'], - 'install_cmd': local_setup_env + local_pyqt5_sip_install, + 'preconfigopts': local_setup_env, + 'configopts': local_pyqt_configopts }), ('PyQtWebEngine', version, { @@ -82,13 +90,18 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip-wheel'], + 'files': ['bin/%s' % x for x in [ + 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ "python -c 'import PyQt5.QtCore'", "sip-wheel --help", + "sip5 --help", + "pyuic5 --help", + "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", + "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", ] modextrapaths = { diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb index 54c02ccf191..01de04b0208 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb @@ -18,15 +18,26 @@ dependencies = [ default_easyblock = 'PythonPackage' +local_sipdir = '%(installdir)s/share/sip' + local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir local_pyqtweb_configopts += "--no-stubs --no-dist-info" +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir + local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_sipver = '5.5.0' @@ -57,10 +68,10 @@ components = [ 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], - 'easyblock': 'Binary', + 'easyblock': 'ConfigureMakePythonPackage', 'start_dir': '%(name)s-%(version)s', - 'skipsteps': ['configure', 'build'], - 'install_cmd': local_setup_env + local_pyqt5_sip_install, + 'preconfigopts': local_setup_env, + 'configopts': local_pyqt_configopts }), ('PyQtWebEngine', version, { 'source_urls': [PYPI_SOURCE], @@ -75,13 +86,17 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'files': ['bin/%s' % x for x in [ + 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ "python -c 'import PyQt5.QtCore'", "sip5 --help", + "pyuic5 --help", + "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", + "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", ] modextrapaths = { diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb index 97b56cff0b2..cc175935b12 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb @@ -86,7 +86,8 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/pyrcc5', 'bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'files': ['bin/%s' % x for x in [ + 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From c26186efb83d45bc17bf86faf76942aa68ab3174 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 25 Oct 2022 16:20:32 +0200 Subject: [PATCH 487/793] Switched to MakeCp easyblock and applied instructions from README --- .../m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb | 22 +++++++++++++------ 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb index 624706433b6..b27d825a42d 100644 --- a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb +++ b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'MakeCp' name = 'MIGRATE-N' version = '5.0.4' @@ -12,7 +12,6 @@ mutations and uncertainty of the genealogy. """ toolchain = {'name': 'foss', 'version': '2021b'} -toolchainopts = {'usempi': True} source_urls = ["https://peterbeerli.com/migrate-html5/download_version4"] sources = ['migrate-%(version)s.src.tar.gz'] @@ -20,22 +19,31 @@ patches = [ 'migrate-%(version)s_install.patch', 'migrate-%(version)s_locale.patch', ] +checksums = [ + 'd25ba8ed112b81ee5fdc77759a5886b0f50ece834fd8db445b9c833742c3a1b9', # migrate-5.0.4.src.tar.gz + 'aaba4dbd8d868f80afd9645ae84d5b8c153de85a4f616a8585950593655d6fcf', # migrate-5.0.4_install.patch + '67f2dec0a2fcd432e12747f979a381f7d5e5ad73b885b485c829e50613aba35b', # migrate-5.0.4_locale.patch +] dependencies = [ ('zlib', '1.2.11'), ] -configopts = '--enable-A4 "CC=$CC" STDCPLUS=-lstdc++' -prebuildopts = 'make mpis && make clean &&' -installopts = "&& make clean && make installmpi" - parallel = 1 - start_dir = 'src' +prebuildopts = './configure --prefix=%(installdir)s --enable-A4 "CC=$CC" STDCPLUS=-lstdc++ && ' +buildopts = ' && make mpis CC="$MPICC"' +files_to_copy = [(['migrate-n', 'migrate-n-mpi'], 'bin')] + sanity_check_paths = { 'files': ['bin/%s' % x for x in ['migrate-n', 'migrate-n-mpi']], 'dirs': [], } +sanity_check_commands = [ + "echo Q | migrate-n", + "echo Q | mpirun -np 1 migrate-n-mpi", +] + moduleclass = 'bio' From cdc56f3ff989905cf61c0d04acbd2c0533db7171 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Oct 2022 17:09:48 +0200 Subject: [PATCH 488/793] fix installation of Python 2.7.18 with GCCcore/11.2.0 (fixes #16467) --- easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb index 40d1364f4e5..6cae29ec4ff 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb @@ -175,6 +175,7 @@ exts_list = [ }), ('backports.entry_points_selectable', '1.1.0', { 'checksums': ['988468260ec1c196dab6ae1149260e2f5472c9110334e5d51adcb77867361f6a'], + 'preinstallopts': "sed -i 's/^author =.*/version = %(version)s/g' setup.cfg && ", }), ('virtualenv', '20.7.0', { 'checksums': ['97066a978431ec096d163e72771df5357c5c898ffdd587048f45e0aecc228094'], @@ -245,6 +246,7 @@ exts_list = [ }), ('backports.functools_lru_cache', '1.6.4', { 'checksums': ['d5ed2169378b67d3c545e5600d363a923b09c456dab1593914935a68ad478271'], + 'preinstallopts': "sed -i 's/^author .*/version = %(version)s/g' setup.cfg && ", }), ('wcwidth', '0.2.5', { 'checksums': ['c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83'], @@ -306,6 +308,7 @@ exts_list = [ }), ('singledispatch', '3.7.0', { 'checksums': ['c1a4d5c1da310c3fd8fccfb8d4e1cb7df076148fd5d858a819e37fffe44f3092'], + 'preinstallopts': "sed -i 's/^author .*/version = %(version)s/g' setup.cfg && ", }), ('sortedcontainers', '2.4.0', { 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], From 5e900a1aa53fc1dc8540e063ecda03a05b4d5c8d Mon Sep 17 00:00:00 2001 From: easybuild Date: Tue, 25 Oct 2022 17:17:07 +0200 Subject: [PATCH 489/793] Backport glibc-2.34 SIGSTKSZ patch --- .../easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-10.1.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-10.2.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-10.3.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-11.1.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-5.3.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-5.4.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-5.5.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-6.3.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-6.4.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-7.1.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-7.2.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-7.3.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-7.4.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-8.1.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-8.2.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-8.3.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-8.4.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-9.1.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-9.2.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-9.3.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-system.eb | 7 +- easybuild/easyconfigs/m/M4/M4-1.4.18.eb | 7 +- .../m/M4/M4-1.4.18_glibc_2.34.patch | 106 ++++++++++++++++++ 24 files changed, 257 insertions(+), 23 deletions(-) create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.18_glibc_2.34.patch diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb index bc8af908fd7..6daf6b4d3cc 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'FCC', 'version': '4.5.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use binutils from the OS, since M4 is itself a dependency of the easybuilt binutils (via flex and Bison) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb index bd7b15d0f99..c2cdc5682d3 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '10.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb index 40d8acc91af..eb7a850b087 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb index aaa4eda2c91..691dd0696ef 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb index c1852324b5b..6730f48fb80 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '11.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb index 90f3441ae31..d63b2609039 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '5.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb index 44174916f39..9c980305317 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb @@ -13,11 +13,17 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] + # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.26', '', SYSTEM)] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb index bb84008fe0d..4b63035ae7b 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '5.5.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb index 42ac0537642..9a72c72b661 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb index abedf0b58b2..c5d9b7af082 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb @@ -16,10 +16,16 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-%(version)s_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb index 70675bd26d4..d6b25a708e0 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '7.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-%(version)s_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb index 95c1d432cdf..20fed34dea2 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '7.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-%(version)s_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb index d435d9cf19f..692b6fd6d43 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-%(version)s_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb index 18817b26e32..e0164f7af7f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '7.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb index f268c01aaed..59a6abb4da2 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '8.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-%(version)s_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb index cdf833ca394..b294b3ad96a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb index b21fcafc4f7..c5bded45603 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb index 30d2b32da00..f8bc2dc62b3 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '8.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb index aac98bc3c12..464d943e7b5 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '9.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb index c70532aeb1f..031f28e5ef4 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '9.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb index 61100b9eb44..96842f7085b 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb index 72020d96254..03d16d2f2b2 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb @@ -15,10 +15,15 @@ toolchainopts = {'optarch': False} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb index 79f53be742f..1c23e05d614 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb @@ -17,10 +17,15 @@ toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18_glibc_2.34.patch b/easybuild/easyconfigs/m/M4/M4-1.4.18_glibc_2.34.patch new file mode 100644 index 00000000000..9935b43323a --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18_glibc_2.34.patch @@ -0,0 +1,106 @@ +c-stack: stop using SIGSTKSZ + +It’s been proposed to stop making SIGSTKSZ an integer constant: +https://sourceware.org/pipermail/libc-alpha/2020-September/118028.html +Also, using SIGSTKSZ in #if did not conform to current POSIX. +Also, avoiding SIGSTKSZ makes the code simpler and easier to grok. +* lib/c-stack.c (SIGSTKSZ): Remove. +(alternate_signal_stack): Now a 64 KiB array, for simplicity. +All uses changed. + +[Retrieved (and backported) from: +https://git.savannah.gnu.org/cgit/gnulib.git/patch/?id=f9e2b20a12a230efa30f1d479563ae07d276a94b] +Signed-off-by: Fabrice Fontaine + +diff -Nura m4-1.4.18.orig/lib/c-stack.c m4-1.4.18/lib/c-stack.c +--- m4-1.4.18.orig/lib/c-stack.c 2021-04-11 19:12:14.086494029 +0200 ++++ m4-1.4.18/lib/c-stack.c 2021-04-11 19:48:46.316862760 +0200 +@@ -50,15 +50,16 @@ + #if ! HAVE_STACK_T && ! defined stack_t + typedef struct sigaltstack stack_t; + #endif +-#ifndef SIGSTKSZ +-# define SIGSTKSZ 16384 +-#elif HAVE_LIBSIGSEGV && SIGSTKSZ < 16384 +-/* libsigsegv 2.6 through 2.8 have a bug where some architectures use +- more than the Linux default of an 8k alternate stack when deciding +- if a fault was caused by stack overflow. */ +-# undef SIGSTKSZ +-# define SIGSTKSZ 16384 +-#endif ++ ++/* Storage for the alternate signal stack. ++ 64 KiB is not too large for Gnulib-using apps, and is large enough ++ for all known platforms. Smaller sizes may run into trouble. ++ For example, libsigsegv 2.6 through 2.8 have a bug where some ++ architectures use more than the Linux default of an 8 KiB alternate ++ stack when deciding if a fault was caused by stack overflow. */ ++static max_align_t alternate_signal_stack[(64 * 1024 ++ + sizeof (max_align_t) - 1) ++ / sizeof (max_align_t)]; + + #include + #include +@@ -128,19 +129,6 @@ + #if (HAVE_SIGALTSTACK && HAVE_DECL_SIGALTSTACK \ + && HAVE_STACK_OVERFLOW_HANDLING) || HAVE_LIBSIGSEGV + +-/* Storage for the alternate signal stack. */ +-static union +-{ +- char buffer[SIGSTKSZ]; +- +- /* These other members are for proper alignment. There's no +- standard way to guarantee stack alignment, but this seems enough +- in practice. */ +- long double ld; +- long l; +- void *p; +-} alternate_signal_stack; +- + static void + null_action (int signo __attribute__ ((unused))) + { +@@ -205,8 +193,8 @@ + + /* Always install the overflow handler. */ + if (stackoverflow_install_handler (overflow_handler, +- alternate_signal_stack.buffer, +- sizeof alternate_signal_stack.buffer)) ++ alternate_signal_stack, ++ sizeof alternate_signal_stack)) + { + errno = ENOTSUP; + return -1; +@@ -279,14 +267,14 @@ + stack_t st; + struct sigaction act; + st.ss_flags = 0; ++ st.ss_sp = alternate_signal_stack; ++ st.ss_size = sizeof alternate_signal_stack; + # if SIGALTSTACK_SS_REVERSED + /* Irix mistakenly treats ss_sp as the upper bound, rather than + lower bound, of the alternate stack. */ +- st.ss_sp = alternate_signal_stack.buffer + SIGSTKSZ - sizeof (void *); +- st.ss_size = sizeof alternate_signal_stack.buffer - sizeof (void *); +-# else +- st.ss_sp = alternate_signal_stack.buffer; +- st.ss_size = sizeof alternate_signal_stack.buffer; ++ st.ss_size -= sizeof (void *); ++ char *ss_sp = st.ss_sp; ++ st.ss_sp = ss_sp + st.ss_size; + # endif + r = sigaltstack (&st, NULL); + if (r != 0) +diff -Nura m4-1.4.18.orig/lib/c-stack.h m4-1.4.18/lib/c-stack.h +--- m4-1.4.18.orig/lib/c-stack.h 2021-04-11 19:12:14.098494042 +0200 ++++ m4-1.4.18/lib/c-stack.h 2021-04-11 19:17:42.138848378 +0200 +@@ -34,7 +34,7 @@ + A null ACTION acts like an action that does nothing. + + ACTION must be async-signal-safe. ACTION together with its callees +- must not require more than SIGSTKSZ bytes of stack space. Also, ++ must not require more than 64 KiB bytes of stack space. Also, + ACTION should not call longjmp, because this implementation does + not guarantee that it is safe to return to the original stack. + From bb3ab265775f54661775dd52f1b834ee4e674399 Mon Sep 17 00:00:00 2001 From: easybuild Date: Tue, 25 Oct 2022 17:42:52 +0200 Subject: [PATCH 490/793] Fix mixed spaces/tabs --- easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18.eb | 4 ++-- 23 files changed, 46 insertions(+), 46 deletions(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb index 6daf6b4d3cc..bc86a842bf0 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb index c2cdc5682d3..23e948da86e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb index eb7a850b087..a8d9bfb5194 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb index 691dd0696ef..70575029ae0 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb index 6730f48fb80..63f864a0d85 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb index d63b2609039..43408ff8fac 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb index 9c980305317..7c7bb607dc6 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb index 4b63035ae7b..1c0ae73d6d8 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb index 9a72c72b661..9b67783cc40 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb index c5d9b7af082..5bb8c417674 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb @@ -18,8 +18,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb index d6b25a708e0..43b5a997994 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb index 20fed34dea2..c6ea670638e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb index 692b6fd6d43..0fd28aca84f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb index e0164f7af7f..3957e4980e2 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb index 59a6abb4da2..3ae81595fa9 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb index b294b3ad96a..a646315f4d9 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb index c5bded45603..bba6ee5bb81 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb index f8bc2dc62b3..84ace55818b 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb index 464d943e7b5..abe9dbefd21 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb index 031f28e5ef4..2db382b9321 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb index 96842f7085b..e0dffd89a28 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb index 03d16d2f2b2..6df13418cc3 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb @@ -16,8 +16,8 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb index 1c23e05d614..d181fe31631 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb @@ -18,8 +18,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ From 8657f4aa2c7c65aa9a4aa66aa3ef599667319c04 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 25 Oct 2022 18:04:47 +0200 Subject: [PATCH 491/793] @jfgrimm revert PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb --- ...PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb | 19 +++---------------- 1 file changed, 3 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb index 400130674cd..2122c835fca 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb @@ -19,24 +19,15 @@ dependencies = [ default_easyblock = 'PythonPackage' -local_sipdir = '%(installdir)s/share/sip' local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " -local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir -local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " local_pyqtweb_configopts += "--no-stubs --no-dist-info" -local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir -local_pyqt_configopts += "--no-stubs " -local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " -# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: -local_pyqt_configopts += "--bindir=%(installdir)s/bin " -local_pyqt_configopts += "--sipdir=%s " % local_sipdir local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_sipver = '5.4.0' @@ -85,17 +76,13 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in [ - 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], + 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ "python -c 'import PyQt5.QtCore'", "sip5 --help", - "pyuic5 --help", - "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", - "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", ] modextrapaths = { From 781250e6de3b80c19a25a58abc3e59e0ddb949d0 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 25 Oct 2022 18:50:40 +0100 Subject: [PATCH 492/793] Patch added to ensure test-jobs are not failing due to blanks (https://github.com/pybind/pybind11/issues/3680) --- ...04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch | 121 ++++++++++++++++++ .../pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb | 11 +- 2 files changed, 131 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/pybind11/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch diff --git a/easybuild/easyconfigs/p/pybind11/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch b/easybuild/easyconfigs/p/pybind11/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch new file mode 100644 index 00000000000..5d0bcd18dba --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch @@ -0,0 +1,121 @@ +From 1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5 Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= +Date: Thu, 3 Feb 2022 18:29:46 +0100 +URL: https://github.com/pybind/pybind11/commit/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch +Subject: [PATCH] test: Strip whitespace when comparing numpy dtypes for 1.22 + compat (#3682) + +* test: Strip whitespace when comparing numpy dtypes for 1.22 compat + +Strip whitespace when comparing numpy dtype str() in order to preserve +test compatibility with both numpy 1.22 and older versions whose output +differ by whitespace. + +Fixes #3680 + +diff --git a/pybind11-2.6.0.orig/tests/test_numpy_dtypes.py b/pybind11-2.6.0/tests/test_numpy_dtypes.py +index f56b776..228ef63 100644 +--- a/pybind11-2.6.0.orig/tests/test_numpy_dtypes.py ++++ b/pybind11-2.6.0/tests/test_numpy_dtypes.py +@@ -33,8 +33,8 @@ def dt_fmt(): + e = "<" if byteorder == "little" else ">" + return ( + "{{'names':['bool_','uint_','float_','ldbl_']," +- " 'formats':['?','" + e + "u4','" + e + "f4','" + e + "f{}']," +- " 'offsets':[0,4,8,{}], 'itemsize':{}}}" ++ "'formats':['?','" + e + "u4','" + e + "f4','" + e + "f{}']," ++ "'offsets':[0,4,8,{}],'itemsize':{}}}" + ) + + +@@ -47,7 +47,7 @@ def simple_dtype_fmt(): + def packed_dtype_fmt(): + from sys import byteorder + +- return "[('bool_', '?'), ('uint_', '{e}u4'), ('float_', '{e}f4'), ('ldbl_', '{e}f{}')]".format( ++ return "[('bool_','?'),('uint_','{e}u4'),('float_','{e}f4'),('ldbl_','{e}f{}')]".format( + np.dtype("longdouble").itemsize, e="<" if byteorder == "little" else ">" + ) + +@@ -72,7 +72,7 @@ def partial_nested_fmt(): + partial_nested_off = 8 + 8 * (ld.alignment > 8) + partial_ld_off = partial_ld_offset() + partial_nested_size = partial_nested_off * 2 + partial_ld_off + ld.itemsize +- return "{{'names':['a'], 'formats':[{}], 'offsets':[{}], 'itemsize':{}}}".format( ++ return "{{'names':['a'],'formats':[{}],'offsets':[{}],'itemsize':{}}}".format( + partial_dtype_fmt(), partial_nested_off, partial_nested_size + ) + +@@ -116,25 +116,25 @@ def test_dtype(simple_dtype): + + e = "<" if byteorder == "little" else ">" + +- assert m.print_dtypes() == [ ++ assert [x.replace(" ", "") for x in m.print_dtypes()] == [ + simple_dtype_fmt(), + packed_dtype_fmt(), +- "[('a', {}), ('b', {})]".format(simple_dtype_fmt(), packed_dtype_fmt()), ++ "[('a',{}),('b',{})]".format(simple_dtype_fmt(), packed_dtype_fmt()), + partial_dtype_fmt(), + partial_nested_fmt(), +- "[('a', 'S3'), ('b', 'S3')]", ++ "[('a','S3'),('b','S3')]", + ( +- "{{'names':['a','b','c','d'], " +- + "'formats':[('S4', (3,)),('" ++ "{{'names':['a','b','c','d']," ++ + "'formats':[('S4',(3,)),('" + + e +- + "i4', (2,)),('u1', (3,)),('" ++ + "i4',(2,)),('u1',(3,)),('" + + e +- + "f4', (4, 2))], " +- + "'offsets':[0,12,20,24], 'itemsize':56}}" ++ + "f4',(4,2))]," ++ + "'offsets':[0,12,20,24],'itemsize':56}}" + ).format(e=e), +- "[('e1', '" + e + "i8'), ('e2', 'u1')]", +- "[('x', 'i1'), ('y', '" + e + "u8')]", +- "[('cflt', '" + e + "c8'), ('cdbl', '" + e + "c16')]", ++ "[('e1','" + e + "i8'),('e2','u1')]", ++ "[('x','i1'),('y','" + e + "u8')]", ++ "[('cflt','" + e + "c8'),('cdbl','" + e + "c16')]", + ] + + d1 = np.dtype( +@@ -228,7 +228,7 @@ def test_recarray(simple_dtype, packed_dtype): + ] + + arr = m.create_rec_partial(3) +- assert str(arr.dtype) == partial_dtype_fmt() ++ assert str(arr.dtype).replace(" ", "") == partial_dtype_fmt() + partial_dtype = arr.dtype + assert "" not in arr.dtype.fields + assert partial_dtype.itemsize > simple_dtype.itemsize +@@ -236,7 +236,7 @@ def test_recarray(simple_dtype, packed_dtype): + assert_equal(arr, elements, packed_dtype) + + arr = m.create_rec_partial_nested(3) +- assert str(arr.dtype) == partial_nested_fmt() ++ assert str(arr.dtype).replace(" ", "") == partial_nested_fmt() + assert "" not in arr.dtype.fields + assert "" not in arr.dtype.fields["a"][0].fields + assert arr.dtype.itemsize > partial_dtype.itemsize +@@ -275,12 +275,12 @@ def test_array_array(): + e = "<" if byteorder == "little" else ">" + + arr = m.create_array_array(3) +- assert str(arr.dtype) == ( +- "{{'names':['a','b','c','d'], " +- + "'formats':[('S4', (3,)),('" ++ assert str(arr.dtype).replace(" ", "") == ( ++ "{{'names':['a','b','c','d']," ++ + "'formats':[('S4',(3,)),('" + + e +- + "i4', (2,)),('u1', (3,)),('{e}f4', (4, 2))], " +- + "'offsets':[0,12,20,24], 'itemsize':56}}" ++ + "i4',(2,)),('u1',(3,)),('{e}f4',(4,2))]," ++ + "'offsets':[0,12,20,24],'itemsize':56}}" + ).format(e=e) + assert m.print_array_array(arr) == [ + "a={{A,B,C,D},{K,L,M,N},{U,V,W,X}},b={0,1}," diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb index 60135a6d7f6..8e9b6e72bfe 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb @@ -1,3 +1,7 @@ +# include patch to fix failing test jobs due to additional white space +# see https://github.com/pybind/pybind11/issues/3680 +# Authors: J. Sassmannshausen / Alexander Grund + name = 'pybind11' version = '2.6.0' @@ -9,7 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/pybind/pybind11/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['90b705137b69ee3b5fc655eaca66d0dc9862ea1759226f7ccd3098425ae69571'] +patches = ['1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch'] +checksums = [ + '90b705137b69ee3b5fc655eaca66d0dc9862ea1759226f7ccd3098425ae69571', + # 1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch: + 'f0ff7416d14f9589b5d100ad021e18690cb08cb662df9d0ac21327d04bdb96fc', +] builddependencies = [ ('binutils', '2.35'), From ad17fc07ee1bdc8748cff9da1619b117e3443e44 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Oct 2022 21:55:37 +0200 Subject: [PATCH 493/793] work around installation problem for extensions in Python 2.7.16 easyconfig due to missing build-backend spec in pyproject.toml --- .../easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb index 630fe512e04..7dfe39787ec 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb @@ -37,6 +37,11 @@ exts_default_options = { 'sanity_pip_check': True, } +# workaround for: AttributeError: 'module' object has no attribute '__legacy__' +# see also https://github.com/pypa/pip/issues/6264 +local_fix_pyproject_toml_cmd = """sed -i 's/\(\[build-system\]\)/\\1\\nbuild-backend="setuptools.build_meta"/g' """ +local_fix_pyproject_toml_cmd += "pyproject.toml && " + # order is important! # package versions updated Sept 13th 2019 exts_list = [ @@ -125,6 +130,7 @@ exts_list = [ ('PyNaCl', '1.3.0', { 'modulename': 'nacl', 'checksums': ['0c6100edd16fefd1557da078c7a31e7b7d7a52ce39fdca2bec29d4f7b6e7600c'], + 'preinstallopts': local_fix_pyproject_toml_cmd, }), ('bcrypt', '3.1.7', { 'checksums': ['0b0069c752ec14172c5f78208f1863d7ad6755a6fae6fe76ec2c80d13be41e42'], @@ -209,9 +215,11 @@ exts_list = [ }), ('importlib_metadata', '0.22', { 'checksums': ['652234b6ab8f2506ae58e528b6fbcc668831d3cc758e1bc01ef438d328b68cdb'], + 'preinstallopts': local_fix_pyproject_toml_cmd, }), ('pluggy', '0.13.0', { 'checksums': ['fa5fa1622fa6dd5c030e9cad086fa19ef6a0cf6d7a2d12318e10cb49d6d68f34'], + 'preinstallopts': local_fix_pyproject_toml_cmd, }), # more-itertools 5.0.0 is the most recent version still supporting Python 2.x ('more-itertools', '5.0.0', { From 36183b5d248d5dfa112a3414b38b6c92c83dccfe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Oct 2022 09:41:15 +0200 Subject: [PATCH 494/793] avoid that ~/.ccache is used when building/installing WebKitGTK+ --- .../easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb index 5e41bdddcfb..d944a2691e6 100644 --- a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb @@ -77,6 +77,9 @@ configopts += "-DENABLE_GAMEPAD=OFF -DUSE_LIBSECRET=OFF -DUSE_LIBHYPHEN=OFF " configopts += "-DUSE_WOFF2=OFF -DENABLE_JOURNALD_LOG=OFF -DENABLE_BUBBLEWRAP_SANDBOX=OFF " configopts += "-DENABLE_INTROSPECTION=OFF -DUSE_LIBNOTIFY=OFF " +prebuildopts = "export CCACHE_DIR=%(builddir)s/ccache && " +preinstallopts = prebuildopts + sanity_check_paths = { 'files': ['bin/WebKitWebDriver', 'lib/libwebkit2gtk-4.1.%s' % SHLIB_EXT, 'lib/libjavascriptcoregtk-4.1.%s' % SHLIB_EXT], From f02b3d7184ab235372c4de70876b1e83bd5b8818 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 26 Oct 2022 09:42:51 +0100 Subject: [PATCH 495/793] remove ExomeDepth from recent R-bundle-Bioconductor --- .../R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb | 3 --- .../R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb | 3 --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 3 --- 3 files changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb index b7133459ca4..761944fd152 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb @@ -1075,9 +1075,6 @@ exts_list = [ ('M3Drop', '1.20.0', { 'checksums': ['b82772303c624ff01418e66cefd751a0f6f9d819ea2cf3c9c20a9acd1fc106e5'], }), - ('ExomeDepth', '1.1.15', { - 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], - }), ('bsseq', '1.30.0', { 'checksums': ['2dada40e222d4f42510deeb99c24043078420a4d3d214d4cc3409d428cfb60c4'], }), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb index 15af98e6e4b..1c4ffc3555e 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb @@ -1060,9 +1060,6 @@ exts_list = [ ('M3Drop', '1.22.0', { 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], }), - ('ExomeDepth', '1.1.15', { - 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], - }), ('bsseq', '1.32.0', { 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], }), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 209068efaa5..e9595a58dd4 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1059,9 +1059,6 @@ exts_list = [ ('M3Drop', '1.22.0', { 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], }), - ('ExomeDepth', '1.1.15', { - 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], - }), ('bsseq', '1.32.0', { 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], }), From ace549bec0cd223ae2c0b2885306453f59cb9945 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 26 Oct 2022 11:49:59 +0200 Subject: [PATCH 496/793] adding easyconfigs: NiBabel-4.0.2-foss-2022a.eb, pydicom-2.3.0-GCCcore-11.3.0.eb --- .../n/NiBabel/NiBabel-4.0.2-foss-2022a.eb | 46 +++++++++++++++++++ .../p/pydicom/pydicom-2.3.0-GCCcore-11.3.0.eb | 26 +++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/n/NiBabel/NiBabel-4.0.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/pydicom/pydicom-2.3.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-4.0.2-foss-2022a.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-4.0.2-foss-2022a.eb new file mode 100644 index 00000000000..2691a91e34a --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-4.0.2-foss-2022a.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'NiBabel' +version = '4.0.2' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Pillow', '9.1.1'), + ('pydicom', '2.3.0'), +] + +use_pip = True + +exts_list = [ + ('bz2file', '0.98', { + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('nibabel', version, { + 'checksums': ['45c49b5349351b45f6c045a91aa02b4f0d367686ff3284632ef95ac65b930786'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-diff', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nib-diff --help", + "parrec2nii --help", +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pydicom/pydicom-2.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pydicom/pydicom-2.3.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a92eebf56b9 --- /dev/null +++ b/easybuild/easyconfigs/p/pydicom/pydicom-2.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pydicom' +version = '2.3.0' + +homepage = 'https://pydicom.github.io/' +description = "Pure python package for DICOM medical file reading and writing." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e50dfa6bc44516816248c750a93b07fa577b867433bd8bf4fd3319a4a19259a5'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('Python', '3.10.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' From 1f1ddd397839cc246317b5cfa9333199ad7068ff Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 26 Oct 2022 12:20:49 +0200 Subject: [PATCH 497/793] adding easyconfigs: IJulia-1.23.3-Julia-1.6.7.eb --- .../i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb diff --git a/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb b/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb new file mode 100644 index 00000000000..54566147c74 --- /dev/null +++ b/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb @@ -0,0 +1,87 @@ +easyblock = 'Bundle' + +name = 'IJulia' +version = '1.23.3' +_julia_ver = '1.6.7' +versionsuffix = "-Julia-%s" % _julia_ver + +homepage = 'https://github.com/JuliaLang/IJulia.jl' +description = "Julia kernel for Jupyter" + +toolchain = SYSTEM + +dependencies = [ + ('Julia', _julia_ver, '-linux-%s' % ARCH, SYSTEM), +] + +exts_defaultclass = 'JuliaPackage' +exts_filter = ("julia -e 'using %(ext_name)s'", "") +exts_default_options = { + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], +} + +exts_list = [ + ('Parsers', '2.4.2', { + 'source_urls': ['https://github.com/JuliaData/Parsers.jl/archive/'], + 'checksums': ['44036a59b047f704d6b7841e3edf12fe2a53aa797254086fdd0709f0cdebac89'], + }), + ('JSON', '0.21.3', { + 'source_urls': ['https://github.com/JuliaIO/JSON.jl/archive/'], + 'checksums': ['bd02a015da24b03f79d55967b29f5ceaba2477b559242576d74f02623bb1b6b1'], + }), + ('MbedTLS', '1.1.7', { + 'source_urls': ['https://github.com/JuliaLang/MbedTLS.jl/archive/'], + 'checksums': ['3df27a16ea31acf4eaf6cc9f3bd25b81960c10662722ffa22b13cb0e6ac11b12'], + }), + ('VersionParsing', '1.3.0', { + 'source_urls': ['https://github.com/JuliaInterop/VersionParsing.jl/archive/'], + 'checksums': ['f90fe419e1a40ef0eccfaaed1d1b7792d9115a059a82d0c23e3c04c944d0f8ca'], + }), + ('Conda', '1.7.0', { + 'source_urls': ['https://github.com/JuliaPy/Conda.jl/archive/'], + 'checksums': ['2077b1192e1cfa206caf441d9d91b0ca83aa935db89918f1fd69cd25c2415ced'], + }), + ('SoftGlobalScope', '1.1.0', { + 'source_urls': ['https://github.com/stevengj/SoftGlobalScope.jl/archive/'], + 'checksums': ['8d4264386c859403938498cd9ddd5e94e10181deba4a3e71d391b16750e3848b'], + }), + ('Preferences', '1.3.0', { + 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], + 'checksums': ['a87c1fc863fcb6240c3f4327776fa01a1f87e0d2df5a0c1850f789ce24469da2'], + }), + ('JLLWrappers', '1.4.1', { + 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], + 'checksums': ['2cb61d4171e8ebc74e36ee20e6e0ba959aa5525a9c2fef5547e0993566018775'], + }), + ('libsodium_jll', '1.0.20+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/libsodium_jll.jl/archive/'], + 'sources': [{'filename': 'libsodium-v%(version)s.tar.gz'}], + 'checksums': ['f7c3a17acc3a478ec10a4a49a0dd04694140f4483644ec9db638706ea9844aba'], + }), + ('ZeroMQ_jll', '4.3.4+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/ZeroMQ_jll.jl/archive/'], + 'sources': [{'filename': 'ZeroMQ-v%(version)s.tar.gz'}], + 'checksums': ['aa98ae3c7e050fc6bdf0b0132bb607dea2f6c062da7870b1ecada9f3c8ea8d72'], + }), + ('ZMQ', '1.2.1', { + 'source_urls': ['https://github.com/JuliaInterop/ZMQ.jl/archive/'], + 'checksums': ['8b42555340d0208e5a36cd5e8f29a3f0d44c13c064382d4b1e5d00c1c4a9dd96'], + }), + (name, version, { + 'source_urls': ['https://github.com/JuliaLang/IJulia.jl/archive/'], + 'checksums': ['1471ed94093efd24bae5e6ff1d3f7fa61901bf8834a737eeae2a9e620f50f07c'], + 'preinstallopts': "mkdir -p %(installdir)s/jupyter && export JUPYTER_DATA_DIR=%(installdir)s/jupyter && ", + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['packages'], +} + +modextrapaths = { + 'JULIA_DEPOT_PATH': '', + 'JUPYTER_PATH': 'jupyter', +} + +moduleclass = 'lib' From 3b68a7b68e8b390f477d58adca126af3e4e24aa8 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 26 Oct 2022 12:18:12 +0100 Subject: [PATCH 498/793] Name of patchfile changed --- .../easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb | 4 ++-- ...5.patch => pybind11-2.6.0_fix-test-extra-whitespace.patch} | 0 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/pybind11/{1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch => pybind11-2.6.0_fix-test-extra-whitespace.patch} (100%) diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb index 8e9b6e72bfe..9eddf8c8ef2 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb @@ -13,10 +13,10 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/pybind/pybind11/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch'] +patches = ['pybind11-2.6.0_fix-test-extra-whitespace.patch'] checksums = [ '90b705137b69ee3b5fc655eaca66d0dc9862ea1759226f7ccd3098425ae69571', - # 1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch: + # pybind11-2.6.0_fix-test-extra-whitespace.patch: 'f0ff7416d14f9589b5d100ad021e18690cb08cb662df9d0ac21327d04bdb96fc', ] diff --git a/easybuild/easyconfigs/p/pybind11/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0_fix-test-extra-whitespace.patch similarity index 100% rename from easybuild/easyconfigs/p/pybind11/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch rename to easybuild/easyconfigs/p/pybind11/pybind11-2.6.0_fix-test-extra-whitespace.patch From 4ddd6621d457e813acbaa22d94b5d1e69e3c46b0 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 26 Oct 2022 13:51:19 +0200 Subject: [PATCH 499/793] adding easyconfigs: dask-2022.10.0-foss-2022a.eb, bokeh-2.4.3-foss-2022a.eb --- .../b/bokeh/bokeh-2.4.3-foss-2022a.eb | 38 ++++++++++ .../d/dask/dask-2022.10.0-foss-2022a.eb | 72 +++++++++++++++++++ 2 files changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-2.4.3-foss-2022a.eb create mode 100644 easybuild/easyconfigs/d/dask/dask-2022.10.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.4.3-foss-2022a.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.4.3-foss-2022a.eb new file mode 100644 index 00000000000..4f2830449ae --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.4.3-foss-2022a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '2.4.3' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('Pillow', '9.1.1'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True + +exts_list = [ + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + (name, version, { + 'checksums': ['ef33801161af379665ab7a34684f2209861e3aefd5c803a21fbbb99d94874b03'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["bokeh --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dask/dask-2022.10.0-foss-2022a.eb b/easybuild/easyconfigs/d/dask/dask-2022.10.0-foss-2022a.eb new file mode 100644 index 00000000000..ab9413891e9 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-2022.10.0-foss-2022a.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'dask' +version = '2022.10.0' + +homepage = 'https://dask.org/' +description = """Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance + at scale for the tools you love.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('SciPy-bundle', '2022.05'), + ('bokeh', '2.4.3'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('locket', '1.0.0', { + 'checksums': ['5c0d4c052a8bbbf750e056a8e65ccd309086f4f0f18a2eac306a8dfa4112a632'], + }), + ('partd', '1.3.0', { + 'checksums': ['ce91abcdc6178d668bcaa431791a5a917d902341cb193f543fe445d494660485'], + }), + ('fsspec', '2021.7.0', { + 'checksums': ['792ebd3b54de0b30f1ce73f0ba0a8bcc864724f2d9f248cb8d0ece47db0cbde8'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('zict', '2.2.0', { + 'checksums': ['d7366c2e2293314112dcf2432108428a67b927b00005619feefc310d12d833f3'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('cloudpickle', '2.2.0', { + 'checksums': ['3f4219469c55453cfe4737e564b67c2a149109dabf7f242478948b895f61106f'], + }), + (name, version, { + 'checksums': ['f277a3b300ecc1d0be232a339f346dff686e0becdb0843c0aaf2ae943d5492d3'], + }), + ('distributed', version, { + 'checksums': ['dcfbc9c528bcd9e4f9686e673956a90172826395ac5b258039e580777d50782f'], + }), + ('dask-mpi', '2022.4.0', { + 'checksums': ['0a04f1d7d35a06cdff506593330d4414ea242c9172498ce191f5742eac499e17'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('dask-jobqueue', '0.8.1', { + 'checksums': ['16fd1b646a073ad3de75dde12a0dfe529b836f21a3bdbcee2a88bef24e9112a7'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["dask-scheduler --help"] + +sanity_pip_check = True + +moduleclass = 'data' From 9a1bce2ff7b11da801999840338254fca578060d Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 26 Oct 2022 17:32:55 +0200 Subject: [PATCH 500/793] adding easyconfigs: ITK-5.2.1-foss-2022a.eb --- .../easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb new file mode 100644 index 00000000000..22f773b4840 --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb @@ -0,0 +1,59 @@ +# Contributors: +# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University +# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) +# Denis Kristak (INUITS) +# +easyblock = 'CMakeMake' + +name = 'ITK' +version = '5.2.1' + +homepage = 'https://itk.org' +description = """Insight Segmentation and Registration Toolkit (ITK) provides + an extensive suite of software tools for registering and segmenting + multidimensional imaging data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +github_account = 'InsightSoftwareConsortium' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['6022b2b64624b8bcec3333fe48d5f74ff6ebceb3bdf98258ba7d7fbbc76b99ab'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Bison', '3.8.2'), + ('Eigen', '3.4.0'), +] +dependencies = [ + ('expat', '2.4.8'), + ('HDF5', '1.12.2'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('VTK', '9.2.0.rc2'), + ('zlib', '1.2.12'), +] + +local_sys_deps = ['EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' +configopts += '-DITK_WRAP_PYTHON:BOOL=OFF ' +configopts += '-DITK_LEGACY_REMOVE:BOOL=OFF ' # needed by SimpleITK +configopts += ' '.join(local_sys_cmake) + +prebuildopts = "LC_ALL=C " + +local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', + 'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters'] + +sanity_check_paths = { + 'files': ['bin/itkTestDriver'] + + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], +} + +moduleclass = 'data' From 806133fd03c318084c697007ecc50286d54a788c Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 26 Oct 2022 20:38:38 +0100 Subject: [PATCH 501/793] adding easyconfigs: TBA-1.0-foss-2020b.eb --- .../easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb new file mode 100644 index 00000000000..d6d7f6ff551 --- /dev/null +++ b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb @@ -0,0 +1,65 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'Tarball' + +name = 'TBA' +version = '1.0' + +homepage = 'https://github.com/jenhantao/tba' +description = """TBA (a Transcription factor Binding Analysis): +TBA is a multi-functional machine learning tool for identifying +transcription factors associated with genomic features""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/jenhantao/tba/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['97acb78e045bbd066d67213c84417f2af7f48fde1f513be22cbb46ad2966ae2c'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Biopython', '1.78'), + ('scikit-learn', '0.23.2'), + ('Seaborn', '0.11.1'), + ('matplotlib', '3.5.1'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('idr', '2.0.3', { + 'source_urls': ['https://github.com/nboley/idr/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['63e3be099b2deadfa8c7ccc3ab83659afe683f6a35bd41b2319c6ad58ca74de6'], + }), + ('joblib', '1.2.0', { + 'checksums': ['e1cee4a79e4af22881164f218d4311f60074197fb707e082e803b61f6d137018'], + }), +] + +postinstallcmds = [ + "mv %(installdir)s/model_training/* %(installdir)s/bin ", + "mv %(installdir)s/default_motifs %(installdir)s/share ", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/train_model_default.sh', 'bin/train_classifier.py', + 'bin/create_features.py', 'bin/idr'], + 'dirs': ['share'], +} + +sanity_check_commands = [ + "idr --version", + "train_classifier.py -h", +] + +moduleclass = 'bio' From 1410906635e24073738aa8d0e83af731e6c5aca3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Wed, 26 Oct 2022 21:40:11 +0100 Subject: [PATCH 502/793] Update TBA-1.0-foss-2020b.eb matplotlib demoted to 3.3.3 to avoid conflicts --- easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb index d6d7f6ff551..c3f0e23f2d8 100644 --- a/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('Biopython', '1.78'), ('scikit-learn', '0.23.2'), ('Seaborn', '0.11.1'), - ('matplotlib', '3.5.1'), + ('matplotlib', '3.3.3'), ] exts_defaultclass = 'PythonPackage' From 3404ec4b937e3ceb332d2b6ccff5fd61b91041da Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Oct 2022 11:16:17 +0200 Subject: [PATCH 503/793] adding easyconfigs: Xmipp-3.22.07-Helios-foss-2022a.eb and patches: Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch, Xmipp-3.22.07-Helios_dont_add_useless_libs.patch, Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch, Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch, Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch, XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch, XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch, XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch, XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch --- .../Xmipp/Xmipp-3.22.07-Helios-foss-2022a.eb | 87 +++++++++++++++++++ ...-Helios_correct_order_of_cu_includes.patch | 19 ++++ ...3.22.07-Helios_dont_add_useless_libs.patch | 21 +++++ ...07-Helios_dont_change_EB_build_flags.patch | 41 +++++++++ ...Helios_drop_useless_CXXFLAGS_setting.patch | 18 ++++ ...07-Helios_fix_scons_Environent_calls.patch | 37 ++++++++ ...07-Helios_fix_scons_Environent_calls.patch | 28 ++++++ ...-3.22.07-Helios_use_CXXFLAGS_from_EB.patch | 24 +++++ ...07-Helios_fix_scons_Environent_calls.patch | 28 ++++++ ...-3.22.07-Helios_use_CXXFLAGS_from_EB.patch | 25 ++++++ 10 files changed, 328 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a.eb create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_add_useless_libs.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a.eb new file mode 100644 index 00000000000..9174334361e --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a.eb @@ -0,0 +1,87 @@ +name = 'Xmipp' +version = '3.22.07-Helios' + +homepage = 'https://github.com/I2PC/scipion/wiki' +description = """Scipion is an image processing framework to obtain 3D +models of macromolecular complexes using Electron Microscopy (3DEM). It +integrates several software packages and presents an unified interface +for both biologists and developers. Scipion allows to execute workflows +combining different software tools, while taking care of formats and +conversions. Additionally, all steps are tracked and can be reproduced +later on. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [ + { + 'source_urls': ['https://github.com/I2PC/xmipp/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': '%(namelower)s-v%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/I2PC/xmippCore/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'xmippCore-v%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src', + }, + { + 'source_urls': ['https://github.com/I2PC/xmippViz/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'xmippViz-v%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src', + }, +] +patches = [ + '%(name)s-%(version)s_fix_scons_Environent_calls.patch', + '%(name)s-%(version)s_drop_useless_CXXFLAGS_setting.patch', + '%(name)s-%(version)s_correct_order_of_cu_includes.patch', + '%(name)s-%(version)s_dont_add_useless_libs.patch', + '%(name)s-%(version)s_dont_change_EB_build_flags.patch', + ('XmippCore-%(version)s_fix_scons_Environent_calls.patch', 'src/xmippCore'), + ('XmippCore-%(version)s_use_CXXFLAGS_from_EB.patch', 'src/xmippCore'), + ('XmippViz-%(version)s_fix_scons_Environent_calls.patch', 'src/xmippViz'), + ('XmippViz-%(version)s_use_CXXFLAGS_from_EB.patch', 'src/xmippViz'), +] +checksums = [ + {'xmipp-v3.22.07-Helios.tar.gz': 'f62e2729130b63d18e518930dd96a7a5250219e40c155abb78942a0642237ecf'}, + {'xmippCore-v3.22.07-Helios.tar.gz': '58e1143626cf807655a4756b165c21578d6f1b1777b43d363a2845d92d0bab8f'}, + {'xmippViz-v3.22.07-Helios.tar.gz': 'e1ce2cbbd57d3307d38538b29194a0190d633e5e062685387a6baf0329ad05b3'}, + {'Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch': + '5b59babad5a445ec7315a809509704d2d07232d2a5d180bfb78ebc8007bd0c95'}, + {'Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch': + '34ed0cb591e1e2788acd3e58696b1f45ce9210836d14ed1c99de1e574e4824e6'}, + {'Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch': + '2b0b2ddf349003be4112f4dca623586a03235214d6e64d232deb26468b52f0e3'}, + {'Xmipp-3.22.07-Helios_dont_add_useless_libs.patch': + '284b8ec1e514fb84b7680c8b3f59b3d5931b564beb444d3301504e3170e9a49e'}, + {'Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch': + '1514eaa5de35b38b5a10e949edf5c94ba95bbd05e0b9fbf70db2ea98967394e3'}, + {'XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch': + '8dcf0f3648f4b3438374ba629a9efa2e5c08eb25ae76ed420513664d21e2246b'}, + {'XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch': + 'd86b0d3ecc339b81c9aa7a33d2b44b428643aa7e2e686529b4bb6b16d36805c2'}, + {'XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch': + '7724fc3953d9c4c308a5755f54229259425fdbad5a909153bd173292434407b9'}, + {'XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch': + 'a8bea23c243174fb27a140a34a064a622cc96f0e7231fd31caf20f90c7ba9555'}, +] + +builddependencies = [ + ('SCons', '4.4.0'), + ('CTPL', '0.0.2'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Java', '11', '', SYSTEM), + ('OpenCV', '4.6.0', '-contrib'), + ('SQLite', '3.38.3'), + ('HDF5', '1.12.2'), + ('LibTIFF', '4.3.0'), + ('libjpeg-turbo', '2.1.3'), + ('LIBSVM', '3.30'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch new file mode 100644 index 00000000000..8b61aa94613 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch @@ -0,0 +1,19 @@ +commit baac03018283296f90c08366e0e092c95d25173b +Author: Ake Sandgren +Date: Tue Oct 18 14:34:34 2022 +0200 + + cuda_gpu_multidim_array.cu is just an include file containing templates. + Needs to be before cuda_gpu_geo_transformer.cu + +diff --git xmipp-3.22.07-Helios/src/xmipp/libraries/reconstruction_cuda/cuda_all.cpp xmipp-3.22.07-Helios/src/xmipp/libraries/reconstruction_cuda/cuda_all.cpp +index f7e5178c..8ccbefd3 100644 +--- xmipp-3.22.07-Helios/src/xmipp/libraries/reconstruction_cuda/cuda_all.cpp ++++ xmipp-3.22.07-Helios/src/xmipp/libraries/reconstruction_cuda/cuda_all.cpp +@@ -31,6 +31,6 @@ + */ + + #include "cuda_gpu_bilib.cu" ++#include "cuda_gpu_multidim_array.cu" + #include "cuda_gpu_geo_transformer.cu" + #include "cuda_gpu_iirconvolve.cu" +-#include "cuda_gpu_multidim_array.cu" diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_add_useless_libs.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_add_useless_libs.patch new file mode 100644 index 00000000000..a0ad7920a2d --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_add_useless_libs.patch @@ -0,0 +1,21 @@ +commit 4c1e2d678c5a33eae2ddb9f0558523d6d697e2b6 +Author: Ake Sandgren +Date: Thu Oct 27 08:04:04 2022 +0200 + + Don't add useless libraries to XmippInterfaceCuda and XmippParallelCuda + +diff --git xmipp-3.22.07-Helios/src/xmipp/SConstruct xmipp-3.22.07-Helios/src/xmipp/SConstruct +index e70ea2cd..077541e8 100644 +--- xmipp-3.22.07-Helios/src/xmipp/SConstruct ++++ xmipp-3.22.07-Helios/src/xmipp/SConstruct +@@ -209,9 +209,7 @@ def addCppLibrary(env, name, dirs=[], tars=[], untarTargets=['configure'], patte + """ + _libs = list(libs) + _libpath = list(libpath)+external_libdirs +- if name == "XmippInterfaceCuda": +- _libs.append("XmippCuda") +- if "Cuda" in name: ++ if name == "XmippCuda": + _libs.append("cudart") + #_libs.append("cuda") + _libs.append("cufft") diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch new file mode 100644 index 00000000000..3c7171f617a --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch @@ -0,0 +1,41 @@ +commit e53881505ae212fa913fc536e60869e9b8e7f73c +Author: Ake Sandgren +Date: Thu Oct 27 09:45:11 2022 +0200 + + Don't change flags from what EasyBuild has decided to use. + +diff --git xmipp-3.22.07-Helios/scripts/config.py xmipp-3.22.07-Helios/scripts/config.py +index 0f58cbe3..b442a035 100644 +--- xmipp-3.22.07-Helios/scripts/config.py ++++ xmipp-3.22.07-Helios/scripts/config.py +@@ -293,7 +293,7 @@ class Config: + self.configDict["CCFLAGS"] += " -std=c99" + if 'g++' in self.get(Config.KEY_CXX): + # optimize for current machine +- self.configDict["CXXFLAGS"] += " -mtune=native -march=native -flto" ++ #self.configDict["CXXFLAGS"] += " -mtune=native -march=native -flto" + if "-std=c99" not in self.configDict["CXXFLAGS"]: + self.configDict["CXXFLAGS"] += " -std=c++17" + if isCIBuild(): +@@ -301,8 +301,8 @@ class Config: + self.configDict["CXXFLAGS"] += " -Werror" + # don't optimize, as it slows down the build + self.configDict["CXXFLAGS"] += " -O0" +- else: +- self.configDict["CXXFLAGS"] += " -O3" ++ #else: ++ # self.configDict["CXXFLAGS"] += " -O3" + if self.is_true("DEBUG"): + self.configDict["CXXFLAGS"] += " -g" + +@@ -315,8 +315,8 @@ class Config: + if self.configDict["LIBDIRFLAGS"] == "": + # /usr/local/lib or /path/to/virtEnv/lib + localLib = "%s/lib" % info['data'] +- self.configDict["LIBDIRFLAGS"] = "-L%s" % localLib +- self.environment.update(LD_LIBRARY_PATH=localLib) ++ #self.configDict["LIBDIRFLAGS"] = "-L%s" % localLib ++ #self.environment.update(LD_LIBRARY_PATH=localLib) + + # extra libs + hdf5InLocalLib = findFileInDirList("libhdf5*", localLib) diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch new file mode 100644 index 00000000000..7e4c8618625 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch @@ -0,0 +1,18 @@ +commit f647cd54c8fa2b0894f347cbf7f13aacc0b8c785 +Author: Ake Sandgren +Date: Tue Oct 18 14:30:08 2022 +0200 + + Drop redundant setting of env var CXXFLAGS to what it already is. + +diff --git xmipp-3.22.07-Helios/src/xmipp/SConstruct xmipp-3.22.07-Helios/src/xmipp/SConstruct +index c921c3c5..e70ea2cd 100644 +--- xmipp-3.22.07-Helios/src/xmipp/SConstruct ++++ xmipp-3.22.07-Helios/src/xmipp/SConstruct +@@ -148,7 +148,6 @@ env['LINKERFORPROGRAMS'] = os.environ.get('LINKERFORPROGRAMS') + env['CCFLAGS'] = os.environ.get('CCFLAGS', '').split() + cxxFlags = os.environ.get('CXXFLAGS', '') + env['CXXFLAGS'] = cxxFlags.split() +-os.environ['CXXFLAGS'] = cxxFlags # FIXME use only env or os.environ in the rest of the code + env['LINKFLAGS'] = os.environ.get('LINKFLAGS', '').split() + + diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch new file mode 100644 index 00000000000..3eb4c9cf326 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch @@ -0,0 +1,37 @@ +commit 8ff0a1295743fae1eb069fe8242e524f348f5937 +Author: Ake Sandgren +Date: Tue Oct 18 14:28:47 2022 +0200 + + Make sure SCons sees the complete environment from EasyBuild. + +diff --git xmipp-3.22.07-Helios/src/xmipp/SConstruct xmipp-3.22.07-Helios/src/xmipp/SConstruct +index 22ea72cf..c921c3c5 100644 +--- xmipp-3.22.07-Helios/src/xmipp/SConstruct ++++ xmipp-3.22.07-Helios/src/xmipp/SConstruct +@@ -236,7 +236,7 @@ def addCppLibrary(env, name, dirs=[], tars=[], untarTargets=['configure'], patte + # the reason is a compilation error for CUDA, which results in a multiple symbol detection + # when the order is different. This has to be fixed in the future by changing the CUDA + # build system FIXME David Strelak +- env2 = Environment() ++ env2 = Environment(ENV=os.environ) + env2['ENV']['PATH'] = env['ENV']['PATH'] + env2['CXXFLAGS']=list(env['CXXFLAGS']) # list(.) causes a true copy and not just a pointer + env2['LINKFLAGS']=list(env['LINKFLAGS']) +@@ -425,7 +425,7 @@ def addProgram(env, name, src=None, pattern=None, installDir=None, + ldLibraryPathCopy = [env['LIBPATH']] + appendUnique(libPathsCopy, external_libdirs) # This order is important, because if we should use Scipion libs, these will be before the system libs + appendUnique(libPathsCopy, env.get('LIBPATH', '').split(os.pathsep)) +- env2 = Environment() ++ env2 = Environment(ENV=os.environ) + env2['ENV']['LD_LIBRARY_PATH'] = env['ENV'].get('LD_LIBRARY_PATH', '') + env2['ENV']['PATH'] = env['ENV']['PATH'] + +@@ -486,7 +486,7 @@ def compilerConfig(env): + + def libraryTest(env, name, lang='c'): + """Check the existence of a concrete C/C++ library.""" +- env2 = Environment(LIBS=env.get('LIBS','')) ++ env2 = Environment(ENV=os.environ,LIBS=env.get('LIBS','')) + conf = Configure(env2) + conf.CheckLib(name, language=lang) + env2 = conf.Finish() diff --git a/easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch b/easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch new file mode 100644 index 00000000000..06c3697efcb --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch @@ -0,0 +1,28 @@ +commit 901b41d324b351995b9256d7ee6b370276274497 +Author: Ake Sandgren +Date: Tue Oct 18 14:21:03 2022 +0200 + + Make sure SCons sees the complete environment from EasyBuild. + +diff --git xmippCore-3.22.07-Helios/SConstruct xmippCore-3.22.07-Helios/SConstruct +index 1c5fec3..40ed01f 100644 +--- xmippCore-3.22.07-Helios/SConstruct ++++ xmippCore-3.22.07-Helios/SConstruct +@@ -207,7 +207,7 @@ def addCppLibrary(env, name, dirs=[], tars=[], untarTargets=['configure'], patte + if not sources and env.TargetInBuild(name): + Exit('No sources found for Library: %s. Exiting!!!' % name) + +- env2 = Environment() ++ env2 = Environment(ENV=os.environ) + env2['ENV']['PATH'] = env['ENV']['PATH'] + env2['CXX'] = env['CXX'] + +@@ -363,7 +363,7 @@ def compilerConfig(env): + + def libraryTest(env, name, lang='c'): + """Check the existence of a concrete C/C++ library.""" +- env2 = Environment(LIBS=env.get('LIBS','')) ++ env2 = Environment(ENV=os.environ,LIBS=env.get('LIBS','')) + conf = Configure(env2) + conf.CheckLib(name, language=lang) + env2 = conf.Finish() diff --git a/easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch b/easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch new file mode 100644 index 00000000000..f1ac9fff312 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch @@ -0,0 +1,24 @@ +commit 36ca78858e442f1df23f5cb6b87c877a864eff44 +Author: Ake Sandgren +Date: Tue Oct 18 14:23:16 2022 +0200 + + Only use CXXFLAGS from EasyBuild. + +diff --git xmippCore-3.22.07-Helios/SConstruct xmippCore-3.22.07-Helios/SConstruct +index 40ed01f..277443d 100644 +--- xmippCore-3.22.07-Helios/SConstruct ++++ xmippCore-3.22.07-Helios/SConstruct +@@ -136,13 +136,7 @@ env['CXX'] = os.environ.get('CXX') + env['LINKERFORPROGRAMS'] = os.environ.get('LINKERFORPROGRAMS') + env['CCFLAGS'] = os.environ.get('CCFLAGS', '').split() + cxxFlags = os.environ.get('CXXFLAGS', '') +-if os.environ.get('DEBUG', '0') == 'True': #FIXME, use 1, true, yes... +- cxxFlags += ' -g' +-else: +- if cxxFlags.find("-O")==-1: +- cxxFlags += (" -O3" if 'TRAVIS' not in os.environ else " -O0") #don't optimize on Travis, as it slows down the build + env['CXXFLAGS'] = cxxFlags.split() +-os.environ['CXXFLAGS'] = cxxFlags # FIXME use only env or os.environ in the rest of the code + env['LINKFLAGS'] = os.environ.get('LINKFLAGS', '').split() + + diff --git a/easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch b/easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch new file mode 100644 index 00000000000..1cdd9c3add5 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch @@ -0,0 +1,28 @@ +commit 0e749b55db29360c9804f8c5e07094b7a5bf0597 +Author: Ake Sandgren +Date: Tue Oct 18 14:25:17 2022 +0200 + + Make sure scons sees the complete environment from EasyBuild. + +diff --git xmippViz-3.22.07-Helios/SConstruct xmippViz-3.22.07-Helios/SConstruct +index dc0a809..32c75be 100644 +--- xmippViz-3.22.07-Helios/SConstruct ++++ xmippViz-3.22.07-Helios/SConstruct +@@ -237,7 +237,7 @@ def addCppLibrary(env, name, dirs=[], tars=[], untarTargets=['configure'], patte + if not sources and env.TargetInBuild(name): + Exit('No sources found for Library: %s. Exiting!!!' % name) + +- env2 = Environment() ++ env2 = Environment(ENV=os.environ) + env2['ENV']['PATH'] = env['ENV']['PATH'] + + mpiArgs = {} +@@ -474,7 +474,7 @@ def compilerConfig(env): + + def libraryTest(env, name, lang='c'): + """Check the existence of a concrete C/C++ library.""" +- env2 = Environment(LIBS=env.get('LIBS', '')) ++ env2 = Environment(ENV=os.environ,LIBS=env.get('LIBS', '')) + conf = Configure(env2) + conf.CheckLib(name, language=lang) + env2 = conf.Finish() diff --git a/easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch b/easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch new file mode 100644 index 00000000000..6d8802ccb21 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch @@ -0,0 +1,25 @@ +commit 3d1e0e6e6da7aa7cc605be2a699f02b6cfbf4ca5 +Author: Ake Sandgren +Date: Tue Oct 18 14:26:22 2022 +0200 + + Only use CXXFLAGS from EasyBuild. + +diff --git xmippViz-3.22.07-Helios/SConstruct xmippViz-3.22.07-Helios/SConstruct +index 32c75be..fecd394 100644 +--- xmippViz-3.22.07-Helios/SConstruct ++++ xmippViz-3.22.07-Helios/SConstruct +@@ -143,14 +143,7 @@ env['CXX'] = os.environ.get('CXX') + env['LINKERFORPROGRAMS'] = os.environ.get('LINKERFORPROGRAMS') + env['CCFLAGS'] = os.environ.get('CCFLAGS', '').split() + cxxFlags = os.environ.get('CXXFLAGS', '') +-if os.environ.get('DEBUG', '0') == 'True': # FIXME, use 1, true, yes... +- cxxFlags += ' -g' +-else: +- if cxxFlags.find("-O") == -1: +- cxxFlags += ( +- " -O3" if 'TRAVIS' not in os.environ else " -O0") # don't optimize on Travis, as it slows down the build + env['CXXFLAGS'] = cxxFlags.split() +-os.environ['CXXFLAGS'] = cxxFlags # FIXME use only env or os.environ in the rest of the code + env['LINKFLAGS'] = os.environ.get('LINKFLAGS', '').split() + + for path in ['JAVA_HOME', 'JAVA_BINDIR']: From 265e2707a3dbc3ef9d9278d71806d80703f5302b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Oct 2022 11:39:09 +0200 Subject: [PATCH 504/793] Add missing CTPL dep --- .../c/CTPL/CTPL-0.0.2-GCC-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/CTPL/CTPL-0.0.2-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CTPL/CTPL-0.0.2-GCC-11.3.0.eb b/easybuild/easyconfigs/c/CTPL/CTPL-0.0.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..360aea103ca --- /dev/null +++ b/easybuild/easyconfigs/c/CTPL/CTPL-0.0.2-GCC-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CmdCp' + +name = 'CTPL' +version = '0.0.2' + +homepage = 'https://github.com/vit-vit/CTPL.git' + +description = "Modern and efficient C++ Thread Pool Library" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'vit-vit' +source_urls = [GITHUB_SOURCE] +sources = ['%(namelower)s_v.%(version)s.tar.gz'] +checksums = ['8c1cec7c570d6d84be1d29283af5039ea27c3e69703bd446d396424bf619816e'] + +dependencies = [ + ('Boost', '1.79.0'), +] + +cmds_map = [('.*', "echo Nothing to build")] + +files_to_copy = [(['ctpl.h', 'ctpl_stl.h'], 'include/CTPL'), 'LICENSE', 'example.cpp'] + +sanity_check_paths = { + 'files': ['include/CTPL/%s' % x for x in ['ctpl.h', 'ctpl_stl.h']], + 'dirs': [] +} + +moduleclass = 'devel' From 191e0c22e05b8d60b8b193c98dc025be20cbf535 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Oct 2022 12:33:45 +0200 Subject: [PATCH 505/793] Add missing SCons dep --- .../s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ ...ns-4.4.0_install_man_pages_correctly.patch | 15 ++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/SCons/SCons-4.4.0_install_man_pages_correctly.patch diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8b3bae7755a --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'SCons' +version = '4.4.0' + +homepage = 'https://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': False, + 'patches': ['SCons-4.4.0_install_man_pages_correctly.patch'], + 'checksums': [ + {'SCons-4.4.0.tar.gz': '7703c4e9d2200b4854a31800c1dbd4587e1fa86e75f58795c740bcfa7eca7eaa'}, + {'SCons-4.4.0_install_man_pages_correctly.patch': + '9d216c2ea8e152ae1531593b17adc4042eb88f1d9524d7f3b08ace5137d6d5e7'}, + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/sconsign'], + 'dirs': ['lib/pythoni%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = ["scons --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.4.0_install_man_pages_correctly.patch b/easybuild/easyconfigs/s/SCons/SCons-4.4.0_install_man_pages_correctly.patch new file mode 100644 index 00000000000..4c482a86c5e --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-4.4.0_install_man_pages_correctly.patch @@ -0,0 +1,15 @@ +Install the man pages in the correct directory. + +Åke Sandgren, 2022-10-27 +diff -ru SCons-4.4.0.orig/setup.cfg SCons-4.4.0/setup.cfg +--- SCons-4.4.0.orig/setup.cfg 2022-07-30 23:16:02.000000000 +0200 ++++ SCons-4.4.0/setup.cfg 2022-10-27 11:55:33.457877253 +0200 +@@ -58,7 +58,7 @@ + SCons.Tool.docbook = *.* + + [options.data_files] +-. = scons.1 ++man/man1 = scons.1 + scons-time.1 + sconsign.1 + From 1edcba7fa4d21e5bc98fef154cf4ddf231c4b8ca Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Oct 2022 12:38:52 +0200 Subject: [PATCH 506/793] SCons: Fix typo --- easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb index 8b3bae7755a..22668b263b2 100644 --- a/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb @@ -29,7 +29,7 @@ exts_list = [ sanity_check_paths = { 'files': ['bin/scons', 'bin/sconsign'], - 'dirs': ['lib/pythoni%(pyshortver)s/site-packages/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], } sanity_check_commands = ["scons --help"] From 882d3673c93229c62dca34816d4b42936ebd190f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Oct 2022 18:39:34 +0200 Subject: [PATCH 507/793] adding easyconfigs: PyQt5-5.15.5-GCCcore-11.3.0.eb --- .../p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb | 102 ++++++++++++++++++ 1 file changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a052b69a2df --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb @@ -0,0 +1,102 @@ +easyblock = 'Bundle' + +name = 'PyQt5' +version = '5.15.5' + +homepage = 'https://www.riverbankcomputing.com/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. +This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'cstd': 'c++11'} + +builddependencies = [('binutils', '2.38')] +dependencies = [ + ('Python', '3.10.4'), + ('Qt5', '5.15.5'), +] + +default_easyblock = 'PythonPackage' + +local_sipdir = '%(installdir)s/share/sip' + +local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' + +local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " + +local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--no-stubs --no-dist-info" + +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir + +local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " +local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_sipver = '5.5.0' +components = [ + ('SIP', local_sipver, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'start_dir': 'sip-%s' % local_sipver, + 'use_pip': True, + 'options': {'modulename': 'PyQt5.sip'}, + }), + ('PyQt-builder', '1.14.0', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'start_dir': 'PyQt-builder-%(version)s', + 'use_pip': True, + }), + ('PyQt5_sip', '12.11.0', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'start_dir': 'PyQt5_sip-%(version)s', + 'use_pip': True, + }), + (name, version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + 'configopts': local_pyqt_configopts + }), + ('PyQtWebEngine', version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + 'configopts': local_pyqtweb_configopts, + 'options': {'modulename': 'PyQt5.QtWebEngine'}, + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in [ + 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import PyQt5.QtCore'", + "sip5 --help", + "pyuic5 --help", + "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", + "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'QT_INSTALL_DATA': 'qsci', +} + +moduleclass = 'vis' From 0b6b8131e2b2f73363367341f60edbf47079e721 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Oct 2022 19:48:44 +0200 Subject: [PATCH 508/793] Add missing checksums --- easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb index a052b69a2df..594f66926cc 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb @@ -45,6 +45,7 @@ components = [ ('SIP', local_sipver, { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['5d024c419b30fea8a6de8c71a560c7ab0bc3c221fbfb14d55a5b865bd58eaac5'], 'start_dir': 'sip-%s' % local_sipver, 'use_pip': True, 'options': {'modulename': 'PyQt5.sip'}, @@ -52,18 +53,21 @@ components = [ ('PyQt-builder', '1.14.0', { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], + 'checksums': ['6755931c6d2f8940553e0334d10c933ce5cc18b64425e94fda1accf4ff774f59'], 'start_dir': 'PyQt-builder-%(version)s', 'use_pip': True, }), ('PyQt5_sip', '12.11.0', { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], + 'checksums': ['b4710fd85b57edef716cc55fae45bfd5bfac6fc7ba91036f1dcc3f331ca0eb39'], 'start_dir': 'PyQt5_sip-%(version)s', 'use_pip': True, }), (name, version, { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], + 'checksums': ['b411b7a8fa03901c9feb1dcbac7ea1fc3ce20b9ae682762b777cd5398749ca2b'], 'easyblock': 'ConfigureMakePythonPackage', 'start_dir': '%(name)s-%(version)s', 'preconfigopts': local_setup_env, @@ -72,6 +76,7 @@ components = [ ('PyQtWebEngine', version, { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], + 'checksums': ['ab47608dccf2b5e4b950d5a3cc704b17711af035024d07a9b71ad29fc103b941'], 'easyblock': 'ConfigureMakePythonPackage', 'start_dir': '%(name)s-%(version)s', 'preconfigopts': local_setup_env, From d56c22e819ef39fad047ae05b6f62527f1961c3c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 28 Oct 2022 07:46:55 +0200 Subject: [PATCH 509/793] adding easyconfigs: PyOpenGL-3.1.6-GCCcore-11.3.0.eb --- .../PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..202415c4bdc --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'PyOpenGL' +version = '3.1.6' + +homepage = 'http://pyopengl.sourceforge.net' +description = """PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + + +builddependencies = [ + ('binutils', '2.38'), + ('bzip2', '1.0.8'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('Mesa', '22.0.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'OpenGL', + 'checksums': ['8ea6c8773927eda7405bffc6f5bb93be81569a7b05c8cac50cd94e969dce5e27'], + }), +] + +moduleclass = 'vis' From e3925ab4dfc73f8c851ed9ea864821152998b6c4 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 28 Oct 2022 08:45:04 +0100 Subject: [PATCH 510/793] fix libsanitzer for glibc 2.36 to build GCCcore 10.x and 11.x --- .../easyconfigs/g/GCCcore/GCCcore-10.1.0.eb | 21 ++++++----- .../easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 36 ++++++++++--------- .../easyconfigs/g/GCCcore/GCCcore-10.3.0.eb | 29 ++++++++------- .../easyconfigs/g/GCCcore/GCCcore-11.1.0.eb | 2 ++ .../easyconfigs/g/GCCcore/GCCcore-11.2.0.eb | 2 ++ 5 files changed, 52 insertions(+), 38 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb index 23a101c3f9f..5ad49480069 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb @@ -31,17 +31,20 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCC-10.x_fix-libsanitizer-cyclades.patch', + 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', ] checksums = [ - '954057239c89d25bc7a62bfbceb58026363ad74f079c63fdba27f95abbf60900', # gcc-10.1.0.tar.gz - 'f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea', # gmp-6.2.0.tar.bz2 - 'c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc', # mpfr-4.0.2.tar.bz2 - '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e', # mpc-1.1.0.tar.gz - '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd', # isl-0.22.1.tar.bz2 - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch - '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch - 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832', # GCC-10.x_fix-libsanitizer-cyclades.patch + {'gcc-10.1.0.tar.gz': '954057239c89d25bc7a62bfbceb58026363ad74f079c63fdba27f95abbf60900'}, + {'gmp-6.2.0.tar.bz2': 'f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea'}, + {'mpfr-4.0.2.tar.bz2': 'c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc'}, + {'mpc-1.1.0.tar.gz': '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e'}, + {'isl-0.22.1.tar.bz2': '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCC-10.x_fix-libsanitizer-cyclades.patch': 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832'}, + {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index d6d21047a9c..880ff3864f6 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -39,24 +39,28 @@ patches = [ 'GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCC-10.x_fix-libsanitizer-cyclades.patch', + 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', ] checksums = [ - '27e879dccc639cd7b0cc08ed575c1669492579529b53c9ff27b0b96265fa867d', # gcc-10.2.0.tar.gz - 'f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea', # gmp-6.2.0.tar.bz2 - 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 - '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e', # mpc-1.1.0.tar.gz - '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd', # isl-0.22.1.tar.bz2 - '58dd9e3eaedf519360d92d84205c3deef0b3fc286685d1c562e245914ef72c66', # newlib-3.3.0.tar.gz - 'a25b6f7761bb61c0d8e2a183bcf51fbaaeeac26868dcfc015e3b16a33fe11705', # nvptx-tools-20180301.tar.gz - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch - '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108', # GCCcore-9.3.0_nvptx_sm_35_default.patch - 'f94fa117f3401b28fda0741f3f45439c09dc956d1ed27f9a3ebe40c0e7e404b6', # GCCcore-10.2.0_fix-has-include-Fortran.patch - '44edbf1cddb2d7037f9606b6995d9ef20ff664b810a3e3ef383420a4366ed278', # GCCcore-10.2.0_fix-ice-on-arm.patch - # GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch - 'fb160374ba691d8267a19dee4268305a6e34123cab9e65176b5168c36e9f0962', - '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch - 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832', # GCC-10.x_fix-libsanitizer-cyclades.patch + {'gcc-10.2.0.tar.gz': '27e879dccc639cd7b0cc08ed575c1669492579529b53c9ff27b0b96265fa867d'}, + {'gmp-6.2.0.tar.bz2': 'f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.1.0.tar.gz': '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e'}, + {'isl-0.22.1.tar.bz2': '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd'}, + {'newlib-3.3.0.tar.gz': '58dd9e3eaedf519360d92d84205c3deef0b3fc286685d1c562e245914ef72c66'}, + {'nvptx-tools-20180301.tar.gz': 'a25b6f7761bb61c0d8e2a183bcf51fbaaeeac26868dcfc015e3b16a33fe11705'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-9.3.0_nvptx_sm_35_default.patch': '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108'}, + {'GCCcore-10.2.0_fix-has-include-Fortran.patch': + 'f94fa117f3401b28fda0741f3f45439c09dc956d1ed27f9a3ebe40c0e7e404b6'}, + {'GCCcore-10.2.0_fix-ice-on-arm.patch': '44edbf1cddb2d7037f9606b6995d9ef20ff664b810a3e3ef383420a4366ed278'}, + {'GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch': + 'fb160374ba691d8267a19dee4268305a6e34123cab9e65176b5168c36e9f0962'}, + {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCC-10.x_fix-libsanitizer-cyclades.patch': 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832'}, + {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb index a3826b1579c..7f9079c65c0 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb @@ -37,21 +37,24 @@ patches = [ 'gcc-10.3.0_fix-ice-in-tsubst.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCC-10.x_fix-libsanitizer-cyclades.patch', + 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', ] checksums = [ - '8fcf994811ad4e5c7ac908e8cf62af2c1982319e5551f62ae72016064dacdf16', # gcc-10.3.0.tar.gz - 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 - 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 - '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz - 'c58922c14ae7d0791a77932f377840890f19bc486b653fa64eba7f1026fb214d', # isl-0.23.tar.bz2 - 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz - '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2', # nvptx-tools-20210115.tar.gz - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch - '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108', # GCCcore-9.3.0_nvptx_sm_35_default.patch - '74e6e019458aa2feb36ae3c45f45e164725ca5edd66f4fe9f873c8ee78c35717', # gcc-10.3.0_fix-ice-in-tsubst.patch - '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch - 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832', # GCC-10.x_fix-libsanitizer-cyclades.patch + {'gcc-10.3.0.tar.gz': '8fcf994811ad4e5c7ac908e8cf62af2c1982319e5551f62ae72016064dacdf16'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'}, + {'isl-0.23.tar.bz2': 'c58922c14ae7d0791a77932f377840890f19bc486b653fa64eba7f1026fb214d'}, + {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'}, + {'nvptx-tools-20210115.tar.gz': '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-9.3.0_nvptx_sm_35_default.patch': '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108'}, + {'gcc-10.3.0_fix-ice-in-tsubst.patch': '74e6e019458aa2feb36ae3c45f45e164725ca5edd66f4fe9f873c8ee78c35717'}, + {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCC-10.x_fix-libsanitizer-cyclades.patch': 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832'}, + {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb index a5a30163948..dde91967953 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb @@ -35,6 +35,7 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCC-10.x_fix-libsanitizer-cyclades.patch', + 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ @@ -50,6 +51,7 @@ checksums = [ {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, {'GCC-10.x_fix-libsanitizer-cyclades.patch': 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832'}, + {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, {'GCCcore-11.3.0_fix-vectorizer.patch': '7dff25b678e2f65b81d9bf0c8402ad46c25a04b0c0d610db50b763ecc5f9ef98'}, ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb index 5efade9fb39..9d40637c25c 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb @@ -34,6 +34,7 @@ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', + 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ @@ -48,6 +49,7 @@ checksums = [ {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, {'GCCcore-11.3.0_fix-vectorizer.patch': '7dff25b678e2f65b81d9bf0c8402ad46c25a04b0c0d610db50b763ecc5f9ef98'}, ] From b4320eab9ed3f4b592917353cb6d3ac4e21607ed Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 28 Oct 2022 13:54:11 +0200 Subject: [PATCH 511/793] adding easyconfigs: cwltool-3.1.20221018083734-GCCcore-10.3.0.eb --- ...ltool-3.1.20221018083734-GCCcore-10.3.0.eb | 115 ++++++++++++++++++ 1 file changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..cfc690a27ae --- /dev/null +++ b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb @@ -0,0 +1,115 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'PythonBundle' + +name = 'cwltool' +version = '3.1.20221018083734' + +homepage = 'https://github.com/common-workflow-language/cwltool' +description = """Common workflow language (CWL) reference implementation.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('make', '4.3'), + ('Check', '0.15.2'), + ('SWIG', '4.0.2'), + ('expat', '2.2.9'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +# The Qt5 dependency of Graphviz (required by pydot) may be long to build and +# requires a lot of disk space and memory! +dependencies = [ + ('Python', '3.9.5'), + ('typing-extensions', '3.10.0.0'), + ('pydot', '1.4.2'), + ('lxml', '4.6.3'), +] + +use_pip = True + +# Fetch the tar.gz, not the whl files! +exts_list = [ + ('argcomplete', '2.0.0', { + 'checksums': ['6372ad78c89d662035101418ae253668445b391755cfe94ea52f1b9d22425b20'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + ('ruamel.yaml.clib', '0.2.7', { + 'modulename': 'ruamel.yaml', + 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], + }), + ('ruamel.yaml', '0.17.14', { + 'modulename': 'ruamel', + 'checksums': ['4185fcfa9e037fea9ffd0bb6172354a03ec98c21e462355d72e068c74e493512'], + }), + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('rdflib', '6.2.0', { + 'checksums': ['62dc3c86d1712db0f55785baf8047f63731fa59b2682be03219cb89262065942'], + }), + ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('schema-salad', '8.3.20221016151607', { + 'modulename': 'schema_salad', + 'checksums': ['c61a517c945cd383445ebecbc085b00766913a3fdd7df9699a0fa4c41728ca1f'], + }), + ('shellescape', '3.8.1', { + 'checksums': ['40b310b30479be771bf3ab28bd8d40753778488bd46ea0969ba0b35038c3ec26'], + }), + ('cwlformat', '2022.2.18', { + 'modulename': 'cwlformat', + 'source_tmpl': 'cwlformat-%(version)s-py3-none-any.whl', + 'checksums': ['d3e2dca192ce10e703ed4eb0bae26539db08d8ddd7c6a6fe9d1406c3f1b53cda'], + }), + ('cwl-upgrader', '1.2.4', { + 'modulename': 'cwlupgrader', + 'checksums': ['b25fc236407343d44cc830ac3f63eed395b8d872fc7e17db92cde583d4a3b2ec'], + }), + ('cwl-utils', '0.20', { + 'modulename': 'cwl_utils', + 'checksums': ['28472aaba50ab4e8380c29f31c27beb63f60a1af1690369ab7bb7e31e71e66d9'], + }), + ('mypy-extensions', '0.4.3', { + 'modulename': 'mypy_extensions', + 'source_tmpl': 'mypy_extensions-%(version)s.tar.gz', + 'checksums': ['2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8'], + }), + ('networkx', '2.8.7', { + 'checksums': ['815383fd52ece0a7024b5fd8408cc13a389ea350cd912178b82eed8b96f82cd3'], + }), + ('prov', '1.5.1', { + 'checksums': ['7a2d72b0df43cd9c6e374d815c8ce3cd5ca371d54f98f837853ac9fcc98aee4c'], + }), + ('bagit', '1.8.1', { + 'checksums': ['37df1330d2e8640c8dee8ab6d0073ac701f0614d25f5252f9e05263409cee60c'], + }), + ('cwltool', '3.1.20221018083734', { + 'checksums': ['06d08f390ed7577ac66c6eef0c98f915363b5e36c04daa1353e3f2d0c5e19f17'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cwltool'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cwltool --version"] + +moduleclass = 'tools' From 9daea5ff0b20098eb2870fcc0dadc296fbb7d437 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 28 Oct 2022 15:28:51 +0200 Subject: [PATCH 512/793] Add missing sanity_pip_check --- .../c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb index cfc690a27ae..1d9ccc685eb 100644 --- a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb @@ -112,4 +112,6 @@ sanity_check_paths = { sanity_check_commands = ["cwltool --version"] +sanity_pip_check = True + moduleclass = 'tools' From 07493ac0283d1ff8b447a97e020d44fdc92f317b Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 28 Oct 2022 17:02:56 +0200 Subject: [PATCH 513/793] Use ruamel.yaml and networkx from EB --- .../cwltool-3.1.20221018083734-GCCcore-10.3.0.eb | 13 ++----------- 1 file changed, 2 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb index 1d9ccc685eb..b40b9c1e883 100644 --- a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb @@ -34,6 +34,8 @@ dependencies = [ ('typing-extensions', '3.10.0.0'), ('pydot', '1.4.2'), ('lxml', '4.6.3'), + ('ruamel.yaml', '0.17.21'), + ('networkx', '2.6.3', '', ('foss', '2021a')), ] use_pip = True @@ -49,14 +51,6 @@ exts_list = [ ('coloredlogs', '15.0.1', { 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], }), - ('ruamel.yaml.clib', '0.2.7', { - 'modulename': 'ruamel.yaml', - 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], - }), - ('ruamel.yaml', '0.17.14', { - 'modulename': 'ruamel', - 'checksums': ['4185fcfa9e037fea9ffd0bb6172354a03ec98c21e462355d72e068c74e493512'], - }), ('isodate', '0.6.1', { 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], }), @@ -91,9 +85,6 @@ exts_list = [ 'source_tmpl': 'mypy_extensions-%(version)s.tar.gz', 'checksums': ['2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8'], }), - ('networkx', '2.8.7', { - 'checksums': ['815383fd52ece0a7024b5fd8408cc13a389ea350cd912178b82eed8b96f82cd3'], - }), ('prov', '1.5.1', { 'checksums': ['7a2d72b0df43cd9c6e374d815c8ce3cd5ca371d54f98f837853ac9fcc98aee4c'], }), From 5822cf971248270b67fcdf12b3f057eff278950d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 28 Oct 2022 18:10:36 +0200 Subject: [PATCH 514/793] Update napari-0.4.15-foss-2021b.eb fox sources list docstring-parser --- easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb index f439e3019c2..18337a90cfd 100644 --- a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb +++ b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb @@ -52,7 +52,7 @@ exts_list = [ 'checksums': ['0310ba8afe52729fa7626325c8d8356a8421c434bf887ac851e58dcf7cf056a6'], }), ('docstring-parser', '0.14.1', { - 'sources': 'docstring_parser-%(version)s.tar.gz', + 'sources': ['docstring_parser-%(version)s.tar.gz'], 'checksums': ['2c77522e31b7c88b1ab457a1f3c9ae38947ad719732260ba77ee8a3deb58622a'], }), ('pep517', '0.12.0', { From 560d52ba93aaf34f7137c70d30baa99999553367 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 18:31:57 +0100 Subject: [PATCH 515/793] adding easyconfigs: svist4get-1.3.1-foss-2020b.eb --- .../s/svist4get/svist4get-1.3.1-foss-2020b.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb new file mode 100644 index 00000000000..8ec2b2b0060 --- /dev/null +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -0,0 +1,59 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'svist4get' +version = '1.3.1' + +homepage = 'https://github.com/art-egorov/svist4get' +description = """Svist4get is a simple bioinformatics tool for visualization of +genomic signal tracks in user-defined genomic windows, either arbitrary selected +by genomic coordinates or anchored to particular transcripts or genes.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('pybedtools', '0.8.2'), + ('Biopython', '1.78'), + ('Pillow', '8.0.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('reportlab', '3.6.9', { + 'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84'], + }), + + ('configs', '3.0.3', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['a5ab09e04e441dac6aa856a71fbf5ffc62954352630f79d311b8f8a31d9ce19c'], + }), + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + ('Wand', '0.6.10', { + 'checksums': ['373f4a7f2866c868c31ce910e1f9b36a92d132640a20068ec17cea3284fedc57'], + }), + ('statistics', '1.0.3.5', { + 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], + }), + + (name, version, { + 'checksums': ['22311fdc956cca531dac7ba924744e8f870a57bc6f27cbe4e8ba9854117e720c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/svist4get', 'bin/svist4get_copier'], + 'dirs': ['lib'], +} + +sanity_check_commands = [ + "svist4get --help", + "svist4get -v", +] + +moduleclass = 'bio' From d12f1b147c7ad739e4603458a4aef74285b2c013 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 18:33:08 +0100 Subject: [PATCH 516/793] adding easyconfigs: TOBIAS-0.14.0-foss-2020b.eb --- .../t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb | 83 +++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb new file mode 100644 index 00000000000..124583e843d --- /dev/null +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb @@ -0,0 +1,83 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'TOBIAS' +version = '0.14.0' + +homepage = 'https://github.com/loosolab/TOBIAS' +description = """TOBIAS is a collection of command-line bioinformatics tools +for performing footprinting analysis on ATAC-seq data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Seaborn', '0.11.1'), + ('pybedtools', '0.8.2'), + ('pyBigWig', '0.3.18'), + ('scikit-learn', '0.23.2'), + ('PyYAML', '5.3.1'), + ('XlsxWriter', '1.4.0'), + ('svist4get', '1.3.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('adjustText', '0.7.3', { + 'checksums': ['b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06'], + 'modulename': 'adjustText', + }), + ('botocore', '1.28.2', { + 'checksums': ['9890005735652555d1183b44bad729603d26922dc08e261e1e0a35a7bf26ba38'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.6.0', { + 'checksums': ['2ed07d3866f523cc561bf4a00fc5535827981b117dd7876f036b0c1aca42c947'], + }), + ('boto3', '1.25.2', { + 'checksums': ['43a93f8cecd882cccb2815cd76fc07a73b076027ab092a1c7cede89cb9b075f8'], + }), + ('kneed', '0.7.0', { + 'checksums': ['340d67fa183a72b0afae19846dd246a6fb7204e8d54243d8b8d3d9932f887c6e'], + }), + ('logomaker', '0.8', { + 'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'], + }), + ('MOODS-python', '1.9.4.1', { + 'checksums': ['b3b5e080cb0cd13c0fd175d0ee0d453fde3e42794fa7ac39a4f6db1ac5ddb4cc'], + 'modulename': 'MOODS', + }), + ('flit_core', '3.7.1', { + 'checksums': ['14955af340c43035dbfa96b5ee47407e377ee337f69e70f73064940d27d0a44f'], + }), + ('typing_extensions', '4.4.0', { + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + ('PyPDF2', '2.11.1', { + 'checksums': ['3c7badd512c21711eb1789c2eadbf96279289c0f94452ee54a86473bfbefd732'], + 'modulename': 'PyPDF2', + }), + + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['ac74c35f981d499425147054f82142d22e52858d402d0c63ab7e8481bd156589'], + }), +] + +sanity_check_paths = { + 'files': ['bin/TOBIAS', 'bin/cluster_sites_by_overlap.py', 'bin/moods-dna.py', 'bin/jp.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "TOBIAS --help", +] + +moduleclass = 'bio' From c5c6cdf960b42a6c5df9d32ae61befdf7973b5bf Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 23:37:54 +0100 Subject: [PATCH 517/793] reportlab patched so it finds EB fontconfig instead system one --- .../s/svist4get/svist4get-1.3.1-foss-2020b.eb | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb index 8ec2b2b0060..c228ca9af49 100644 --- a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -16,17 +16,19 @@ dependencies = [ ('Python', '3.8.6'), ('pybedtools', '0.8.2'), ('Biopython', '1.78'), - ('Pillow', '8.0.1'), + ('Pillow', '9.2.0'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('reportlab', '3.6.9', { - 'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84'], + ('reportlab', '3.6.12', { + 'patches': ['reportlab-3.6.12-fontconfig.patch'], + 'checksums': ['b13cebf4e397bba14542bcd023338b6ff2c151a3a12aabca89eecbf972cb361a', + # reportlab-3.6.12-fontconfig.patch: + '2cc9b40e09650b7404ee9c4d72b134739acc89bacac3da58131cef2308726297'], }), - ('configs', '3.0.3', { 'sources': ['%(name)s-%(version)s.zip'], 'checksums': ['a5ab09e04e441dac6aa856a71fbf5ffc62954352630f79d311b8f8a31d9ce19c'], @@ -40,7 +42,6 @@ exts_list = [ ('statistics', '1.0.3.5', { 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], }), - (name, version, { 'checksums': ['22311fdc956cca531dac7ba924744e8f870a57bc6f27cbe4e8ba9854117e720c'], }), @@ -52,7 +53,7 @@ sanity_check_paths = { } sanity_check_commands = [ - "svist4get --help", + "svist4get --help", "svist4get -v", ] From 479ed72ae7168d43ea554240fc34c381c8c88929 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 23:39:29 +0100 Subject: [PATCH 518/793] adding easyconfigs: Pillow-9.2.0-GCCcore-10.2.0.eb --- .../p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..38e7492daf9 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '9.2.0' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = [ + '75e636fd3e0fb872693f23ccb8a5ff2cd578801251f3a4f6854c6a5d437d3c04', # Pillow-8.0.1.tar.gz +] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.1.0'), + ('freetype', '2.10.3') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' From af342d68b218ed49e52240d56a5d750c226b883f Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 23:49:12 +0100 Subject: [PATCH 519/793] Patchfile added --- .../reportlab-3.6.12-fontconfig.patch | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/svist4get/reportlab-3.6.12-fontconfig.patch diff --git a/easybuild/easyconfigs/s/svist4get/reportlab-3.6.12-fontconfig.patch b/easybuild/easyconfigs/s/svist4get/reportlab-3.6.12-fontconfig.patch new file mode 100644 index 00000000000..92e6ce51369 --- /dev/null +++ b/easybuild/easyconfigs/s/svist4get/reportlab-3.6.12-fontconfig.patch @@ -0,0 +1,25 @@ +Patch to make sure the fontconfig from EasyBuild will be found +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/reportlab-3.6.12.orig/setup.py b/reportlab-3.6.12/setup.py +index 4b380b6..2ccfa93 100644 +--- a/reportlab-3.6.12.orig/setup.py ++++ b/reportlab-3.6.12/setup.py +@@ -277,14 +277,11 @@ class inc_lib_dirs: + # darwin ports installation directories + aDir(L, "/opt/local/lib") + aDir(I, "/opt/local/include") +- aDir(I, "/usr/local/include") +- aDir(L, "/usr/local/lib") +- aDir(I, "/usr/include") +- aDir(L, "/usr/lib") +- aDir(I, "/usr/include/freetype2") + if addrSize==64: +- aDir(L, "/usr/lib/lib64") +- aDir(L, "/usr/lib/x86_64-linux-gnu") ++ freepath = os.getenv("EBROOTFREETYPE") ++ aDir(L, pjoin(freepath, "lib64")) ++ aDir(I, pjoin(freepath, "include/freetype2")) ++ + else: + aDir(L, "/usr/lib/lib32") + prefix = sysconfig.get_config_var("prefix") From 160c1da84942a6311bb12c0a5e0e90835668b57c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Sat, 29 Oct 2022 00:38:28 +0100 Subject: [PATCH 520/793] Update svist4get-1.3.1-foss-2020b.eb Missing ImageMagick added (picked up OS installation before) --- easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb index c228ca9af49..d9b689ae40e 100644 --- a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -17,6 +17,7 @@ dependencies = [ ('pybedtools', '0.8.2'), ('Biopython', '1.78'), ('Pillow', '9.2.0'), + ('ImageMagick', '7.0.10-35'), ] use_pip = True From ca066e8f6222f3c8ab16b502e2d614d92ebf7af2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Sat, 29 Oct 2022 00:53:11 +0100 Subject: [PATCH 521/793] Update svist4get-1.3.1-foss-2020b.eb Pillow downgraded to 8.0.1, reportlab downgraded to 3.6.9 due to conflicts with TOBIAS --- .../easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb index d9b689ae40e..a6339d51f19 100644 --- a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.8.6'), ('pybedtools', '0.8.2'), ('Biopython', '1.78'), - ('Pillow', '9.2.0'), + ('Pillow', '8.0.1'), ('ImageMagick', '7.0.10-35'), ] @@ -24,9 +24,9 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('reportlab', '3.6.12', { + ('reportlab', '3.6.9', { 'patches': ['reportlab-3.6.12-fontconfig.patch'], - 'checksums': ['b13cebf4e397bba14542bcd023338b6ff2c151a3a12aabca89eecbf972cb361a', + 'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84', # reportlab-3.6.12-fontconfig.patch: '2cc9b40e09650b7404ee9c4d72b134739acc89bacac3da58131cef2308726297'], }), From d9798882dc8f2681816c6e473b6107257f534715 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Sat, 29 Oct 2022 09:12:32 +0100 Subject: [PATCH 522/793] Update TOBIAS-0.14.0-foss-2020b.eb Empty line removed --- easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb index 124583e843d..862d4fe55c1 100644 --- a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb @@ -64,7 +64,6 @@ exts_list = [ 'checksums': ['3c7badd512c21711eb1789c2eadbf96279289c0f94452ee54a86473bfbefd732'], 'modulename': 'PyPDF2', }), - (name, version, { 'sources': ['%(namelower)s-%(version)s.tar.gz'], 'checksums': ['ac74c35f981d499425147054f82142d22e52858d402d0c63ab7e8481bd156589'], From 769fde96b1588d61317942682d27a64a0f4a25b1 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 29 Oct 2022 12:14:17 +0200 Subject: [PATCH 523/793] adding easyconfigs: make-4.3-GCCcore-11.3.0.eb, tmux-3.3a-GCCcore-11.3.0.eb --- .../m/make/make-4.3-GCCcore-11.3.0.eb | 29 +++++++++++++++ .../t/tmux/tmux-3.3a-GCCcore-11.3.0.eb | 36 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/m/make/make-4.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/make/make-4.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/make/make-4.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..508f420c75e --- /dev/null +++ b/easybuild/easyconfigs/m/make/make-4.3-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'make' +version = '4.3' + +homepage = 'https://www.gnu.org/software/make/make.html' +description = "GNU version of make utility" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e05fdde47c5f7ca45cb697e973894ff4f5d79e13b750ed57d7b66d8defc78e19'] + +builddependencies = [('binutils', '2.38')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"] + +sanity_check_paths = { + 'files': ['bin/gmake', 'bin/make'], + 'dirs': [] +} + +sanity_check_commands = [ + "gmake --help", + "make --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..de3e3e02e01 --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '3.3a' + +homepage = 'https://github.com/tmux/tmux/' +description = """tmux is a terminal multiplexer: it enables a number of +terminals to be created, accessed, and controlled from a single screen. tmux +may be detached from a screen and continue running in the background, then +later reattached.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e4fd347843bd0772c4f48d6dde625b0b109b7a380ff15db21e97c11a4dcdf93f'] + +builddependencies = [ + ('binutils', '2.38'), + ('Bison', '3.8.2'), + ('make', '4.3'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('libevent', '2.1.12'), + ('ncurses', '6.3'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +moduleclass = 'tools' From b40096676f0a96b0c47cb55a576e3f489cc73ac3 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 31 Oct 2022 02:29:29 +0000 Subject: [PATCH 524/793] Add OpenBLAS patches to disable FMA in [cz]cal and fix crash in zdot --- .../o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 5 ++ .../o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb | 5 ++ .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 5 ++ .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 5 ++ .../OpenBLAS-0.3.21_avoid-crash-in-zdot.patch | 19 ++++++ ...AS-0.3.21_disable-fma-in-cscal-zscal.patch | 68 +++++++++++++++++++ 6 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_avoid-crash-in-zdot.patch create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index 93e65aa9221..c4b29c67422 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -19,6 +19,8 @@ patches = [ 'OpenBLAS-%(version)s_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch', 'OpenBLAS-%(version)s_fix-segfault-ztrsv.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', ] checksums = [ {'v0.3.17.tar.gz': 'df2934fa33d04fd84d839ca698280df55c690c86a5a1133b3f7266fce1de279f'}, @@ -31,6 +33,9 @@ checksums = [ {'OpenBLAS-0.3.17_fix-segfault-ztrsv.patch': 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': + 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb index 866cd7de515..762a9558bfb 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -18,6 +18,8 @@ patches = [ 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.17_fix-segfault-ztrsv.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', ] checksums = [ {'v0.3.18.tar.gz': '1632c1e8cca62d8bed064b37747e331a1796fc46f688626337362bf0d16aeadb'}, @@ -28,6 +30,9 @@ checksums = [ {'OpenBLAS-0.3.17_fix-segfault-ztrsv.patch': 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': + 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index c654f92e700..98f44c83e7c 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -17,6 +17,8 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', ] checksums = [ {'v0.3.20.tar.gz': '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c'}, @@ -26,6 +28,9 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': + 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index bb82984319e..4496c0bc5b3 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -17,6 +17,8 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', ] checksums = [ {'v0.3.20.tar.gz': '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c'}, @@ -26,6 +28,9 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': + 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_avoid-crash-in-zdot.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_avoid-crash-in-zdot.patch new file mode 100644 index 00000000000..d96341d6de5 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_avoid-crash-in-zdot.patch @@ -0,0 +1,19 @@ +Avoid crash with GCC 11's vectorizer involving 256-bit ymm registers. + +See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=107451 + +Bart Oldeman + +diff --git a/kernel/x86_64/zdot.c b/kernel/x86_64/zdot.c +index 27397ccf..e1d43be1 100644 +--- a/kernel/x86_64/zdot.c ++++ b/kernel/x86_64/zdot.c +@@ -97,7 +97,7 @@ extern int blas_level1_thread_with_return_value(int mode, BLASLONG m, BLASLONG n + + + +-static void zdot_compute (BLASLONG n, FLOAT *x, BLASLONG inc_x, FLOAT *y, BLASLONG inc_y,OPENBLAS_COMPLEX_FLOAT *result) ++__attribute__((target("prefer-vector-width=128"))) static void zdot_compute (BLASLONG n, FLOAT *x, BLASLONG inc_x, FLOAT *y, BLASLONG inc_y,OPENBLAS_COMPLEX_FLOAT *result) + { + BLASLONG i; + BLASLONG ix,iy; diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch new file mode 100644 index 00000000000..6e2cb2e62e0 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch @@ -0,0 +1,68 @@ +From e7e3aa29482281edba46a27fcd452d7ed630f46a Mon Sep 17 00:00:00 2001 +From: Bart Oldeman +Date: Thu, 27 Oct 2022 17:20:44 -0400 +Subject: [PATCH] x86_64: prevent GCC and Clang from generating FMAs in + cscal/zscal. + +If e.g. -march=haswell is set in CFLAGS, GCC generates FMAs by default, which +is inconsistent with the microkernels, none of which use FMAs. These +inconsistencies cause a few failures in the LAPACK testcases, where +eigenvalue results with/without eigenvectors are compared. + +Moreover using FMAs for multiplication of complex numbers can give surprising +results, see 22aa81f for more information. + +This uses the same syntax as used in 22aa81f for zarch (s390x). +--- + kernel/x86_64/cscal.c | 13 +++++++++++++ + kernel/x86_64/zscal.c | 13 +++++++++++++ + 2 files changed, 26 insertions(+) + +diff --git a/kernel/x86_64/cscal.c b/kernel/x86_64/cscal.c +index dc3f688c69..6ae66d9731 100644 +--- a/kernel/x86_64/cscal.c ++++ b/kernel/x86_64/cscal.c +@@ -25,6 +25,19 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE + USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + *****************************************************************************/ + ++/* ++ * Avoid contraction of floating point operations, specifically fused ++ * multiply-add, because they can cause unexpected results in complex ++ * multiplication. ++ */ ++#if defined(__GNUC__) && !defined(__clang__) ++#pragma GCC optimize ("fp-contract=off") ++#endif ++ ++#if defined(__clang__) ++#pragma clang fp contract(off) ++#endif ++ + #include "common.h" + + +diff --git a/kernel/x86_64/zscal.c b/kernel/x86_64/zscal.c +index 3744c98bb7..dfdb4230b6 100644 +--- a/kernel/x86_64/zscal.c ++++ b/kernel/x86_64/zscal.c +@@ -25,6 +25,19 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE + USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + *****************************************************************************/ + ++/* ++ * Avoid contraction of floating point operations, specifically fused ++ * multiply-add, because they can cause unexpected results in complex ++ * multiplication. ++ */ ++#if defined(__GNUC__) && !defined(__clang__) ++#pragma GCC optimize ("fp-contract=off") ++#endif ++ ++#if defined(__clang__) ++#pragma clang fp contract(off) ++#endif ++ + #include "common.h" + + From e2abe951628c519b1dc970064b3c36682e02d0ec Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 31 Oct 2022 11:28:16 +0100 Subject: [PATCH 525/793] adding easyconfigs: MotionCor2-1.5.0-GCCcore-11.3.0.eb --- .../MotionCor2-1.5.0-GCCcore-11.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6c70f59b67b --- /dev/null +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Ake Sandgren +# HPC2N +# Umea University + +name = 'MotionCor2' +version = '1.5.0' + +homepage = 'https://msg.ucsf.edu/' +description = """MotionCor2 correct anisotropic image motion at the +single pixel level across the whole frame, suitable for both single +particle and tomographic images. Iterative, patch-based motion detection +is combined with spatial and temporal constraints and dose weighting. + +Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, +Yifan Cheng and David A. Agard (2016) Anisotropic Correction of +Beam-induced Motion for Improved Single-particle Electron +Cryo-microscopy, Nature Methods, submitted. +BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960 +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +# No longer directly downloadable, available from https://msg.ucsf.edu/software +sources = [ + '%(name)s_%(version)s.zip', +] +checksums = ['cdb7b9aceb42d52e2a4c7a5e80270371376aea412d21fa1f1f28d4cc71c81834'] + +# CUDA is a build dependency to make sure it gets installed. +# It's actually a runtime dependency, but that's handled in the wrapper to +# make sure it doesn't conflict with whatever toolchain happens to be loaded. +# Change CUDA version to match the latest one used in this version +# of MotionCor2 +builddependencies = [ + ('binutils', '2.38'), + ('CUDA', '11.6.0', '', SYSTEM), +] + +dependencies = [ + ('LibTIFF', '4.3.0'), +] + +moduleclass = 'bio' From e71962b1ce6e45abbd51a7b7372828216bde1819 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 31 Oct 2022 11:57:54 +0100 Subject: [PATCH 526/793] add LMERConvenienceFunctions extension for R v4.2.1 --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 49b9a97d1a0..e3da8a7d9fa 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3358,6 +3358,12 @@ exts_list = [ ('AMAPVox', '0.12.0', { 'checksums': ['b30fefef8661e27ffe3883665204b623eda2143dbcd3084a1d5810f8ea834c85'], }), + ('LCFdata', '2.0', { + 'checksums': ['b58f4d93b9023dd1ba2db96a59ddfc058397085933d8de4cdb38ee064d5e7bf4'], + }), + ('LMERConvenienceFunctions', '3.0', { + 'checksums': ['eb430de9fbf836173f716960d60afc2de91de7f986471f406c3ca9027142e849'], + }), ] moduleclass = 'lang' From abc4ba47ae726bf6f7b18947f076e352b596221a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85ke=20Sandgren?= Date: Mon, 31 Oct 2022 12:50:33 +0100 Subject: [PATCH 527/793] Update easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb index 6c70f59b67b..13e710f1fd7 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb @@ -26,6 +26,7 @@ sources = [ '%(name)s_%(version)s.zip', ] checksums = ['cdb7b9aceb42d52e2a4c7a5e80270371376aea412d21fa1f1f28d4cc71c81834'] +download_instructions = """Visit https://msg.ucsf.edu/software and fill in the form to download %s""" % sources[0] # CUDA is a build dependency to make sure it gets installed. # It's actually a runtime dependency, but that's handled in the wrapper to From 32c0d75f717c18624bb44eceae50c0ba5636bc62 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85ke=20Sandgren?= Date: Mon, 31 Oct 2022 12:50:45 +0100 Subject: [PATCH 528/793] Update easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb index 13e710f1fd7..1ce57f532b7 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb @@ -21,7 +21,6 @@ BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960 toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -# No longer directly downloadable, available from https://msg.ucsf.edu/software sources = [ '%(name)s_%(version)s.zip', ] From 64400bf1141f3e8e49a6f2b590870a6284356a57 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 31 Oct 2022 15:14:37 +0100 Subject: [PATCH 529/793] adding easyconfigs: cdsapi-0.5.1-GCCcore-11.3.0.eb --- .../c/cdsapi/cdsapi-0.5.1-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/cdsapi/cdsapi-0.5.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/cdsapi/cdsapi-0.5.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cdsapi/cdsapi-0.5.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c70d2401d59 --- /dev/null +++ b/easybuild/easyconfigs/c/cdsapi/cdsapi-0.5.1-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'cdsapi' +version = '0.5.1' + +homepage = 'https://pypi.org/project/cdsapi' +description = "Climate Data Store API" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['19f3e92f1996cc1115d0b0281617edeaecf3eefca03fbd384cfbc520d5f0476d'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('tqdm', '4.64.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' From bdf19a088b0c99038d13c2911447c4b78f81d8e3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 1 Nov 2022 08:37:25 +0100 Subject: [PATCH 530/793] add missing build dependency on Perl for GStreamer. And make sure to not make files suid. --- .../GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb | 9 +++++++- .../g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb | 9 +++++++- .../GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb | 9 +++++++- .../GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb | 9 +++++++- .../GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb | 9 +++++++- .../GStreamer-1.18_fix_bad_suid.patch | 22 +++++++++++++++++++ .../GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb | 9 +++++++- 7 files changed, 70 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.18_fix_bad_suid.patch diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb index 3c94c21acae..1e320e100bf 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb @@ -13,9 +13,16 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['0e8e2f7118be437cba879353970cf83c2acced825ecb9275ba05d9186ef07c00'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.16.0.tar.xz': '0e8e2f7118be437cba879353970cf83c2acced825ecb9275ba05d9186ef07c00'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ + ('Perl', '5.28.1'), ('Bison', '3.0.5'), ('flex', '2.6.4'), ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb index 92e0c55eca2..370fa85b4cf 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb @@ -13,9 +13,16 @@ toolchain = {'name': 'GCC', 'version': '8.3.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['e3f044246783fd685439647373fa13ba14f7ab0b346eadd06437092f8419e94e'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.16.2.tar.xz': 'e3f044246783fd685439647373fa13ba14f7ab0b346eadd06437092f8419e94e'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ + ('Perl', '5.30.0'), ('Bison', '3.3.2'), ('flex', '2.6.4'), ('GObject-Introspection', '1.63.1', '-Python-3.7.4'), diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb index a4c5be90916..cc7e4f4623c 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb @@ -13,11 +13,18 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.18.4.tar.xz': '9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ ('Meson', '0.55.3'), ('Ninja', '1.10.1'), + ('Perl', '5.32.0'), ('Bison', '3.7.1'), ('flex', '2.6.4'), ('GObject-Introspection', '1.66.1'), diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb index 2c38b4b9151..11f4d5afc2e 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb @@ -13,11 +13,18 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.18.4.tar.xz': '9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ ('Meson', '0.58.0'), ('Ninja', '1.10.2'), + ('Perl', '5.32.1'), ('Bison', '3.7.6'), ('flex', '2.6.4'), ('GObject-Introspection', '1.68.0'), diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb index 7d550bd31b6..45f9ea5e5d0 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb @@ -13,11 +13,18 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['55862232a63459bbf56abebde3085ca9aec211b478e891dacea4d6df8cafe80a'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.18.5.tar.xz': '55862232a63459bbf56abebde3085ca9aec211b478e891dacea4d6df8cafe80a'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ ('Meson', '0.58.2'), ('Ninja', '1.10.2'), + ('Perl', '5.34.0'), ('Bison', '3.7.6'), ('flex', '2.6.4'), ('GObject-Introspection', '1.68.0'), diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18_fix_bad_suid.patch b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18_fix_bad_suid.patch new file mode 100644 index 00000000000..4fff14d8b7a --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18_fix_bad_suid.patch @@ -0,0 +1,22 @@ +Do NOT make files setuid or try to do setcap. +That's a recipe for disaster. + +Åke Sandgren, 20221031 +diff -ru gstreamer-1.20.2.orig/libs/gst/helpers/ptp_helper_post_install.sh gstreamer-1.20.2/libs/gst/helpers/ptp_helper_post_install.sh +--- gstreamer-1.20.2.orig/libs/gst/helpers/ptp_helper_post_install.sh 2022-05-03 00:29:29.000000000 +0200 ++++ gstreamer-1.20.2/libs/gst/helpers/ptp_helper_post_install.sh 2022-10-31 16:39:11.959435316 +0100 +@@ -11,14 +11,10 @@ + setuid-root) + echo "$0: permissions before: " + ls -l "$ptp_helper" +- chown root "$ptp_helper" || true +- chmod u+s "$ptp_helper" || true + echo "$0: permissions after: " + ls -l "$ptp_helper" + ;; + capabilities) +- echo "Calling $setcap cap_net_bind_service,cap_net_admin+ep $ptp_helper" +- $setcap cap_net_bind_service,cap_net_admin+ep "$ptp_helper" || true + ;; + none) + echo "No perms/caps to set for $ptp_helper" diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb index df69820328f..d942105b5f7 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb @@ -13,11 +13,18 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['df24e8792691a02dfe003b3833a51f1dbc6c3331ae625d143b17da939ceb5e0a'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.20.2.tar.xz': 'df24e8792691a02dfe003b3833a51f1dbc6c3331ae625d143b17da939ceb5e0a'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ ('Meson', '0.62.1'), ('Ninja', '1.10.2'), + ('Perl', '5.34.1'), ('Bison', '3.8.2'), ('flex', '2.6.4'), ('GObject-Introspection', '1.72.0'), From 9914b1c520060e5cea9fdc0621f431d86ae42fbb Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 1 Nov 2022 15:10:58 +0100 Subject: [PATCH 531/793] adding easyconfigs: wandb-0.13.4-GCCcore-11.3.0.eb --- .../w/wandb/wandb-0.13.4-GCCcore-11.3.0.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/w/wandb/wandb-0.13.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/w/wandb/wandb-0.13.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/w/wandb/wandb-0.13.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1fdb7113a4e --- /dev/null +++ b/easybuild/easyconfigs/w/wandb/wandb-0.13.4-GCCcore-11.3.0.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'wandb' +version = '0.13.4' + +homepage = 'https://www.wandb.com/' +description = """ +CLI and Python API for Weights and Biases: a tool for visualizing and tracking +your machine learning experiments.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('GitPython', '3.1.27'), + ('PyYAML', '6.0'), + ('protobuf-python', '3.19.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('yaspin', '2.1.0', { + 'checksums': ['c8d34eca9fda3f4dfbe59f57f3cf0f3641af3eefbf1544fbeb9b3bacf82c580a'], + }), + ('shortuuid', '1.0.9', { + 'checksums': ['459f12fa1acc34ff213b1371467c0325169645a31ed989e268872339af7563d5'], + }), + ('setproctitle', '1.3.2', { + 'checksums': ['b9fb97907c830d260fa0658ed58afd48a86b2b88aac521135c352ff7fd3477fd'], + }), + ('sentry-sdk', '1.8.0', { + 'checksums': ['9c68e82f7b1ad78aee6cdef57c2c0f6781ddd9ffa8848f4503c5a8e02b360eea'], + }), + ('charset-normalizer', '2.0.12', { + 'checksums': ['2857e29ff0d34db842cd7ca3230549d1a697f96ee6d3fb071cfa6c7393832597'], + }), + ('promise', '2.3', { + 'checksums': ['dfd18337c523ba4b6a58801c164c1904a9d4d1b1747c7d5dbf45b693a49d93d0'], + }), + ('pathtools', '0.1.2', { + 'checksums': ['7c35c5421a39bb82e58018febd90e3b6e5db34c5443aaaf742b3f33d4655f1c0'], + }), + ('docker-pycreds', '0.4.0', { + 'modulename': 'dockerpycreds', + 'checksums': ['6ce3270bcaf404cc4c3e27e4b6c70d3521deae82fb508767870fdbf772d584d4'], + }), + (name, version, { + 'checksums': ['51e2672e12cca94680f6bcff0af80822d562e6b7846036050fc5bdd00240ea75'], + }), +] + +sanity_check_paths = { + 'files': ['bin/wandb', 'bin/wb'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ['wandb --help'] + +moduleclass = 'tools' From 20cbc3a794cc30e10944f430a07c2a336a9782d7 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 1 Nov 2022 15:15:17 +0100 Subject: [PATCH 532/793] adding easyconfigs: SimpleITK-2.1.1.2-foss-2022a.eb --- .../SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb new file mode 100644 index 00000000000..9a0f8d8c8e2 --- /dev/null +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb @@ -0,0 +1,50 @@ +easyblock = 'CMakeMake' + +name = 'SimpleITK' +version = '2.1.1.2' + +homepage = 'https://www.simpleitk.org' +description = """SimpleITK is a simplified programming interface to the algorithms and data structures of + the Insight Toolkit (ITK).""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_allow-lua54-for-code-generation.patch'] +checksums = [ + '5c0689b007d449ce0ce17a9ea322152315fb17ed32949005a974d3d9c2f58da3', # SimpleITK-2.1.1.2.tar.gz + # SimpleITK-2.1.1.2_allow-lua54-for-code-generation.patch + 'd1a45b1b64a226b3c22bf83c2f40f7f0e8f0a7d74bea1b2e7f5c5b6ed88b1522', +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('SWIG', '4.0.2'), + ('Lua', '5.4.4'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('ITK', '5.2.1'), + ('scikit-build', '0.15.0'), +] + +start_dir = 'SimpleITK' + +configopts = "-DWRAP_DEFAULT:BOOL=OFF -DWRAP_PYTHON=BOOL:ON " + +postinstallcmds = [ + "cd %(builddir)s/easybuild_obj/Wrapping/Python && " + "pip install --ignore-installed --no-deps --prefix=%(installdir)s . ", +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['lib/libSimpleITK_ITKBiasCorrection-%(version_major_minor)s.a'], + 'dirs': ['include/%(name)s-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import %(name)s'"] + +moduleclass = 'tools' From c5c539d4f0362b6f0d87358de38fb0948af5030b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 1 Nov 2022 15:17:03 +0100 Subject: [PATCH 533/793] adding easyconfigs: MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb, MONAI-1.0.1-foss-2022a.eb, einops-0.4.1-GCCcore-11.3.0.eb --- .../e/einops/einops-0.4.1-GCCcore-11.3.0.eb | 29 +++++++++++ .../MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb | 50 +++++++++++++++++++ .../m/MONAI/MONAI-1.0.1-foss-2022a.eb | 48 ++++++++++++++++++ 3 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/e/einops/einops-0.4.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/einops/einops-0.4.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/e/einops/einops-0.4.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e31c2fbbbba --- /dev/null +++ b/easybuild/easyconfigs/e/einops/einops-0.4.1-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'einops' +version = '0.4.1' + +homepage = 'https://einops.rocks/' +description = """ +Flexible and powerful tensor operations for readable and reliable code. +Supports numpy, pytorch, tensorflow, jax, and others.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['65ede824fa54ce99ba969c61152f9948eb8cad08d5f0ca97c95e3804bafcce48'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..bd6d8765a06 --- /dev/null +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'MONAI' +version = '1.0.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://monai.io/' +description = """ +MONAI is a PyTorch-based, open-source framework for deep learning in healthcare +imaging, part of PyTorch Ecosystem. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'Project-MONAI' + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', versionsuffix), + ('einops', '0.4.1'), + ('ITK', '5.2.1'), + ('NiBabel', '4.0.2'), + ('scikit-image', '0.19.3'), + ('tensorboard', '2.10.0'), + ('torchvision', '0.13.1', versionsuffix), + ('tqdm', '4.64.0'), +] + +exts_list = [ + (name, version, { + 'preinstallopts': 'BUILD_MONAI=1', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'checksums': ['dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b'], + }), +] + +use_pip = True + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb new file mode 100644 index 00000000000..0d272341e2c --- /dev/null +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'MONAI' +version = '1.0.1' + +homepage = 'https://monai.io/' +description = """ +MONAI is a PyTorch-based, open-source framework for deep learning in healthcare +imaging, part of PyTorch Ecosystem. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'Project-MONAI' + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), + ('einops', '0.4.1'), + ('ITK', '5.2.1'), + ('NiBabel', '4.0.2'), + ('scikit-image', '0.19.3'), + ('tensorboard', '2.10.0'), + ('torchvision', '0.13.1'), + ('tqdm', '4.64.0'), +] + +exts_list = [ + (name, version, { + 'preinstallopts': 'BUILD_MONAI=1', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'checksums': ['dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b'], + }), +] + +use_pip = True + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], + 'dirs': [''], +} + +moduleclass = 'vis' From 269db8f055bb836dc74be57f242a48c0a75e1f53 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 1 Nov 2022 15:22:48 +0100 Subject: [PATCH 534/793] adding easyconfigs: scikit-image-0.19.3-foss-2022a.eb, imageio-2.22.2-foss-2022a.eb --- .../i/imageio/imageio-2.22.2-foss-2022a.eb | 25 +++++++++++ .../scikit-image-0.19.3-foss-2022a.eb | 43 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/i/imageio/imageio-2.22.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/scikit-image/scikit-image-0.19.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.22.2-foss-2022a.eb b/easybuild/easyconfigs/i/imageio/imageio-2.22.2-foss-2022a.eb new file mode 100644 index 00000000000..a340e81b29e --- /dev/null +++ b/easybuild/easyconfigs/i/imageio/imageio-2.22.2-foss-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'imageio' +version = '2.22.2' + +homepage = 'https://imageio.github.io' +description = """Imageio is a Python library that provides an easy interface to read and write a wide range of + image data, including animated images, video, volumetric data, and scientific formats.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['db7010cd10712518819a4187baf61b05988361ea20c23e829918727b27acb977'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Pillow', '9.1.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.19.3-foss-2022a.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.19.3-foss-2022a.eb new file mode 100644 index 00000000000..2cc7bce06b1 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.19.3-foss-2022a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'scikit-image' +version = '0.19.3' + +homepage = 'https://scikit-image.org/' +description = "scikit-image is a collection of algorithms for image processing." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('matplotlib', '3.5.2'), + ('Pillow', '9.1.1'), + ('networkx', '2.8.4'), + ('dask', '2022.10.0'), + ('imageio', '2.22.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('PyWavelets', '1.4.1', { + 'modulename': 'pywt', + 'checksums': ['6437af3ddf083118c26d8f97ab43b0724b956c9f958e9ea788659f6a2834ba93'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.6.0', { + 'checksums': ['57d20ec4b10dd694d2b05bb64bc6b109c6e85a6c1405794ce87ed8b341ab3f44'], + }), + ('tifffile', '2022.10.10', { + 'checksums': ['50b61ba943b866d191295bc38a00191c9fdab23ece063544c7f1a264e3f6aa8e'], + }), + (name, version, { + 'modulename': 'skimage', + 'checksums': ['24b5367de1762da6ee126dd8f30cc4e7efda474e0d7d70685433f0e3aa2ec450'], + }), +] + +moduleclass = 'vis' From beaed9282b95ecc76803630bfad3d7c46d1fce1c Mon Sep 17 00:00:00 2001 From: robogast Date: Tue, 1 Nov 2022 17:07:18 +0100 Subject: [PATCH 535/793] added comments to ASAP patch files, updated checksums accordingly --- easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch | 4 ++++ easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb | 6 +++--- easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch | 6 ++++++ easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch | 3 +++ 4 files changed, 16 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch index b4ca984d421..d836a0466d2 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch @@ -1,3 +1,7 @@ +# Author: Robert Jan Schlimbach (SURF) +# ASAP/2.1 forgets a few headers, in this case cmath +# Possibly fixed if https://github.com/computationalpathologygroup/ASAP/pull/241 gets merged + diff --git a/annotation/ImageScopeRepository.cpp b/annotation/ImageScopeRepository.cpp index 6916a58..c135cb3 100644 --- a/annotation/ImageScopeRepository.cpp diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb index 7dd82903d65..1a9c9bccc8b 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb @@ -19,9 +19,9 @@ patches = [ ] checksums = [ '7ba9f39d09bada808f760c5dc9ac0cda0d221fd1393a0a3f9decfd6b5e913b3c', # ASAP-2.1.tar.gz - 'dbdf26324a7521b4beaa7ec2c0585f0816619cd73b3125efd313eb48c4813a43', # ASAP-2.1-libjpeg.patch - 'f578bb3ec4cbce573d4b9acd695eb55446592f4ac00551656a06f113ba09a9a7', # ASAP-2.1-pugixml.patch - 'e33d83853e0bd51113a886d0793504ce0abfb15fdf88410a19287d46fafd33c4', # ASAP-2.1-cmath.patch + '78337d0250c567335f1a356f8761587000170b71a87b3e546b6b9330d3236b0f', # ASAP-2.1-libjpeg.patch + 'ab6104fb19515d0b042944bbe95fa67f55f47ef3bf18a91d337e0ca476c7385d', # ASAP-2.1-pugixml.patch + '15cf6bf2ab65ce37338ea571d80ced59b4e35cf82e434b2ccec7b534778f4a33', # ASAP-2.1-cmath.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch index eeab7c05144..b2030303872 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch @@ -1,3 +1,9 @@ +# Author: Robert Jan Schlimbach (SURF) +# ASAP/2.1 uses DCMKT jpeg sources directly by manually setting a PATH +# see https://github.com/computationalpathologygroup/ASAP/issues/32 +# we simply replace DCMTK jpeg with the default jpeglib header. +# Need to rename jpeg_mem_src to avoid a resulting name conflic. + diff --git a/multiresolutionimageinterface/VSIImage.cpp b/multiresolutionimageinterface/VSIImage.cpp index 509bb18..1763201 100644 --- a/multiresolutionimageinterface/VSIImage.cpp diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch index 2b4a652369f..751d179cb19 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch @@ -1,3 +1,6 @@ +# Author: Robert Jan Schlimbach (SURF) +# Patch to make ASAP/2.1 accept pugixml as non-header-only shared lib + diff --git a/annotation/CMakeLists.txt b/annotation/CMakeLists.txt index 114babe..2156cd3 100644 --- a/annotation/CMakeLists.txt From a0732b63add05a61e1f72e0aa5d57bf2af2c8e94 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Wed, 2 Nov 2022 15:53:44 +0100 Subject: [PATCH 536/793] adding easyconfigs: ESM-2-2.0.0-foss-2021a.eb --- .../e/ESM-2/ESM-2-2.0.0-foss-2021a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb new file mode 100644 index 00000000000..d33ee519c80 --- /dev/null +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'ESM-2' +version = '2.0.0' + +homepage = 'https://github.com/facebookresearch/esm' +description = """ESM-2 outperforms all tested single-sequence protein language models + across a range of structure prediction tasks. ESMFold harnesses the ESM-2 language model to generate + accurate structure predictions end to end directly from the sequence of a protein.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://pypi.python.org/packages/source/f/fair-esm'] +sources = ['fair-esm-%(version)s.tar.gz'] +checksums = ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'] + +dependencies = [ + ('Python', '3.9.5'), + ('PyTorch', '1.10.0'), +] + +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'esm'} + +sanity_check_commands = [ + "python -c 'import esm.pretrained'", +] + +moduleclass = 'bio' From d73fe2ec878074d495f94b2e8e7889ecb91cafa5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 3 Nov 2022 00:34:10 +0100 Subject: [PATCH 537/793] build nodejs with external OpenSSL and ICU --- .../n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb | 32 +++++++++++++------ .../n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb | 25 ++++++++++----- .../n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 25 ++++++++++----- 3 files changed, 57 insertions(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb index deaf600ec19..b75eb3495ef 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'nodejs' version = '14.17.0' # LTS on 2021-06-03 -local_libversion = '83' +_libversion = '83' homepage = 'https://nodejs.org' description = """Node.js is a platform built on Chrome's JavaScript runtime @@ -14,11 +14,16 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['http://%(name)s.org/dist/v%(version)s/'] sources = ['node-v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_fix-argument-list-too-long.patch'] +patches = [ + '%(name)s-%(version)s_fix-argument-list-too-long.patch', + '%(name)s-%(version)s_use_new_icu69_calls.patch', +] checksums = [ '6114e82d3256136dc85a509d835442fbdf2f8430dcd8bfa7c304097344d06fb7', # node-v14.17.0.tar.gz # nodejs-14.17.0_fix-argument-list-too-long.patch 'b0eac4b478a9268c8902ec701f99e1445eeba2a70927bfacdeb5ba243e668550', + # nodejs-14.17.0_use_new_icu69_calls.patch + '24fbc749d225b395184aa9c4c3880665026ced898474d77259c597f6b790e290', ] builddependencies = [ @@ -26,21 +31,30 @@ builddependencies = [ ('Python', '3.9.5'), ] +dependencies = [ + ('ICU', '69.1'), + ('OpenSSL', '1.1', '', True), +] + +# Use ICU and OpenSSL from EasyBuild +_common_configopts = "--with-intl=system-icu --shared-openssl " + configopts = [ - '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library - '--shared --with-intl=none', # Build libnode.so in a second run + _common_configopts, # Static build + '--shared %s' % _common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode +_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in _extra_sonames] +_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, _libversion) + postinstallcmds = [ - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s %s %s" % (_libnode_real, x) for x in _extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [_libnode_real] + _extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb index 569932aa452..e81302ffc40 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'nodejs' version = '14.17.6' # LTS on 2020-08-31 -local_libversion = '83' +_libversion = '83' homepage = 'https://nodejs.org' description = """Node.js is a platform built on Chrome's JavaScript runtime @@ -21,21 +21,30 @@ builddependencies = [ ('Python', '3.9.6', '-bare'), ] +dependencies = [ + ('ICU', '69.1'), + ('OpenSSL', '1.1', '', True), +] + +# Use ICU and OpenSSL from EasyBuild +_common_configopts = "--with-intl=system-icu --shared-openssl " + configopts = [ - '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library - '--shared --with-intl=none', # Build libnode.so in a second run + _common_configopts, # Static build + '--shared %s' % _common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode +_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in _extra_sonames] +_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, _libversion) + postinstallcmds = [ - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s %s %s" % (_libnode_real, x) for x in _extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [_libnode_real] + _extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb index 3fe69b1af4c..73aeb628575 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'nodejs' version = '16.15.1' # LTS on 2022-06-12 -local_libversion = '93' +_libversion = '93' homepage = 'https://nodejs.org' description = """Node.js is a platform built on Chrome's JavaScript runtime @@ -21,21 +21,30 @@ builddependencies = [ ('Python', '3.10.4', '-bare'), ] +dependencies = [ + ('ICU', '71.1'), + ('OpenSSL', '1.1', '', True), +] + +# Use ICU and OpenSSL from EasyBuild +_common_configopts = "--with-intl=system-icu --shared-openssl " + configopts = [ - '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library - '--shared --with-intl=none', # Build libnode.so in a second run + _common_configopts, # Static build + '--shared %s' % _common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode +_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in _extra_sonames] +_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, _libversion) + postinstallcmds = [ - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s %s %s" % (_libnode_real, x) for x in _extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [_libnode_real] + _extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } From 9a403292a75a1d9a16753c4ac9404a04da4446a7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 3 Nov 2022 00:43:07 +0100 Subject: [PATCH 538/793] add patch to fix ICU v69 support in nodejs v14 --- .../nodejs-14.17.0_use_new_icu69_calls.patch | 92 +++++++++++++++++++ 1 file changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-14.17.0_use_new_icu69_calls.patch diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0_use_new_icu69_calls.patch b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0_use_new_icu69_calls.patch new file mode 100644 index 00000000000..9b635d20f3d --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0_use_new_icu69_calls.patch @@ -0,0 +1,92 @@ +From 035c305ce7761f51328b45f1bd83e26aef267c9d Mon Sep 17 00:00:00 2001 +From: Frank Tang +Date: Thu, 15 Oct 2020 22:44:27 -0700 +Subject: [PATCH] [Intl] call new ListFormatter::createInstance + +The one we currently using is now marked as internal and to be removed +for 68. Migrating to the style which already avaiable in ICU 67-1. + +Bug: v8:11031 +Change-Id: I668382a2e1b8602ddca02bf231c5008a6c92bf2d +Reviewed-on: https://chromium-review.googlesource.com/c/v8/v8/+/2477751 +Reviewed-by: Jakob Kummerow +Commit-Queue: Frank Tang +Cr-Commit-Position: refs/heads/master@{#70638} +--- + +diff --git a/deps/v8/src/objects/js-list-format.cc b/deps/v8/src/objects/js-list-format.cc +index b17d38c..e48a387 100644 +--- a/deps/v8/src/objects/js-list-format.cc ++++ b/deps/v8/src/objects/js-list-format.cc +@@ -29,46 +29,27 @@ + namespace internal { + + namespace { +-const char* kStandard = "standard"; +-const char* kOr = "or"; +-const char* kUnit = "unit"; +-const char* kStandardShort = "standard-short"; +-const char* kOrShort = "or-short"; +-const char* kUnitShort = "unit-short"; +-const char* kStandardNarrow = "standard-narrow"; +-const char* kOrNarrow = "or-narrow"; +-const char* kUnitNarrow = "unit-narrow"; + +-const char* GetIcuStyleString(JSListFormat::Style style, +- JSListFormat::Type type) { ++UListFormatterWidth GetIcuWidth(JSListFormat::Style style) { ++ switch (style) { ++ case JSListFormat::Style::LONG: ++ return ULISTFMT_WIDTH_WIDE; ++ case JSListFormat::Style::SHORT: ++ return ULISTFMT_WIDTH_SHORT; ++ case JSListFormat::Style::NARROW: ++ return ULISTFMT_WIDTH_NARROW; ++ } ++ UNREACHABLE(); ++} ++ ++UListFormatterType GetIcuType(JSListFormat::Type type) { + switch (type) { + case JSListFormat::Type::CONJUNCTION: +- switch (style) { +- case JSListFormat::Style::LONG: +- return kStandard; +- case JSListFormat::Style::SHORT: +- return kStandardShort; +- case JSListFormat::Style::NARROW: +- return kStandardNarrow; +- } ++ return ULISTFMT_TYPE_AND; + case JSListFormat::Type::DISJUNCTION: +- switch (style) { +- case JSListFormat::Style::LONG: +- return kOr; +- case JSListFormat::Style::SHORT: +- return kOrShort; +- case JSListFormat::Style::NARROW: +- return kOrNarrow; +- } ++ return ULISTFMT_TYPE_OR; + case JSListFormat::Type::UNIT: +- switch (style) { +- case JSListFormat::Style::LONG: +- return kUnit; +- case JSListFormat::Style::SHORT: +- return kUnitShort; +- case JSListFormat::Style::NARROW: +- return kUnitNarrow; +- } ++ return ULISTFMT_TYPE_UNITS; + } + UNREACHABLE(); + } +@@ -143,7 +124,7 @@ + icu::Locale icu_locale = r.icu_locale; + UErrorCode status = U_ZERO_ERROR; + icu::ListFormatter* formatter = icu::ListFormatter::createInstance( +- icu_locale, GetIcuStyleString(style_enum, type_enum), status); ++ icu_locale, GetIcuType(type_enum), GetIcuWidth(style_enum), status); + if (U_FAILURE(status) || formatter == nullptr) { + delete formatter; + THROW_NEW_ERROR(isolate, NewRangeError(MessageTemplate::kIcuError), From d2457c0740f4846fa8f8224974ed8a2ab3712e04 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 3 Nov 2022 01:02:47 +0100 Subject: [PATCH 539/793] fix dependency on OpenSSL to use SYSTEM template --- easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb index b75eb3495ef..bf1db1aa052 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb @@ -33,7 +33,7 @@ builddependencies = [ dependencies = [ ('ICU', '69.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # Use ICU and OpenSSL from EasyBuild diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb index e81302ffc40..a6fe9b552ba 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb @@ -23,7 +23,7 @@ builddependencies = [ dependencies = [ ('ICU', '69.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # Use ICU and OpenSSL from EasyBuild diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb index 73aeb628575..bcd9c8dded1 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ dependencies = [ ('ICU', '71.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # Use ICU and OpenSSL from EasyBuild From 8da47cb621791fe7fce2c92e31742c0306ee1850 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Thu, 3 Nov 2022 08:28:15 +0100 Subject: [PATCH 540/793] added download_dep_fail --- easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb index d33ee519c80..e3ea302ffec 100644 --- a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb @@ -20,6 +20,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True sanity_pip_check = True options = {'modulename': 'esm'} From 0273721033e985b841678403fb7827b93ba087e9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 3 Nov 2022 08:39:24 +0100 Subject: [PATCH 541/793] adding easyconfigs: ctffind-4.1.14-foss-2022a.eb --- .../c/ctffind/ctffind-4.1.14-foss-2022a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022a.eb new file mode 100644 index 00000000000..59e562d1e6b --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022a.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# +# Author: Ake Sandgren, HPC2N, Umea University +# +# Author: Thomas Hoffmann, EMBL Heidelberg + +easyblock = 'ConfigureMake' + +name = 'ctffind' +version = '4.1.14' + +homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' +description = """Program for finding CTFs of electron micrographs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-%(version)s_asm-fix.patch', + '%(name)s-%(version)s_void-functions.patch' +] +checksums = [ + 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz + 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch + '0a578328062881d86b10585f1b0efa81b7a1826baf3e7bcc5c749bba73e96d10', # ctffind-4.1.14_void-functions.patch +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libjpeg-turbo', '2.1.3'), + ('LibTIFF', '4.3.0'), + ('GSL', '2.7',), + ('wxWidgets', '3.2.1'), +] + +configopts = '--enable-openmp ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ctffind'], + 'dirs': [], +} + +moduleclass = 'bio' From c92ba4b925937d47cbd836691b10c67e665dcd88 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jurij=20Pe=C4=8Dar?= Date: Thu, 3 Nov 2022 11:30:49 +0100 Subject: [PATCH 542/793] adding easyconfigs: Nextflow-22.10.1.eb --- .../n/Nextflow/Nextflow-22.10.1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb new file mode 100644 index 00000000000..896a6c321e3 --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb @@ -0,0 +1,33 @@ +easyblock = 'Binary' + +name = 'Nextflow' +version = '22.10.1' + +homepage = 'https://www.%(namelower)s.io/' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/%(namelower)s-io/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s-all'] +checksums = ['c5edc9fc81d9c6eb4f628505f14f8bb4fe044d4fc7d9ef60654ba0d73abf5a80'] + +dependencies = [('Java', '11', '', True)] + +install_cmd = "[ -d %(builddir)s/bin ] || mkdir -p %(installdir)s/bin &&" +install_cmd += "cp %(builddir)s/%(namelower)s-%(version)s-all %(installdir)s/bin &&" +install_cmd += "cd %(installdir)s/bin && ln -s %(namelower)s-%(version)s-all %(namelower)s &&" +install_cmd += "chmod +x %(installdir)s/bin/%(namelower)s-%(version)s-all" + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-%(version)s-all', 'bin/%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [ + "%(namelower)s -v", + "%(namelower)s help", +] + +moduleclass = 'tools' From 88a15c893eb2a0f1767a8255c201dba3c630e450 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 3 Nov 2022 12:07:54 +0100 Subject: [PATCH 543/793] adding easyconfigs: DRAGMAP-1.3.0-foss-2021b.eb --- .../d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb b/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb new file mode 100644 index 00000000000..23c3faed318 --- /dev/null +++ b/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'DRAGMAP' +version = '1.3.0' + +homepage = 'https://github.com/Illumina/DRAGMAP' +description = 'Dragmap is the Dragen mapper/aligner Open Source Software.' + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/Illumina/DRAGMAP/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['baf546c2f53b13e2bce4c937201e38459f3ce2f1069722ca670d8726a4bae224'] + +skipsteps = ['configure'] +prebuildopts = 'sed -i "s|-msse4.2 -mavx2|$CXXFLAGS|g" config.mk &&' +buildopts = 'CC="$CC" CXX="$CXX"' +preinstallopts = 'mkdir %(installdir)s/bin &&' +installopts = 'DESTDIR=%(installdir)s' + +dependencies = { + ('Boost', '1.77.0'), + ('googletest', '1.11.0'), +} + +sanity_check_paths = { + 'files': ['bin/dragen-os'], + 'dirs': [] +} + +sanity_check_commands = ['dragen-os --help'] + +moduleclass = 'bio' From fb6f9fc133fc94006fca6494e9a68f2f99d09e78 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 3 Nov 2022 11:12:18 +0000 Subject: [PATCH 544/793] adding easyconfigs: bsddb3-6.2.9-GCCcore-11.3.0.eb --- .../b/bsddb3/bsddb3-6.2.9-GCCcore-11.3.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8a366485ad0 --- /dev/null +++ b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-11.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'bsddb3' +version = '6.2.9' + +homepage = 'https://pypi.org/project/bsddb3/' +description = """bsddb3 is a nearly complete Python binding of the +Oracle/Sleepycat C API for the Database Environment, Database, Cursor, +Log Cursor, Sequence and Transaction objects.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +components = [ + ('DB', '5.3.28', { + 'source_urls': ['https://github.com/berkeleydb/libdb/releases/download/v%(version)s/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['e0a992d740709892e81f9d93f06daf305cf73fb81b545afe72478043172c3628'], + 'start_dir': '%(namelower)s-%(version)s', + }), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'preinstallopts': "unset LIBS && BERKELEYDB_DIR=%(installdir)s/ ", + 'checksums': ['70d05ec8dc568f42e70fc919a442e0daadc2a905a1cfb7ca77f549d49d6e7801'], + }), +] + +sanity_check_paths = { + 'files': ['bin/db_archive', 'include/db.h', 'lib/libdb.a', + 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'data' From d81b3437d6dc0a92a91c540fcaab2d9e9c5cb279 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:15:40 +0200 Subject: [PATCH 545/793] adding easyconfigs: imagecodecs-2022.9.26-foss-2021a.eb --- .../imagecodecs-2022.9.26-foss-2021a.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb new file mode 100644 index 00000000000..55bf95340ff --- /dev/null +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb @@ -0,0 +1,72 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL) +easyblock = 'PythonBundle' + +name = 'imagecodecs' +version = '2022.9.26' + +homepage = 'https://github.com/cgohlke/imagecodecs' +description = """Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, +compression, and decompression functions for use in the tifffile, czifile, zarr, and other +scientific image input/output modules.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +local_openjpeg_maj_min = '2.4' +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # required for numpy + ('matplotlib', '3.4.2'), + ('Brotli', '1.0.9'), + ('bzip2', '1.0.8'), + ('Blosc', '1.21.0'), + ('Blosc2', '2.0.4'), + ('CFITSIO', '3.49'), + ('CharLS', '2.3.4'), + ('giflib', '5.2.1'), + ('jxrlib', '1.1'), + ('LittleCMS', '2.12'), + ('LERC', '3.0'), + ('libaec', '1.0.6'), + ('libavif', '0.11.1'), + ('libdeflate', '1.8'), + ('libjpeg-turbo', '2.0.6'), + ('libjxl', '0.5'), + ('LibLZF', '3.6'), + ('libpng', '1.6.37'), + ('XZ', '5.2.5'), + ('LibTIFF', '4.2.0'), + ('libwebp', '1.2.0'), + ('lz4', '1.9.3'), + ('OpenJPEG', local_openjpeg_maj_min + '.0'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), + ('zlib-ng', '2.0.6'), + ('Zopfli', '1.0.3'), + ('zfp', '1.0.0'), + ('zstd', '1.4.9'), + ('Brunsli', '0.1'), + ('HDF5', '1.12.1'), + ('h5py', '3.2.1'), + ('libheif', '1.12.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('bitshuffle', '0.3.5', { + 'source_urls': ['https://github.com/kiyo-masui/bitshuffle/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['c3f4461d8013e3d9db0d58defec77b143164652de505a1fba3df088eaa19be2f'], + }), + (name, version, { + 'extract_cmd': "tar -xvf %s && find . -type f -print0 | xargs -0 dos2unix", + 'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-2.4/:$CPATH && ", + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'checksums': ['04d5757d8fd7819844b0f8d9eed05025dca4962f280d0010b42c7c9c993fe371'], + }), +] + +moduleclass = 'lib' From 5ee258f18cb9d63a4c80caa2564e33f4403711c4 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:33:37 +0200 Subject: [PATCH 546/793] adding easyconfigs: Blosc2-2.0.4-GCCcore-10.3.0.eb --- .../b/Blosc2/Blosc2-2.0.4-GCCcore-10.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.4-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..7736eae4911 --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.4-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Blosc2' +version = '2.0.4' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['90c78edcc262759dd16d243141513310624bb4fda3d98ac34dcfb78255e151c1'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a', + 'lib/libblosc2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 341cb16b6e28ac08e6907fc122a61c5535e5b2af Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:36:30 +0200 Subject: [PATCH 547/793] adding easyconfigs: CFITSIO-3.49-GCCcore-10.3.0.eb --- .../c/CFITSIO/CFITSIO-3.49-GCCcore-10.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..1b080d80935 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.3.0.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '3.49' + +homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = ['%%(namelower)s-%s.tar.gz' % version] +patches = ['CFITSIO-3.48_install_test_data.patch'] +checksums = [ + '5b65a20d5c53494ec8f638267fca4a629836b7ac8dd0ef0266834eab270ed4b3', # cfitsio-3.49.tar.gz + 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c', # CFITSIO-3.48_install_test_data.patch +] + +# curl for HTTPs support +dependencies = [('cURL', '7.76.0')] + +builddependencies = [('binutils', '2.36.1')] + +# make would create just static libcfitsio.a. +# Let's create dynamic lib and testprog too. +buildopts = '&& make shared && make testprog' + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + ('cd %(installdir)s/share && testprog'), +] + +moduleclass = 'lib' From e34a43b98c10d409280e46bb0ac8151e9bcb5c8c Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:39:12 +0200 Subject: [PATCH 548/793] adding easyconfigs: jxrlib-1.1-GCCcore-10.3.0.eb --- .../j/jxrlib/jxrlib-1.1-GCCcore-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..6257a6cbb8b --- /dev/null +++ b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author:: Denis Kristak (INUITS) +# Update: Thomas Hoffmann (EMBL) +## + +easyblock = 'CMakeMake' + +name = 'jxrlib' +version = '1.1' + +homepage = 'https://github.com/4creators/jxrlib' +description = """Open source implementation of jpegxr""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://deb.debian.org/debian/pool/main/j/jxrlib/'] +sources = ['%(name)s_%(version)s.orig.tar.gz'] +patches = [('jxrlib-%(version)s_cmake.patch', 1)] +checksums = [ + 'c7287b86780befa0914f2eeb8be2ac83e672ebd4bd16dc5574a36a59d9708303', # jxrlib_1.1.orig.tar.gz + 'e96ea8b418fdab10e9cbc2f4cad95ca1f59a826ce7379c6a3192882050689a74', # jxrlib-1.1_cmake.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': ['bin/JxrDecApp', 'bin/JxrEncApp', "lib/libjpegxr.%s" % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['JxrDecApp', 'JxrEncApp'] + +modextrapaths = {'CPATH': 'include/jxrlib'} + +moduleclass = 'lib' From 133d1c682e91c11e2605e369b85a4fd5620a2e93 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:40:26 +0200 Subject: [PATCH 549/793] adding easyconfigs: LERC-3.0-GCCcore-10.3.0.eb --- .../l/LERC/LERC-3.0-GCCcore-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..b1976a9c3c2 --- /dev/null +++ b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +# Updated: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'LERC' +version = '3.0' + +homepage = 'https://github.com/Esri/lerc' +description = """LERC is an open-source image or raster format which supports rapid encoding and decoding +for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, +so the precision of the original input image is preserved (within user defined error bounds).""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/Esri/lerc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8c0148f5c22d823eff7b2c999b0781f8095e49a7d3195f13c68c5541dd5740a1'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +postinstallcmds = [ + "cd %(builddir)s/lerc-%(version)s/src/LercTest && sed -i -e 's@../LercLib/include/@@' main.cpp", + "cp %(builddir)s/lerc-%(version)s/src/LercTest/main.cpp %(installdir)s/test.c", +] + +sanity_check_commands = [ + "mkdir -p %(builddir)s && cd %(builddir)s && g++ %(installdir)s/test.c -o lerctest -lLerc && ./lerctest", +] + +sanity_check_paths = { + 'files': ['include/Lerc_c_api.h', 'include/Lerc_types.h', 'lib/libLerc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 8745875102720aad4cfb7057f4d6c948f013bd65 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:41:40 +0200 Subject: [PATCH 550/793] adding easyconfigs: libaec-1.0.6-GCCcore-10.3.0.eb --- .../l/libaec/libaec-1.0.6-GCCcore-10.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..7ed6541d683 --- /dev/null +++ b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'libaec' +version = '1.0.6' + +homepage = 'https://gitlab.dkrz.de/k202009/libaec' +description = """Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers +(samples). The library achieves best results for low entropy data as often encountered in space imaging +instrument data or numerical model output from weather or climate simulations. While floating point representations +are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['abab8c237d85c982bb4d6bde9b03c1f3d611dcacbd58bca55afac2496d61d4be'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +sanity_check_paths = { + 'files': ['bin/aec', 'include/libaec.h', 'include/szlib.h', 'lib/libaec.a', 'lib/libaec.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = ["aec --help"] + +moduleclass = 'lib' From 558ec0d37917214b025769dc27d7b9f58d21c91d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:42:44 +0200 Subject: [PATCH 551/793] adding easyconfigs: libavif-0.11.1-foss-2021a.eb --- .../l/libavif/libavif-0.11.1-foss-2021a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2021a.eb b/easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2021a.eb new file mode 100644 index 00000000000..2f4ed93c1c9 --- /dev/null +++ b/easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2021a.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'libavif' +version = '0.11.1' + +homepage = 'https://github.com/AOMediaCodec/libavif' +description = """This library aims to be a friendly, portable C implementation of the AV1 Image File Format, +as described here: https://aomediacodec.github.io/av1-avif/ +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/AOMediaCodec/libavif/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0eb49965562a0e5e5de58389650d434cff32af84c34185b6c9b7b2fccae06d4e'] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('NASM', '2.15.05'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('Rust', '1.52.1'), +] + +sanity_check_paths = { + 'files': ['lib/libavif.%s' % SHLIB_EXT, 'include/avif/avif.h'], + 'dirs': [], +} + +moduleclass = 'tools' From a24bdbaeacba00b74f4fde6ee3551355c153b925 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:46:49 +0200 Subject: [PATCH 552/793] adding easyconfigs: LibLZF-3.6-GCCcore-10.3.0.eb --- .../l/LibLZF/LibLZF-3.6-GCCcore-10.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..63540846348 --- /dev/null +++ b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'ConfigureMake' + +name = 'LibLZF' +version = '3.6' + +homepage = 'http://oldhome.schmorp.de/marc/liblzf.html' +description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files +and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still +written in portable C.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['http://dist.schmorp.de/liblzf/Attic/'] +sources = ['liblzf-%(version)s.tar.gz'] +checksums = ['9c5de01f7b9ccae40c3f619d26a7abec9986c06c36d260c179cedd04b89fb46a'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +sanity_check_commands = ['lzf -h'] + +sanity_check_paths = { + 'files': ['bin/lzf', 'lib/liblzf.a'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'lib' From 06597b301e85a56bda66dce126cb5e90bb3a4909 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:47:53 +0200 Subject: [PATCH 553/793] adding easyconfigs: zlib-ng-2.0.6-GCCcore-10.3.0.eb --- .../z/zlib-ng/zlib-ng-2.0.6-GCCcore-10.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.6-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..529355b3749 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.6-GCCcore-10.3.0.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +# Updated: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'zlib-ng' +version = '2.0.6' + +homepage = 'https://github.com/zlib-ng/zlib-ng' +description = """zlib data compression library for the next generation systems""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/zlib-ng/zlib-ng/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8258b75a72303b661a238047cb348203d88d9dddf85d480ed885f375916fcab6'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +configopts = ' -DZLIB_ENABLE_TESTS=True ' + +sanity_check_paths = { + 'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' From 3e4cb429acf96e8bee8dff44e638024f2cd727f0 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:49:01 +0200 Subject: [PATCH 554/793] adding easyconfigs: Zopfli-1.0.3-GCCcore-10.3.0.eb --- .../z/Zopfli/Zopfli-1.0.3-GCCcore-10.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..d08922dc6c9 --- /dev/null +++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +# Updated: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Zopfli' +version = '1.0.3' + +homepage = 'https://github.com/google/zopfli' +description = """Zopfli Compression Algorithm is a compression library programmed in C to perform +very good, but slow, deflate or zlib compression.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/zopfli/archive/refs/tags/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['e955a7739f71af37ef3349c4fa141c648e8775bceb2195be07e86f8e638814bd'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF', +] + +sanity_check_paths = { + 'files': ['bin/zopfli', 'include/zopfli.h', 'lib/libzopfli.a', 'lib/libzopfli.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["zopfli --help"] + +moduleclass = 'tools' From 1ec9bfdd271c08ac548e4c04e30cc65abc656207 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:50:02 +0200 Subject: [PATCH 555/793] adding easyconfigs: zfp-1.0.0-GCCcore-10.3.0.eb --- .../z/zfp/zfp-1.0.0-GCCcore-10.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..3901a6550a2 --- /dev/null +++ b/easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-10.3.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'MakeCp' + +name = 'zfp' +version = '1.0.0' + +homepage = 'https://github.com/LLNL/zfp' +description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays. +zfp provides compressed-array classes that support high throughput read and write random access to individual array +elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications +that read and write large data sets to and from disk.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/LLNL/zfp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['fe13b03141ee9b571692aed42ff76cf37c9dcda40f9a43a808870dca3558a57c'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +prebuildopts = "sed -i 's/FLAGS = -O3/FLAGS = $CFLAGS/g' Makefile && " +buildopts = 'ZFP_WITH_OPENMP=1' + +runtest = 'test' + +files_to_copy = ['bin', 'include', 'lib'] + +sanity_check_paths = { + 'files': ['bin/zfp', 'bin/testzfp', 'include/zfp.h', 'lib/libzfp.a'], + 'dirs': ['include/zfp'], +} + +sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"] + +moduleclass = 'lib' From 9fe9959d6f35c302b56e8636f829179890846879 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:51:37 +0200 Subject: [PATCH 556/793] adding easyconfigs: Brunsli-0.1-GCCcore-10.3.0.eb --- .../b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..20cd4b20aef --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """Brunsli is a lossless JPEG repacking library.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('Highway', '0.12.2'), +] + +# skip use of third_party directory, since we provide Brotli via a proper dependency +preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon"' + +buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" + +# also install dbrunsli binary and missing libraries +postinstallcmds = [ + "mkdir %(installdir)s/bin", + "cp dbrunsli %(installdir)s/bin/", + "cp libbrunsli*.a %(installdir)s/lib*/", + "cp libbrunsli*.%s %%(installdir)s/lib*/" % SHLIB_EXT, +] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['include/brunsli', 'lib'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' From 21102edbd215c924de05f0e9fde3c45ea1049084 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:52:42 +0200 Subject: [PATCH 557/793] adding easyconfigs: libheif-1.12.0-GCC-10.3.0.eb --- .../l/libheif/libheif-1.12.0-GCC-10.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..bb5cb6bf57c --- /dev/null +++ b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'libheif' +version = '1.12.0' + +homepage = 'https://github.com/strukturag/libheif' +description = "libheif is an HEIF and AVIF file format decoder and encoder" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e1ac2abb354fdc8ccdca71363ebad7503ad731c84022cf460837f0839e171718'] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('libde265', '1.0.8'), + ('x265', '3.5'), + ('Gdk-Pixbuf', '2.42.6'), +] + +# build both static and shared libraries +configopts = [ + "-DBUILD_SHARED_LIBS=OFF", + "-DBUILD_SHARED_LIBS=ON", +] + +sanity_check_paths = { + 'files': ['bin/heif-info', 'lib/libheif.a', 'lib/libheif.%s' % SHLIB_EXT, 'lib/pkgconfig/libheif.pc'], + 'dirs': ['include/libheif'], +} + +sanity_check_commands = ["heif-info --help"] + +moduleclass = 'tools' From f1d51b596f316a30aad8436d5d0715de30c16f56 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 3 Nov 2022 17:51:18 +0100 Subject: [PATCH 558/793] Rename package name --- .../Chemaxon-Marvin-21.14.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/c/{Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb => Chemaxon-Marvin/Chemaxon-Marvin-21.14.eb} (99%) diff --git a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb b/easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-21.14.eb similarity index 99% rename from easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb rename to easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-21.14.eb index adadbfe31a0..69f794a1422 100644 --- a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb +++ b/easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-21.14.eb @@ -10,7 +10,7 @@ # Summary and License fields must be present in package: (main package) easyblock = 'Binary' -name = 'Chemaxon_Marvin' +name = 'Chemaxon-Marvin' version = '21.14' homepage = 'https://chemaxon.com/products/marvin' From 1da56a693b2a047860ea239717bb1698d7a6aff3 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 19:11:22 +0200 Subject: [PATCH 559/793] adding easyconfigs: libde265-1.0.8-GCC-10.3.0.eb --- .../l/libde265/libde265-1.0.8-GCC-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb new file mode 100644 index 00000000000..647d345e73e --- /dev/null +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'libde265' +version = '1.0.8' + +homepage = 'https://github.com/strukturag/libde265' +description = "libde265 is an open source implementation of the h.265 video codec" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['24c791dd334fa521762320ff54f0febfd3c09fc978880a8c5fbc40a88f21d905'] + +builddependencies = [('CMake', '3.20.1')] + +sanity_check_paths = { + 'files': ['bin/dec265', 'bin/enc265', 'lib/liblibde265.%s' % SHLIB_EXT], + 'dirs': ['include/libde265', 'lib/cmake/libde265'], +} + +sanity_check_commands = [ + "dec265 --help", + "enc265 --help", +] + +moduleclass = 'tools' From afd61fb09cc2d8ed5970973f8b96f842e415f025 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jurij=20Pe=C4=8Dar?= Date: Thu, 3 Nov 2022 20:21:06 +0100 Subject: [PATCH 560/793] shortened Java dependency and removed test -d --- easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb index 896a6c321e3..cb17ec4556a 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb @@ -13,9 +13,9 @@ source_urls = ['https://github.com/%(namelower)s-io/%(namelower)s/releases/downl sources = ['%(namelower)s-%(version)s-all'] checksums = ['c5edc9fc81d9c6eb4f628505f14f8bb4fe044d4fc7d9ef60654ba0d73abf5a80'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11')] -install_cmd = "[ -d %(builddir)s/bin ] || mkdir -p %(installdir)s/bin &&" +install_cmd = "mkdir -p %(installdir)s/bin &&" install_cmd += "cp %(builddir)s/%(namelower)s-%(version)s-all %(installdir)s/bin &&" install_cmd += "cd %(installdir)s/bin && ln -s %(namelower)s-%(version)s-all %(namelower)s &&" install_cmd += "chmod +x %(installdir)s/bin/%(namelower)s-%(version)s-all" From db3c378611f30e7b425ea94e91f13d8f62b69c6c Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 3 Nov 2022 20:56:45 +0000 Subject: [PATCH 561/793] adding easyconfigs: KITE-1.1-gompi-2022a.eb --- .../k/KITE/KITE-1.1-gompi-2022a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb diff --git a/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb b/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb new file mode 100644 index 00000000000..d1f4c2ad3a1 --- /dev/null +++ b/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb @@ -0,0 +1,38 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'KITE' +version = '1.1' + +homepage = 'https://github.com/quantum-kite/kite' +description = """KITE is an open-source Python/C++ software suite for efficient real-space tight-binding (TB) +simulations of electronic structure and bulk quantum transport properties of disordered systems scalable to +multi billions of atomic orbitals.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://github.com/quantum-kite/kite/archive/'] +sources = ['%(version)s.tar.gz'] + +checksums = [ + 'a480fe46f2220ab6c2d6b9914e0673580121de703523dc22658fe50dc676e47e', # 1.1.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('Eigen', '3.4.0'), + ('HDF5', '1.12.2'), +] + +sanity_check_paths = { + 'files': ['bin/KITEx'], + 'dirs': [], +} + +moduleclass = 'chem' From 3efeea3c0dc2ebb94dd4b36bbc782b97b232c8fe Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 4 Nov 2022 10:55:52 +0100 Subject: [PATCH 562/793] Move to toolchain foss-2021a + Report issue with cwlformat upstream --- ...ore-10.3.0.eb => cwltool-3.1.20221018083734-foss-2021a.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/cwltool/{cwltool-3.1.20221018083734-GCCcore-10.3.0.eb => cwltool-3.1.20221018083734-foss-2021a.eb} (96%) diff --git a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb similarity index 96% rename from easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb index b40b9c1e883..15b2225906c 100644 --- a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb @@ -14,7 +14,7 @@ version = '3.1.20221018083734' homepage = 'https://github.com/common-workflow-language/cwltool' description = """Common workflow language (CWL) reference implementation.""" -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchain = {'name': 'foss', 'version': '2021a'} builddependencies = [ ('binutils', '2.36.1'), @@ -35,7 +35,7 @@ dependencies = [ ('pydot', '1.4.2'), ('lxml', '4.6.3'), ('ruamel.yaml', '0.17.21'), - ('networkx', '2.6.3', '', ('foss', '2021a')), + ('networkx', '2.6.3'), ] use_pip = True From 1d8333aba2e19716d792229dd353060d401c30a6 Mon Sep 17 00:00:00 2001 From: robogast Date: Fri, 4 Nov 2022 14:44:45 +0100 Subject: [PATCH 563/793] adding easyconfigs: CUDA-11.8.0.eb, cuDNN-8.6.0.163-CUDA-11.8.0.eb, NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb, UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb, GDRCopy-2.3-GCCcore-12.2.0.eb --- easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb | 17 ++++++ .../c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb | 33 ++++++++++++ .../g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb | 52 +++++++++++++++++++ .../NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb | 24 +++++++++ ...-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb | 42 +++++++++++++++ 5 files changed, 168 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb create mode 100644 easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb create mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb new file mode 100644 index 00000000000..e0ea509fe8b --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb @@ -0,0 +1,17 @@ +name = 'CUDA' +version = '11.8.0' +local_nv_version = '520.61.05' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = ['9223c4af3aebe4a7bbed9abd9b163b03a1b34b855fbc2b4a0d1b706ac09a5a16'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb new file mode 100644 index 00000000000..23f76bb3dca --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb @@ -0,0 +1,33 @@ +name = 'cuDNN' +version = '8.6.0.163' +versionsuffix = '-CUDA-%(cudaver)s' +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# note: cuDNN is tied to specific to CUDA versions, +# see also https://docs.nvidia.com/deeplearning/cudnn/support-matrix/index.html#cudnn-cuda-hardware-versions +local_short_ver = '.'.join(version.split('.')[:3]) +local_cuda_major = '11' # Is there a way to make this parametric? '%(cudaver)'.split(...) obviously doesn't work... + +source_urls = [ + 'https://developer.download.nvidia.com/compute/redist/cudnn/v%s/local_installers/%%(cudashortver)s/' % local_short_ver # noqa: E501 +] +sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] +checksums = ['bbc396df47294c657edc09c600674d608cb1bfc80b82dcf4547060c21711159e'] + +dependencies = [('CUDA', '11.8.0')] + +sanity_check_paths = { + 'files': [ + 'include/cudnn.h', 'lib64/libcudnn_adv_infer_static.a', 'lib64/libcudnn_adv_train_static.a', + 'lib64/libcudnn_cnn_infer_static.a', 'lib64/libcudnn_cnn_train_static.a', + 'lib64/libcudnn_ops_infer_static.a', 'lib64/libcudnn_ops_train_static.a', + 'lib64/libcudnn.%s' % SHLIB_EXT + ], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0fb6d9b4864 --- /dev/null +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'GDRCopy' +version = '2.3' + +homepage = 'https://github.com/NVIDIA/gdrcopy' +description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['b85d15901889aa42de6c4a9233792af40dd94543e82abe0439e544c87fd79475'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.3'), +] + +prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found +buildopts = "config lib prefix=%(installdir)s" + +installopts = 'prefix=%(installdir)s' + +github_account = 'NVIDIA' +# This easyconfig only installs the library of GDRCopy. Please keep in mind +# that GDRCopy also needs the following kernel modules at runtime: +# +# 1. Kernel module for GDRCopy: improves Host to GPU communication +# https://github.com/NVIDIA/gdrcopy +# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' +# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 +# +# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication +# https://github.com/Mellanox/nv_peer_memory +# RPM: 'nvidia_peer_memory' +# Requirements: Mellanox HCA with MLNX_OFED 2.1 +# +# These kernel modules are not listed as system dependencies to lower the system +# requirements to build this easyconfig, as they are not needed for the build. + +skipsteps = ['configure'] +install_cmd = "make lib_install" + +sanity_check_paths = { + 'files': ['lib/libgdrapi.so'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb new file mode 100644 index 00000000000..eaacb222314 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb @@ -0,0 +1,24 @@ +name = 'NCCL' +version = '2.15.5' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +checksums = ['f4ac3c74d469c9cd718f82e1477759785db9b9f8cc9d9ecc103485805b8394a3'] + +builddependencies = [('binutils', '2.39')] +buildopts = ['NVCC_APPEND_FLAGS="-allow-unsupported-compiler"'] # CUDA 11.8 doesn't officially support GCC 12.2 yet... + +dependencies = [ + ('CUDA', '11.8.0', '', SYSTEM), + ('UCX-CUDA', '1.13.1', versionsuffix), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb new file mode 100644 index 00000000000..e2d761a00ca --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb @@ -0,0 +1,42 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.13.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications + +This module adds the UCX CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['ucx-%(version)s.tar.gz'] +patches = [ + '%(name)s-1.11.0_link_against_existing_UCX_libs.patch', +] +checksums = [ + {'ucx-1.13.1.tar.gz': 'efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('UCX', version), + ('CUDA', '11.8.0', '', SYSTEM), + ('GDRCopy', '2.3'), +] + +moduleclass = 'lib' From faf4b17772355e79fa62b0eb7a94c5d5403199ca Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 4 Nov 2022 15:30:30 +0100 Subject: [PATCH 564/793] Move to networkx 2.5.1 to satisfy multi-variant deps for networkx in foss-2021a --- .../c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb index 15b2225906c..170d12542ff 100644 --- a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb +++ b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb @@ -35,7 +35,7 @@ dependencies = [ ('pydot', '1.4.2'), ('lxml', '4.6.3'), ('ruamel.yaml', '0.17.21'), - ('networkx', '2.6.3'), + ('networkx', '2.5.1'), ] use_pip = True From 620492f519a44217ea0461e28baee7f421e53d64 Mon Sep 17 00:00:00 2001 From: robogast Date: Fri, 4 Nov 2022 17:14:30 +0100 Subject: [PATCH 565/793] removed NCCL, UCX-CUDA, GDCopy --- .../g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb | 52 ------------------- .../NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb | 24 --------- ...-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb | 42 --------------- 3 files changed, 118 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb delete mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb delete mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb deleted file mode 100644 index 0fb6d9b4864..00000000000 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GDRCopy' -version = '2.3' - -homepage = 'https://github.com/NVIDIA/gdrcopy' -description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -toolchainopts = {'pic': True} - -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['b85d15901889aa42de6c4a9233792af40dd94543e82abe0439e544c87fd79475'] - -builddependencies = [ - ('binutils', '2.39'), - ('Autotools', '20220317'), - ('pkgconf', '1.9.3'), -] - -prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found -buildopts = "config lib prefix=%(installdir)s" - -installopts = 'prefix=%(installdir)s' - -github_account = 'NVIDIA' -# This easyconfig only installs the library of GDRCopy. Please keep in mind -# that GDRCopy also needs the following kernel modules at runtime: -# -# 1. Kernel module for GDRCopy: improves Host to GPU communication -# https://github.com/NVIDIA/gdrcopy -# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' -# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 -# -# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication -# https://github.com/Mellanox/nv_peer_memory -# RPM: 'nvidia_peer_memory' -# Requirements: Mellanox HCA with MLNX_OFED 2.1 -# -# These kernel modules are not listed as system dependencies to lower the system -# requirements to build this easyconfig, as they are not needed for the build. - -skipsteps = ['configure'] -install_cmd = "make lib_install" - -sanity_check_paths = { - 'files': ['lib/libgdrapi.so'], - 'dirs': ['include'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb deleted file mode 100644 index eaacb222314..00000000000 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'NCCL' -version = '2.15.5' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'https://developer.nvidia.com/nccl' -description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective -communication primitives that are performance optimized for NVIDIA GPUs.""" - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} - -github_account = 'NVIDIA' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s-1.tar.gz'] -checksums = ['f4ac3c74d469c9cd718f82e1477759785db9b9f8cc9d9ecc103485805b8394a3'] - -builddependencies = [('binutils', '2.39')] -buildopts = ['NVCC_APPEND_FLAGS="-allow-unsupported-compiler"'] # CUDA 11.8 doesn't officially support GCC 12.2 yet... - -dependencies = [ - ('CUDA', '11.8.0', '', SYSTEM), - ('UCX-CUDA', '1.13.1', versionsuffix), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb deleted file mode 100644 index e2d761a00ca..00000000000 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'EB_UCX_Plugins' - -name = 'UCX-CUDA' -version = '1.13.1' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'http://www.openucx.org/' -description = """Unified Communication X -An open-source production grade communication framework for data centric -and high-performance applications - -This module adds the UCX CUDA support. -""" - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['ucx-%(version)s.tar.gz'] -patches = [ - '%(name)s-1.11.0_link_against_existing_UCX_libs.patch', -] -checksums = [ - {'ucx-1.13.1.tar.gz': 'efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828'}, - {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': - 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3'}, -] - -builddependencies = [ - ('binutils', '2.39'), - ('Autotools', '20220317'), - ('pkgconf', '1.9.3'), -] - -dependencies = [ - ('zlib', '1.2.12'), - ('UCX', version), - ('CUDA', '11.8.0', '', SYSTEM), - ('GDRCopy', '2.3'), -] - -moduleclass = 'lib' From 5d266b29427ef54b284728e5910e7452828143bb Mon Sep 17 00:00:00 2001 From: robogast Date: Fri, 4 Nov 2022 18:24:15 +0100 Subject: [PATCH 566/793] added ppc64le & sbsa checksums --- .../easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb index 23f76bb3dca..bc2f6803e9b 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb @@ -16,7 +16,14 @@ source_urls = [ 'https://developer.download.nvidia.com/compute/redist/cudnn/v%s/local_installers/%%(cudashortver)s/' % local_short_ver # noqa: E501 ] sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] -checksums = ['bbc396df47294c657edc09c600674d608cb1bfc80b82dcf4547060c21711159e'] +checksums = [{ + '%%(namelower)s-linux-x86_64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'bbc396df47294c657edc09c600674d608cb1bfc80b82dcf4547060c21711159e', + '%%(namelower)s-linux-ppc64le-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'c8a25e7e3df1bb9c4e18a4f24dd5f25cfd4bbe8b7054e34008e53b2be4f58a80', + '%%(namelower)s-linux-sbsa-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'a0202278d3cbd4f3adc3f7816bff6071621cb042b0903698b477acac8928ac06', +}] dependencies = [('CUDA', '11.8.0')] From 1a68db0bf0aba9ac35ef256bdce1d4970dad0c46 Mon Sep 17 00:00:00 2001 From: robogast Date: Fri, 4 Nov 2022 18:51:21 +0100 Subject: [PATCH 567/793] added checksums for CUDA ppc and sbsa --- easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb index e0ea509fe8b..4fc4d6173ce 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb @@ -12,6 +12,13 @@ toolchain = SYSTEM source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] -checksums = ['9223c4af3aebe4a7bbed9abd9b163b03a1b34b855fbc2b4a0d1b706ac09a5a16'] +checksums = [{ + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '9223c4af3aebe4a7bbed9abd9b163b03a1b34b855fbc2b4a0d1b706ac09a5a16', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + 'f917fb7617033223938543ad3ae923190d99507acc08a399d752a2868e87349d', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + 'e6e9a8d31163c9776b5e313fd7590877c5684e1ecddee741154f95704d4ed27c' +}] moduleclass = 'system' From a8bcc6962a63d55b527445fd11bd1c2fb5676907 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 7 Nov 2022 11:06:14 +0100 Subject: [PATCH 568/793] adding easyconfigs: JupyterLab-3.5.0-GCCcore-11.3.0.eb, jupyter-server-1.21.0-GCCcore-11.3.0.eb --- .../JupyterLab-3.5.0-GCCcore-11.3.0.eb | 56 +++++++++++++++++++ .../jupyter-server-1.21.0-GCCcore-11.3.0.eb | 41 ++++++++++++++ 2 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb create mode 100755 easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1ce74b3d8a8 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'JupyterLab' +version = '3.5.0' + +homepage = "https://jupyter.org/" +description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar + building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, + etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter + Notebook.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), + ('jupyter-server', '1.21.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('json5', '0.9.10', { + 'checksums': ['ad9f048c5b5a4c3802524474ce40a622fae789860a86f10cc4f7e5f9cf9b46ab'], + }), + ('notebook_shim', '0.1.0', { + 'checksums': ['7897e47a36d92248925a2143e3596f19c60597708f7bef50d81fcd31d7263e85'], + }), + ('nbclassic', '0.4.8', { + 'checksums': ['c74d8a500f8e058d46b576a41e5bc640711e1032cf7541dde5f73ea49497e283'], + }), + ('jupyterlab_server', '2.13.0', { + 'checksums': ['2040298a133458aa22f287a877d6bb91ff973f6298d562264f9f7b75e92a5ace'], + }), + ('jupyterlab', version, { + 'checksums': ['e02556c8ea1b386963c4b464e4618aee153c5416b07ab481425c817a033323a2'], + }), +] + +sanity_check_commands = ["jupyter lab --help"] + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} +modextravars = { + # only one path allowed as JUPYTERLAB_DIR + 'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb new file mode 100755 index 00000000000..b511014596e --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server' +version = '1.21.0' + +homepage = "https://jupyter.org/" +description = """The Jupyter Server provides the backend (i.e. the core services, APIs, and REST +endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and +Voila.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.1', { + 'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'], + }), + ('websocket-client', '1.4.2', { + 'modulename': 'websocket', + 'checksums': ['d6e8f90ca8e2dd4e8027c4561adeb9456b54044312dba655e7cae652ceb9ae59'], + }), + ('jupyter_server', version, { + 'checksums': ['d0adca19913a3763359be7f0b8c2ea8bfde356f4b8edd8e3149d7d0fbfaa248b'], + }), +] + +moduleclass = 'tools' From 8cbbb761cbf86493124b68bf8606370c00923544 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 7 Nov 2022 11:14:36 +0100 Subject: [PATCH 569/793] adding easyconfigs: nglview-3.0.3-foss-2021a.eb, MDAnalysis-2.0.0-foss-2021a.eb --- .../MDAnalysis/MDAnalysis-2.0.0-foss-2021a.eb | 45 +++++++++++++++++++ .../n/nglview/nglview-3.0.3-foss-2021a.eb | 44 ++++++++++++++++++ 2 files changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021a.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021a.eb new file mode 100644 index 00000000000..64300f8f2f7 --- /dev/null +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021a.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'MDAnalysis' +version = '2.0.0' + +homepage = 'https://www.mdanalysis.org/' +description = """MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) +simulations in many popular formats.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('Biopython', '1.79'), + ('networkx', '2.5.1'), + ('tqdm', '4.61.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('GridDataFormats', '0.6.0', { + 'modulename': 'gridData', + 'checksums': ['f14e00e8b795f8021f6069935e1133352224775c9bd97f395beb2bcd64a19b86'], + }), + ('gsd', '2.5.1', { + 'checksums': ['76bf228b1d8e95e7d6a334e8cc7712c0bd8c256148007f7ce88a489c21996593'], + }), + ('msgpack', '1.0.3', { + 'checksums': ['51fdc7fb93615286428ee7758cecc2f374d5ff363bdd884c7ea622a7a327a81e'], + }), + ('mmtf-python', '1.1.2', { + 'modulename': 'mmtf', + 'checksums': ['a5caa7fcd2c1eaa16638b5b1da2d3276cbd3ed3513f0c2322957912003b6a8df'], + }), + (name, version, { + 'modulename': name, + 'checksums': ['aa3079d1a82305eba58cf567fac8fc231940184ed88f9a4451be8433f4a06d3e'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb b/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb new file mode 100644 index 00000000000..f4c5a62bada --- /dev/null +++ b/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'nglview' +version = '3.0.3' + +homepage = 'https://github.com/arose/nglview' +description = "IPython widget to interactively view molecular structures and trajectories." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('IPython', '7.25.0'), + ('JupyterLab', '3.2.8'), + ('nodejs', '14.17.0'), + ('MDAnalysis', '2.0.0'), # optional +] + +use_pip = True + +exts_list = [ + ('versioneer', '0.24', { + 'checksums': ['1b8dba9e51e2f0e04c7e8545216eecdea2d63e1bd5569448ee66c549f7e7782f'], + }), + (name, version, { + 'use_pip_extras': 'MDAnalysis', + 'checksums': ['3253c44bd071e4701c288de44997471608487d5191ab3d3b7736c8651335c1af'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/nglview'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} + +moduleclass = 'chem' From a2d2c2cfde8ad1f2de5a1feac758a05e809ac1ed Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 7 Nov 2022 12:26:56 +0100 Subject: [PATCH 570/793] downgrade dependency of nglview-3.0.3-foss-2021a.eb on JupyterLab to v3.0.16 --- easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb b/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb index f4c5a62bada..0d555c1e891 100644 --- a/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb +++ b/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb @@ -12,7 +12,7 @@ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('IPython', '7.25.0'), - ('JupyterLab', '3.2.8'), + ('JupyterLab', '3.0.16'), ('nodejs', '14.17.0'), ('MDAnalysis', '2.0.0'), # optional ] From 439cb7b0e790eca1a8b3be13cce88776e67a3a91 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 7 Nov 2022 14:01:02 +0100 Subject: [PATCH 571/793] adding easyconfigs: MCU-3366c85-gomkl-2021a.eb, matplotlib-3.4.2-gomkl-2021a.eb, spglib-python-1.16.1-gomkl-2021a.eb --- .../m/MCU/MCU-3366c85-gomkl-2021a.eb | 33 ++++++++++ .../matplotlib-3.4.2-gomkl-2021a.eb | 64 +++++++++++++++++++ .../spglib-python-1.16.1-gomkl-2021a.eb | 27 ++++++++ 3 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-gomkl-2021a.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.1-gomkl-2021a.eb diff --git a/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb b/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb new file mode 100644 index 00000000000..74d3aa4c388 --- /dev/null +++ b/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'MCU' +version = '3366c85' # There is a 0.2 release but it's too old and it doesn't work + +homepage = 'https://hungqpham.com/mcu/' +description = """A package for periodic wavefunction and crystallography analysis. + mcu is designed to support large scale analysis and topological descriptions for periodic wavefunction.""" + +toolchain = {'name': 'gomkl', 'version': '2021a'} + +source_urls = ['https://github.com/hungpham2017/mcu/archive/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['96553924c57ca27d2e4d8668be2c97fc6019c139f91950a798733c5575a8b44a'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('spglib-python', '1.16.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'mcu'} + +sanity_check_commands = [ + "python -c 'from mcu import VASP'", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-gomkl-2021a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-gomkl-2021a.eb new file mode 100644 index 00000000000..ca47ecae358 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-gomkl-2021a.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.4.2' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'gomkl', 'version': '2021a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('cppy', '1.1.0') +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('libpng', '1.6.37'), + ('freetype', '2.10.4'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '8.2.0'), + ('Qhull', '2020.2') +] + +use_pip = True +sanity_pip_check = True + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' setup.cfg.template >setup.cfg && " + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['950a199911a8d94683a6b10321f9345d5a3a8433ec58b217ace979e18f16e248'], + }), + (name, version, { + 'preinstallopts': _fix_setup + _include_path, + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['d8d994cefdff9aaba45166eb3de4f5211adb4accac85cbf97137e98f26ea0219'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.1-gomkl-2021a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.1-gomkl-2021a.eb new file mode 100644 index 00000000000..6079d940a72 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.1-gomkl-2021a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.16.1' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." + +toolchain = {'name': 'gomkl', 'version': '2021a'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['9fd2fefbd83993b135877a69c498d8ddcf20a9980562b65b800cfb4cdadad003'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'spglib'} + +moduleclass = 'chem' From 1972ddbd3fce77cd788f6444cade40df3d9d2bd3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 7 Nov 2022 14:16:27 +0100 Subject: [PATCH 572/793] style fix --- easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb b/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb index 74d3aa4c388..5a722540235 100644 --- a/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb +++ b/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'MCU' -version = '3366c85' # There is a 0.2 release but it's too old and it doesn't work +version = '3366c85' # There is a 0.2 release but it's too old and it doesn't work homepage = 'https://hungqpham.com/mcu/' description = """A package for periodic wavefunction and crystallography analysis. From 088501e33cb81906978c5b9c7a678b3eaefbe120 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Mon, 7 Nov 2022 14:48:45 +0100 Subject: [PATCH 573/793] Moved dependencies to its usual place --- .../easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb b/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb index 23c3faed318..e6bb3dd3a74 100644 --- a/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb +++ b/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb @@ -12,17 +12,17 @@ source_urls = ['https://github.com/Illumina/DRAGMAP/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] checksums = ['baf546c2f53b13e2bce4c937201e38459f3ce2f1069722ca670d8726a4bae224'] +dependencies = { + ('Boost', '1.77.0'), + ('googletest', '1.11.0'), +} + skipsteps = ['configure'] prebuildopts = 'sed -i "s|-msse4.2 -mavx2|$CXXFLAGS|g" config.mk &&' buildopts = 'CC="$CC" CXX="$CXX"' preinstallopts = 'mkdir %(installdir)s/bin &&' installopts = 'DESTDIR=%(installdir)s' -dependencies = { - ('Boost', '1.77.0'), - ('googletest', '1.11.0'), -} - sanity_check_paths = { 'files': ['bin/dragen-os'], 'dirs': [] From 773580293233ea6b9387985596155d641eaeadef Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 7 Nov 2022 15:55:10 +0100 Subject: [PATCH 574/793] Switched to new JuliaPackage easyblock + changed True to SYSTEM as requested --- ...Estimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb | 79 +++++++++++++++++-- 1 file changed, 71 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb index ca021785912..d9bb1bafff0 100644 --- a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb @@ -1,4 +1,4 @@ -easyblock = 'Tarball' +easyblock = 'Bundle' name = 'MultilevelEstimators' version = '0.1.0' @@ -12,20 +12,83 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'} dependencies = [ ('Python', '3.9.6'), - ('Julia', local_julia_ver, '-linux-%s' % ARCH, True), + ('Julia', local_julia_ver, '-linux-%s' % ARCH, SYSTEM), ] -postinstallcmds = [ - "cd %(installdir)s && mkdir pkgs", - """export JULIA_DEPOT_PATH=%%(installdir)s/pkgs && - julia -e 'using Pkg;Pkg.add(url="%s")' """ % homepage +exts_defaultclass = 'JuliaPackage' +exts_filter = ("julia -e 'using %(ext_name)s'", "") +exts_default_options = { + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], +} + +exts_list = [ + ('Preferences', '1.3.0', { + 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], + }), + ('JLLWrappers', '1.4.1', { + 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], + }), + ('OpenSpecFun_jll', '0.5.5+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/OpenSpecFun_jll.jl/archive/'], + 'sources': ['OpenSpecFun-v%(version)s.tar.gz'], + }), + ('InverseFunctions', '0.1.8', { + 'source_urls': ['https://github.com/JuliaMath/InverseFunctions.jl/archive/'], + }), + ('DocStringExtensions', '0.9.2', { + 'source_urls': ['https://github.com/JuliaDocs/DocStringExtensions.jl/archive/'], + }), + ('IrrationalConstants', '0.1.1', { + 'source_urls': ['https://github.com/JuliaMath/IrrationalConstants.jl/archive/'], + }), + ('Compat', '4.3.0', { + 'source_urls': ['https://github.com/JuliaLang/Compat.jl/archive/'], + }), + ('ChainRulesCore', '1.15.6', { + 'source_urls': ['https://github.com/JuliaDiff/ChainRulesCore.jl/archive/'], + }), + ('ChangesOfVariables', '0.1.4', { + 'source_urls': ['https://github.com/JuliaMath/ChangesOfVariables.jl/archive/'], + }), + ('LogExpFunctions', '0.3.18', { + 'source_urls': ['https://github.com/JuliaStats/LogExpFunctions.jl/archive/'], + }), + ('SpecialFunctions', '1.8.7', { + 'source_urls': ['https://github.com/JuliaMath/SpecialFunctions.jl/archive/'], + }), + ('TranscodingStreams', '0.9.9', { + 'source_urls': ['https://github.com/JuliaIO/TranscodingStreams.jl/archive/'], + }), + ('Reexport', '1.2.2', { + 'source_urls': ['https://github.com/simonster/Reexport.jl/archive/'], + }), + ('OrderedCollections', '1.4.1', { + 'source_urls': ['https://github.com/JuliaCollections/OrderedCollections.jl/archive/'], + }), + ('MacroTools', '0.5.10', { + 'source_urls': ['https://github.com/FluxML/MacroTools.jl/archive/'], + }), + ('Requires', '1.3.0', { + 'source_urls': ['https://github.com/JuliaPackaging/Requires.jl/archive/'], + }), + ('FileIO', '1.16.0', { + 'source_urls': ['https://github.com/JuliaIO/FileIO.jl/archive/'], + }), + ('JLD2', '0.4.24', { + 'source_urls': ['https://github.com/JuliaIO/JLD2.jl/archive/'], + }), + (name, version, { + 'source_urls': ['https://github.com/PieterjanRobbe/MultilevelEstimators.jl/archive/'], + }), ] sanity_check_paths = { 'files': [], - 'dirs': ["pkgs"] + 'dirs': ['packages'] } -modextrapaths = {'JULIA_DEPOT_PATH': 'pkgs'} +modextrapaths = { + 'JULIA_DEPOT_PATH': '', +} moduleclass = 'lib' From 04340fd1ae7c02dc8d1a01fd471374ba2ee8cced Mon Sep 17 00:00:00 2001 From: eb-test Date: Mon, 7 Nov 2022 16:00:29 +0100 Subject: [PATCH 575/793] add new SPOTlight package --- .../R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb index 1c4ffc3555e..cb2f31c3821 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb @@ -43,7 +43,7 @@ exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_s # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends # !! order of packages is important !! -# packages updated on 4th May 2022 +# packages updated on 7th Nov 2022 exts_list = [ ('BiocGenerics', '0.42.0', { 'checksums': ['0cb6fa74a389693d253a9f61935d335fcfcc1dfe5acbba78b3cc43c1af5d6947'], @@ -1060,6 +1060,9 @@ exts_list = [ ('M3Drop', '1.22.0', { 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], }), + ('ExomeDepth', '1.1.15', { + 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], + }), ('bsseq', '1.32.0', { 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], }), @@ -1087,6 +1090,9 @@ exts_list = [ ('CAGEr', '2.2.0', { 'checksums': ['1cd64f6b045a5e246ae92cd709234c806edfcc25463819df0bd32fe4f4b2fd0d'], }), + ('SPOTlight', '1.0.0', { + 'checksums': ['f6baf718e468292960884a1aacdf8295f0864d771f5eb0f2088fb9a1bc00dcc0'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 98ae750d79d281d348741e7007089e48573c348f Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 7 Nov 2022 16:01:58 +0100 Subject: [PATCH 576/793] Added checksums for all packages --- ...Estimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb index d9bb1bafff0..e048be328cf 100644 --- a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb @@ -24,61 +24,80 @@ exts_default_options = { exts_list = [ ('Preferences', '1.3.0', { 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], + 'checksums': ['a87c1fc863fcb6240c3f4327776fa01a1f87e0d2df5a0c1850f789ce24469da2'], }), ('JLLWrappers', '1.4.1', { 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], + 'checksums': ['2cb61d4171e8ebc74e36ee20e6e0ba959aa5525a9c2fef5547e0993566018775'], }), ('OpenSpecFun_jll', '0.5.5+0', { 'source_urls': ['https://github.com/JuliaBinaryWrappers/OpenSpecFun_jll.jl/archive/'], 'sources': ['OpenSpecFun-v%(version)s.tar.gz'], + 'checksums': ['6d1df617dd0a80fc0de5bc41a092e51f72782dbfd296c64e151707733cb57b6f'], }), ('InverseFunctions', '0.1.8', { 'source_urls': ['https://github.com/JuliaMath/InverseFunctions.jl/archive/'], + 'checksums': ['6b3e72037c2198268bc5247daeb14eaa5cf2b37f41c7c735b3cd2355bad1584b'], }), ('DocStringExtensions', '0.9.2', { 'source_urls': ['https://github.com/JuliaDocs/DocStringExtensions.jl/archive/'], + 'checksums': ['ff7869968381f17b24b3f471a88dd96b7008e8b8d7a14079d4667d87db0037dd'], }), ('IrrationalConstants', '0.1.1', { 'source_urls': ['https://github.com/JuliaMath/IrrationalConstants.jl/archive/'], + 'checksums': ['2eccfb55449d25d363d96ce116c45b39110d1572248e04e136ec4c37fe84ba96'], }), ('Compat', '4.3.0', { 'source_urls': ['https://github.com/JuliaLang/Compat.jl/archive/'], + 'checksums': ['0d792ec0912a8d3ed30329fc44073e964be3cd314671594dd16f8570c51b2c19'], }), ('ChainRulesCore', '1.15.6', { 'source_urls': ['https://github.com/JuliaDiff/ChainRulesCore.jl/archive/'], + 'checksums': ['79e22fc981fa7c44b3efc2f07903f555c5520dc38d0d3d31b6390980c786cb60'], }), ('ChangesOfVariables', '0.1.4', { 'source_urls': ['https://github.com/JuliaMath/ChangesOfVariables.jl/archive/'], + 'checksums': ['2eb2eb59711d53d284a9cc998e9facf3a1720cfde26eb672676cbe944fa9224a'], }), ('LogExpFunctions', '0.3.18', { 'source_urls': ['https://github.com/JuliaStats/LogExpFunctions.jl/archive/'], + 'checksums': ['f169c5512f79746987858dd19d05d6fdd4017f2b817d9cd8831bde3c3e398a82'], }), ('SpecialFunctions', '1.8.7', { 'source_urls': ['https://github.com/JuliaMath/SpecialFunctions.jl/archive/'], + 'checksums': ['3f2ecec0506fe47cfa5e436ac510e2a82d39f74fceaeb422572cf06d90f2096a'], }), ('TranscodingStreams', '0.9.9', { 'source_urls': ['https://github.com/JuliaIO/TranscodingStreams.jl/archive/'], + 'checksums': ['c341df1b582e6289fd5d5bd682111876b01582792687c0812fd093c085b12e68'], }), ('Reexport', '1.2.2', { 'source_urls': ['https://github.com/simonster/Reexport.jl/archive/'], + 'checksums': ['2566f7776aae9697cbf15765fc32187f46dd51200abc953a0266863ad67132b3'], }), ('OrderedCollections', '1.4.1', { 'source_urls': ['https://github.com/JuliaCollections/OrderedCollections.jl/archive/'], + 'checksums': ['ad6d191a2bf6f0c04abaf795fa93b3db6c3f3fb97498b464fcf7297b3a4bf6b6'], }), ('MacroTools', '0.5.10', { 'source_urls': ['https://github.com/FluxML/MacroTools.jl/archive/'], + 'checksums': ['0c61fe20a40346b0d1c248ff57e047b669ae47ad2d971b2ca7b91efdddff71ac'], }), ('Requires', '1.3.0', { 'source_urls': ['https://github.com/JuliaPackaging/Requires.jl/archive/'], + 'checksums': ['8af4dac29839e796a651b8cb6a325b6f9c7eee5d5620b3e366b64f58325ebeb7'], }), ('FileIO', '1.16.0', { 'source_urls': ['https://github.com/JuliaIO/FileIO.jl/archive/'], + 'checksums': ['c447263eb2fac0bd1c7822b97b64f4274e8eeb52bdd5fdc8dc413342a547759f'], }), ('JLD2', '0.4.24', { 'source_urls': ['https://github.com/JuliaIO/JLD2.jl/archive/'], + 'checksums': ['fdcc4a9af9eaaa9013724deb2649ba00aa987ae5d3753a7af389ab7720bf19a9'], }), (name, version, { 'source_urls': ['https://github.com/PieterjanRobbe/MultilevelEstimators.jl/archive/'], + 'checksums': ['53bd629506cbe2472c9fb061a5a64523478556264e7fc98a3b6503dc1e7ef039'], }), ] From 4906ccbb280b753019ab454bea1fbca708772df4 Mon Sep 17 00:00:00 2001 From: eb-test Date: Mon, 7 Nov 2022 16:07:01 +0100 Subject: [PATCH 577/793] add it also to 2022a --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index e9595a58dd4..cac7fb0b26b 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -45,7 +45,7 @@ exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_s # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends # !! order of packages is important !! -# packages updated on 7th July 2022 +# packages updated on 7th Nov 2022 exts_list = [ ('BiocGenerics', '0.42.0', { 'checksums': ['0cb6fa74a389693d253a9f61935d335fcfcc1dfe5acbba78b3cc43c1af5d6947'], @@ -1059,6 +1059,9 @@ exts_list = [ ('M3Drop', '1.22.0', { 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], }), + ('ExomeDepth', '1.1.15', { + 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], + }), ('bsseq', '1.32.0', { 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], }), @@ -1083,6 +1086,9 @@ exts_list = [ ('CAGEr', '2.2.0', { 'checksums': ['1cd64f6b045a5e246ae92cd709234c806edfcc25463819df0bd32fe4f4b2fd0d'], }), + ('SPOTlight', '1.0.0', { + 'checksums': ['f6baf718e468292960884a1aacdf8295f0864d771f5eb0f2088fb9a1bc00dcc0'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 4ac5f57ff988d0e8fbf891c789b2d8f57279e5ef Mon Sep 17 00:00:00 2001 From: eb-test Date: Mon, 7 Nov 2022 16:12:58 +0100 Subject: [PATCH 578/793] remove ExomeDepth as is gone due to #16492 --- .../R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb | 3 --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 3 --- 2 files changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb index cb2f31c3821..9c7b01b9137 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb @@ -1060,9 +1060,6 @@ exts_list = [ ('M3Drop', '1.22.0', { 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], }), - ('ExomeDepth', '1.1.15', { - 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], - }), ('bsseq', '1.32.0', { 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], }), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index cac7fb0b26b..db12f43dc2b 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1059,9 +1059,6 @@ exts_list = [ ('M3Drop', '1.22.0', { 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], }), - ('ExomeDepth', '1.1.15', { - 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], - }), ('bsseq', '1.32.0', { 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], }), From e303fcc683a3d7e3052020d25087157fdad982c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Nov 2022 16:17:19 +0100 Subject: [PATCH 579/793] define $GTKDOCIZE as 'echo' before generating configure script for recent HarfBuzz versions (fixes #16567) --- .../easyconfigs/h/HarfBuzz/HarfBuzz-2.8.1-GCCcore-10.3.0.eb | 3 ++- .../easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb | 3 ++- .../easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.1-GCCcore-10.3.0.eb index 5662fb3cc49..61d5d7f6ffc 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.1-GCCcore-10.3.0.eb @@ -30,7 +30,8 @@ dependencies = [ ('freetype', '2.10.4'), ] -preconfigopts = "./autogen.sh && " +# define $GTKDOCIZE to 'echo' as workaround for https://github.com/easybuilders/easybuild-easyconfigs/issues/16567 +preconfigopts = "GTKDOCIZE=echo ./autogen.sh && " configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb index 57ecf2bd16c..2be2036a9b2 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb @@ -27,7 +27,8 @@ dependencies = [ ('freetype', '2.11.0'), ] -preconfigopts = "./autogen.sh && " +# define $GTKDOCIZE to 'echo' as workaround for https://github.com/easybuilders/easybuild-easyconfigs/issues/16567 +preconfigopts = "GTKDOCIZE=echo ./autogen.sh && " configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb index af1f8d0d274..389711e5230 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb @@ -27,7 +27,8 @@ dependencies = [ ('freetype', '2.12.1'), ] -preconfigopts = "./autogen.sh && " +# define $GTKDOCIZE to 'echo' as workaround for https://github.com/easybuilders/easybuild-easyconfigs/issues/16567 +preconfigopts = "GTKDOCIZE=echo ./autogen.sh && " configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " sanity_check_paths = { From 2ce828930e93303842546c5914ddb1458a4c6b7b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Nov 2022 16:55:38 +0100 Subject: [PATCH 580/793] disable use of -Werror in recent NSS easyconfigs --- easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb | 5 ++++- easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb | 5 ++++- easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb | 5 ++++- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb index 1153b4b58a8..cc653fd5135 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb @@ -31,8 +31,11 @@ dependencies = [ # building in parallel fails parallel = 1 +# disable use of -Werror to work around compilation errors with newer glibc versions, +# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 +buildopts = "NSS_ENABLE_WERROR=0 " # fix for not being able to find header files -buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +buildopts += 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' # fix c standard causing missing functions buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' # also install pkgconfig file (see patch) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb index 0ea01ba44d0..55fbfa38a92 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb @@ -34,8 +34,11 @@ dependencies = [ # building in parallel fails parallel = 1 +# disable use of -Werror to work around compilation errors with newer glibc versions, +# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 +buildopts = "NSS_ENABLE_WERROR=0 " # fix for not being able to find header files -buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +buildopts += 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' # fix c standard causing missing functions buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' # also install pkgconfig file (see patch) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb index 3cea93f9ab6..40d16c445eb 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb @@ -32,8 +32,11 @@ dependencies = [ # building in parallel fails parallel = 1 +# disable use of -Werror to work around compilation errors with newer glibc versions, +# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 +buildopts = "NSS_ENABLE_WERROR=0 " # fix for not being able to find header files -buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +buildopts += 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' # fix c standard causing missing functions buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' # also install pkgconfig file (see patch) From 589da76b23b7828955ee9c4a8021e71a9b269e5f Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Mon, 7 Nov 2022 17:50:26 +0100 Subject: [PATCH 581/793] adding easyconfigs: InParanoid-5.0.79d8e39-GCC-10.3.0.eb --- .../InParanoid-5.0.79d8e39-GCC-10.3.0.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb new file mode 100644 index 00000000000..61194783a6d --- /dev/null +++ b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb @@ -0,0 +1,65 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'Tarball' + +name = 'InParanoid' +version = '5.0.79d8e39' + +homepage = 'https://inparanoid.sbc.su.se' +description = """InParanoid: ortholog groups with inparalogs.""" +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://bitbucket.org/sonnhammergroup/inparanoid/get/'] +sources = ['79d8e39bb243d403ce57b699c1ae104a8a640389.tar.gz'] +checksums = ['efe1a35bbb70608385780c4bf62969a29c46dd8132fbe472034422d23ad4b0c2'] # for commit 79d8e39 + +builddependencies = [('binutils', '2.36.1')] + +# NOTE some dependencies are not listed on the web site such as Java! +dependencies = [ + ('Perl', '5.32.1'), # brings libmoose-perl and libparallel-forkmanager-perl + ('BioPerl', '1.7.8'), + ('Java', '11', '', SYSTEM), + ('BLAST', '2.2.26', '-Linux_x86_64', SYSTEM), + ('DIAMOND', '2.0.13'), +] + +# NOTE inparanoid.pl uses only local (same directory) paths, so patch it +postinstallcmds = ["rm -rf %(installdir)s/docker/ %(installdir)s/singularity/ && " + "chmod a+rx %(installdir)s/*.pl && " + "chmod -x %(installdir)s/*.jar && " + "perl -i -pe 's|helpfile = \"help\"|helpfile = \"%(installdir)s/help\"|' " + "%(installdir)s/inparanoid.pl && " + "perl -i -pe 's|seqstat = \"|seqstat = \"%(installdir)s/|' " + "%(installdir)s/inparanoid.pl && " + "perl -i -pe 's|blastParser = \"|blastParser = \"%(installdir)s/|' " + "%(installdir)s/inparanoid.pl && " + "perl -i -pe 's|diamondParser = \"|diamondParser = \"%(installdir)s/|' " + "%(installdir)s/inparanoid.pl && " + "perl -i -pe 's|copy\(\"\./|copy\(\"%(installdir)s/|' " + "%(installdir)s/inparanoid.pl && " + "perl -i -pe 's|\./\$blastParser|\$blastParser|g' " + "%(installdir)s/inparanoid.pl && " + "perl -i -pe 's|#!.*perl|#!/usr/bin/env perl|' %(installdir)s/*.pl"] + +sanity_check_paths = { + 'files': ['inparanoid.pl', 'blast_parser.pl', 'diamondParser.pl'], + 'dirs': ['matrices'], +} + +modextrapaths = { + 'PATH': '', +} + +sanity_check_commands = ["inparanoid.pl -input-dir %(installdir)s/testInput/ && " + "rm -Rf %(installdir)s/output/"] + +moduleclass = 'bio' From e300c9937fb0e36dbf415eaea0a264063fd206a4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 8 Nov 2022 09:30:36 +0100 Subject: [PATCH 582/793] fixed naming and versioning --- .../mcu-2021-04-06-gomkl-2021a.eb} | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/m/{MCU/MCU-3366c85-gomkl-2021a.eb => mcu/mcu-2021-04-06-gomkl-2021a.eb} (76%) diff --git a/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb b/easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb similarity index 76% rename from easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb rename to easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb index 5a722540235..5a34c8b03a6 100644 --- a/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb +++ b/easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb @@ -1,7 +1,8 @@ easyblock = 'PythonPackage' -name = 'MCU' -version = '3366c85' # There is a 0.2 release but it's too old and it doesn't work +name = 'mcu' +local_commit = '3366c85' +version = '2021-04-06' # There is a 0.2 release but it's too old and it doesn't work homepage = 'https://hungqpham.com/mcu/' description = """A package for periodic wavefunction and crystallography analysis. @@ -10,7 +11,7 @@ description = """A package for periodic wavefunction and crystallography analysi toolchain = {'name': 'gomkl', 'version': '2021a'} source_urls = ['https://github.com/hungpham2017/mcu/archive/'] -sources = [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] checksums = ['96553924c57ca27d2e4d8668be2c97fc6019c139f91950a798733c5575a8b44a'] dependencies = [ @@ -24,8 +25,6 @@ use_pip = True download_dep_fail = True sanity_pip_check = True -options = {'modulename': 'mcu'} - sanity_check_commands = [ "python -c 'from mcu import VASP'", ] From f184bf0f4a276c02194f833960c6c5b1b42f3bc7 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 09:45:01 +0100 Subject: [PATCH 583/793] adding easyconfigs: Godon-20210913-x86_64.eb --- .../g/Godon/Godon-20210913-x86_64.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb diff --git a/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb b/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb new file mode 100644 index 00000000000..576e9b6362d --- /dev/null +++ b/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb @@ -0,0 +1,42 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +# Compilation with GO looks to use a broken dependency +# +# SO use the pre-compiled binaries! +## + +easyblock = 'Binary' + +name = 'Godon' +version = '20210913' +versionsuffix = '-x86_64' + +software_license = 'LicenseGPLv3' + +homepage = 'https://bitbucket.org/Davydov/godon/' +description = """Godon is codon models software written in Go.""" + +toolchain = SYSTEM + +source_urls = ['https://bitbucket.org/Davydov/godon/downloads'] +sources = ['godon-master-linux-gnu-x86_64'] +checksums = ['159058f7577093548f3ced1540d1ff9fd5f7915cdfcb8f8cd7fb40f5c202fcca'] + + +extract_sources = False + +postinstallcmds = ["mkdir -p %(installdir)s/bin/ && cd %(installdir)s/bin/ && " + "ln -s ../godon-master-linux-gnu-x86_64 godon"] + +sanity_check_paths = { + 'files': ["bin/godon"], + 'dirs': ['bin'], +} + +sanity_check_commands = ["godon --help"] + +moduleclass = 'bio' From 34ffbf8e8618aad39c9188e3097f1e3464e69110 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 10:18:21 +0100 Subject: [PATCH 584/793] adding easyconfigs: NanoLyse-1.2.1-foss-2021a.eb --- .../n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb new file mode 100644 index 00000000000..a6b362f5ae5 --- /dev/null +++ b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb @@ -0,0 +1,56 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'PythonBundle' + +name = 'NanoLyse' +version = '1.2.1' + +homepage = 'https://github.com/wdecoster/nanolyse' +description = """Remove reads mapping to the lambda phage genome from a fastq file.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('make', '4.3'), + ('Check', '0.15.2'), + ('SWIG', '4.0.2'), + ('expat', '2.2.9'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Biopython', '1.79'), +] + +use_pip = True + +# Fetch the tar.gz, not the whl files! +exts_list = [ + ('mappy', '2.24', { + 'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'], + }), + ('NanoLyse', '1.2.1', { + 'checksums': ['933ee668da805fc9ec9fa86c9fca81a073438d45b5f64e23cf606c01e715b1d5'], + }), +] + +sanity_check_paths = { + 'files': ['bin/NanoLyse'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoLyse --version"] + +sanity_pip_check = True + +moduleclass = 'bio' From 147604a643395b467b19273f00aeaafa1ef7a1f6 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 11:14:17 +0100 Subject: [PATCH 585/793] adding easyconfigs: PyDamage-0.70-foss-2021a.eb --- .../p/PyDamage/PyDamage-0.70-foss-2021a.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb b/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb new file mode 100644 index 00000000000..45477aba7e9 --- /dev/null +++ b/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb @@ -0,0 +1,65 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'PythonBundle' + +name = 'PyDamage' +version = '0.70' + +homepage = 'https://github.com/maxibor/pydamage' +description = """Pydamage, is a Python software to automate the process of +contig damage identification and estimation. After modelling the ancient DNA +damage using the C to T transitions, Pydamage uses a likelihood ratio test +to discriminate between truly ancient, and modern contigs originating from +sample contamination.""" +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('make', '4.3'), + ('Check', '0.15.2'), + ('SWIG', '4.0.2'), + ('expat', '2.2.9'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Biopython', '1.79'), + ('Pysam', '0.16.0.1'), + ('statsmodels', '0.12.2'), + ('matplotlib', '3.4.2'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +# Fetch the tar.gz, not the whl files! +exts_list = [ + ('kneed', '0.7.0', { + 'checksums': ['340d67fa183a72b0afae19846dd246a6fb7204e8d54243d8b8d3d9932f887c6e'], + }), + ('pydamage', '0.70', { + 'checksums': ['1dcd6ebae431f758c9434785c668351f82926847f9eda76413e96b7481138d78'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pydamage'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pydamage --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From ff135866cea1a5bb953de5ccdc4ee508a3a51e05 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Tue, 8 Nov 2022 11:46:10 +0100 Subject: [PATCH 586/793] Update imagecodecs-2022.9.26-foss-2021a.eb --- .../i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb index 55bf95340ff..2a32ac22f2e 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb @@ -47,7 +47,7 @@ dependencies = [ ('zfp', '1.0.0'), ('zstd', '1.4.9'), ('Brunsli', '0.1'), - ('HDF5', '1.12.1'), + ('HDF5', '1.10.7'), ('h5py', '3.2.1'), ('libheif', '1.12.0'), ] From 91d4154016519c6f550bbf367df983561d14aeca Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 12:02:18 +0100 Subject: [PATCH 587/793] adding easyconfigs: CAT-BAT-5.2.3-GCC-10.3.0.eb --- .../c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb new file mode 100644 index 00000000000..20b588f3e11 --- /dev/null +++ b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb @@ -0,0 +1,48 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'Tarball' + +name = 'CAT-BAT' +version = '5.2.3' + +homepage = 'https://github.com/dutilh/CAT' +description = """Tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs).""" +# software_license = 'LicenseMIT' + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/dutilh/CAT/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['19a8eb28c0ebd3fc5a04b006d305a916dd1af00a32b70d2f30df35f32ca2929b'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('DIAMOND', '2.0.13'), + ('prodigal', '2.6.3'), +] + +postinstallcmds = ["cd %(installdir)s/ && ln -s CAT_pack bin && " + "chmod a+rx %(installdir)s/CAT_pack/*.py && " + "sed -i 's@/usr/bin/env/ python3@/usr/bin/env python3@' " + "%(installdir)s/CAT_pack/check.py"] + +sanity_check_paths = { + 'files': ['CAT_pack/CAT', 'README.md'], + 'dirs': ['CAT_pack'], +} + +modextrapaths = { + 'PATH': '', +} + +sanity_check_commands = ["CAT --help"] + +moduleclass = 'bio' From 3e5ad955853e91bd8fee4cfd83c76779def2febc Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 12:28:40 +0100 Subject: [PATCH 588/793] Fix install cmd + Remove empty line + Dont test bin/ dir already tested --- .../easyconfigs/g/Godon/Godon-20210913-x86_64.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb b/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb index 576e9b6362d..7014125e51c 100644 --- a/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb +++ b/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb @@ -23,18 +23,19 @@ description = """Godon is codon models software written in Go.""" toolchain = SYSTEM source_urls = ['https://bitbucket.org/Davydov/godon/downloads'] -sources = ['godon-master-linux-gnu-x86_64'] +sources = [{ + 'download_filename': 'godon-master-linux-gnu-x86_64', + 'filename': 'godon', +}] checksums = ['159058f7577093548f3ced1540d1ff9fd5f7915cdfcb8f8cd7fb40f5c202fcca'] - extract_sources = False -postinstallcmds = ["mkdir -p %(installdir)s/bin/ && cd %(installdir)s/bin/ && " - "ln -s ../godon-master-linux-gnu-x86_64 godon"] +install_cmd = "mkdir -p %(installdir)s/bin/ && mv godon %(installdir)s/bin/" sanity_check_paths = { 'files': ["bin/godon"], - 'dirs': ['bin'], + 'dirs': [], } sanity_check_commands = ["godon --help"] From 6ee549a5cf2a9b1d30e4e8b69786b57a1dc0fad7 Mon Sep 17 00:00:00 2001 From: eb-test Date: Tue, 8 Nov 2022 12:55:52 +0100 Subject: [PATCH 589/793] include tqdm as extension in the idemux bundle to avoid multivariant deps on GCCcore-10.2.0 --- .../easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb index d156b3c22fc..2b39682fdb8 100644 --- a/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb @@ -19,15 +19,17 @@ builddependencies = [ dependencies = [ ('Python', '3.8.6'), ('coverage', '5.5'), - ('tqdm', '4.60.0'), ] use_pip = True exts_list = [ ('pytest-runner', '5.3.0', { - 'checksums': ['ca3f58ff4957e8be6c54c55d575b235725cbbcf4dc0d5091c29c6444cfc8a5fe'], 'modulename': 'ptr', + 'checksums': ['ca3f58ff4957e8be6c54c55d575b235725cbbcf4dc0d5091c29c6444cfc8a5fe'], + }), + ('tqdm', '4.60.0', { + 'checksums': ['ebdebdb95e3477ceea267decfc0784859aa3df3e27e22d23b83e9b272bf157ae'], }), (name, version, { 'checksums': ['590980baaf810c8a02705efd50eb4ace644c360470fc3dc4491d077bbb6b26fc'], From 3f68011737a67fa7a0e1187f937ef408406e2b9e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 14:06:41 +0100 Subject: [PATCH 590/793] Remove useless buildrequirements + Add missing minimap2 requirement --- .../n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb index a6b362f5ae5..fe176ac7b26 100644 --- a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb @@ -13,31 +13,26 @@ version = '1.2.1' homepage = 'https://github.com/wdecoster/nanolyse' description = """Remove reads mapping to the lambda phage genome from a fastq file.""" +software_license = 'LicenseGPLv3' toolchain = {'name': 'foss', 'version': '2021a'} builddependencies = [ ('binutils', '2.36.1'), - ('CMake', '3.20.1'), - ('make', '4.3'), - ('Check', '0.15.2'), - ('SWIG', '4.0.2'), - ('expat', '2.2.9'), - ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), ] dependencies = [ ('Python', '3.9.5'), ('Biopython', '1.79'), + ('minimap2', '2.20'), ] use_pip = True # Fetch the tar.gz, not the whl files! exts_list = [ - ('mappy', '2.24', { - 'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'], + ('mappy', '2.20', { + 'checksums': ['00c8720783ac982b514b01b86349ede9809eeaccdf1328acb5a16dfeef51458b'], }), ('NanoLyse', '1.2.1', { 'checksums': ['933ee668da805fc9ec9fa86c9fca81a073438d45b5f64e23cf606c01e715b1d5'], From ee0deec486b0c0b1b2f976ef15ed3d96e0c4a1c5 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 14:35:16 +0100 Subject: [PATCH 591/793] Remove useless buildrequirements --- easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb index fe176ac7b26..b31eb661ab9 100644 --- a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb @@ -17,10 +17,6 @@ software_license = 'LicenseGPLv3' toolchain = {'name': 'foss', 'version': '2021a'} -builddependencies = [ - ('binutils', '2.36.1'), -] - dependencies = [ ('Python', '3.9.5'), ('Biopython', '1.79'), From ce4fe5319f93754c1005cef4e927d338322174c4 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 14:53:39 +0100 Subject: [PATCH 592/793] Use postinstall cmd list + Use fix_perl_shebang_for + Test if testInput/ exists + Test outside of the install dir --- .../InParanoid-5.0.79d8e39-GCC-10.3.0.eb | 38 +++++++++---------- 1 file changed, 17 insertions(+), 21 deletions(-) diff --git a/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb index 61194783a6d..5bfa4ca673a 100644 --- a/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb @@ -21,8 +21,6 @@ source_urls = ['https://bitbucket.org/sonnhammergroup/inparanoid/get/'] sources = ['79d8e39bb243d403ce57b699c1ae104a8a640389.tar.gz'] checksums = ['efe1a35bbb70608385780c4bf62969a29c46dd8132fbe472034422d23ad4b0c2'] # for commit 79d8e39 -builddependencies = [('binutils', '2.36.1')] - # NOTE some dependencies are not listed on the web site such as Java! dependencies = [ ('Perl', '5.32.1'), # brings libmoose-perl and libparallel-forkmanager-perl @@ -33,33 +31,31 @@ dependencies = [ ] # NOTE inparanoid.pl uses only local (same directory) paths, so patch it -postinstallcmds = ["rm -rf %(installdir)s/docker/ %(installdir)s/singularity/ && " - "chmod a+rx %(installdir)s/*.pl && " - "chmod -x %(installdir)s/*.jar && " - "perl -i -pe 's|helpfile = \"help\"|helpfile = \"%(installdir)s/help\"|' " - "%(installdir)s/inparanoid.pl && " - "perl -i -pe 's|seqstat = \"|seqstat = \"%(installdir)s/|' " - "%(installdir)s/inparanoid.pl && " - "perl -i -pe 's|blastParser = \"|blastParser = \"%(installdir)s/|' " - "%(installdir)s/inparanoid.pl && " - "perl -i -pe 's|diamondParser = \"|diamondParser = \"%(installdir)s/|' " - "%(installdir)s/inparanoid.pl && " - "perl -i -pe 's|copy\(\"\./|copy\(\"%(installdir)s/|' " - "%(installdir)s/inparanoid.pl && " - "perl -i -pe 's|\./\$blastParser|\$blastParser|g' " - "%(installdir)s/inparanoid.pl && " - "perl -i -pe 's|#!.*perl|#!/usr/bin/env perl|' %(installdir)s/*.pl"] +postinstallcmds = [ + "rm -rf %(installdir)s/docker/ %(installdir)s/singularity/", + "chmod a+rx %(installdir)s/*.pl", + "chmod -x %(installdir)s/*.jar", + "perl -i -pe 's|helpfile = \"help\"|helpfile = \"%(installdir)s/help\"|' %(installdir)s/inparanoid.pl", + "perl -i -pe 's|seqstat = \"|seqstat = \"%(installdir)s/|' %(installdir)s/inparanoid.pl", + "perl -i -pe 's|blastParser = \"|blastParser = \"%(installdir)s/|' %(installdir)s/inparanoid.pl", + "perl -i -pe 's|diamondParser = \"|diamondParser = \"%(installdir)s/|' %(installdir)s/inparanoid.pl", + "perl -i -pe 's|copy\(\"\./|copy\(\"%(installdir)s/|' %(installdir)s/inparanoid.pl", + "perl -i -pe 's|\./\$blastParser|\$blastParser|g' %(installdir)s/inparanoid.pl", +] + +fix_perl_shebang_for = ['*.pl'] sanity_check_paths = { 'files': ['inparanoid.pl', 'blast_parser.pl', 'diamondParser.pl'], - 'dirs': ['matrices'], + 'dirs': ['matrices', 'testInput'], } modextrapaths = { 'PATH': '', } -sanity_check_commands = ["inparanoid.pl -input-dir %(installdir)s/testInput/ && " - "rm -Rf %(installdir)s/output/"] +sanity_check_commands = [ + "cd %(builddir)s && inparanoid.pl -input-dir %(installdir)s/testInput/", +] moduleclass = 'bio' From 931102f16450a7734781e26800043cb245d7c4f5 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 15:10:45 +0100 Subject: [PATCH 593/793] Remove useless builddependencies --- .../p/PyDamage/PyDamage-0.70-foss-2021a.eb | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb b/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb index 45477aba7e9..c2ff6ff71da 100644 --- a/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb @@ -21,17 +21,6 @@ software_license = 'LicenseGPLv3' toolchain = {'name': 'foss', 'version': '2021a'} -builddependencies = [ - ('binutils', '2.36.1'), - ('CMake', '3.20.1'), - ('make', '4.3'), - ('Check', '0.15.2'), - ('SWIG', '4.0.2'), - ('expat', '2.2.9'), - ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), -] - dependencies = [ ('Python', '3.9.5'), ('Biopython', '1.79'), From ab1ac7f2f6f502670404cc6a381cc4eb927f508b Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 15:22:49 +0100 Subject: [PATCH 594/793] Remove useless buildrequirements + Use postinstallcmds list + Remove useless PATH extension --- .../c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb index 20b588f3e11..6707fbe1fc7 100644 --- a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb @@ -21,28 +21,23 @@ source_urls = ['https://github.com/dutilh/CAT/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] checksums = ['19a8eb28c0ebd3fc5a04b006d305a916dd1af00a32b70d2f30df35f32ca2929b'] -builddependencies = [('binutils', '2.36.1')] - dependencies = [ ('Python', '3.9.5'), ('DIAMOND', '2.0.13'), ('prodigal', '2.6.3'), ] -postinstallcmds = ["cd %(installdir)s/ && ln -s CAT_pack bin && " - "chmod a+rx %(installdir)s/CAT_pack/*.py && " - "sed -i 's@/usr/bin/env/ python3@/usr/bin/env python3@' " - "%(installdir)s/CAT_pack/check.py"] +postinstallcmds = [ + "cd %(installdir)s/ && ln -s CAT_pack bin", + "chmod a+rx %(installdir)s/CAT_pack/*.py", + "sed -i 's@/usr/bin/env/ python3@/usr/bin/env python3@' %(installdir)s/CAT_pack/check.py", +] sanity_check_paths = { 'files': ['CAT_pack/CAT', 'README.md'], 'dirs': ['CAT_pack'], } -modextrapaths = { - 'PATH': '', -} - sanity_check_commands = ["CAT --help"] moduleclass = 'bio' From 73e4fa376f981612261e656a0101bc52eccbe3ab Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 15:48:32 +0100 Subject: [PATCH 595/793] Use version in binary name --- easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb b/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb index 7014125e51c..aa401a18c4f 100644 --- a/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb +++ b/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb @@ -25,13 +25,14 @@ toolchain = SYSTEM source_urls = ['https://bitbucket.org/Davydov/godon/downloads'] sources = [{ 'download_filename': 'godon-master-linux-gnu-x86_64', - 'filename': 'godon', + 'filename': 'godon-%(version)s-linux-gnu-x86_64', }] checksums = ['159058f7577093548f3ced1540d1ff9fd5f7915cdfcb8f8cd7fb40f5c202fcca'] extract_sources = False -install_cmd = "mkdir -p %(installdir)s/bin/ && mv godon %(installdir)s/bin/" +install_cmd = "mkdir -p %(installdir)s/bin/ && cp -a godon-%(version)s-linux-gnu-x86_64 %(installdir)s/bin/ && " +install_cmd += "cd %(installdir)s/bin && ln -s godon-%(version)s-linux-gnu-x86_64 godon" sanity_check_paths = { 'files': ["bin/godon"], From 629be09f0cbcff3655396ddbf63e1d7b7c77c2a9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 8 Nov 2022 15:47:37 +0000 Subject: [PATCH 596/793] Add HiCcompare and dependencies --- ...le-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 33 ++++++++++++------- 1 file changed, 21 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index db12f43dc2b..d34e406d5d8 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -222,9 +222,9 @@ exts_list = [ ('Rgraphviz', '2.40.0', { 'patches': ['Rgraphviz-2.28.0_fno-tree-vectorize.patch'], 'checksums': [ - '94a4ce168efe39046fe10e2d75a9e459158716b4ef6ef977a0ced725f871cee4', # Rgraphviz_2.40.0.tar.gz - # Rgraphviz-2.28.0_fno-tree-vectorize.patch - '15783e9daba6f63c8e655858468a99e9f4f088468dbe3b414825e5844cf6b4a9', + {'Rgraphviz_2.40.0.tar.gz': '94a4ce168efe39046fe10e2d75a9e459158716b4ef6ef977a0ced725f871cee4'}, + {'Rgraphviz-2.28.0_fno-tree-vectorize.patch': + '15783e9daba6f63c8e655858468a99e9f4f088468dbe3b414825e5844cf6b4a9'}, ], }), ('RNASeqPower', '1.36.0', { @@ -443,17 +443,17 @@ exts_list = [ ('dada2', '1.24.0', { 'patches': ['dada2-1.16.0-remove-sse-on-aarch64.patch'], 'checksums': [ - '9dd083928fc06d53cdb0a2e2d35be7c304fac74a300f8d3c3026022859b5725b', # dada2_1.24.0.tar.gz - # dada2-1.16.0-remove-sse-on-aarch64.patch - 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935', + {'dada2_1.24.0.tar.gz': '9dd083928fc06d53cdb0a2e2d35be7c304fac74a300f8d3c3026022859b5725b'}, + {'dada2-1.16.0-remove-sse-on-aarch64.patch': + 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935'}, ], }), ('LEA', '3.8.0', { 'patches': ['LEA-3.0.0_support_aarch64_and_ppc64le.patch'], 'checksums': [ - 'c0fd5b5a66aff94d65b8961409c226966aa96a02eb7d1e9a9e75382226e5b774', # LEA_3.8.0.tar.gz - # LEA-3.0.0_support_aarch64_and_ppc64le.patch - 'caeaae7aa0577540bc9c03b54ce5a0fe4ff1a28ac503106e2b3acd1b9db82881', + {'LEA_3.8.0.tar.gz': 'c0fd5b5a66aff94d65b8961409c226966aa96a02eb7d1e9a9e75382226e5b774'}, + {'LEA-3.0.0_support_aarch64_and_ppc64le.patch': + 'caeaae7aa0577540bc9c03b54ce5a0fe4ff1a28ac503106e2b3acd1b9db82881'}, ], }), ('tximport', '1.24.0', { @@ -720,9 +720,9 @@ exts_list = [ ('RProtoBufLib', '2.8.0', { 'patches': ['RProtoBufLib-2.8.0_fix-protobuf-build.patch'], 'checksums': [ - 'f7160c1623f50f0e23d14e7e99a2e6c018186871f7f1f68c9171031f6ae678d7', # RProtoBufLib_2.8.0.tar.gz - # RProtoBufLib-2.8.0_fix-protobuf-build.patch - '8775d74e2288000c57575f4ef45a875b4a377ac02f89efa947699ea786bedf64', + {'RProtoBufLib_2.8.0.tar.gz': 'f7160c1623f50f0e23d14e7e99a2e6c018186871f7f1f68c9171031f6ae678d7'}, + {'RProtoBufLib-2.8.0_fix-protobuf-build.patch': + '8775d74e2288000c57575f4ef45a875b4a377ac02f89efa947699ea786bedf64'}, ], }), ('cytolib', '2.8.0', { @@ -1086,6 +1086,15 @@ exts_list = [ ('SPOTlight', '1.0.0', { 'checksums': ['f6baf718e468292960884a1aacdf8295f0864d771f5eb0f2088fb9a1bc00dcc0'], }), + ('CGHcall', '2.58.0', { + 'checksums': ['c5e86b9234685462b7330c85b91ca648a801a76c99f3e98cd509ac47ee8afae2'], + }), + ('QDNAseq', '1.32.0', { + 'checksums': ['75bbde9b6cc55cd6a47b9f466358033a180b480def2144abdcc93a2a8e066668'], + }), + ('HiCcompare', '1.18.0', { + 'checksums': ['b9320fa7a9f10832e2ac7ade0245f85ac4c2c26edef2580078888f5e1050ee2d'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 09d88f791a5e9a6659f4ab7a76a4f9b1d8b24d41 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 17:11:16 +0100 Subject: [PATCH 597/793] adding easyconfigs: pullseq-1.0.2-GCCcore-10.3.0.eb --- .../p/pullseq/pullseq-1.0.2-GCCcore-10.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..bd94483da59 --- /dev/null +++ b/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'pullseq' +version = '1.0.2' + +homepage = 'https://github.com/bcthomas/pullseq' +description = "Utility program for extracting sequences from a fasta/fastq file" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/bcthomas/pullseq/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['a295d7e0e2d64ed05d293d795d1716376707e465f2c42ede6454f27db586c85f'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Autotools', '20210128'), +] +dependencies = [ + ('PCRE', '8.44'), +] + +preconfigopts = "./bootstrap && " + +buildopts = 'CFLAGS="$CFLAGS -fcommon"' + +sanity_check_paths = { + 'files': ['bin/pullseq', 'bin/seqdiff'], + 'dirs': [], +} + +sanity_check_commands = [ + "pullseq --help 2>&1 | grep 'pullseq - a bioinformatics tool'", + "seqdiff --help 2>&1 | grep 'seqdiff - a bioinformatics tool'", +] + +moduleclass = 'bio' From fe12a8b8778e44b8765d8b97ead5176f1b84e1fc Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 17:12:16 +0100 Subject: [PATCH 598/793] adding easyconfigs: IDBA-UD-1.1.3-GCC-10.3.0.eb --- .../i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.3.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.3.0.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.3.0.eb new file mode 100644 index 00000000000..6b69859e259 --- /dev/null +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.3.0.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Updated: Pavel Grochal (INUITS) +# License: GPLv2 + +# "make install" doesnt copy all the compiled binaries so we use the "MakeCp" easyblock +# to be sure everything is copied and we run ./configure in prebuildopts + +# modified by Tom Strempel +easyblock = 'MakeCp' + +name = 'IDBA-UD' +version = '1.1.3' + +homepage = 'https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/' +description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads +Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. +IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth +contigs are removed iteratively with cutoff threshold from low to high to reduce the errors +in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled +locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD +can iterate k value of de Bruijn graph to a very large value with less gaps and less branches +to form long contigs in both low-depth and high-depth regions.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/loneknightpy/idba/releases/download/%(version)s'] +sources = ['idba-%(version)s.tar.gz'] +checksums = ['030e24463c6d725c1c202baabf773b605b51e310844fd0f27f4688ecfbae26d0'] + +prebuildopts = './configure && ' + +# we delete every .o and Makefile file which is left in bin folder +buildopts = ' && rm -fr bin/*.o bin/Makefile*' + +files_to_copy = ["bin", "script", "ChangeLog", "NEWS"] + +pretestopts = "cd test && " +runtest = "check" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran", + "idba_ud", "parallel_blat", "idba_tran_test"]], + 'dirs': [""], +} + +moduleclass = 'bio' From 2ee8b1f495828d5a226a4dabd775c8ed35a00ab2 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 17:13:18 +0100 Subject: [PATCH 599/793] adding easyconfigs: FragGeneScan-1.31-GCCcore-10.3.0.eb --- .../FragGeneScan-1.31-GCCcore-10.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..4870fb3bdfa --- /dev/null +++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'FragGeneScan' +version = '1.31' + +homepage = 'https://omics.informatics.indiana.edu/FragGeneScan/' +description = "FragGeneScan is an application for finding (fragmented) genes in short reads." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s%(version)s.tar.gz'] +checksums = ['cd3212d0f148218eb3b17d24fcd1fc897fb9fee9b2c902682edde29f895f426c'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [("Perl", "5.32.1")] + +fix_perl_shebang_for = ['*.pl'] + +prebuildopts = "make clean && " +buildopts = 'CC="$CC" CFLAG="$CFLAGS" fgs && chmod -R go+rx *.pl train example' + +files_to_copy = ['FragGeneScan', 'run_FragGeneScan.pl', 'example', 'train'] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['FragGeneScan', 'run_FragGeneScan.pl'], + 'dirs': ['example', 'train'], +} + +sanity_check_commands = [ + './run_FragGeneScan.pl help', + './run_FragGeneScan.pl -genome=./example/NC_000913.fna -out=./example/NC_000913-fgs -complete=1 -train=complete' +] + +moduleclass = 'bio' From 79d2a7ababdee961b9316a5c7d938dc14827b96c Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 17:30:10 +0100 Subject: [PATCH 600/793] adding easyconfigs: SSW-1.1-GCCcore-10.3.0.eb --- .../s/SSW/SSW-1.1-GCCcore-10.3.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f8abd16d82d --- /dev/null +++ b/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.3.0.eb @@ -0,0 +1,48 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'SSW' +version = '1.1' + +homepage = 'https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library' +description = """SSW is a fast implementation of the Smith-Waterman algorithm, which uses the + Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the + instruction level. SSW library provides an API that can be flexibly used by programs written in + C, C++ and other languages. We also provide a software that can do protein and genome alignment + directly. Current version of our implementation is ~50 times faster than an ordinary + Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path + (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and + location heuristically. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.1_build-cpp-lib.patch'] +checksums = [ + 'cdbc20740daeb188ed39413ea5ff9ae4cf72c4d7ccff1d2de2cac0446d64d99f', # v1.1.tar.gz + 'fe0d1f536ecd526dda8879b2f41b62c3c82b39d236f023ee735c1c18d584f06a', # SSW-1.1_build-cpp-lib.patch +] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('zlib', '1.2.11')] + +start_dir = 'src' + +buildopts = 'default' + +files_to_copy = [ + (['ssw_test'], 'bin'), + (['*.%s*' % SHLIB_EXT], 'lib'), + (['*.h'], 'include/ssw'), +] + +sanity_check_paths = { + 'files': ['bin/ssw_test', 'lib/libssw.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 50ebf6f6d3dd2e38a69642179c28121ea1c97578 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 17:33:12 +0100 Subject: [PATCH 601/793] adding easyconfigs: fermi-lite-20190320-GCCcore-10.3.0.eb --- .../fermi-lite-20190320-GCCcore-10.3.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..6daf5a68037 --- /dev/null +++ b/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.3.0.eb @@ -0,0 +1,46 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'fermi-lite' +version = '20190320' +local_commit = 'b499514' + +homepage = 'https://github.com/lh3/fermi-lite' +description = """Standalone C library for assembling Illumina short reads in small regions.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = [ + '%(name)s-20190320_avoid-bwa-namespace-conflict.patch', + '%(name)s-20190320_build-shared-lib.patch', +] +checksums = [ + 'ea1230e298b8e7193a996b5aceeff7fea44ef00852b0b87d4fcb504bdca0e712', # b499514.tar.gz + # fermi-lite-20190320_avoid-bwa-namespace-conflict.patch + '27600733f1cea8b1d1503b1a67b9d41526e907c1b6321313ff51194e166c1842', + '43398559fbb3910d6d3d1a41af3fb16bf8f26bd7cc34176dfc9a068a551c3f50', # fermi-lite-20190320_build-shared-lib.patch +] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('zlib', '1.2.11')] + +prebuildopts = 'CFLAGS="$CFLAGS -fcommon"' + +files_to_copy = [ + (['fml-asm'], 'bin'), + (['*.a', '*.%s*' % SHLIB_EXT], 'lib'), + (['*.h'], 'include/fml'), + 'test', +] + +sanity_check_paths = { + 'files': ['bin/fml-asm', 'lib/libfml.a', 'lib/libfml.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From 143e7ae01b8298310d9b79667fe7e979aa8d1ef9 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 8 Nov 2022 20:55:07 +0100 Subject: [PATCH 602/793] adding easyconfigs: CMake-3.24.3-GCCcore-11.3.0.eb --- .../c/CMake/CMake-3.24.3-GCCcore-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d5b6ac8b205 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +name = 'CMake' +version = '3.24.3' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b53aa10fa82bff84ccdb59065927b72d3bee49f4d86261249fc0984b3b367291'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('cURL', '7.83.0'), + ('libarchive', '3.6.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +moduleclass = 'devel' From ae07a8f91ee2a5a1c4b720658ec2fc1fcd369551 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Nov 2022 22:32:24 +0100 Subject: [PATCH 603/793] {tools}[GCCcore/12.2.0] XZ v5.2.7 --- .../easyconfigs/g/gettext/gettext-0.21.1.eb | 39 +++++++++++++++++++ .../x/XZ/XZ-5.2.7-GCCcore-12.2.0.eb | 37 ++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.21.1.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.7-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21.1.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21.1.eb new file mode 100644 index 00000000000..9525991ab15 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21.1.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.21.1' + +homepage = 'https://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +# This is a basic stripped down version of gettext without any +# dependencies on other packages used as initial builddep for XZ +# It is the first step in the cyclic dependency chain of +# XZ -> libxml2 -> gettext -> XZ + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e8c3650e1d8cee875c4f355642382c1df83058bd5a11ee8555c0cf276d646d45'] + +dependencies = [ + ('ncurses', '6.3'), +] + +configopts = '--without-emacs --with-included-libxml --without-xz --without-bzip2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.7-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2942a648d38 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.7-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.7' + +homepage = 'https://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://tukaani.org/xz/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b65f1d0c2708e57716f4dd2216989a73847ac6fdb4168ffceb155767e22b834b'] + +builddependencies = [ + # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.21.1', '', SYSTEM), + ('binutils', '2.39'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ['bin/lzmainfo', 'bin/unxz', 'bin/xz'], + 'dirs': [] +} + +sanity_check_commands = [ + "xz --help", + "unxz --help", +] + +moduleclass = 'tools' From 5c72c29cf95f639526b7bf4a98a508dc018b365f Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 09:19:27 +0100 Subject: [PATCH 604/793] adding easyconfigs: MaxBin-2.2.7-gompi-2021a.eb --- .../m/MaxBin/MaxBin-2.2.7-gompi-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021a.eb diff --git a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021a.eb b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021a.eb new file mode 100644 index 00000000000..338bf18f42b --- /dev/null +++ b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021a.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'MaxBin' +version = '2.2.7' + +# https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html doesn't work +homepage = 'https://sourceforge.net/projects/maxbin/' +description = """MaxBin is software for binning assembled metagenomic sequences +based on an Expectation-Maximization algorithm.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['cb6429e857280c2b75823c8cd55058ed169c93bc707a46bde0c4383f2bffe09e'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Perl', '5.32.1'), + ('Bowtie2', '2.4.4'), + ('FragGeneScan', '1.31'), + ('HMMER', '3.3.2'), + ('IDBA-UD', '1.1.3'), +] + +prebuildopts = "cd src && " + +files_to_copy = ['*'] + +fix_perl_shebang_for = ['run_MaxBin.pl'] + +sanity_check_paths = { + 'files': ['run_MaxBin.pl', 'src/MaxBin'], + 'dirs': [], +} + +modextrapaths = {'PATH': ['', 'src']} + +moduleclass = 'bio' From 54362da083f45edc31479bd1ab614bff278f0250 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 09:24:51 +0100 Subject: [PATCH 605/793] adding easyconfigs: DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb --- .../DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..12a3da12443 --- /dev/null +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb @@ -0,0 +1,59 @@ +easyblock = 'Tarball' + +name = 'DAS_Tool' +version = '1.1.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/cmks/DAS_Tool' +description = """DAS Tool is an automated method that integrates the results of a flexible number of binning + algorithms to calculate an optimized, non-redundant set of bins from a single assembly.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/cmks/DAS_Tool/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch'] +checksums = [ + '2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a', # 1.1.1.tar.gz + 'dc89e6ab7129d170d24da28720cec0937b4d958b5ae46049373d57dde8b8a27a', # DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch +] + +dependencies = [ + ('R', '4.1.0'), + ('Python', '3.9.5'), + ('Ruby', '3.0.1'), + ('pullseq', '1.0.2'), + ('prodigal', '2.6.3'), + ('BLAST+', '2.11.0'), +] + +exts_defaultclass = 'RPackage' + +exts_list = [ + (name, version, { + 'modulename': 'DASTool', + 'source_tmpl': 'DASTool_%(version)s.tar.gz', + 'source_urls': ['https://github.com/cmks/DAS_Tool/raw/%(version)s/package/'], + 'checksums': ['8d33997baaaec00d253b2d749cf1ace004ccdea2275b763d4d0f1c969916b72b'], + }), +] + +postinstallcmds = [ + "cd %(installdir)s; unzip db.zip", + "chmod a+x %(installdir)s/DAS_Tool", +] + +sanity_check_paths = { + 'files': ['DAS_Tool', 'arc.all.faa', 'arc.scg.lookup'], + 'dirs': ['DASTool/R'], +} + +sanity_check_commands = ['DAS_Tool -h | grep "DAS Tool version %s"' % version] +# Help gets printed correctly, but the error code is 1 + +modextrapaths = { + 'PATH': '', + 'R_LIBS_SITE': '', +} + +moduleclass = 'bio' From e71706e9dd6b6e09e219cffb16ff75435eddb9cc Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 09:40:14 +0100 Subject: [PATCH 606/793] Add comment for the shebang fix + Test bin/CAT symlink --- easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb index 6707fbe1fc7..12d6688ec5a 100644 --- a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb @@ -30,11 +30,12 @@ dependencies = [ postinstallcmds = [ "cd %(installdir)s/ && ln -s CAT_pack bin", "chmod a+rx %(installdir)s/CAT_pack/*.py", + # fix shebang in check.py script ('/env/' should be '/env') "sed -i 's@/usr/bin/env/ python3@/usr/bin/env python3@' %(installdir)s/CAT_pack/check.py", ] sanity_check_paths = { - 'files': ['CAT_pack/CAT', 'README.md'], + 'files': ['CAT_pack/CAT', 'bin/CAT', 'README.md'], 'dirs': ['CAT_pack'], } From ae21dff077b8bc7fa0551fb94f3ad0a726d41495 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 09:48:00 +0100 Subject: [PATCH 607/793] adding easyconfigs: MetaBAT-2.15-gompi-2021a.eb --- .../m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb new file mode 100644 index 00000000000..a94f4f9953a --- /dev/null +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'MetaBAT' +version = '2.15' + +homepage = 'https://bitbucket.org/berkeleylab/metabat' +description = "An efficient tool for accurately reconstructing single genomes from complex microbial communities" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Perl', '5.32.1'), + ('Boost', '1.76.0'), + ('zlib', '1.2.11'), + ('SAMtools', '1.13'), + ('XZ', '5.2.5'), + ('bzip2', '1.0.8'), +] + +fix_perl_shebang_for = ['bin/*.pl'] + +prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " + +sanity_check_paths = { + 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], + 'dirs': [""], +} + +moduleclass = 'bio' From ccc288eca099a7be7cdb8e893ae776dd3007b65e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 09:53:09 +0100 Subject: [PATCH 608/793] adding easyconfigs: MEGAHIT-1.2.9-GCCcore-10.3.0.eb --- .../m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..279dcf61042 --- /dev/null +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'MEGAHIT' +version = '1.2.9' + +homepage = 'https://github.com/voutcn/megahit' +description = """An ultra-fast single-node solution for large and complex +metagenomics assembly via succinct de Bruijn graph""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/voutcn/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['09026eb07cc4e2d24f58b0a13f7a826ae8bb73da735a47cb1cbe6e4693118852'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('bzip2', '1.0.8'), + ('gzip', '1.10'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%(namelower)s', + 'bin/%(namelower)s_core', + 'bin/%(namelower)s_core_no_hw_accel', + 'bin/%(namelower)s_core_popcnt', + 'bin/%(namelower)s_toolkit', + ], + 'dirs': [], +} + +sanity_check_commands = [ + "megahit --version", + "megahit --test", +] + +moduleclass = 'bio' From 4b5d1b297e33663fbba1e6ba9d92012874f65491 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 10:02:35 +0100 Subject: [PATCH 609/793] Rename file on download + Better version string --- ...9-GCC-10.3.0.eb => InParanoid-5.0-20220607-GCC-10.3.0.eb} | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/i/InParanoid/{InParanoid-5.0.79d8e39-GCC-10.3.0.eb => InParanoid-5.0-20220607-GCC-10.3.0.eb} (92%) diff --git a/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0-20220607-GCC-10.3.0.eb similarity index 92% rename from easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb rename to easybuild/easyconfigs/i/InParanoid/InParanoid-5.0-20220607-GCC-10.3.0.eb index 5bfa4ca673a..97e0d20fb04 100644 --- a/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0-20220607-GCC-10.3.0.eb @@ -9,7 +9,8 @@ easyblock = 'Tarball' name = 'InParanoid' -version = '5.0.79d8e39' +version = '5.0-20220607' +local_commit = '79d8e39bb243d403ce57b699c1ae104a8a640389' homepage = 'https://inparanoid.sbc.su.se' description = """InParanoid: ortholog groups with inparalogs.""" @@ -18,7 +19,7 @@ software_license = 'LicenseGPLv3' toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://bitbucket.org/sonnhammergroup/inparanoid/get/'] -sources = ['79d8e39bb243d403ce57b699c1ae104a8a640389.tar.gz'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] checksums = ['efe1a35bbb70608385780c4bf62969a29c46dd8132fbe472034422d23ad4b0c2'] # for commit 79d8e39 # NOTE some dependencies are not listed on the web site such as Java! From ddbbb99b4554786f94cdc18bc15a84f28b09c540 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 14:36:38 +0100 Subject: [PATCH 610/793] adding easyconfigs: typing-extensions-4.3.0-GCCcore-10.3.0.eb --- .../typing-extensions-4.3.0-GCCcore-10.3.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..d62b98215f8 --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '4.3.0' + +homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' +description = 'Typing Extensions - Backported and Experimental Type Hints for Python' + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '3.9.5')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From 29b4e32d07b930856f8c5fdac6fe5ca882efbbd1 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 9 Nov 2022 15:46:39 +0100 Subject: [PATCH 611/793] adding easyconfigs: Seaborn-0.12.1-foss-2022a.eb --- .../s/Seaborn/Seaborn-0.12.1-foss-2022a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.1-foss-2022a.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.1-foss-2022a.eb new file mode 100644 index 00000000000..e3f97801473 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.1-foss-2022a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.12.1' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bb1eb1d51d3097368c187c3ef089c0288ec1fe8aa1c69fb324c68aa1d02df4c1'] + +dependencies = [ + ('Python', '3.10.4'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' From 601a39e5412437b1ef3c1358501c3fccbdc2b6d1 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 15:48:32 +0100 Subject: [PATCH 612/793] adding easyconfigs: freebayes-1.3.6-foss-2021a-R-4.1.0.eb, vcflib-1.0.3-foss-2021a-R-4.1.0.eb, SeqLib-1.2.0-GCC-10.3.0.eb --- .../freebayes-1.3.6-foss-2021a-R-4.1.0.eb | 54 +++++++++++++++ .../s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb | 49 +++++++++++++ .../vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb | 69 +++++++++++++++++++ 3 files changed, 172 insertions(+) create mode 100644 easybuild/easyconfigs/f/freebayes/freebayes-1.3.6-foss-2021a-R-4.1.0.eb create mode 100644 easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.6-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.6-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..cc4ea323667 --- /dev/null +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.6-foss-2021a-R-4.1.0.eb @@ -0,0 +1,54 @@ +easyblock = 'MesonNinja' + +name = 'freebayes' +version = '1.3.6' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/freebayes/freebayes' +description = "Bayesian haplotype-based genetic polymorphism discovery and genotyping." + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-1.3.6_find-external-libs.patch', + '%(name)s-1.3.5_fix-includes.patch', + '%(name)s-1.3.6_install-libs-headers.patch', +] +checksums = [ + 'd668c0b433cc0f11498ace10e48d72a7f0f40ca23b391b72e975ffafd1c13044', # v1.3.6.tar.gz + '4836a9ceaa9044e6e66b3ca0387b058a5e0505ddeaa62c428b526b5e234aff3b', # freebayes-1.3.6_find-external-libs.patch + '4c6c74b30bf3b2f04b8a50bbdef26e74f6e2412f3efbd81512226e557c2a53d1', # freebayes-1.3.5_fix-includes.patch + '5ba006ca6956905bbd81107a17e02287c515890ee25884c444ebf5b95da1caae', # freebayes-1.3.6_install-libs-headers.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('R', '4.1.0'), + ('parallel', '20210622'), + ('libffi', '3.3'), + ('VCFtools', '0.1.16'), + ('vcflib', '1.0.3', versionsuffix), + ('SeqLib', '1.2.0'), +] + +configopts = "--buildtype release" + +sanity_check_paths = { + 'files': ['bin/freebayes', 'bin/bamleftalign', 'scripts/freebayes-parallel'], + 'dirs': [], +} + +sanity_check_commands = ["freebayes --help"] + +modextrapaths = {'PATH': ['scripts']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..21b5647395b --- /dev/null +++ b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb @@ -0,0 +1,49 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'SeqLib' +version = '1.2.0' + +homepage = 'https://github.com/walaj/SeqLib' +description = """C++ interface to HTSlib, BWA-MEM and Fermi.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'walaj' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version_major_minor)s.0_avoid-bwa-fml-namespace-conflict.patch', + '%(name)s-%(version_major_minor)s.0_use-external-deps.patch', +] +checksums = [ + '6892bdb5cae88d8d8acbbfadd351cfa00004bc7c0fd1ae912dc1ff1ccfd61a70', # 1.2.0.tar.gz + # SeqLib-1.2.0_avoid-bwa-fml-namespace-conflict.patch + '9be9229bcf34db8e4bd1fd49614bb55d84c12df263ca7174980f7f4b1bd63da9', + '413f0ad8e0963d8922205d31e0c361cfa98a10f93e7d3e0506e0bed539ec70eb', # SeqLib-1.2.0_use-external-deps.patch +] + +builddependencies = [('Autotools', '20210128')] + +dependencies = [ + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), + ('bzip2', '1.0.8'), + ('JsonCpp', '1.9.4'), + ('BWA', '0.7.17'), + ('HTSlib', '1.12'), + ('fermi-lite', '20190320'), + ('SSW', '1.1'), + ('PCRE', '8.44'), +] + +preconfigopts = "autoreconf -i -f && " + +sanity_check_paths = { + 'files': ['bin/seqtools', 'lib/libseqlib.%s' % SHLIB_EXT], + 'dirs': [], +} +sanity_check_commands = ["seqtools"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..1fd858e08a4 --- /dev/null +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb @@ -0,0 +1,69 @@ +# Author: Jasper Grimm (UoY) +# Updated: Denis Kristak (INUITS) +easyblock = 'CMakeMake' + +name = 'vcflib' +version = '1.0.3' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/vcflib/vcflib' +description = """vcflib provides methods to manipulate and interpret sequence variation as it can be + described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended + to concisely describe reference-indexed genetic variations between individuals.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_use-external-deps.patch', + 'vcflib-1.0.3_fix-shared-linking.patch', +] +checksums = [ + '5fd05f46dc251a56a322809da92c93c85318036aa9ac39a2eefc4fbd39b5df6c', # v1.0.3.tar.gz + '89f99efb35eb3a5fdc5a7fdeb96c204b1af481194bcd788c939c600a985fa8a4', # vcflib-1.0.3_use-external-deps.patch + '2584e33e447c07a66eefc46263161873498910e19035f9beed1600cbd05fd4b0', # vcflib-1.0.3_fix-shared-linking.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Perl', '5.32.1'), + ('R', '4.1.0'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('HTSlib', '1.12'), + ('tabixpp', '1.1.0'), + ('intervaltree', '0.1'), + ('fastahack', '1.0.0'), + ('filevercmp', '20191210'), + ('fsom', '20141119'), + ('multichoose', '1.0.3'), + ('smithwaterman', '20160702'), +] + +preconfigopts = "find %(builddir)s/%(name)s-%(version)s/src -type f -regextype egrep -regex '.*\.(h|cpp)' -exec sed -i" +preconfigopts += " -e 's|SmithWatermanGotoh.h|smithwaterman/SmithWatermanGotoh.h|g'" +preconfigopts += " -e 's|IntervalTree.h|intervaltree/IntervalTree.h|g'" +preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|filevercmp.h|filevercmp/filevercmp.h|g'" +preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" +preconfigopts += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " + +postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] + +modextrapaths = {'PATH': ['scripts']} + +sanity_check_paths = { + 'files': ['bin/vcfannotate', 'bin/vcfcombine', 'lib/libvcflib.%s' % SHLIB_EXT], + 'dirs': ['scripts'], +} + +sanity_check_commands = ["vcfremap"] + +moduleclass = 'bio' From 08832cc28564f07f4ac02d2e0166396122caae1d Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 17:16:19 +0100 Subject: [PATCH 613/793] Update to the last version --- ...re-10.3.0.eb => typing-extensions-4.4.0-GCCcore-10.3.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/t/typing-extensions/{typing-extensions-4.3.0-GCCcore-10.3.0.eb => typing-extensions-4.4.0-GCCcore-10.3.0.eb} (83%) diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.4.0-GCCcore-10.3.0.eb similarity index 83% rename from easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.4.0-GCCcore-10.3.0.eb index d62b98215f8..ea51e13ece0 100644 --- a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.4.0-GCCcore-10.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'typing-extensions' -version = '4.3.0' +version = '4.4.0' homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' description = 'Typing Extensions - Backported and Experimental Type Hints for Python' @@ -9,7 +9,7 @@ description = 'Typing Extensions - Backported and Experimental Type Hints for Py toolchain = {'name': 'GCCcore', 'version': '10.3.0'} sources = ['typing_extensions-%(version)s.tar.gz'] -checksums = ['e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6'] +checksums = ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'] builddependencies = [('binutils', '2.36.1')] From 5781cd9d12fdde97531d3919ed60857da00b9d6f Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 17:51:19 +0100 Subject: [PATCH 614/793] templating the name, but hardcoding the patch version --- easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb | 4 ++-- .../easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb index 21b5647395b..27a50312ce6 100644 --- a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb @@ -14,8 +14,8 @@ github_account = 'walaj' source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] patches = [ - '%(name)s-%(version_major_minor)s.0_avoid-bwa-fml-namespace-conflict.patch', - '%(name)s-%(version_major_minor)s.0_use-external-deps.patch', + '%(name)s-1.2.0_avoid-bwa-fml-namespace-conflict.patch', + '%(name)s-1.2.0_use-external-deps.patch', ] checksums = [ '6892bdb5cae88d8d8acbbfadd351cfa00004bc7c0fd1ae912dc1ff1ccfd61a70', # 1.2.0.tar.gz diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb index 1fd858e08a4..9061ba602b3 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb @@ -16,8 +16,8 @@ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] patches = [ - '%(name)s-%(version)s_use-external-deps.patch', - 'vcflib-1.0.3_fix-shared-linking.patch', + '%(name)s-1.0.3_use-external-deps.patch', + '%(name)s-1.0.3_fix-shared-linking.patch', ] checksums = [ '5fd05f46dc251a56a322809da92c93c85318036aa9ac39a2eefc4fbd39b5df6c', # v1.0.3.tar.gz From 8c9b31f081ea5134b06804aad059bd2d6508637a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 21:18:46 +0100 Subject: [PATCH 615/793] adding easyconfigs: libxml2-2.10.3-GCCcore-12.2.0.eb --- .../libxml2/libxml2-2.10.3-GCCcore-12.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.10.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.10.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.10.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..899bcfe4e7f --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.10.3-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.10.3' + +homepage = 'http://xmlsoft.org/' + +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['5d2cc3d78bec3dbe212a9d7fa629ada25a7da928af432c93060ff5c17ee28a9c'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('XZ', '5.2.7'), + ('zlib', '1.2.12'), +] + +moduleclass = 'lib' From c1c8a42c28f4823a37f93e483f0a044e77353494 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 21:51:53 +0100 Subject: [PATCH 616/793] adding easyconfigs: Python-3.10.8-GCCcore-12.2.0-bare.eb, SQLite-3.39.4-GCCcore-12.2.0.eb, Tcl-8.6.12-GCCcore-12.2.0.eb, libffi-3.4.4-GCCcore-12.2.0.eb, bzip2-1.0.8-GCCcore-12.2.0.eb, UnZip-6.0-GCCcore-12.2.0.eb --- .../b/bzip2/bzip2-1.0.8-GCCcore-12.2.0.eb | 27 ++++++++++ .../l/libffi/libffi-3.4.4-GCCcore-12.2.0.eb | 29 +++++++++++ .../Python-3.10.8-GCCcore-12.2.0-bare.eb | 35 +++++++++++++ .../s/SQLite/SQLite-3.39.4-GCCcore-12.2.0.eb | 39 ++++++++++++++ .../t/Tcl/Tcl-8.6.12-GCCcore-12.2.0.eb | 41 +++++++++++++++ .../u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb | 52 +++++++++++++++++++ 6 files changed, 223 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0-bare.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.39.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.12-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d2ce38e1732 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/%(name)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.39'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f9c248d7fd7 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.4.4' + +homepage = 'https://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libffi/libffi/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d66c56ad259a82cf2a9dfc408b32bf5da52371500b84745f7fb8b645712df676'] + +builddependencies = [ + ('binutils', '2.39'), +] + +configopts = '--disable-exec-static-tramp ' + +sanity_check_paths = { + 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0-bare.eb new file mode 100644 index 00000000000..39fbf14affe --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0-bare.eb @@ -0,0 +1,35 @@ +name = 'Python' +version = '3.10.8' +versionsuffix = '-bare' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['f400c3fb394b8bef1292f6dc1292c5fadc3533039a5bc0c3e885f3e16738029a'] + +builddependencies = [ + ('UnZip', '6.0'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('binutils', '2.39'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.12'), + ('libreadline', '8.2'), + ('ncurses', '6.3'), + ('SQLite', '3.39.4'), + ('XZ', '5.2.7'), + ('libffi', '3.4.4'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +install_pip = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.39.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.39.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..cc6b559ef73 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.39.4-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.39.4' +local_filename_version = '3390400' + +homepage = 'https://www.sqlite.org/' +description = "SQLite: SQL Database Engine in a C Library" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.sqlite.org/2022/'] +sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)] +checksums = ['f31d445b48e67e284cf206717cc170ab63cbe4fd7f79a82793b772285e78fdbb'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('libreadline', '8.2'), + ('Tcl', '8.6.12'), +] + +# enable additional APIs that provide access to meta-data about tables and queries +# needed for GDAL when it used as a dep for QGIS +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -DSQLITE_ENABLE_COLUMN_METADATA"' + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +sanity_check_commands = [ + 'sqlite3 --version | grep ^%(version)s', +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.12-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.12-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d86abbb9d4d --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.12-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.12' + +homepage = 'https://www.tcl.tk/' +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['26c995dd0f167e48b11961d891ee555f680c175f7173ff8cb829f4ebcde4c1a6'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('zlib', '1.2.12'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh'] + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', + 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2b85900a4d8 --- /dev/null +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'UnZip' +version = '6.0' + +homepage = 'http://www.info-zip.org/UnZip.html' +description = """UnZip is an extraction utility for archives compressed +in .zip format (also called "zipfiles"). Although highly compatible both +with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's +own Zip program, our primary objectives have been portability and +non-MSDOS functionality.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +patches = [ + 'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch', +] +checksums = [ + '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37', # unzip60.tar.gz + # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch + '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe', +] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile CC="$CC" D_USE_BZ2=-DUSE_BZIP2 L_BZ2=-lbz2 ' +buildopts += 'LF2="$LDFLAGS" ' +# Note: CF is multiple lines +buildopts += 'CF="$CFLAGS $CPPFLAGS -I. -DACORN_FTYPE_NFS -DWILD_STOP_AT_DIR -DLARGE_FILE_SUPPORT ' +buildopts += '-DUNICODE_SUPPORT -DUNICODE_WCHAR -DUTF8_MAYBE_NATIVE -DNO_LCHMOD ' +buildopts += '-DDATE_FORMAT=DF_YMD -DUSE_BZIP2 -DIZ_HAVE_UXUIDGID -DNOMEMCPY -DNO_WORKING_ISPRINT" unzips ' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/unzip', 'bin/zipinfo'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["unzip -v"] + +moduleclass = 'tools' From 4e58dc480e02a1ef47a382bc40ee872bcbc203e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 21:53:58 +0100 Subject: [PATCH 617/793] adding easyconfigs: cURL-7.86.0-GCCcore-12.2.0.eb --- .../c/cURL/cURL-7.86.0-GCCcore-12.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.86.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.86.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.86.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..4e108bdbc19 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.86.0-GCCcore-12.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.86.0' + +homepage = 'https://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3dfdd39ba95e18847965cd3051ea6d22586609d9011d91df7bc5521288987a82'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = '--with-zlib ' +configopts += '--with-ssl=$EBROOTOPENSSL ' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/curl'], +} + +moduleclass = 'tools' From 8df94ddb722ef38af443951adf5ed0f462661a03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 21:54:12 +0100 Subject: [PATCH 618/793] adding easyconfigs: libarchive-3.6.1-GCCcore-12.2.0.eb --- .../libarchive-3.6.1-GCCcore-12.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..8cc05cbcb01 --- /dev/null +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libarchive' +version = '3.6.1' + +homepage = 'https://www.libarchive.org/' + +description = """ + Multi-format archive and compression library +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.libarchive.org/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['c676146577d989189940f1959d9e3980d28513d74eedfbc6b7f15ea45fe54ee2'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('XZ', '5.2.7'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], + 'dirs': ['bin', 'share/man/man3'], +} + +moduleclass = 'tools' From 4dd41bfb994262fabb743d9e4da47cd4b3ab0881 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 21:55:24 +0100 Subject: [PATCH 619/793] adding easyconfigs: CMake-3.24.3-GCCcore-12.2.0.eb --- .../c/CMake/CMake-3.24.3-GCCcore-12.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..86db778efcb --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +name = 'CMake' +version = '3.24.3' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b53aa10fa82bff84ccdb59065927b72d3bee49f4d86261249fc0984b3b367291'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('cURL', '7.86.0'), + ('libarchive', '3.6.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +moduleclass = 'devel' From b0f5a08b7873d0bcf346dbda7b49417980638983 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 21:57:44 +0100 Subject: [PATCH 620/793] adding easyconfigs: FlexiBLAS-3.2.1-GCC-12.2.0.eb, BLIS-0.9.0-GCC-12.2.0.eb, OpenBLAS-0.3.21-GCC-12.2.0.eb --- .../b/BLIS/BLIS-0.9.0-GCC-12.2.0.eb | 42 ++++++++++++++ .../f/FlexiBLAS/FlexiBLAS-3.2.1-GCC-12.2.0.eb | 58 +++++++++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb | 47 +++++++++++++++ 3 files changed, 147 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.1-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.2.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.2.0.eb new file mode 100644 index 00000000000..3fdd482cf5a --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '0.9.0' + +homepage = 'https://github.com/flame/blis/' +description = """BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/flame/blis/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_disable_power9_kernels.patch', + '%(name)s-%(version)s_enable_ppc_autodetect.patch', +] +checksums = [ + '1135f664be7355427b91025075562805cdc6cc730d3173f83533b2c5dcc2f308', # 0.9.0.tar.gz + # BLIS-0.9.0_disable_power9_kernels.patch + 'ed7a326bc5c5c21c42faefbec2fd7be609d1c7236981b466475edace39307279', + # BLIS-0.9.0_enable_ppc_autodetect.patch + 'f373fb252c0d14036fb631f048091976cceb02abb3e570a97fbaeac2fbb12328', +] +builddependencies = [ + ('Python', '3.10.8', '-bare'), + ('Perl', '5.36.0'), +] + +configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.1-GCC-12.2.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.1-GCC-12.2.0.eb new file mode 100644 index 00000000000..9a77c6b3a77 --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.1-GCC-12.2.0.eb @@ -0,0 +1,58 @@ +easyblock = 'Bundle' + +name = 'FlexiBLAS' +version = '3.2.1' + +homepage = 'https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release' +description = """FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation +used by a program without recompiling or relinking it.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +local_extra_flags = "-fstack-protector-strong -fstack-clash-protection" +toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': local_extra_flags} + +builddependencies = [ + ('CMake', '3.24.3'), + ('Python', '3.10.8', '-bare'), # required for running the tests + ('BLIS', '0.9.0'), +] + +dependencies = [ + ('OpenBLAS', '0.3.21'), +] + +# note: first listed backend will be used as default by FlexiBLAS, +# unless otherwise specified via easyconfig parameter flexiblas_default +local_backends = ['OpenBLAS', 'BLIS'] + +# imkl supplies its backend via the imkl module, not as a dependency +if ARCH == 'x86_64': + local_backends.append('imkl') + +default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} +sanity_check_all_components = True + +# Also build and install LAPACKE, which FlexiBLAS does not support yet +components = [ + (name, version, { + 'source_urls': ['https://github.com/mpimd-csc/flexiblas/releases/download/v%(version)s/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['5be7e508e2dbb751b3bf372639d8e82a11f79e9ef6cbf243b64981c24a5703cf'], + 'backends': local_backends, + }), + ('LAPACK', '3.10.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/Reference-LAPACK/lapack/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['cd005cd021f144d7d5f7f33c943942db9f03a28d110d6a3b80d718a295f7f714'], + 'configopts': ('-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON ' + '-DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON ' + '-DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas'), + 'sanity_check_paths': { + 'files': ['lib/liblapacke.%s' % SHLIB_EXT, 'include/flexiblas/lapacke.h'], + 'dirs': [], + }, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb new file mode 100644 index 00000000000..eee3ebc9454 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb @@ -0,0 +1,47 @@ +name = 'OpenBLAS' +version = '0.3.21' + +homepage = 'http://www.openblas.net/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', +] +checksums = [ + {'v0.3.21.tar.gz': 'f36ba3d7a60e7c8bcc54cd9aaa9b1223dd42eaf02c811791c37e8ca707c241ca'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': + 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, +] + +builddependencies = [ + # required by LAPACK test suite + ('Python', '3.10.8', '-bare'), +] + +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' From b23bc8abe61cca25d721e9efdcbd8a0733275e9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 22:06:22 +0100 Subject: [PATCH 621/793] adding easyconfigs: hwloc-2.8.0-GCCcore-12.2.0.eb, libpciaccess-0.17-GCCcore-12.2.0.eb, xorg-macros-1.19.3-GCCcore-12.2.0.eb --- .../h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb | 45 +++++++++++++++++++ .../libpciaccess-0.17-GCCcore-12.2.0.eb | 26 +++++++++++ .../xorg-macros-1.19.3-GCCcore-12.2.0.eb | 27 +++++++++++ 3 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f6483901c2b --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '2.8.0' + +homepage = 'https://www.open-mpi.org/projects/hwloc/' + +description = """ + The Portable Hardware Locality (hwloc) software package provides a portable + abstraction (across OS, versions, architectures, ...) of the hierarchical + topology of modern architectures, including NUMA memory nodes, sockets, shared + caches, cores and simultaneous multithreading. It also gathers various system + attributes such as cache and memory information as well as the locality of I/O + devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily + aims at helping applications with gathering information about modern computing + hardware so as to exploit it accordingly and efficiently. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['20b2bd4df436827d8e50f7afeafb6f967259f2fb374ce7330244f8d0ed2dde6f'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('numactl', '2.0.16'), + ('libxml2', '2.10.3'), + ('libpciaccess', '0.17'), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL " +configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " + +sanity_check_paths = { + 'files': ['bin/lstopo', 'include/hwloc/linux.h', + 'lib/libhwloc.%s' % SHLIB_EXT], + 'dirs': ['share/man/man3'], +} +sanity_check_commands = ['lstopo'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0c9005d81c0 --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.17' + +homepage = 'https://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_GZ] +checksums = ['bf6985a77d2ecb00e2c79da3edfb26b909178ffca3f2e9d14ed0620259ab733b'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('xorg-macros', '1.19.3'), +] + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..23dad904c35 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.3' + +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['8205d210a580da0938f5ce4392a96b60cf1d9a5f792eaa1474fa4c1977aef4d0'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' From 7fd3bc769e202c71bff87cb387d7223b27583fc8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 22:34:01 +0100 Subject: [PATCH 622/793] adding easyconfigs: OpenMPI-4.1.4-GCC-12.2.0.eb, libevent-2.1.12-GCCcore-12.2.0.eb, libfabric-1.16.1-GCCcore-12.2.0.eb, PMIx-4.2.2-GCCcore-12.2.0.eb, UCC-1.1.0-GCCcore-12.2.0.eb --- .../libevent-2.1.12-GCCcore-12.2.0.eb | 38 ++++++++++++ .../libfabric-1.16.1-GCCcore-12.2.0.eb | 62 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb | 62 +++++++++++++++++++ .../p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb | 45 ++++++++++++++ .../u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb | 37 +++++++++++ 5 files changed, 244 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.16.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..99908875d8c --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.12' + +homepage = 'https://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['92e6de1be9ec176428fd2367677e61ceffc2ee1cb119035037a27d346b0403bb'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.16.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.16.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..97eacfc006e --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.16.1-GCCcore-12.2.0.eb @@ -0,0 +1,62 @@ +easyblock = 'ConfigureMake' + +name = 'libfabric' +version = '1.16.1' + +homepage = 'https://ofiwg.github.io/libfabric/' +description = """ +Libfabric is a core component of OFI. It is the library that defines and exports +the user-space API of OFI, and is typically the only software that applications +deal with directly. It works in conjunction with provider libraries, which are +often integrated directly into libfabric. +""" + +# The psm3 provider (enabled by default) requires an AVX capable system to run +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ofiwg/libfabric/releases/download/v%(version)s'] +sources = [SOURCE_TAR_BZ2] +patches = [ + '%(name)s-1.12.1_disable-psm3-avx-config.patch', +] +checksums = [ + {'libfabric-1.16.1.tar.bz2': '53f992d33f9afe94b8a4ea3d105504887f4311cf4b68cea99a24a85fcc39193f'}, + {'libfabric-1.12.1_disable-psm3-avx-config.patch': + '129be05a824b41eeb7bddac3c23aa421a13f7dde622948df942a265ccc96125a'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('numactl', '2.0.16'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +# Regenerate build files to pick up psm3-axv-config patch +preconfigopts = "./autogen.sh &&" + +# Disable deprecated "sockets" provider +configopts = "--disable-sockets " + +# Disable usNIC provider by default as this requires specific osdependencies +# If you want to enable this provider you need to uncomment the following line: +# osdependencies.append(('libnl3-devel', 'libnl3-dev')) +configopts += "--disable-usnic " + +buildopts = "V=1" + +sanity_check_paths = { + 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + + ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = ['fi_info'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb new file mode 100644 index 00000000000..09a6bc393d3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb @@ -0,0 +1,62 @@ +name = 'OpenMPI' +version = '4.1.4' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', + 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', +] +checksums = [ + '92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d', # openmpi-4.1.4.tar.bz2 + # OpenMPI-4.1.1_build-with-internal-cuda-header.patch + '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83', + # OpenMPI-4.1.1_opal-datatype-cuda-performance.patch + 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e', +] + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('Perl', '5.36.0'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('hwloc', '2.8.0'), + ('libevent', '2.1.12'), + ('UCX', '1.13.1'), + ('libfabric', '1.16.1'), + ('PMIx', '4.2.2'), + ('UCC', '1.1.0'), +] + +# Update configure to include changes from the "internal-cuda" patch +# by running a subset of autogen.pl sufficient to achieve this +# without doing the full, long-running regeneration. +preconfigopts = ' && '.join([ + 'cd config', + 'autom4te --language=m4sh opal_get_version.m4sh -o opal_get_version.sh', + 'cd ..', + 'autoconf', + 'autoheader', + 'aclocal', + 'automake', + '' +]) + +# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. +configopts = '--with-cuda=internal ' + +# disable MPI1 compatibility for now, see what breaks... +# configopts += '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..ffe8c9fba65 --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'PMIx' +version = '4.2.2' + +homepage = 'https://pmix.org/' +description = """Process Management for Exascale Environments +PMI Exascale (PMIx) represents an attempt to +provide an extended version of the PMI standard specifically designed +to support clusters up to and including exascale sizes. The overall +objective of the project is not to branch the existing pseudo-standard +definitions - in fact, PMIx fully supports both of the existing PMI-1 +and PMI-2 APIs - but rather to (a) augment and extend those APIs to +eliminate some current restrictions that impact scalability, and (b) +provide a reference implementation of the PMI-server that demonstrates +the desired level of scalability. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['935b2f492e4bc409017f1425a83366aa72a7039605ea187c9fac7bb1371cd73c'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('libevent', '2.1.12'), + ('zlib', '1.2.12'), + ('hwloc', '2.8.0'), +] + +configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' +configopts += ' --with-hwloc=$EBROOTHWLOC' +configopts += ' --enable-pmix-binaries' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], + 'dirs': ['etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b5ff6ef4e42 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'UCC' +version = '1.1.0' + +homepage = 'https://www.openucx.org/' +description = """UCC (Unified Collective Communication) is a collective +communication operations API and library that is flexible, complete, and +feature-rich for current and emerging programming models and runtimes. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['74c8ba75037b5bd88cb703e8c8ae55639af3fecfd4428912a433c010c97b4df7'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('UCX', '1.13.1'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/ucc_info'], + 'dirs': ['include', 'lib'] +} + +sanity_check_commands = ["ucc_info -c"] + +moduleclass = 'lib' From 2fea5fff4cb20690af3a56e49a6441a8c231675e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 22:36:23 +0100 Subject: [PATCH 623/793] adding easyconfigs: gompi-2022.10.eb --- .../easyconfigs/g/gompi/gompi-2022.10.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2022.10.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-2022.10.eb b/easybuild/easyconfigs/g/gompi/gompi-2022.10.eb new file mode 100644 index 00000000000..9d5e2752969 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2022.10.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gompi' +version = '2022.10' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '12.2.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # includes both GCC and binutils + ('OpenMPI', '4.1.4', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' From b0e358cbfd08891ead6d086aadc81b452d909c49 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 22:37:21 +0100 Subject: [PATCH 624/793] adding easyconfigs: FFTW-3.3.10-GCC-12.2.0.eb, FFTW.MPI-3.3.10-gompi-2022.10.eb --- .../FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.10.eb | 19 +++++++++++++++++++ .../f/FFTW/FFTW-3.3.10-GCC-12.2.0.eb | 17 +++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.10.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.10.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.10.eb new file mode 100644 index 00000000000..dacac34b6e3 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.10.eb @@ -0,0 +1,19 @@ +name = 'FFTW.MPI' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2022.10'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-12.2.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-12.2.0.eb new file mode 100644 index 00000000000..90dce63b19c --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-12.2.0.eb @@ -0,0 +1,17 @@ +name = 'FFTW' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +runtest = 'check' + +moduleclass = 'numlib' From 443aca94e6dfeb2c4eb16dc0f412566ccb62af31 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 22:39:30 +0100 Subject: [PATCH 625/793] {toolchain} foss/2022.10 --- easybuild/easyconfigs/f/foss/foss-2022.10.eb | 28 ++++++++++++ .../easyconfigs/h/HPL/HPL-2.3-foss-2022.10.eb | 21 +++++++++ .../ScaLAPACK-2.2.0-gompi-2022.10-fb.eb | 43 +++++++++++++++++++ 3 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/f/foss/foss-2022.10.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022.10.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.10-fb.eb diff --git a/easybuild/easyconfigs/f/foss/foss-2022.10.eb b/easybuild/easyconfigs/f/foss/foss-2022.10.eb new file mode 100644 index 00000000000..023dc177384 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2022.10.eb @@ -0,0 +1,28 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2022.10' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '12.2.0' + +# toolchain used to build foss dependencies +local_comp_mpi_tc = ('gompi', version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('OpenMPI', '4.1.4', '', ('GCC', local_gccver)), + ('FlexiBLAS', '3.2.1', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), + ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022.10.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022.10.eb new file mode 100644 index 00000000000..453f6a14c83 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022.10.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2022.10'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.10-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.10-fb.eb new file mode 100644 index 00000000000..5b5a3e57d38 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.10-fb.eb @@ -0,0 +1,43 @@ +name = 'ScaLAPACK' +version = '2.2.0' +versionsuffix = '-fb' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2022.10'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57', # scalapack-2.2.0.tgz + 'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906', # ScaLAPACK-2.2.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('FlexiBLAS', '3.2.1'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' From c6a622be78d7044e477d203e1a9ddec8af7bf375 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 22:49:33 +0100 Subject: [PATCH 626/793] construct 'buildopts' value in a more transparent way in UnZip easyconfig --- .../u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb index 2b85900a4d8..042b74c404e 100644 --- a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb @@ -33,12 +33,19 @@ dependencies = [ skipsteps = ['configure'] -buildopts = '-f unix/Makefile CC="$CC" D_USE_BZ2=-DUSE_BZIP2 L_BZ2=-lbz2 ' -buildopts += 'LF2="$LDFLAGS" ' -# Note: CF is multiple lines -buildopts += 'CF="$CFLAGS $CPPFLAGS -I. -DACORN_FTYPE_NFS -DWILD_STOP_AT_DIR -DLARGE_FILE_SUPPORT ' -buildopts += '-DUNICODE_SUPPORT -DUNICODE_WCHAR -DUTF8_MAYBE_NATIVE -DNO_LCHMOD ' -buildopts += '-DDATE_FORMAT=DF_YMD -DUSE_BZIP2 -DIZ_HAVE_UXUIDGID -DNOMEMCPY -DNO_WORKING_ISPRINT" unzips ' +local_cf = ['$CFLAGS', '$CPPFLAGS', '-I.', '-DACORN_FTYPE_NFS', '-DWILD_STOP_AT_DIR', '-DLARGE_FILE_SUPPORT' + '-DUNICODE_SUPPORT', '-DUNICODE_WCHAR', '-DUTF8_MAYBE_NATIVE', '-DNO_LCHMOD', '-DDATE_FORMAT=DF_YMD', + '-DUSE_BZIP2', '-DIZ_HAVE_UXUIDGID', '-DNOMEMCPY', '-DNO_WORKING_ISPRINT'] + +buildopts = ' '.join([ + "-f unix/Makefile", + 'CC="$CC"', + 'D_USE_BZ2=-DUSE_BZIP2', + 'L_BZ2=-lbz2', + 'LF2="$LDFLAGS"', + 'CF="%s"' % ' '.join(local_cf), + 'unzips', +]) installopts = '-f unix/Makefile prefix=%(installdir)s ' From 2745967c83fc6c5dd3c06b2c051338d7a9b0f294 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 10 Nov 2022 08:54:23 +0000 Subject: [PATCH 627/793] adding easyconfigs: OSU-Micro-Benchmarks-6.2-gompi-2022.10.eb --- .../OSU-Micro-Benchmarks-6.2-gompi-2022.10.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022.10.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022.10.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022.10.eb new file mode 100644 index 00000000000..9326eb7240e --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022.10.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '6.2' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2022.10'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bb9dbc87dcf8ec6785977a61f6fceee8febf1a682488eaab4c58cf50e4fa985f'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From a010106a159d8b9ad639128420ba6861ef42f21f Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 09:59:48 +0100 Subject: [PATCH 628/793] adding easyconfigs: python-libsbml-5.19.2-foss-2021a.eb --- .../python-libsbml-5.19.2-foss-2021a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb new file mode 100644 index 00000000000..3ff630bebf1 --- /dev/null +++ b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb @@ -0,0 +1,51 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'PythonBundle' + +name = 'python-libsbml' +version = '5.19.2' + +homepage = 'https://sbml.org/' +description = """LibSBML Python API.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('make', '4.3'), + ('Check', '0.15.2'), + ('SWIG', '4.0.2'), + ('expat', '2.2.9'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), +] + +use_pip = True + +# NOTE Use version 5.19.2 because is the last one provided as tarball and not as weird whl +exts_list = [ + (name, version, { + 'modulename': 'libsbml', + 'checksums': ['b11a79a5421abba9f8874ebbc1c479cbdb3c1827697db74b687705632583a0e5'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 2538811517d07628a0d89709afd06376df1898bb Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 10:20:48 +0100 Subject: [PATCH 629/793] Add missing sanity_pip_check --- .../p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb index 3ff630bebf1..ebe73922184 100644 --- a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb @@ -48,4 +48,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_pip_check = True + moduleclass = 'bio' From 23b69b499eb00902e17dd2c31bb5e82d0706b1ba Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 10 Nov 2022 10:52:08 +0000 Subject: [PATCH 630/793] switch 'www.cpan.org' to 'cpan.metacpan.org' in extension source_urls for recent Perl easyconfigs --- .../p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 42 +++++++++---------- .../p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 42 +++++++++---------- .../p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 42 +++++++++---------- 3 files changed, 63 insertions(+), 63 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb index b998f1d93d0..9c3e8483a03 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb @@ -110,47 +110,47 @@ exts_list = [ }), ('IPC::System::Simple', '1.30', { 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JK/JKEENAN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN/'], 'checksums': ['22e6f5222b505ee513058fdca35ab7a1eab80539b98e5ca4a923a70a8ae9ba9e'], }), ('Importer', '0.026', { 'source_tmpl': 'Importer-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], 'checksums': ['e08fa84e13cb998b7a897fc8ec9c3459fcc1716aff25cc343e36ef875891b0ef'], }), ('Term::Table', '0.016', { 'source_tmpl': 'Term-Table-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], 'checksums': ['8fb4fbb8e96a2d6c514949eb8cfd7e66319bcb1cbf7cea0ab19af887a72d97bf'], }), ('Scope::Guard', '0.21', { 'source_tmpl': 'Scope-Guard-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CH/CHOCOLATE/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE/'], 'checksums': ['8c9b1bea5c56448e2c3fadc65d05be9e4690a3823a80f39d2f10fdd8f777d278'], }), ('Sub::Info', '0.002', { 'source_tmpl': 'Sub-Info-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], 'checksums': ['ea3056d696bdeff21a99d340d5570887d39a8cc47bff23adfc82df6758cdd0ea'], }), ('Test2::Require::Module', '0.000145', { 'source_tmpl': 'Test2-Suite-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], 'checksums': ['ed44be739c8879fe178d3107b238f2db960d52797db0058de53be5b84600358b'], }), ('Test2::Plugin::NoWarnings', '0.09', { 'source_tmpl': 'Test2-Plugin-NoWarnings-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DR/DROLSKY/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], 'checksums': ['be3dd800042eef362bf17d2056cf9e934dee91ccce98e4f178b8fb5772f2fb74'], }), ('Class::Tiny', '1.008', { 'source_tmpl': 'Class-Tiny-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DA/DAGOLDEN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], 'checksums': ['ee058a63912fa1fcb9a72498f56ca421a2056dc7f9f4b67837446d6421815615'], }), ('Test::File::ShareDir::Dist', '1.001002', { 'source_tmpl': 'Test-File-ShareDir-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/K/KE/KENTNL/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL/'], 'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'], }), ('DateTime::Locale', '1.35', { @@ -210,12 +210,12 @@ exts_list = [ }), ('CPAN::Meta::Check', '0.014', { 'source_tmpl': 'CPAN-Meta-Check-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/L/LE/LEONT/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT/'], 'checksums': ['28a0572bfc1c0678d9ce7da48cf521097ada230f96eb3d063fcbae1cfe6a351f'], }), ('Test::Without::Module', '0.20', { 'source_tmpl': 'Test-Without-Module-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CO/CORION/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION/'], 'checksums': ['8e9aeb7c32a6c6d0b8a93114db2a8c072721273a9d9a2dd4f9ca86cfd28aa524'], }), ('DateTime', '1.58', { @@ -1051,7 +1051,7 @@ exts_list = [ }), ('Test::Needs', '0.002009', { 'source_tmpl': 'Test-Needs-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/H/HA/HAARG/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], 'checksums': ['571c21193ad16195df58b06b268798796a391b398c443271721d2cc0fb7c4ac3'], }), ('HTTP::Daemon', '6.14', { @@ -1131,12 +1131,12 @@ exts_list = [ }), ('Module::Runtime::Conflicts', '0.003', { 'source_tmpl': 'Module-Runtime-Conflicts-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], 'checksums': ['707cdc75038c70fe91779b888ac050f128565d3967ba96680e1b1c7cc9733875'], }), ('Test::CleanNamespaces', '0.24', { 'source_tmpl': 'Test-CleanNamespaces-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], 'checksums': ['338d5569e8e89a654935f843ec0bc84aaa486fe8dd1898fb9cab3eccecd5327a'], }), ('Moose', '2.2201', { @@ -1221,7 +1221,7 @@ exts_list = [ }), ('Test::More::UTF8', '0.05', { 'source_tmpl': 'Test-More-UTF8-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/M/MO/MONS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MO/MONS/'], 'checksums': ['b9f1c4b36a97cdfefaa53ed1115dd38f4b483037775f6559ee1df14acfd1ce04'], }), ('Text::Template', '1.60', { @@ -1231,17 +1231,17 @@ exts_list = [ }), ('PadWalker', '2.5', { 'source_tmpl': 'PadWalker-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/R/RO/ROBIN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN/'], 'checksums': ['07b26abb841146af32072a8d68cb90176ffb176fd9268e6f2f7d106f817a0cd0'], }), ('Devel::Cycle', '1.12', { 'source_tmpl': 'Devel-Cycle-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/L/LD/LDS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LD/LDS/'], 'checksums': ['fd3365c4d898b2b2bddbb78a46d507a18cca8490a290199547dab7f1e7390bc2'], }), ('Test::Memory::Cycle', '1.06', { 'source_tmpl': 'Test-Memory-Cycle-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/P/PE/PETDANCE/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'], 'checksums': ['9d53ddfdc964cd8454cb0da4c695b6a3ae47b45839291c34cb9d8d1cfaab3202'], }), ('PDF::API2', '2.043', { @@ -1301,12 +1301,12 @@ exts_list = [ }), ('Set::Object', '1.42', { 'source_tmpl': 'Set-Object-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/R/RU/RURBAN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN/'], 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], }), ('Heap', '0.80', { 'source_tmpl': 'Heap-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JM/JMM/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JM/JMM/'], 'checksums': ['ccda29f3c93176ad0fdfff4dd6f5e4ac90b370cba4b028386b7343bf64139bde'], }), ('Graph', '0.9725', { @@ -1376,7 +1376,7 @@ exts_list = [ }), ('Variable::Magic', '0.62', { 'source_tmpl': 'Variable-Magic-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/V/VP/VPIT/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/V/VP/VPIT/'], 'checksums': ['3f9a18517e33f006a9c2fc4f43f01b54abfe6ff2eae7322424f31069296b615c'], }), ('B::Hooks::EndOfScope', '0.26', { diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb index 1424b9a1a56..78044193927 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb @@ -110,47 +110,47 @@ exts_list = [ }), ('IPC::System::Simple', '1.30', { 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JK/JKEENAN'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], 'checksums': ['22e6f5222b505ee513058fdca35ab7a1eab80539b98e5ca4a923a70a8ae9ba9e'], }), ('Importer', '0.026', { 'source_tmpl': 'Importer-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['e08fa84e13cb998b7a897fc8ec9c3459fcc1716aff25cc343e36ef875891b0ef'], }), ('Term::Table', '0.016', { 'source_tmpl': 'Term-Table-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['8fb4fbb8e96a2d6c514949eb8cfd7e66319bcb1cbf7cea0ab19af887a72d97bf'], }), ('Scope::Guard', '0.21', { 'source_tmpl': 'Scope-Guard-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CH/CHOCOLATE'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE'], 'checksums': ['8c9b1bea5c56448e2c3fadc65d05be9e4690a3823a80f39d2f10fdd8f777d278'], }), ('Sub::Info', '0.002', { 'source_tmpl': 'Sub-Info-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['ea3056d696bdeff21a99d340d5570887d39a8cc47bff23adfc82df6758cdd0ea'], }), ('Test2::Require::Module', '0.000145', { 'source_tmpl': 'Test2-Suite-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['ed44be739c8879fe178d3107b238f2db960d52797db0058de53be5b84600358b'], }), ('Test2::Plugin::NoWarnings', '0.09', { 'source_tmpl': 'Test2-Plugin-NoWarnings-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DR/DROLSKY'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], 'checksums': ['be3dd800042eef362bf17d2056cf9e934dee91ccce98e4f178b8fb5772f2fb74'], }), ('Class::Tiny', '1.008', { 'source_tmpl': 'Class-Tiny-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DA/DAGOLDEN'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], 'checksums': ['ee058a63912fa1fcb9a72498f56ca421a2056dc7f9f4b67837446d6421815615'], }), ('Test::File::ShareDir::Dist', '1.001002', { 'source_tmpl': 'Test-File-ShareDir-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/K/KE/KENTNL'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], 'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'], }), ('DateTime::Locale', '1.36', { @@ -210,12 +210,12 @@ exts_list = [ }), ('CPAN::Meta::Check', '0.014', { 'source_tmpl': 'CPAN-Meta-Check-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/L/LE/LEONT/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT/'], 'checksums': ['28a0572bfc1c0678d9ce7da48cf521097ada230f96eb3d063fcbae1cfe6a351f'], }), ('Test::Without::Module', '0.20', { 'source_tmpl': 'Test-Without-Module-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CO/CORION/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION/'], 'checksums': ['8e9aeb7c32a6c6d0b8a93114db2a8c072721273a9d9a2dd4f9ca86cfd28aa524'], }), ('DateTime', '1.58', { @@ -1051,7 +1051,7 @@ exts_list = [ }), ('Test::Needs', '0.002009', { 'source_tmpl': 'Test-Needs-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/H/HA/HAARG/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], 'checksums': ['571c21193ad16195df58b06b268798796a391b398c443271721d2cc0fb7c4ac3'], }), ('HTTP::Daemon', '6.14', { @@ -1131,12 +1131,12 @@ exts_list = [ }), ('Module::Runtime::Conflicts', '0.003', { 'source_tmpl': 'Module-Runtime-Conflicts-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], 'checksums': ['707cdc75038c70fe91779b888ac050f128565d3967ba96680e1b1c7cc9733875'], }), ('Test::CleanNamespaces', '0.24', { 'source_tmpl': 'Test-CleanNamespaces-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], 'checksums': ['338d5569e8e89a654935f843ec0bc84aaa486fe8dd1898fb9cab3eccecd5327a'], }), ('Moose', '2.2201', { @@ -1221,7 +1221,7 @@ exts_list = [ }), ('Test::More::UTF8', '0.05', { 'source_tmpl': 'Test-More-UTF8-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/M/MO/MONS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MO/MONS/'], 'checksums': ['b9f1c4b36a97cdfefaa53ed1115dd38f4b483037775f6559ee1df14acfd1ce04'], }), ('Text::Template', '1.61', { @@ -1231,17 +1231,17 @@ exts_list = [ }), ('PadWalker', '2.5', { 'source_tmpl': 'PadWalker-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/R/RO/ROBIN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN/'], 'checksums': ['07b26abb841146af32072a8d68cb90176ffb176fd9268e6f2f7d106f817a0cd0'], }), ('Devel::Cycle', '1.12', { 'source_tmpl': 'Devel-Cycle-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/L/LD/LDS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LD/LDS/'], 'checksums': ['fd3365c4d898b2b2bddbb78a46d507a18cca8490a290199547dab7f1e7390bc2'], }), ('Test::Memory::Cycle', '1.06', { 'source_tmpl': 'Test-Memory-Cycle-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/P/PE/PETDANCE/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'], 'checksums': ['9d53ddfdc964cd8454cb0da4c695b6a3ae47b45839291c34cb9d8d1cfaab3202'], }), ('PDF::API2', '2.043', { @@ -1301,12 +1301,12 @@ exts_list = [ }), ('Set::Object', '1.42', { 'source_tmpl': 'Set-Object-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/R/RU/RURBAN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN/'], 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], }), ('Heap', '0.80', { 'source_tmpl': 'Heap-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JM/JMM/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JM/JMM/'], 'checksums': ['ccda29f3c93176ad0fdfff4dd6f5e4ac90b370cba4b028386b7343bf64139bde'], }), ('Graph', '0.9725', { @@ -1376,7 +1376,7 @@ exts_list = [ }), ('Variable::Magic', '0.62', { 'source_tmpl': 'Variable-Magic-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/V/VP/VPIT/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/V/VP/VPIT/'], 'checksums': ['3f9a18517e33f006a9c2fc4f43f01b54abfe6ff2eae7322424f31069296b615c'], }), ('B::Hooks::EndOfScope', '0.26', { diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb index df8c81ece83..9e66a846bc3 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -110,47 +110,47 @@ exts_list = [ }), ('IPC::System::Simple', '1.30', { 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JK/JKEENAN'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], 'checksums': ['22e6f5222b505ee513058fdca35ab7a1eab80539b98e5ca4a923a70a8ae9ba9e'], }), ('Importer', '0.026', { 'source_tmpl': 'Importer-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['e08fa84e13cb998b7a897fc8ec9c3459fcc1716aff25cc343e36ef875891b0ef'], }), ('Term::Table', '0.016', { 'source_tmpl': 'Term-Table-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['8fb4fbb8e96a2d6c514949eb8cfd7e66319bcb1cbf7cea0ab19af887a72d97bf'], }), ('Scope::Guard', '0.21', { 'source_tmpl': 'Scope-Guard-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CH/CHOCOLATE'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE'], 'checksums': ['8c9b1bea5c56448e2c3fadc65d05be9e4690a3823a80f39d2f10fdd8f777d278'], }), ('Sub::Info', '0.002', { 'source_tmpl': 'Sub-Info-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['ea3056d696bdeff21a99d340d5570887d39a8cc47bff23adfc82df6758cdd0ea'], }), ('Test2::Require::Module', '0.000145', { 'source_tmpl': 'Test2-Suite-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['ed44be739c8879fe178d3107b238f2db960d52797db0058de53be5b84600358b'], }), ('Test2::Plugin::NoWarnings', '0.09', { 'source_tmpl': 'Test2-Plugin-NoWarnings-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DR/DROLSKY'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], 'checksums': ['be3dd800042eef362bf17d2056cf9e934dee91ccce98e4f178b8fb5772f2fb74'], }), ('Class::Tiny', '1.008', { 'source_tmpl': 'Class-Tiny-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DA/DAGOLDEN'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], 'checksums': ['ee058a63912fa1fcb9a72498f56ca421a2056dc7f9f4b67837446d6421815615'], }), ('Test::File::ShareDir::Dist', '1.001002', { 'source_tmpl': 'Test-File-ShareDir-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/K/KE/KENTNL'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], 'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'], }), ('DateTime::Locale', '1.36', { @@ -210,12 +210,12 @@ exts_list = [ }), ('CPAN::Meta::Check', '0.014', { 'source_tmpl': 'CPAN-Meta-Check-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/L/LE/LEONT/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT/'], 'checksums': ['28a0572bfc1c0678d9ce7da48cf521097ada230f96eb3d063fcbae1cfe6a351f'], }), ('Test::Without::Module', '0.20', { 'source_tmpl': 'Test-Without-Module-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CO/CORION/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION/'], 'checksums': ['8e9aeb7c32a6c6d0b8a93114db2a8c072721273a9d9a2dd4f9ca86cfd28aa524'], }), ('DateTime', '1.58', { @@ -1051,7 +1051,7 @@ exts_list = [ }), ('Test::Needs', '0.002009', { 'source_tmpl': 'Test-Needs-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/H/HA/HAARG/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], 'checksums': ['571c21193ad16195df58b06b268798796a391b398c443271721d2cc0fb7c4ac3'], }), ('HTTP::Daemon', '6.14', { @@ -1131,12 +1131,12 @@ exts_list = [ }), ('Module::Runtime::Conflicts', '0.003', { 'source_tmpl': 'Module-Runtime-Conflicts-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], 'checksums': ['707cdc75038c70fe91779b888ac050f128565d3967ba96680e1b1c7cc9733875'], }), ('Test::CleanNamespaces', '0.24', { 'source_tmpl': 'Test-CleanNamespaces-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], 'checksums': ['338d5569e8e89a654935f843ec0bc84aaa486fe8dd1898fb9cab3eccecd5327a'], }), ('Moose', '2.2201', { @@ -1221,7 +1221,7 @@ exts_list = [ }), ('Test::More::UTF8', '0.05', { 'source_tmpl': 'Test-More-UTF8-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/M/MO/MONS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MO/MONS/'], 'checksums': ['b9f1c4b36a97cdfefaa53ed1115dd38f4b483037775f6559ee1df14acfd1ce04'], }), ('Text::Template', '1.61', { @@ -1231,17 +1231,17 @@ exts_list = [ }), ('PadWalker', '2.5', { 'source_tmpl': 'PadWalker-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/R/RO/ROBIN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN/'], 'checksums': ['07b26abb841146af32072a8d68cb90176ffb176fd9268e6f2f7d106f817a0cd0'], }), ('Devel::Cycle', '1.12', { 'source_tmpl': 'Devel-Cycle-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/L/LD/LDS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LD/LDS/'], 'checksums': ['fd3365c4d898b2b2bddbb78a46d507a18cca8490a290199547dab7f1e7390bc2'], }), ('Test::Memory::Cycle', '1.06', { 'source_tmpl': 'Test-Memory-Cycle-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/P/PE/PETDANCE/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'], 'checksums': ['9d53ddfdc964cd8454cb0da4c695b6a3ae47b45839291c34cb9d8d1cfaab3202'], }), ('PDF::API2', '2.043', { @@ -1301,12 +1301,12 @@ exts_list = [ }), ('Set::Object', '1.42', { 'source_tmpl': 'Set-Object-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/R/RU/RURBAN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN/'], 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], }), ('Heap', '0.80', { 'source_tmpl': 'Heap-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JM/JMM/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JM/JMM/'], 'checksums': ['ccda29f3c93176ad0fdfff4dd6f5e4ac90b370cba4b028386b7343bf64139bde'], }), ('Graph', '0.9725', { @@ -1376,7 +1376,7 @@ exts_list = [ }), ('Variable::Magic', '0.62', { 'source_tmpl': 'Variable-Magic-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/V/VP/VPIT/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/V/VP/VPIT/'], 'checksums': ['3f9a18517e33f006a9c2fc4f43f01b54abfe6ff2eae7322424f31069296b615c'], }), ('B::Hooks::EndOfScope', '0.26', { From 6b3b897fcfa09c66a861fd71c41e229a2e3c4df5 Mon Sep 17 00:00:00 2001 From: easybuild Date: Thu, 10 Nov 2022 13:09:59 +0000 Subject: [PATCH 631/793] adding easyconfigs: Centrifuge-1.0.4-gompi-2021a.eb --- .../Centrifuge-1.0.4-gompi-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2021a.eb diff --git a/easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2021a.eb b/easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2021a.eb new file mode 100644 index 00000000000..d73a84e0a4c --- /dev/null +++ b/easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2021a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Centrifuge' +version = '1.0.4' + +homepage = 'https://ccb.jhu.edu/software/centrifuge' +description = 'Classifier for metagenomic sequences' + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/DaehwanKimLab/centrifuge/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + '929daed0f84739f7636cc1ea2757527e83373f107107ffeb5937a403ba5201bc', # v1.0.4.tar.gz +] + +dependencies = [ + ('NGS', '2.10.9'), + ('ncbi-vdb', '2.10.9'), +] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CXXFLAGS" ' +buildopts += 'USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINUSVDB' + +installopts = "prefix=%(installdir)s" + +fix_perl_shebang_for = ['bin/centrifuge*.pl'] + +sanity_check_paths = { + 'files': ['bin/centrifuge%s' % x for x in ['', '-build', '-build-bin', '-class', '-download', + '-inspect', '-inspect-bin']], + 'dirs': [], +} + +sanity_check_commands = ["centrifuge --help"] + +moduleclass = 'bio' From 41f160ccd11862234a24aa8308ad16c8f36ecfdf Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 14:57:01 +0100 Subject: [PATCH 632/793] Update to version 1.1.3, the last one with the R tarball --- ...021a-R-4.1.0.eb => DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/d/DAS_Tool/{DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb => DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb} (88%) diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb similarity index 88% rename from easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb rename to easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb index 12a3da12443..8889f759be9 100644 --- a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb @@ -1,7 +1,7 @@ easyblock = 'Tarball' name = 'DAS_Tool' -version = '1.1.1' +version = '1.1.3' versionsuffix = '-R-%(rver)s' homepage = 'https://github.com/cmks/DAS_Tool' @@ -14,7 +14,7 @@ source_urls = ['https://github.com/cmks/DAS_Tool/archive/'] sources = ['%(version)s.tar.gz'] patches = ['DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch'] checksums = [ - '2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a', # 1.1.1.tar.gz + 'c2d41a38a7a92d53d412ac3f2b8ab5b9fa64c56021aa5c4dd51fefd7c96b68f4', # 1.1.3.tar.gz 'dc89e6ab7129d170d24da28720cec0937b4d958b5ae46049373d57dde8b8a27a', # DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch ] @@ -34,7 +34,7 @@ exts_list = [ 'modulename': 'DASTool', 'source_tmpl': 'DASTool_%(version)s.tar.gz', 'source_urls': ['https://github.com/cmks/DAS_Tool/raw/%(version)s/package/'], - 'checksums': ['8d33997baaaec00d253b2d749cf1ace004ccdea2275b763d4d0f1c969916b72b'], + 'checksums': ['050ba4fa061ceb398a6881652b4b5f14736581a35edd00ef9ae4cea986f38d18'], }), ] From b6783e1df0dcc157bccab2574dd932728a292ba7 Mon Sep 17 00:00:00 2001 From: easybuild Date: Thu, 10 Nov 2022 15:38:01 +0000 Subject: [PATCH 633/793] Fix Perl version in gompi-2021a in ncbi-vdb update --- .../n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2021a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2021a.eb diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2021a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2021a.eb new file mode 100644 index 00000000000..aa5ea3306c4 --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2021a.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '2.10.9' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +github_account = 'ncbi' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch'] +checksums = [ + '3707f81412dbf6ce2b29d3e65e364116c86acc534543e5a084cf8a666b81960d', # ncbi-vdb-2.10.9.tar.gz + 'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133', # ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch +] + +builddependencies = [('Perl', '5.32.1')] + +dependencies = [ + ('NGS', '2.10.9'), + ('file', '5.40'), # provides libmagic + ('HDF5', '1.10.7'), + ('libxml2', '2.9.10'), + ('bzip2', '1.0.8'), +] + +# add addtional libraries needed to statically link HDF5 from EB +preconfigopts = "sed -i 's/-lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz/' setup/konfigure.perl &&" + +configopts = "--build-prefix=%(builddir)s " # change default build directory +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS --with-ngs-java-prefix=$EBROOTNGS/jar/ngs-java.jar " +configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" + +# replace hardcoded optimization flags with EB settings +prebuildopts = "find build/ -name \"Makefile*\" -exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && EBFLAGS=\"$CFLAGS\" " +preinstallopts = 'EBFLAGS="$CFLAGS" ' + +sanity_check_paths = { + 'files': ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a')] + + [('lib/libncbi-%s.%s' % (l, e), 'lib64/libncbi-%s.%s' % (l, e)) + for l in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'bio' From e443f54e1cfd4976395154afd6ce8e69f18b4476 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 16:44:08 +0100 Subject: [PATCH 634/793] Update to last version after fixes on the pypi side --- ...9.2-foss-2021a.eb => python-libsbml-5.19.7-foss-2021a.eb} | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/p/python-libsbml/{python-libsbml-5.19.2-foss-2021a.eb => python-libsbml-5.19.7-foss-2021a.eb} (83%) diff --git a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb similarity index 83% rename from easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb rename to easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb index ebe73922184..4fb837dd9a0 100644 --- a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb @@ -9,7 +9,7 @@ easyblock = 'PythonBundle' name = 'python-libsbml' -version = '5.19.2' +version = '5.19.7' homepage = 'https://sbml.org/' description = """LibSBML Python API.""" @@ -35,11 +35,10 @@ dependencies = [ use_pip = True -# NOTE Use version 5.19.2 because is the last one provided as tarball and not as weird whl exts_list = [ (name, version, { 'modulename': 'libsbml', - 'checksums': ['b11a79a5421abba9f8874ebbc1c479cbdb3c1827697db74b687705632583a0e5'], + 'checksums': ['447b1fde7aceccd11a93dc9f589ffd9319ba854d7b7583f911259a8b0127ab7b'], }), ] From d523a904efe69621d9267ed6d2519dd6fd43f5d4 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 18:30:34 +0100 Subject: [PATCH 635/793] adding easyconfigs: Filtlong-0.2.1-GCC-10.3.0.eb --- .../f/Filtlong/Filtlong-0.2.1-GCC-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-10.3.0.eb b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-10.3.0.eb new file mode 100644 index 00000000000..8ed16b2cc4c --- /dev/null +++ b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-10.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'Filtlong' +version = '0.2.1' + +homepage = 'https://github.com/rrwick/Filtlong' +description = """Filtlong is a tool for filtering long reads by quality. It can take a set + of long reads and produce a smaller, better subset. It uses both read length (longer is better) + and read identity (higher is better) when choosing which reads pass the filter""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/rrwick/Filtlong/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e6f47675e87f98cf2481a60bef5cad38396f1e4db653a5c1673139f37770273a'] + +unpack_options = '--strip-components=1' + +parallel = 1 + +dependencies = [ + ('zlib', '1.2.11'), +] + +files_to_copy = ["*"] + +sanity_check_paths = { + 'files': ['bin/filtlong'], + 'dirs': [] +} + +sanity_check_commands = ["filtlong --help"] + +moduleclass = 'bio' From 820ea192af5b7d8eff4735f91552097e21283438 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 10 Nov 2022 18:34:21 +0100 Subject: [PATCH 636/793] Sanity check now checks for the exact folder --- .../MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb index e048be328cf..b26dd65738e 100644 --- a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb @@ -103,7 +103,7 @@ exts_list = [ sanity_check_paths = { 'files': [], - 'dirs': ['packages'] + 'dirs': ['packages/%(name)s'] } modextrapaths = { From fae36b681c85e52a93d7bada9ffd39c902a7eb8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Nov 2022 21:06:20 +0100 Subject: [PATCH 637/793] strip out sanity_check_paths from python-libsbml easyconfig, PythonBundle checks by non-empty lib/python*/site-packages by default --- .../p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb index 4fb837dd9a0..04cf6dfe9e0 100644 --- a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb +++ b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb @@ -42,11 +42,6 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_pip_check = True moduleclass = 'bio' From 342043332611daa94060ef014943f504a78a909a Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 11 Nov 2022 09:10:51 +0100 Subject: [PATCH 638/793] adding easyconfigs: COBRApy-0.26.0-foss-2021a.eb --- .../c/COBRApy/COBRApy-0.26.0-foss-2021a.eb | 98 +++++++++++++++++++ 1 file changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb new file mode 100644 index 00000000000..7cce7c9bf0f --- /dev/null +++ b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb @@ -0,0 +1,98 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'PythonBundle' + +name = 'COBRApy' +version = '0.26.0' + +homepage = 'https://opencobra.github.io/cobrapy/' +description = """COBRApy is a package for constraint-based modeling of metabolic networks.""" +software_license = 'LicenseGPLv2' + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('ruamel.yaml', '0.17.21'), + ('SciPy-bundle', '2021.05'), + ('sympy', '1.8'), + ('GLPK', '5.0'), + ('python-libsbml', '5.19.7'), +] + +use_pip = True + +exts_list = [ + ('typing-extensions', '4.4.0', { + 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '12.6.0', { + 'checksums': ['ba3a3775974105c221d31141f2c116f4fd65c5ceb0698657a11e9f295ec93fd0'], + }), + ('pydantic', '1.10.2', { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), + ('swiglpk', '5.0.8', { + 'checksums': ['9b933d7ba17c619f5d838b6b3216647bcf8a2e22cd67ea89b0f2e2f50f7be0ae'], + }), + ('optlang', '1.6.0', { + 'checksums': ['b503b05e4f434c5c69e4aac90b2dfd3cba9fa8ae24899a9a820017ce1d3d370c'], + }), + ('importlib_resources', '5.10.0', { + 'checksums': ['c01b1b94210d9849f286b86bb51bcea7cd56dde0600d8db721d7b81330711668'], + }), + ('rfc3986', '1.5.0', { + 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.2', { + 'checksums': ['25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421'], + }), + ('h11', '0.12.0', { + 'checksums': ['47222cb6067e4a307d535814917cd98fd0a57b6788ce715755fa2b6c28b56042'], + }), + ('httpcore', '0.15.0', { + 'checksums': ['18b68ab86a3ccf3e7dc0f43598eaddcf472b602aba29f9aa6ab85fe2ada3980b'], + }), + ('httpx', '0.23.0', { + 'checksums': ['f28eac771ec9eb4866d3fb4ab65abd42d38c424739e80c08d8d20570de60b0ef'], + }), + ('diskcache', '5.4.0', { + 'checksums': ['8879eb8c9b4a2509a5e633d2008634fb2b0b35c2b36192d89655dbde02419644'], + }), + # More recent versions of pipdeptree do not provide the same methods + ('pipdeptree', '1.0.0', { + 'checksums': ['5fe866a38113d28d527033ececc57b8e86df86b7c29edbacb33f41ee50f75b31'], + }), + ('versioneer', '0.28', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['11ffc09427ac99db4ce61bdc85785dae819618d0de28153adfce3085956125a8'], + }), + ('depinfo', '1.7.0', { + 'checksums': ['770c82e02f7f1f58c8ff87f8ad132ef3b5f5acbce586b838fadd0eb25b131340'], + }), + ('cobra', version, { + 'checksums': ['4c19ed3a1af8376479cc276b83fb3ceb3a373c75353f4d9d41995c6fe81e03ad'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From 1201ed530f22a9375fc7f6a6573afc42bd2b7dc1 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 11 Nov 2022 10:44:25 +0100 Subject: [PATCH 639/793] adding easyconfigs: Porechop-0.2.4-GCCcore-10.3.0.eb --- .../Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..06648897819 --- /dev/null +++ b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonPackage' + +name = 'Porechop' +version = '0.2.4' + +homepage = 'https://github.com/rrwick/Porechop' +description = """Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. + Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, + it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments + to effectively find adapters, even at low sequence identity""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/rrwick/Porechop/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'] + +dependencies = [ + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['%(namelower)s -h'] + +moduleclass = 'bio' From 2043a13a426aa1d8fd61052c72c9710e986dfc09 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 11 Nov 2022 11:00:31 +0100 Subject: [PATCH 640/793] Add missing binutils --- .../easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb index 06648897819..b637b657763 100644 --- a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb @@ -20,6 +20,10 @@ source_urls = ['https://github.com/rrwick/Porechop/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'] +builddependencies = [ + ('binutils', '2.36.1'), +] + dependencies = [ ('Python', '3.9.5'), ] From 94bb82b0263edae500c8a5f18340d6911d15e914 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 11 Nov 2022 16:34:14 +0000 Subject: [PATCH 641/793] Adjust disable-fma-in-cscal-zscal.patch for GCC 12 For some reason (GCC bug report pending) -ffp-contract=off is not sufficient for GCC 12, so we also need -mno-fma, implemented via a GCC pragma. --- .../o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb | 6 +- ...CC-12.2.0_disable-fma-in-cscal-zscal.patch | 73 +++++++++++++++++++ 2 files changed, 76 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb index eee3ebc9454..b0244cb98ce 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb @@ -17,7 +17,7 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', - 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', ] checksums = [ @@ -28,8 +28,8 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, - {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': - 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch': + '9784e93567d100960a4c34d86e215bd7aa70bb28b0bc2c6bf1b22c6a05d56003'}, {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch new file mode 100644 index 00000000000..ff665e1300d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch @@ -0,0 +1,73 @@ +From e7e3aa29482281edba46a27fcd452d7ed630f46a Mon Sep 17 00:00:00 2001 +From: Bart Oldeman +Date: Thu, 27 Oct 2022 17:20:44 -0400 +Subject: [PATCH] x86_64: prevent GCC and Clang from generating FMAs in + cscal/zscal. + +If e.g. -march=haswell is set in CFLAGS, GCC generates FMAs by default, which +is inconsistent with the microkernels, none of which use FMAs. These +inconsistencies cause a few failures in the LAPACK testcases, where +eigenvalue results with/without eigenvectors are compared. + +Moreover using FMAs for multiplication of complex numbers can give surprising +results, see 22aa81f for more information. + +This uses the same syntax as used in 22aa81f for zarch (s390x). + +Edit: 2022-11-11: add no-fma target since fp-contract=off isn't sufficient for +GCC 12.2. +--- + kernel/x86_64/cscal.c | 14 +++++++++++++ + kernel/x86_64/zscal.c | 14 +++++++++++++ + 2 files changed, 28 insertions(+) + +diff --git a/kernel/x86_64/cscal.c b/kernel/x86_64/cscal.c +index dc3f688c69..6ae66d9731 100644 +--- a/kernel/x86_64/cscal.c ++++ b/kernel/x86_64/cscal.c +@@ -25,6 +25,20 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE + USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + *****************************************************************************/ + ++/* ++ * Avoid contraction of floating point operations, specifically fused ++ * multiply-add, because they can cause unexpected results in complex ++ * multiplication. ++ */ ++#if defined(__GNUC__) && !defined(__clang__) ++#pragma GCC optimize ("fp-contract=off") ++#pragma GCC target ("no-fma") ++#endif ++ ++#if defined(__clang__) ++#pragma clang fp contract(off) ++#endif ++ + #include "common.h" + + +diff --git a/kernel/x86_64/zscal.c b/kernel/x86_64/zscal.c +index 3744c98bb7..dfdb4230b6 100644 +--- a/kernel/x86_64/zscal.c ++++ b/kernel/x86_64/zscal.c +@@ -25,6 +25,20 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE + USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + *****************************************************************************/ + ++/* ++ * Avoid contraction of floating point operations, specifically fused ++ * multiply-add, because they can cause unexpected results in complex ++ * multiplication. ++ */ ++#if defined(__GNUC__) && !defined(__clang__) ++#pragma GCC optimize ("fp-contract=off") ++#pragma GCC target ("no-fma") ++#endif ++ ++#if defined(__clang__) ++#pragma clang fp contract(off) ++#endif ++ + #include "common.h" + + From 984f088a26a28517e2f3979ed8f1328cef4b9d35 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 11 Nov 2022 17:42:25 +0000 Subject: [PATCH 642/793] adding easyconfigs: MITgcmutils-0.1.2-foss-2022a.eb --- .../MITgcmutils-0.1.2-foss-2022a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb b/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb new file mode 100644 index 00000000000..4459e4473f3 --- /dev/null +++ b/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb @@ -0,0 +1,46 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'MITgcmutils' +version = '0.1.2' + +homepage = 'https://mitgcm.org/' +description = """A numerical model designed for study of the atmosphere, ocean, +and climate, MITgcm’s flexible non-hydrostatic formulation enables it to +efficiently simulate fluid phenomena over a wide range of scales; its adjoint +capabilities enable it to be applied to sensitivity questions and to parameter +and state estimation problems. By employing fluid equation isomorphisms, a +single dynamical kernel can be used to simulate flow of both the atmosphere +and ocean. The model is developed to perform efficiently on a wide variety of +computational platforms.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('tqdm', '4.64.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['5f15e0ad7a1e2451532facd3e83e8a0a2cea41d5c04df8272c4d31780e28ab2d'], + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'modulename': 'MITgcmutils', + }), +] + +sanity_check_paths = { + 'files': ['bin/gluemncbig'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "gluemncbig --help", +] + +moduleclass = 'geo' From 769aeff75110baf1235fe12cb7848ba33ce3057b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 17:30:32 +0100 Subject: [PATCH 643/793] avoid that zlib + htslib are downloaded and built during installation of MetaBAT --- .../m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb | 7 ++-- .../MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb | 7 ++-- .../m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb | 8 +++-- .../m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb | 7 ++-- .../m/MetaBAT/MetaBAT-2.15_zlib-htslib.patch | 35 +++++++++++++++++++ 5 files changed, 56 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_zlib-htslib.patch diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb index 7746c998d4c..a40c2edb844 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'gompi', 'version': '2019a'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] +patches = ['MetaBAT-2.15_zlib-htslib.patch'] checksums = [ 'd43d5e91afa8f2d211a913739127884669516bfbed870760597fcee2b513abe2', # v2.14.tar.gz ] @@ -35,9 +36,11 @@ dependencies = [ ('bzip2', '1.0.6'), ] -fix_perl_shebang_for = ['bin/*.pl'] +configopts = '-DZLIB_LIBRARY="$EBROOTZLIB/lib/libz.a" -DHTSLIB_LIBRARY="$EBROOTSAMTOOLS/lib/libhts.a" ' +# SAMtools's libhts.a requires additional libraries like cURL to be linked +configopts += '-DCMAKE_EXE_LINKER_FLAGS_RELEASE="-lcurl -llzma -lbz2 -lssl -lcrypto" ' -prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " +fix_perl_shebang_for = ['bin/*.pl'] sanity_check_paths = { 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb index 827c80520e1..d8416cf32df 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] +patches = ['MetaBAT-2.15_zlib-htslib.patch'] checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] builddependencies = [ @@ -29,9 +30,11 @@ dependencies = [ ('bzip2', '1.0.8'), ] -fix_perl_shebang_for = ['bin/*.pl'] +configopts = '-DZLIB_LIBRARY="$EBROOTZLIB/lib/libz.a" -DHTSLIB_LIBRARY="$EBROOTSAMTOOLS/lib/libhts.a" ' +# SAMtools's libhts.a requires additional libraries like cURL to be linked +configopts += '-DCMAKE_EXE_LINKER_FLAGS_RELEASE="-lcurl -llzma -lbz2 -lssl -lcrypto" ' -prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " +fix_perl_shebang_for = ['bin/*.pl'] sanity_check_paths = { 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb index a94f4f9953a..6ad2548c41f 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'gompi', 'version': '2021a'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] +patches = ['MetaBAT-2.15_zlib-htslib.patch'] checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] builddependencies = [ @@ -26,11 +27,14 @@ dependencies = [ ('SAMtools', '1.13'), ('XZ', '5.2.5'), ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), ] -fix_perl_shebang_for = ['bin/*.pl'] +configopts = '-DZLIB_LIBRARY="$EBROOTZLIB/lib/libz.a" -DHTSLIB_LIBRARY="$EBROOTSAMTOOLS/lib/libhts.a" ' +# SAMtools's libhts.a requires additional libraries like cURL to be linked +configopts += '-DCMAKE_EXE_LINKER_FLAGS_RELEASE="-lcurl -llzma -lbz2 -lssl -lcrypto" ' -prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " +fix_perl_shebang_for = ['bin/*.pl'] sanity_check_paths = { 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb index 3a2f07771f6..670e4554b36 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'gompi', 'version': '2021b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] +patches = ['MetaBAT-2.15_zlib-htslib.patch'] checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] builddependencies = [ @@ -28,9 +29,11 @@ dependencies = [ ('bzip2', '1.0.8'), ] -fix_perl_shebang_for = ['bin/*.pl'] +configopts = '-DZLIB_LIBRARY="$EBROOTZLIB/lib/libz.a" -DHTSLIB_LIBRARY="$EBROOTSAMTOOLS/lib/libhts.a" ' +# SAMtools's libhts.a requires additional libraries like cURL to be linked +configopts += '-DCMAKE_EXE_LINKER_FLAGS_RELEASE="-lcurl -llzma -lbz2 -lssl -lcrypto" ' -prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " +fix_perl_shebang_for = ['bin/*.pl'] sanity_check_paths = { 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_zlib-htslib.patch b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_zlib-htslib.patch new file mode 100644 index 00000000000..9914848cdc0 --- /dev/null +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_zlib-htslib.patch @@ -0,0 +1,35 @@ +avoid downloading and building of zlib and htslib, since they're provided as dependencies by EasyBuild +author: Kenneth Hoste (HPC-UGent) +--- berkeleylab-metabat-0db17a40717d/CMakeLists.txt.orig 2022-11-11 12:11:10.473978638 +0000 ++++ berkeleylab-metabat-0db17a40717d/CMakeLists.txt 2022-11-11 12:12:34.246072148 +0000 +@@ -8,8 +8,8 @@ + message("Installing ${CMAKE_BUILD_TYPE} MetaBAT into ${CMAKE_INSTALL_PREFIX}") + + include(${CMAKE_ROOT}/Modules/ExternalProject.cmake) +-include(cmake/zlib.cmake) +-include(cmake/htslib.cmake) ++set(zlib_LIB ${ZLIB_LIBRARY}) ++set(htslib_LIB ${HTSLIB_LIBRARY}) + + set(CMAKE_CXX_STANDARD 11) + set(CMAKE_CXX_STANDARD_REQUIRED ON) +--- berkeleylab-metabat-0db17a40717d/src/CMakeLists.txt.orig 2022-11-11 12:23:52.313823937 +0000 ++++ berkeleylab-metabat-0db17a40717d/src/CMakeLists.txt 2022-11-11 12:24:18.424465217 +0000 +@@ -36,7 +36,7 @@ + foreach(target ${targets}) + + add_executable(${target} ${target}.cpp) +- add_dependencies(${target} htslib zlib check_git_repository) ++ add_dependencies(${target} check_git_repository) + target_link_libraries(${target} ${zlib_LIB} ${Boost_LIBRARIES} ${EXTRALIBS} ) + + endforeach() +@@ -48,7 +48,7 @@ + set(targets jgi_summarize_bam_contig_depths contigOverlaps) + foreach(target ${targets}) + add_executable(${target} ${target}.cpp) +- add_dependencies(${target} htslib zlib check_git_repository) ++ add_dependencies(${target} check_git_repository) + target_link_libraries(${target} ${htslib_LIB} ${zlib_LIB} ${Boost_LIBRARIES} ) + endforeach() + From 417104a83c72d19e3c91bf1101521ff57d57b4d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 18:10:03 +0100 Subject: [PATCH 644/793] add checksum for MetaBAT patch --- easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb | 3 ++- .../m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb | 5 ++++- easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb | 5 ++++- easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb | 5 ++++- 4 files changed, 14 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb index a40c2edb844..d906664f6db 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb @@ -16,7 +16,8 @@ source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] patches = ['MetaBAT-2.15_zlib-htslib.patch'] checksums = [ - 'd43d5e91afa8f2d211a913739127884669516bfbed870760597fcee2b513abe2', # v2.14.tar.gz + {'v2.14.tar.gz': 'd43d5e91afa8f2d211a913739127884669516bfbed870760597fcee2b513abe2'}, + {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, ] multi_deps = {'Python': ['3.7.2', '2.7.15']} diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb index d8416cf32df..de525664832 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] patches = ['MetaBAT-2.15_zlib-htslib.patch'] -checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] +checksums = [ + {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, + {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, +] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb index 6ad2548c41f..5c65ffd3edd 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'gompi', 'version': '2021a'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] patches = ['MetaBAT-2.15_zlib-htslib.patch'] -checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] +checksums = [ + {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, + {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, +] builddependencies = [ ('binutils', '2.36.1'), diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb index 670e4554b36..ef62c68ea78 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'gompi', 'version': '2021b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] patches = ['MetaBAT-2.15_zlib-htslib.patch'] -checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] +checksums = [ + {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, + {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, +] builddependencies = [ ('binutils', '2.37'), From b6a4a54e13289acabe9a2b2bfc897082a1cfcf8d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 19:44:39 +0100 Subject: [PATCH 645/793] remove duplicate zlib dependency in MetaBAT easyconfig --- easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb index 5c65ffd3edd..a552166e24f 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb @@ -30,7 +30,6 @@ dependencies = [ ('SAMtools', '1.13'), ('XZ', '5.2.5'), ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), ] configopts = '-DZLIB_LIBRARY="$EBROOTZLIB/lib/libz.a" -DHTSLIB_LIBRARY="$EBROOTSAMTOOLS/lib/libhts.a" ' From cfe4dd28c0745b9c39dbb3ad52f6d999df63a780 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 20:39:25 +0100 Subject: [PATCH 646/793] adding easyconfigs: Python-2.7.18-GCCcore-12.2.0-bare.eb --- .../Python-2.7.18-GCCcore-12.2.0-bare.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.2.0-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.2.0-bare.eb new file mode 100644 index 00000000000..f8c443163d4 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.2.0-bare.eb @@ -0,0 +1,32 @@ +name = 'Python' +version = '2.7.18' +versionsuffix = '-bare' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] + +builddependencies = [ + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('binutils', '2.39'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.12'), + ('libreadline', '8.2'), + ('ncurses', '6.3'), + ('SQLite', '3.39.4'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +install_pip = True + +moduleclass = 'lang' From c058550aa3096feff13dad0032c03fafa0353539 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 20:39:36 +0100 Subject: [PATCH 647/793] adding easyconfigs: Ninja-1.11.1-GCCcore-12.2.0.eb --- .../n/Ninja/Ninja-1.11.1-GCCcore-12.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e6cefd164e7 --- /dev/null +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CmdCp' + +name = 'Ninja' +version = '1.11.1' + +homepage = 'https://ninja-build.org/' +description = "Ninja is a small build system with a focus on speed." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/ninja-build/ninja/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['31747ae633213f1eda3842686f83c2aa1412e0f5691d1c14dbbcc67fe7400cea'] + +builddependencies = [ + ('binutils', '2.39'), + ('Python', '3.10.8', '-bare'), +] + +cmds_map = [('.*', "./configure.py --bootstrap")] + +files_to_copy = [(['ninja'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ninja'], + 'dirs': [], +} + +sanity_check_commands = ["ninja --version"] + +moduleclass = 'tools' From 308e86a4dc784296d2b8ab229053dece648d25bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 20:41:58 +0100 Subject: [PATCH 648/793] adding easyconfigs: GMP-6.2.1-GCCcore-12.2.0.eb --- .../g/GMP/GMP-6.2.1-GCCcore-12.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..8d18902ab40 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-12.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.2.1' + +homepage = 'https://gmplib.org/' +description = """ + GMP is a free library for arbitrary precision arithmetic, operating on signed + integers, rational numbers, and floating point numbers. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'precise': True, 'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.39'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +# copy libgmp.so* to /lib to make sure that it is picked up by tests +# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) +pretestopts = "mkdir -p %%(installdir)s/lib && cp -a .libs/libgmp.%s* %%(installdir)s/lib && " % SHLIB_EXT +testopts = " && rm -r %(installdir)s/lib" + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (l, e) for l in ['gmp', 'gmpxx'] for e in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'], + 'dirs': ['share'], +} + +moduleclass = 'math' From d4066666ae8b2a9c03a5be3c9ea6003233b5c06e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 20:45:21 +0100 Subject: [PATCH 649/793] adding easyconfigs: gettext-0.21.1-GCCcore-12.2.0.eb --- .../gettext/gettext-0.21.1-GCCcore-12.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a7ad515633f --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.21.1' + +homepage = 'https://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e8c3650e1d8cee875c4f355642382c1df83058bd5a11ee8555c0cf276d646d45'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('libxml2', '2.10.3'), + ('ncurses', '6.3'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + +moduleclass = 'tools' From 5d1c5cfe5d37610f8848161c87e052cf33263eea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 20:45:33 +0100 Subject: [PATCH 650/793] adding easyconfigs: git-2.38.1-GCCcore-12.2.0-nodocs.eb --- .../g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb diff --git a/easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb new file mode 100644 index 00000000000..7760dcfd6bd --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb @@ -0,0 +1,47 @@ +## +# Author: Robert Mijakovic +## +# updated to 2.33.1 +# J. Sassmannshausen / GSTT + +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.38.1' +versionsuffix = '-nodocs' + +homepage = 'https://git-scm.com' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/git/git/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['91456b031324f7909f35e067dcfb907956d1a5c3d2069cfc5b4549e42089e546'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('cURL', '7.86.0'), + ('expat', '2.4.9'), + ('gettext', '0.21.1'), + ('Perl', '5.36.0'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': ['libexec/git-core', 'share'], +} + +moduleclass = 'tools' From 6b678b7965f224d22583846ef4afa0f505c71d03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 20:55:20 +0100 Subject: [PATCH 651/793] adding easyconfigs: libpng-1.6.38-GCCcore-12.2.0.eb --- .../l/libpng/libpng-1.6.38-GCCcore-12.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.38-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.38-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.38-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..c3a6b1c3387 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.38-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.38' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' + +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e2b5e1b4329650992c041996cf1269681b341191dc07ffed816c555769cceb77'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('zlib', '1.2.12')] + +local_majminver = '%(version_major)s%(version_minor)s' + +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', + 'lib/libpng.a', 'lib/libpng.%s' % SHLIB_EXT, + 'lib/libpng%s.a' % local_majminver, + 'lib/libpng%s.%s' % (local_majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % local_majminver, 'share/man'], +} + +moduleclass = 'lib' From 9b05a53e14a92631d2f30667058f21e5f866908a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 21:29:25 +0100 Subject: [PATCH 652/793] adding easyconfigs: Rust-1.65.0-GCCcore-12.2.0.eb --- .../r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..757f1d6d4bf --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.65.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.60_sysroot-fix-interpreter.patch'] +checksums = [ + {'rustc-1.65.0-src.tar.gz': '5828bb67f677eabf8c384020582b0ce7af884e1c84389484f7f8d00dd82c0038'}, + {'Rust-1.60_sysroot-fix-interpreter.patch': 'b59ed4c2591fc9098277299be21dd6752654f6f193d8652b7d21cb0fa0dd8716'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('Python', '3.10.8', '-bare'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " + +# avoid build dependency on Ninja, which requires Python, +# since Rust is a build dependency for cryptography that is included with Python +configopts += "--set=llvm.ninja=false " + +# Use ./x.py to bootstrap so that options like -j N are correctly passed through +# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy +# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) +build_cmd = "./x.py build" +install_cmd = "./x.py install -j %(parallel)s" + +# avoid failure when home directory is an NFS mount, +# see https://github.com/rust-lang/cargo/issues/6652 +prebuildopts = "export CARGO_HOME=%(builddir)s/cargo && " +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], + 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], +} + +sanity_check_commands = [ + "cargo --version", + "rustc --version", +] + +moduleclass = 'lang' From cbb0c9c3e4a057557cc1edc382a421fae6d4e1d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Nov 2022 17:25:15 +0100 Subject: [PATCH 653/793] adding easyconfigs: Python-3.10.8-GCCcore-12.2.0.eb --- .../p/Python/Python-3.10.8-GCCcore-12.2.0.eb | 510 ++++++++++++++++++ 1 file changed, 510 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f0bca199736 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb @@ -0,0 +1,510 @@ +name = 'Python' +version = '3.10.8' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['f400c3fb394b8bef1292f6dc1292c5fadc3533039a5bc0c3e885f3e16738029a'] + +builddependencies = [ + ('UnZip', '6.0'), + ('Rust', '1.65.0'), # required for setuptools-rust, which is needed for cryptography + ('pkgconf', '1.9.3'), + ('git', '2.38.1', '-nodocs'), # required for pbr +] + +dependencies = [ + ('binutils', '2.39'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.12'), + ('libreadline', '8.2'), + ('ncurses', '6.3'), + ('SQLite', '3.39.4'), + ('XZ', '5.2.7'), + ('GMP', '6.2.1'), # required for pycrypto + ('libffi', '3.4.4'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +install_pip = True + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, +} + +# order is important! +# package versions updated 12 Nov 2022 +exts_list = [ + ('wheel', '0.38.4', { + 'checksums': ['965f5259b566725405b05e7cf774052044b1ed30119b5d586b2703aafe8719ac'], + }), + ('setuptools', '65.5.1', { + 'checksums': ['e197a19aa8ec9722928f2206f8de752def0e4c9fc6953527360d1c36d94ddb2f'], + }), + ('pip', '22.3.1', { + 'checksums': ['65fd48317359f3af8e593943e6ae1506b66325085ea64b706a998c6e83eeaf38'], + }), + ('blist', '1.3.6', { + 'patches': [ + 'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch', + 'Python-3.10-bist-1.3.6-compatibility.patch', + ], + 'checksums': [ + {'blist-1.3.6.tar.gz': '3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'}, + {'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch': + '18a643d1d1565b05df7dcc9a612a86dcf7b3b352435032f6425a61b597f911d0'}, + {'Python-3.10-bist-1.3.6-compatibility.patch': + '0fb2d92e06b2c39bfc79e229e6fde6053f9aa9538733029377c9a743650a4741'}, + ], + }), + ('pbr', '5.11.0', { + 'checksums': ['b97bc6695b2aff02144133c2e7399d5885223d42b7912ffaec2ca3898e673bfe'], + }), + ('Cython', '0.29.32', { + 'checksums': ['8733cf4758b79304f2a4e39ebfac5e92341bce47bcceb26c1254398b2f8c1af7'], + }), + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('toml', '0.10.2', { + 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], + }), + ('flit-core', '3.8.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + 'checksums': ['b305b30c99526df5e63d6022dd2310a0a941a187bd3884f4c8ef0418df6c39f3'], + }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('packaging', '21.3', { + 'checksums': ['dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb'], + }), + ('setuptools-scm', '7.0.5', { + 'sources': ['setuptools_scm-%(version)s.tar.gz'], + 'checksums': ['031e13af771d6f892b941adb6ea04545bbf91ebc5ce68c78aaf3fff6e1fb4844'], + }), + ('python-dateutil', '2.8.2', { + 'modulename': 'dateutil', + 'checksums': ['0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86'], + }), + ('decorator', '5.1.1', { + 'checksums': ['637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330'], + }), + ('liac-arff', '2.5.0', { + 'modulename': 'arff', + 'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'patches': ['pycrypto-2.6.1_remove-usr-include.patch'], + 'checksums': [ + {'pycrypto-2.6.1.tar.gz': 'f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'}, + {'pycrypto-2.6.1_remove-usr-include.patch': + '06c3d3bb290305e1360a023ea03f9281116c230de62382e6be9474996086712e'}, + ], + }), + ('ecdsa', '0.18.0', { + 'checksums': ['190348041559e21b22a1d65cee485282ca11a6f81d503fddb84d5017e9ed1e49'], + }), + ('ipaddress', '1.0.23', { + 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], + }), + ('asn1crypto', '1.5.1', { + 'checksums': ['13ae38502be632115abf8a24cbe5f4da52e3b5231990aff31123c805306ccb9c'], + }), + ('idna', '3.4', { + 'checksums': ['814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4'], + }), + ('pycparser', '2.21', { + 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], + }), + ('cffi', '1.15.1', { + 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], + }), + ('semantic-version', '2.10.0', { + 'sources': ['semantic_version-%(version)s.tar.gz'], + 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], + }), + ('typing-extensions', '4.4.0', { + 'sources': ['typing_extensions-%(version)s.tar.gz'], + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + ('setuptools-rust', '1.5.2', { + 'checksums': ['d8daccb14dc0eae1b6b6eb3ecef79675bd37b4065369f79c35393dd5c55652c7'], + }), + ('cryptography', '38.0.3', { + 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", + 'checksums': ['bfbe6ee19615b07a98b1d2287d6a6073f734735b49ee45b11324d85efc4d5cbd'], + }), + ('pyasn1', '0.4.8', { + 'checksums': ['aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba'], + }), + ('PyNaCl', '1.5.0', { + 'modulename': 'nacl', + 'checksums': ['8ac7448f09ab85811607bdd21ec2464495ac8b7c66d146bf545b0f08fb9220ba'], + }), + ('bcrypt', '4.0.1', { + 'checksums': 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['ff53056589300976e960f75afb792dfbfc9c78dcbb5a448e207a17b643826360'], + }), + ('cachy', '0.3.0', { + 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], + }), + ('msgpack', '1.0.4', { + 'checksums': ['f5d869c18f030202eb412f08b28d2afeea553d6613aee89e200d7aca7ef01f5f'], + }), + ('CacheControl', '0.12.11', { + 'checksums': ['a5b9fcc986b184db101aa280b42ecdcdfc524892596f606858e0b7a8b4d9e144'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('poetry-core', '1.3.2', { + 'modulename': 'poetry.core', + 'checksums': ['0ab006a40cb38d6a38b97264f6835da2f08a96912f2728ce668e9ac6a34f686f'], + }), + ('glob2', '0.7', { + 'checksums': ['85c3dbd07c8aa26d63d7aacee34fa86e9a91a3873bc30bf62ec46e531f92ab8c'], + }), + ('dulwich', '0.20.50', { + 'checksums': ['50a941796b2c675be39be728d540c16b5b7ce77eb9e1b3f855650ece6832d2be'], + }), + ('poetry-plugin-export', '1.2.0', { + 'sources': ['poetry_plugin_export-%(version)s.tar.gz'], + 'checksums': ['9a1dd42765408931d7831738749022651d43a2968b67c988db1b7a567dfe41ef'], + }), + ('poetry', '1.2.2', { + 'checksums': ['6d9ed0b1b826a0a79190f2078d7d78483fa24bf2494f3b170e354eaa5e7b5ea1'], + }), + ('fsspec', '2022.11.0', { + 'checksums': ['259d5fd5c8e756ff2ea72f42e7613c32667dc2049a4ac3d84364a7ca034acb8b'], + }), + ('threadpoolctl', '3.1.0', { + 'checksums': ['a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), +] + +moduleclass = 'lang' From f67e8904af10fc8f97f28f3099d48e6275948ae1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Nov 2022 17:53:44 +0100 Subject: [PATCH 654/793] add patch to fix installation of MetaBAT 2.15 on aarch64 --- .../MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb | 6 +++- .../m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb | 6 +++- .../m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb | 6 +++- .../m/MetaBAT/MetaBAT-2.15_fix-aarch64.patch | 31 +++++++++++++++++++ 4 files changed, 46 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_fix-aarch64.patch diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb index de525664832..0852b759a00 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb @@ -11,10 +11,14 @@ toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] -patches = ['MetaBAT-2.15_zlib-htslib.patch'] +patches = [ + 'MetaBAT-2.15_zlib-htslib.patch', + 'MetaBAT-2.15_fix-aarch64.patch', +] checksums = [ {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, + {'MetaBAT-2.15_fix-aarch64.patch': '061b43d6c0ac4a9acf3bd7cf3c62efc856661993a61e7d4652ed68aafb7aa7af'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb index a552166e24f..dc2afdaad6f 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb @@ -10,10 +10,14 @@ toolchain = {'name': 'gompi', 'version': '2021a'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] -patches = ['MetaBAT-2.15_zlib-htslib.patch'] +patches = [ + 'MetaBAT-2.15_zlib-htslib.patch', + 'MetaBAT-2.15_fix-aarch64.patch', +] checksums = [ {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, + {'MetaBAT-2.15_fix-aarch64.patch': '061b43d6c0ac4a9acf3bd7cf3c62efc856661993a61e7d4652ed68aafb7aa7af'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb index ef62c68ea78..3ffd2f88277 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb @@ -10,10 +10,14 @@ toolchain = {'name': 'gompi', 'version': '2021b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] -patches = ['MetaBAT-2.15_zlib-htslib.patch'] +patches = [ + 'MetaBAT-2.15_zlib-htslib.patch', + 'MetaBAT-2.15_fix-aarch64.patch', +] checksums = [ {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, + {'MetaBAT-2.15_fix-aarch64.patch': '061b43d6c0ac4a9acf3bd7cf3c62efc856661993a61e7d4652ed68aafb7aa7af'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_fix-aarch64.patch b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_fix-aarch64.patch new file mode 100644 index 00000000000..b3029a247bf --- /dev/null +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_fix-aarch64.patch @@ -0,0 +1,31 @@ +fixes "error: impossible constraint in asm" when building on aarch64/amr64 +see https://bitbucket.org/berkeleylab/metabat/issues/151 +From a01eafa174e01f6a46ef71b63daa7695d2c3834e Mon Sep 17 00:00:00 2001 +From: Rob Egan +Date: Mon, 26 Sep 2022 09:19:32 -0700 +Subject: [PATCH] removed unused function using assembly types + +--- + src/metabat2.h | 6 ------ + 1 file changed, 6 deletions(-) + +diff --git a/src/metabat2.h b/src/metabat2.h +index b1cb5d3..7accc1a 100644 +--- a/src/metabat2.h ++++ b/src/metabat2.h +@@ -258,12 +258,6 @@ public: + + void gen_tnf_graph(Graph& g, Similarity cutoff); + +-unsigned long long rdtsc() { +- unsigned int lo, hi; +- __asm__ __volatile__ ("rdtsc" : "=a" (lo), "=d" (hi)); +- return ((unsigned long long) hi << 32) | lo; +-} +- + static void trim_fasta_label(std::string &label) { + size_t pos = label.find_first_of(" \t"); + if (pos != std::string::npos) +-- +2.38.1 + From 74a363dc9bb8126ba79a85f38bbca34ed71d2365 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Mon, 14 Nov 2022 09:39:37 +0100 Subject: [PATCH 655/793] Fix DIAMOND duplicate choice in the foss-2021a toolchain --- easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb index 12d6688ec5a..5ff808c82d1 100644 --- a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb @@ -23,7 +23,7 @@ checksums = ['19a8eb28c0ebd3fc5a04b006d305a916dd1af00a32b70d2f30df35f32ca2929b'] dependencies = [ ('Python', '3.9.5'), - ('DIAMOND', '2.0.13'), + ('DIAMOND', '2.0.11'), ('prodigal', '2.6.3'), ] From 63eeebd063e2da748b043d0f1db1cac6af62b2af Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 14 Nov 2022 10:52:16 +0000 Subject: [PATCH 656/793] Add ROntoTools extension to Bioconductor bundle --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index d34e406d5d8..43c53a70184 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1095,6 +1095,9 @@ exts_list = [ ('HiCcompare', '1.18.0', { 'checksums': ['b9320fa7a9f10832e2ac7ade0245f85ac4c2c26edef2580078888f5e1050ee2d'], }), + ('ROntoTools', '2.24.0', { + 'checksums': ['dec7ec0d6d709fbdb44d595d776fc462420957e5c23c7bd6d2d63f5a44df04dd'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 6f6478bc51b997eef54222864da8107f2698ff48 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 14 Nov 2022 14:01:50 +0000 Subject: [PATCH 657/793] adding easyconfigs: xmitgcm-0.5.2-foss-2022a.eb --- .../x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb new file mode 100644 index 00000000000..aeac427c9c5 --- /dev/null +++ b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb @@ -0,0 +1,41 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'xmitgcm' +version = '0.5.2' + +homepage = 'https://github.com/MITgcm/xmitgcm' +description = """xmitgcm is a python package for reading MITgcm binary +MDS files into xarray data structures. By storing data in dask arrays, +xmitgcm enables parallel, out-of-core analysis of MITgcm output data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('MITgcmutils', '0.1.2'), + ('dask', '2022.10.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cachetools', '5.2.0', { + 'checksums': ['6a94c6402995a99c3970cc7e4884bb60b4a8639938157eeed436098bf9831757'], + }), + ('xarray', '2022.9.0', { + 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], + }), + (name, version, { + 'checksums': ['7dda45fdf6182a859f5c441cd5928a7c99d41c8bcea9fccf471b7011791b1131'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From e2a48ad045d3f29e3cf5d23f371f553569013015 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Mon, 14 Nov 2022 15:16:34 +0100 Subject: [PATCH 658/793] Add SWIG as missing requirement --- easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb index 7cce7c9bf0f..54f52a70197 100644 --- a/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb @@ -22,6 +22,7 @@ dependencies = [ ('ruamel.yaml', '0.17.21'), ('SciPy-bundle', '2021.05'), ('sympy', '1.8'), + ('SWIG', '4.0.2'), ('GLPK', '5.0'), ('python-libsbml', '5.19.7'), ] From 38ed74ce899c2df641b51fd6718d377cd98d1c68 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 14 Nov 2022 16:25:41 +0100 Subject: [PATCH 659/793] adding easyconfigs: GD-2.75-GCCcore-11.3.0.eb, Circos-0.69-9-GCCcore-11.3.0.eb --- .../c/Circos/Circos-0.69-9-GCCcore-11.3.0.eb | 41 +++++++++++++ .../g/GD/GD-2.75-GCCcore-11.3.0.eb | 57 +++++++++++++++++++ 2 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/c/Circos/Circos-0.69-9-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/GD/GD-2.75-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/Circos/Circos-0.69-9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Circos/Circos-0.69-9-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..bdb8092c8c6 --- /dev/null +++ b/easybuild/easyconfigs/c/Circos/Circos-0.69-9-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'Tarball' + +name = 'Circos' +version = '0.69-9' + +homepage = 'http://www.circos.ca/' +description = """Circos is a software package for visualizing data and information. + It visualizes data in a circular layout - this makes Circos ideal for exploring + relationships between objects or positions.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://circos.ca/distribution/'] +sources = [SOURCELOWER_TGZ] +checksums = ['34d8d7ebebf3f553d62820f8f4a0a57814b610341f836b4740c46c3057f789d2'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Perl', '5.34.1'), + ('GD', '2.75'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/%(name)s'], +} + +modextrapaths = {'PERL5LIB': 'lib'} + +sanity_check_commands = [('perl', '-e "use Circos"')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GD/GD-2.75-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GD/GD-2.75-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d889cb7d1f5 --- /dev/null +++ b/easybuild/easyconfigs/g/GD/GD-2.75-GCCcore-11.3.0.eb @@ -0,0 +1,57 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester (The Francis Crick Insitute, London, UK) +# Update to v2.71: Alex Domingo (Vrije Universiteit Brussel) +# Update to v2.73: Sebastien Moretti (SIB Swiss Institute of Bioinformatics) +# + +easyblock = 'Bundle' + +name = 'GD' +version = '2.75' + +homepage = 'https://github.com/lstein/Perl-GD' +description = """GD.pm - Interface to Gd Graphics Library""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Perl', '5.34.1'), + ('X11', '20220504'), + ('libgd', '2.3.3'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('ExtUtils::PkgConfig', '1.16', { + 'source_tmpl': 'ExtUtils-PkgConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['bbeaced995d7d8d10cfc51a3a5a66da41ceb2bc04fedcab50e10e6300e801c6e'], + }), + (name, version, { + 'source_tmpl': 'release_%(version_major)s_%(version_minor)s.tar.gz', + 'source_urls': ['https://github.com/lstein/Perl-GD/archive/'], + 'checksums': ['b82ca67fa67446f16ee7ba8bccee2062644816a83cb2ee4e4de2fa3ee8ab359d'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bdf2gdfont.pl', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/%(name)s.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/%(name)s'], +} + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +moduleclass = 'bio' From f7403cdf9b53f80c37ad83c1451761ed7dd872d1 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 14 Nov 2022 18:43:51 +0000 Subject: [PATCH 660/793] adding easyconfigs: oceanspy-0.2.0-foss-2022a.eb --- .../o/oceanspy/oceanspy-0.2.0-foss-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb new file mode 100644 index 00000000000..d73a95fced8 --- /dev/null +++ b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb @@ -0,0 +1,40 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'oceanspy' +version = '0.2.0' + +homepage = 'https://github.com/hainegroup/oceanspy' +description = """OceanSpy - A Python package to facilitate ocean model data analysis +and visualization.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('dask', '2022.10.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xarray', '2022.9.0', { + 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], + }), + ('xgcm', '0.8.0', { + 'checksums': ['99e7e2fc9268fb13827f8849dbae279eaaa4960d51872d62bc38293605b0215f'], + }), + + (name, version, { + 'checksums': ['8c684ecdfe03bade171e17f5ae6bedd422e51db6faffed0303e1839051d40614'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From 2e3e7bd67c1faf07c838a1d64a13f28d22334417 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2022 20:16:32 +0100 Subject: [PATCH 661/793] use new EasyBuild logo in README --- README.rst | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/README.rst b/README.rst index cb4636846ac..b06cc3cf03a 100644 --- a/README.rst +++ b/README.rst @@ -1,7 +1,8 @@ -.. image:: https://github.com/easybuilders/easybuild-easyconfigs/workflows/easyconfigs%20unit%20tests/badge.svg - -.. image:: https://easybuilders.github.io/easybuild/images/easybuild_logo_small.png +.. image:: https://github.com/easybuilders/easybuild/raw/develop/logo/png/easybuild_logo_2022_horizontal_dark_bg_transparent.png :align: center + :height: 400px + +.. image:: https://github.com/easybuilders/easybuild-easyconfigs/workflows/easyconfigs%20unit%20tests/badge.svg `EasyBuild `_ is a software build and installation framework that allows you to manage (scientific) software From 09ce7360d06affcf127854d9b8eab140c80d18c4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 14 Nov 2022 23:50:27 +0100 Subject: [PATCH 662/793] use new SYSTEM constant in dependencies of MATLAB-Engine-2021a-GCCcore-10.2.0.eb --- .../m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb index 3418f6ddc56..83a3d5d719c 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb @@ -10,7 +10,7 @@ description = """The MATLAB Engine API for Python provides a package for Python toolchain = {'name': 'GCCcore', 'version': '10.2.0'} dependencies = [ - ('MATLAB', version, '', True), + ('MATLAB', version, '', SYSTEM), ('Python', '3.8.6'), ] From a62c38ef82a9fb81bca8a34f8413b6e13ed3a465 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 14 Nov 2022 23:50:59 +0100 Subject: [PATCH 663/793] use new SYSTEM constant in dependencies of MATLAB-Engine-2021a-GCCcore-11.2.0.eb --- .../m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb index 9380e93ff8a..e60cc61f004 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb @@ -10,7 +10,7 @@ description = """The MATLAB Engine API for Python provides a package for Python toolchain = {'name': 'GCCcore', 'version': '11.2.0'} dependencies = [ - ('MATLAB', version, '', True), + ('MATLAB', version, '', SYSTEM), ('Python', '3.9.6'), ] From 98b2773c34a35e4ab8ad8f3472e39ef421ad26f4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 15 Nov 2022 00:32:14 +0100 Subject: [PATCH 664/793] enable support in MATLAB-Engine for Python version used in EasyBuild --- .../m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb index e60cc61f004..c1558fb7dc9 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb @@ -17,9 +17,11 @@ dependencies = [ use_pip = False download_dep_fail = True +# Enable support for this current version of Python +prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " +prebuildopts += "sed -i 's/^_supported_versions =.*/_supported_versions = ["%(pyshortver)s"]/' setup.py &&" # Since this setup.py does not provide a separate --build-base for the install # step, both build and install must be performed in a single command. -prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" skipsteps = ['install'] From 72f2ed94534866e8ff42ee891c4566e1644d08a2 Mon Sep 17 00:00:00 2001 From: adam Date: Tue, 15 Nov 2022 08:52:30 +0000 Subject: [PATCH 665/793] Fix modulename and add sanity_check_command --- easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb index 6e3329bd511..5deaefa438c 100644 --- a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb +++ b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb @@ -27,7 +27,7 @@ exts_list = [ (name, version, { 'source_tmpl': 'scoary-%(version)s.tar.gz', 'checksums': ['f433343422c5805a70a20f7fe83851490ae3cdf07745c65680de5feea40a6dca'], - 'modulename': False, + 'modulename': 'scoary.methods', }), ] @@ -38,4 +38,6 @@ sanity_check_paths = { sanity_pip_check = True +sanity_check_commands = [('scoary', '--version')] + moduleclass = 'bio' From dbf74553f8ff671f9a520098289c2103b03e979a Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 15 Nov 2022 10:02:33 +0000 Subject: [PATCH 666/793] adding easyconfigs: gsw-3.6.16-foss-2022a.eb --- .../g/gsw/gsw-3.6.16-foss-2022a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb b/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb new file mode 100644 index 00000000000..aa8438cd21e --- /dev/null +++ b/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb @@ -0,0 +1,42 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'gsw' +version = '3.6.16' + +homepage = 'https://github.com/TEOS-10/GSW-python' +description = """This Python implementation of the Thermodynamic Equation of +Seawater 2010 (TEOS-10) is based primarily on numpy ufunc wrappers of the GSW-C +implementation. This library replaces the original python-gsw pure-python +implementation.. The primary reasons for this change are that by building on +the C implementation we reduce code duplication and we gain an immediate update +to the 75-term equation. +Additional benefits include a major increase in speed, a reduction in memory +usage, and the inclusion of more functions. The penalty is that a C +(or MSVC C++ for Windows) compiler is required to build the package from source.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + + (name, version, { + 'checksums': ['d24d820c8b43dbf72206cf5e3b0ed800b05aa85ca40afd39c9abd19849714197'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From e932e0d6366d8b05d06f1bdfd5a5db95a44e2f83 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Nov 2022 11:15:02 +0100 Subject: [PATCH 667/793] clean up version of Python dependency in pyWannier90 easyconfig --- .../p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb index ec32ef804a9..f4d75a875c3 100644 --- a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb +++ b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb @@ -32,12 +32,8 @@ builddependencies = [ ('pybind11', '2.6.2'), ] -local_pymaj = '3' -local_pymin = '9' -local_pymajmin = local_pymaj + local_pymin - dependencies = [ - ('Python', '%s.%s.5' % (local_pymaj, local_pymin)), + ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('PySCF', '1.7.6'), ] From e9fde4dae46df5bd922be8ec679aa7ec2cb5731d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 15 Nov 2022 11:46:23 +0100 Subject: [PATCH 668/793] Fix matlab version for 2021b --- .../MATLAB-Engine-2021b-GCCcore-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a188c57dcad --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'MATLAB-Engine' +version = '2021b' + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('MATLAB', version, '', True), + ('Python', '3.9.6'), +] + +use_pip = False +download_dep_fail = True + +# Since this setup.py does not provide a separate --build-base for the install +# step, both build and install must be performed in a single command. +prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " +buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" + +skipsteps = ['install'] + +# Test that connection with MATLAB can be established successfully +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +sanity_pip_check = True + +options = {'modulename': 'matlab.engine'} + +moduleclass = 'math' From 65119867029b4e74a665ec7013ddcaa8f4fb6b61 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 15 Nov 2022 10:50:13 +0000 Subject: [PATCH 669/793] adding easyconfigs: pyproj-3.4.0-GCCcore-11.3.0.eb --- .../p/pyproj/pyproj-3.4.0-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyproj/pyproj-3.4.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pyproj/pyproj-3.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pyproj/pyproj-3.4.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2fecab55426 --- /dev/null +++ b/easybuild/easyconfigs/p/pyproj/pyproj-3.4.0-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'pyproj' +version = '3.4.0' + +homepage = 'https://pyproj4.github.io/pyproj' +description = "Python interface to PROJ4 library for cartographic transformations" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a708445927ace9857f52c3ba67d2915da7b41a8fdcd9b8f99a4c9ed60a75eb33'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('PROJ', '9.0.0'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = "export PROJ_DIR=$EBROOTPROJ && " + +sanity_check_paths = { + 'files': ['bin/pyproj'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['pyproj --help'] + +sanity_pip_check = True + +moduleclass = 'data' From 6481ad003ff37ddc871a31436c89826013f7e268 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 15 Nov 2022 14:01:28 +0100 Subject: [PATCH 670/793] adding easyconfigs: Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb, OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb and patches: Xmipp-3.22.07-Helios_fix_missing_cuda_compatibility.cu_include.patch, Xmipp-3.22.07-Helios_fix_opencv_cuda_detection.patch --- ...CV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb | 99 +++++++++++++++++++ ...p-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb | 92 +++++++++++++++++ ...issing_cuda_compatibility.cu_include.patch | 55 +++++++++++ ....07-Helios_fix_opencv_cuda_detection.patch | 25 +++++ 4 files changed, 271 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_missing_cuda_compatibility.cu_include.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_opencv_cuda_detection.patch diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb new file mode 100644 index 00000000000..70276c87526 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb @@ -0,0 +1,99 @@ +name = 'OpenCV' +version = '4.6.0' +versionsuffix = '-CUDA-%(cudaver)s-contrib' + +# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake +local_ippicv_hash = 'a56b6ac6f030c312b2dce17430eef13aed9af274' + +homepage = 'https://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products. + Includes extra modules for OpenCV from the contrib repository.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'cstd': 'c++14'} + +sources = [ + { + 'source_urls': ['https://github.com/%(namelower)s/%(namelower)s/archive/'], + 'download_filename': '%(version)s.zip', + 'filename': SOURCELOWER_ZIP + }, + { + 'source_urls': ['https://github.com/%(namelower)s/opencv_contrib/archive/'], + 'download_filename': '%(version)s.zip', + 'filename': '%(namelower)s_contrib-%(version)s.zip' + }, + { + 'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], + 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', + 'extract_cmd': 'cp %s %(builddir)s' + }, +] +checksums = [ + '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359', # opencv-4.6.0.zip + '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3', # opencv_contrib-4.6.0.zip + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz +] + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('zlib', '1.2.12'), + ('FFmpeg', '4.4.2'), + ('freetype', '2.12.1'), + ('HarfBuzz', '4.2.1'), + ('libjpeg-turbo', '2.1.3'), + ('OpenJPEG', '2.5.0'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('libwebp', '1.2.4'), + ('OpenEXR', '3.1.5'), + ('JasPer', '2.0.33'), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.12', '-Java-%(javaver)s', SYSTEM), + ('GLib', '2.72.1'), + ('GTK4', '4.7.0'), + ('HDF5', '1.12.2'), + ('CUDA', '11.7.0', '', SYSTEM), + ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', SYSTEM), +] + +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = " ".join([ + "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules", + "-DFREETYPE_FOUND=ON", + "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/", + "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES_XXXXX=ON", + "-DHARFBUZZ_FOUND=ON", + "-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz", + "-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON", + "-DBUILD_opencv_python2=OFF", + "-DCUDA_NVCC_FLAGS=--std=c++14", +]) + +enhance_sanity_check = True + +local_contrib_libs = [ + 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', + 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', + 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', + 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' +] + +sanity_check_paths = { + 'files': ['lib64/libopencv_%s.%s' % (x, SHLIB_EXT) for x in local_contrib_libs], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..4093b1d0ecf --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,92 @@ +name = 'Xmipp' +version = '3.22.07-Helios' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/I2PC/scipion/wiki' +description = """Scipion is an image processing framework to obtain 3D +models of macromolecular complexes using Electron Microscopy (3DEM). It +integrates several software packages and presents an unified interface +for both biologists and developers. Scipion allows to execute workflows +combining different software tools, while taking care of formats and +conversions. Additionally, all steps are tracked and can be reproduced +later on. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [ + { + 'source_urls': ['https://github.com/I2PC/xmipp/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': '%(namelower)s-v%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/I2PC/xmippCore/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'xmippCore-v%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src', + }, + { + 'source_urls': ['https://github.com/I2PC/xmippViz/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'xmippViz-v%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src', + }, +] +patches = [ + '%(name)s-%(version)s_fix_scons_Environent_calls.patch', + '%(name)s-%(version)s_drop_useless_CXXFLAGS_setting.patch', + '%(name)s-%(version)s_correct_order_of_cu_includes.patch', + '%(name)s-%(version)s_dont_add_useless_libs.patch', + '%(name)s-%(version)s_dont_change_EB_build_flags.patch', + '%(name)s-%(version)s_fix_missing_cuda_compatibility.cu_include.patch', + '%(name)s-%(version)s_fix_opencv_cuda_detection.patch', + ('XmippCore-%(version)s_fix_scons_Environent_calls.patch', 'src/xmippCore'), + ('XmippCore-%(version)s_use_CXXFLAGS_from_EB.patch', 'src/xmippCore'), + ('XmippViz-%(version)s_fix_scons_Environent_calls.patch', 'src/xmippViz'), + ('XmippViz-%(version)s_use_CXXFLAGS_from_EB.patch', 'src/xmippViz'), +] +checksums = [ + {'xmipp-v3.22.07-Helios.tar.gz': 'f62e2729130b63d18e518930dd96a7a5250219e40c155abb78942a0642237ecf'}, + {'xmippCore-v3.22.07-Helios.tar.gz': '58e1143626cf807655a4756b165c21578d6f1b1777b43d363a2845d92d0bab8f'}, + {'xmippViz-v3.22.07-Helios.tar.gz': 'e1ce2cbbd57d3307d38538b29194a0190d633e5e062685387a6baf0329ad05b3'}, + {'Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch': + '5b59babad5a445ec7315a809509704d2d07232d2a5d180bfb78ebc8007bd0c95'}, + {'Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch': + '34ed0cb591e1e2788acd3e58696b1f45ce9210836d14ed1c99de1e574e4824e6'}, + {'Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch': + '2b0b2ddf349003be4112f4dca623586a03235214d6e64d232deb26468b52f0e3'}, + {'Xmipp-3.22.07-Helios_dont_add_useless_libs.patch': + '284b8ec1e514fb84b7680c8b3f59b3d5931b564beb444d3301504e3170e9a49e'}, + {'Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch': + '1514eaa5de35b38b5a10e949edf5c94ba95bbd05e0b9fbf70db2ea98967394e3'}, + {'XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch': + '8dcf0f3648f4b3438374ba629a9efa2e5c08eb25ae76ed420513664d21e2246b'}, + {'XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch': + 'd86b0d3ecc339b81c9aa7a33d2b44b428643aa7e2e686529b4bb6b16d36805c2'}, + {'XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch': + '7724fc3953d9c4c308a5755f54229259425fdbad5a909153bd173292434407b9'}, + {'XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch': + 'a8bea23c243174fb27a140a34a064a622cc96f0e7231fd31caf20f90c7ba9555'}, +] + +builddependencies = [ + ('SCons', '4.4.0'), + ('CTPL', '0.0.2'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('UCX-CUDA', '1.12.1', versionsuffix), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Java', '11', '', SYSTEM), + ('OpenCV', '4.6.0', versionsuffix + '-contrib'), + ('SQLite', '3.38.3'), + ('HDF5', '1.12.2'), + ('LibTIFF', '4.3.0'), + ('libjpeg-turbo', '2.1.3'), + ('LIBSVM', '3.30'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_missing_cuda_compatibility.cu_include.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_missing_cuda_compatibility.cu_include.patch new file mode 100644 index 00000000000..52dc98a1212 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_missing_cuda_compatibility.cu_include.patch @@ -0,0 +1,55 @@ +Fix support for CUDA arch < 6.0 + +Åke Sandgren, 2022-11-14 +diff --git a/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.cu b/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.cu +index 83189250..f125e47d 100644 +--- a/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.cu ++++ b/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.cu +@@ -28,8 +28,9 @@ + + #include "cuda_compatibility.h" + ++#if defined(__CUDA_ARCH__) + #if __CUDA_ARCH__ < 600 +-__device__ double atomicAdd(double* address, double val) ++static __inline__ __device__ double atomicAdd(double* address, double val) + { + unsigned long long int* address_as_ull = + (unsigned long long int*)address; +@@ -47,6 +48,7 @@ __device__ double atomicAdd(double* address, double val) + return __longlong_as_double(old); + } + #endif ++#endif + + + #endif /* LIBRARIES_RECONSTRUCTION_CUDA_CUDA_COMPATIBILITY_CU_ */ +diff --git a/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.h b/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.h +index 3bb44e0f..279ccbcb 100644 +--- a/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.h ++++ b/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.h +@@ -27,7 +27,11 @@ + #define LIBRARIES_RECONSTRUCTION_CUDA_CUDA_COMPATIBILITY_H_ + + +-__device__ double atomicAdd(double* address, double val); ++#if defined(__CUDA_ARCH__) ++#if __CUDA_ARCH__ < 600 ++static __inline__ __device__ double atomicAdd(double* address, double val); ++#endif ++#endif + + + #endif /* LIBRARIES_RECONSTRUCTION_CUDA_CUDA_COMPATIBILITY_H_ */ +diff --git a/src/xmipp/libraries/reconstruction_cuda/cuda_correlation.cu b/src/xmipp/libraries/reconstruction_cuda/cuda_correlation.cu +index c7dea8fb..9e267336 100644 +--- a/src/xmipp/libraries/reconstruction_cuda/cuda_correlation.cu ++++ b/src/xmipp/libraries/reconstruction_cuda/cuda_correlation.cu +@@ -27,6 +27,7 @@ + #define LIBRARIES_RECONSTRUCTION_CUDA_CUDA_CORRELATION_CU_ + + #include "cuda_compatibility.h" ++#include "cuda_compatibility.cu" + + /** + * Function computes sum and sum squared for each 2D signal diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_opencv_cuda_detection.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_opencv_cuda_detection.patch new file mode 100644 index 00000000000..0575ef6a225 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_opencv_cuda_detection.patch @@ -0,0 +1,25 @@ +Fix detection of OpenCV >= 3 + +Åke Sandgren, 2022-11-14 +diff --git a/src/xmipp/SConscript b/src/xmipp/SConscript +index a767fb99..89777947 100644 +--- a/src/xmipp/SConscript ++++ b/src/xmipp/SConscript +@@ -46,7 +46,7 @@ debug = get('DEBUG') + matlab = get('MATLAB') + opencv = env.GetOption('opencv') and get('OPENCV') + opencvsupportscuda = get('OPENCVSUPPORTSCUDA') +-opencv_3 = get('OPENCV3') ++opencv_ver = int(os.environ.get('OPENCV_VERSION', '0')) + starpu = get('STARPU') + + if opencv: +@@ -55,7 +55,7 @@ if opencv: + 'opencv_video', + 'libopencv_calib3d'] + if opencvsupportscuda: +- if opencv_3: ++ if opencv_ver >= 3: + opencvLibs+=['libopencv_cudaoptflow', 'libopencv_cudaarithm'] + else: + opencvLibs+=['libopencv_gpu'] From 5b850bac0acb053edd023b59e930b9216ae39022 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 15 Nov 2022 14:02:35 +0100 Subject: [PATCH 671/793] adding easyconfigs: NanoPlot-1.33.0-foss-2021a.eb, nanomath-1.2.1-foss-2021a.eb, nanoget-1.18.1-foss-2021a.eb, pauvre-0.2.3-foss-2021a.eb --- .../n/NanoPlot/NanoPlot-1.33.0-foss-2021a.eb | 47 +++++++++++++++++++ .../n/nanoget/nanoget-1.18.1-foss-2021a.eb | 29 ++++++++++++ .../n/nanomath/nanomath-1.2.1-foss-2021a.eb | 33 +++++++++++++ .../p/pauvre/pauvre-0.2.3-foss-2021a.eb | 40 ++++++++++++++++ 4 files changed, 149 insertions(+) create mode 100644 easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/n/nanoget/nanoget-1.18.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/n/nanomath/nanomath-1.2.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/pauvre/pauvre-0.2.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-foss-2021a.eb b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-foss-2021a.eb new file mode 100644 index 00000000000..400d3660c4d --- /dev/null +++ b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-foss-2021a.eb @@ -0,0 +1,47 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'NanoPlot' +version = '1.33.0' + +homepage = 'https://github.com/wdecoster/NanoPlot' +description = "Plotting suite for long read sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['caf69a5789625e746814238cb4f0d510ed6768a094566e8f1dcaa77933c4d6fd'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('Pysam', '0.16.0.1'), + ('nanomath', '1.2.1'), + ('nanoget', '1.18.1'), + ('Seaborn', '0.11.2'), + ('plotly.py', '5.1.0'), + ('pauvre', '0.2.3'), + ('statsmodels', '0.12.2'), + ('Arrow', '6.0.0'), # for pyarrow + ('Kaleido', '0.2.1'), +] + +download_dep_fail = True +use_pip = True + +# replace strict Seaborn & pauvre version requirement with minimal version requirements +preinstallopts = "sed -i 's/==0/>=0/g' setup.py && " + +sanity_check_paths = { + 'files': ['bin/NanoPlot'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoPlot --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nanoget/nanoget-1.18.1-foss-2021a.eb b/easybuild/easyconfigs/n/nanoget/nanoget-1.18.1-foss-2021a.eb new file mode 100644 index 00000000000..82b4f0b5841 --- /dev/null +++ b/easybuild/easyconfigs/n/nanoget/nanoget-1.18.1-foss-2021a.eb @@ -0,0 +1,29 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'nanoget' +version = '1.18.1' + +homepage = 'https://github.com/wdecoster/nanoget' +description = "Functions to extract information from Oxford Nanopore sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e4fa37ab1bccc3287947f5792acad3c96fd1c02cb9c0a1f5d218d26bcdbe1632'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('Pysam', '0.16.0.1'), + ('nanomath', '1.2.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nanomath/nanomath-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/n/nanomath/nanomath-1.2.1-foss-2021a.eb new file mode 100644 index 00000000000..5d1a69c2f73 --- /dev/null +++ b/easybuild/easyconfigs/n/nanomath/nanomath-1.2.1-foss-2021a.eb @@ -0,0 +1,33 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'nanomath' +version = '1.2.1' + +homepage = 'https://github.com/wdecoster/nanomath' +description = "A few simple math function for other Oxford Nanopore processing scripts" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +use_pip = True + +exts_list = [ + ('Python-Deprecated', '1.1.0', { + 'modulename': 'deprecated', + 'checksums': ['a242b3c1721f97912330b12cd5529abfa5b3876084a6c60a2c683a87d4b0dd6f'], + }), + (name, version, { + 'checksums': ['3c611c3b0a8fa364b8afe87c948f31d5d8009a212c28954382e926f36f90e060'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/pauvre/pauvre-0.2.3-foss-2021a.eb b/easybuild/easyconfigs/p/pauvre/pauvre-0.2.3-foss-2021a.eb new file mode 100644 index 00000000000..5bd495d2adb --- /dev/null +++ b/easybuild/easyconfigs/p/pauvre/pauvre-0.2.3-foss-2021a.eb @@ -0,0 +1,40 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'pauvre' +version = '0.2.3' + +homepage = 'https://github.com/conchoecia/pauvre' +description = "Tools for plotting Oxford Nanopore and other long-read data" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ba756bc9025ae7edafd91092d12a57864f018958fd46b548e9eeda7167ee197d'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('scikit-learn', '0.24.2'), + ('matplotlib', '3.4.2'), +] + +download_dep_fail = True +use_pip = True + +# fix incorrect requirement, correct name is 'scikit-learn' +preinstallopts = "sed -i 's/sklearn/scikit-learn/g' setup.py && " + +sanity_check_paths = { + 'files': ['bin/pauvre'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pauvre --help"] + +sanity_pip_check = True + +moduleclass = 'math' From d6d8efaeb2b212f224ca7aadbd451f3185d63702 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 15 Nov 2022 13:04:53 +0000 Subject: [PATCH 672/793] adding easyconfigs: basemap-1.3.6-foss-2022a.eb --- .../b/basemap/basemap-1.3.6-foss-2022a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb b/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb new file mode 100644 index 00000000000..9b019b172c7 --- /dev/null +++ b/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb @@ -0,0 +1,51 @@ +# The newer version require also the installation of basemap-data. +# Conveniently, the tarball contains that too, so that is the one +# being used here. +# Based on basemap-1.2.2-foss-2020a-Python-3.8.2.eb +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'basemap' +version = '1.3.6' + +homepage = 'https://matplotlib.org/basemap/' +description = """The matplotlib basemap toolkit is a library for plotting +2D data on maps in Python""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('matplotlib', '3.5.2'), + ('GEOS', '3.10.3'), + ('Pillow', '9.1.1'), + ('pyproj', '3.4.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyshp', '2.3.1', { + 'modulename': 'shapefile', + 'checksums': ['4caec82fd8dd096feba8217858068bacb2a3b5950f43c048c6dc32a3489d5af1'], + }), + ('basemap_data', version, { + 'modulename': 'mpl_toolkits.basemap_data', + 'preinstallopts': 'cd packages/%(name)s && GEOS_DIR=$EBROOTGEOS', + 'sources': ['v%(version)s.tar.gz'], + 'source_urls': ['https://github.com/matplotlib/basemap/archive/'], + 'checksums': ['42adbd039b4afbe93ca2fa32cfab456d4fd590cb8ed1c28e4aa94dcb957b58ac'], + }), + (name, version, { + 'modulename': 'mpl_toolkits.basemap', + 'prebuildopts': 'GEOS_DIR=$EBROOTGEOS', + 'preinstallopts': 'cd packages/%(name)s && GEOS_DIR=$EBROOTGEOS', + 'sources': ['v%(version)s.tar.gz'], + 'source_urls': ['https://github.com/matplotlib/basemap/archive/'], + 'checksums': ['42adbd039b4afbe93ca2fa32cfab456d4fd590cb8ed1c28e4aa94dcb957b58ac'], + }), +] + +moduleclass = 'vis' From 92db9c418e97d27131129390c58cfc7b640eb856 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 15 Nov 2022 14:28:06 +0100 Subject: [PATCH 673/793] delete easyconfig MATLAB-Engine-2021a-GCCcore-11.2.0.eb --- .../MATLAB-Engine-2021a-GCCcore-11.2.0.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb deleted file mode 100644 index c1558fb7dc9..00000000000 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'MATLAB-Engine' -version = '2021a' - -homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' -description = """The MATLAB Engine API for Python provides a package for Python - to call MATLAB as a computational engine.""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -dependencies = [ - ('MATLAB', version, '', SYSTEM), - ('Python', '3.9.6'), -] - -use_pip = False -download_dep_fail = True - -# Enable support for this current version of Python -prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " -prebuildopts += "sed -i 's/^_supported_versions =.*/_supported_versions = ["%(pyshortver)s"]/' setup.py &&" -# Since this setup.py does not provide a separate --build-base for the install -# step, both build and install must be performed in a single command. -buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" - -skipsteps = ['install'] - -# Test that connection with MATLAB can be established successfully -sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] - -sanity_pip_check = True - -options = {'modulename': 'matlab.engine'} - -moduleclass = 'math' From 2f5588ac858d263d70cd36b50c30f9fe558bce4d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Nov 2022 14:58:22 +0100 Subject: [PATCH 674/793] clean up version of Python dependency in pyWannier90 easyconfig --- .../p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb index 2a045c216cc..3a1d4b39c48 100644 --- a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb +++ b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb @@ -32,12 +32,8 @@ builddependencies = [ ('pybind11', '2.6.2'), ] -local_pymaj = '3' -local_pymin = '9' -local_pymajmin = local_pymaj + local_pymin - dependencies = [ - ('Python', '%s.%s.5' % (local_pymaj, local_pymin)), + ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('PySCF', '1.7.6'), ] From 128ac0711acc1726eb87226ec706e199781e4048 Mon Sep 17 00:00:00 2001 From: alberta Date: Tue, 15 Nov 2022 15:04:34 +0100 Subject: [PATCH 675/793] adding easyconfigs: resolos-0.3.5.eb --- .../easyconfigs/r/resolos/resolos-0.3.5.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb diff --git a/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb b/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb new file mode 100644 index 00000000000..f588b3b926d --- /dev/null +++ b/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'resolos' +version = '0.3.5' + +homepage = 'https://gitlab.unige.ch/resolos/resolos' +description = """Resolos is a toolkit written in Python for maintaining reproducible environments for scientific computations. +It's main goal is to enable researchers to easily replicate environments through space (running code on HPC environment) +and time (environment preservation for long term archival). +For installation and detailed usage, check out the documentation.""" + +toolchain = {'name': 'system', 'version': ''} + +# source_urls = [PYPI_SOURCE] +# Link copy from pypi.org | PYPI_SOURCE is not working +sources = ["https://files.pythonhosted.org/packages/15/0b/fa95a349434f77d8afc775dd999152d7612b6baed52083981ac84eaa41e9/resolos-0.3.5.tar.gz"] +checksums = ['c0fb50e36866fa591f0a7ab3567e9037c97d96f34614e86ee9cad1b62c689de2'] + + +use_pip = True +use_pip_for_deps = True +moduleclass = 'data' + +sanity_check_commands = ["r3s info"] +sanity_check_paths = { + 'files': ["bin/r3s"], + 'dirs': [] +} From fb8f6c3b3fed32f72044265daa3bbc02ca00dca6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Nov 2022 16:48:12 +0100 Subject: [PATCH 676/793] {toolchain} intel/2022.11 --- .../h/HPL/HPL-2.3-intel-2022.11.eb | 21 ++++++++++++ .../easyconfigs/i/iimpi/iimpi-2022.11.eb | 18 ++++++++++ .../imkl-FFTW-2022.2.1-iimpi-2022.11.eb | 11 +++++++ easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb | 18 ++++++++++ .../impi-2021.7.1-intel-compilers-2022.2.1.eb | 16 +++++++++ .../intel-compilers-2022.2.1.eb | 33 +++++++++++++++++++ .../easyconfigs/i/intel/intel-2022.11.eb | 22 +++++++++++++ 7 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.11.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2022.11.eb create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022.11.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2022.11.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.11.eb new file mode 100644 index 00000000000..6b5eb683de8 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.11.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2022.11'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2022.11.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2022.11.eb new file mode 100644 index 00000000000..49aa4591617 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2022.11.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2022.11' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2022.2.1' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', '2021.7.1', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022.11.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022.11.eb new file mode 100644 index 00000000000..ff00372cf4e --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022.11.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2022.2.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2022.11'} + +dependencies = [('imkl', version, '', SYSTEM)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb new file mode 100644 index 00000000000..3daf55958a3 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb @@ -0,0 +1,18 @@ +name = 'imkl' +version = '2022.2.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19038/'] +sources = ['l_onemkl_p_%(version)s.16993_offline.sh'] +checksums = ['eedd4b795720de776b1fc5f542ae0fac37ec235cdb567f7c2ee3182e73e3e59d'] + +interfaces = False + +installopts = "--download-cache=%(builddir)s/cache --download-dir=%(builddir)s/download --log-dir=%(builddir)s/log" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb new file mode 100644 index 00000000000..68aeb9beb63 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb @@ -0,0 +1,16 @@ +name = 'impi' +version = '2021.7.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19010/'] +sources = ['l_mpi_oneapi_p_%(version)s.16815_offline.sh'] +checksums = ['90e7804f2367d457cd4cbf7aa29f1c5676287aa9b34f93e7c9a19e4b8583fff7'] + +dependencies = [('UCX', '1.13.1')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb new file mode 100644 index 00000000000..a6ae8170105 --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb @@ -0,0 +1,33 @@ +name = 'intel-compilers' +version = '2022.2.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19030/'], + 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.16991_offline.sh', + }, + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18998/'], + 'filename': 'l_fortran-compiler_p_%(version)s.16992_offline.sh', + }, +] +checksums = [ + {'l_dpcpp-cpp-compiler_p_2022.2.1.16991_offline.sh': + '3f0f02f9812a0cdf01922d2df9348910c6a4cb4f9dfe50fc7477a59bbb1f7173'}, + {'l_fortran-compiler_p_2022.2.1.16992_offline.sh': + '64f1d1efbcdc3ac2182bec18313ca23f800d94f69758db83a1394490d9d4b042'}, +] + +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/intel/intel-2022.11.eb b/easybuild/easyconfigs/i/intel/intel-2022.11.eb new file mode 100644 index 00000000000..9dd32ad27d5 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2022.11.eb @@ -0,0 +1,22 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2022.11' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2022.2.1' +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', '2021.7.1', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', SYSTEM), + ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From ed16eb8d76b55f3a37df562ae89fd33ff850c127 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 15 Nov 2022 16:38:33 +0000 Subject: [PATCH 677/793] adding easyconfigs: zarr-2.13.3-foss-2022a.eb --- .../z/zarr/zarr-2.13.3-foss-2022a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb new file mode 100644 index 00000000000..ff8bb790e8f --- /dev/null +++ b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb @@ -0,0 +1,41 @@ +easyblock = "PythonBundle" + +name = 'zarr' +version = '2.13.3' + +homepage = 'https://zarr.readthedocs.io/en/stable/' +description = """Zarr is a Python package providing an implementation of compressed, +chunked, N-dimensional arrays, designed for use in parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('entrypoints', '0.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('asciitree', '0.3.3', { + 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], + }), + ('fasteners', '0.18', { + 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], + }), + ('monotonic', '1.6', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/atdt/monotonic/archive'], + 'checksums': ['9609c249aed584fd714811014870650d08d6f6414402b5a190663c49bf83b221'], + }), + ('numcodecs', '0.10.2', { + 'checksums': ['22838c6b3fd986bd9c724039b88870057f790e22b20e6e1cbbaa0de142dd59c4'], + }), + (name, version, { + 'checksums': ['db24b090616c638f65e33a6bc5d956d642221182961515ccbc28b17fb0d0b48c'], + }), +] + +moduleclass = 'data' From 5a553631d9eab4892c2ef75825406ec479bea08e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 15 Nov 2022 17:41:54 +0100 Subject: [PATCH 678/793] Use SWIG as builddependencies --- easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb index 54f52a70197..50daf951ccb 100644 --- a/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb @@ -17,12 +17,15 @@ software_license = 'LicenseGPLv2' toolchain = {'name': 'foss', 'version': '2021a'} +builddependencies = [ + ('SWIG', '4.0.2'), +] + dependencies = [ ('Python', '3.9.5'), ('ruamel.yaml', '0.17.21'), ('SciPy-bundle', '2021.05'), ('sympy', '1.8'), - ('SWIG', '4.0.2'), ('GLPK', '5.0'), ('python-libsbml', '5.19.7'), ] From 11f9457cddcb386b1bfd6aaf2e2759386ffb852e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 15 Nov 2022 19:13:34 +0100 Subject: [PATCH 679/793] Add missing checksums --- .../x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb index 4093b1d0ecf..fc96f59b860 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb @@ -60,6 +60,10 @@ checksums = [ '284b8ec1e514fb84b7680c8b3f59b3d5931b564beb444d3301504e3170e9a49e'}, {'Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch': '1514eaa5de35b38b5a10e949edf5c94ba95bbd05e0b9fbf70db2ea98967394e3'}, + {'Xmipp-3.22.07-Helios_fix_missing_cuda_compatibility.cu_include.patch': + 'b478c08a6a260021b4b91e5a8f6d9c5637eafdedcd99fcb672fe356d1744d349'}, + {'Xmipp-3.22.07-Helios_fix_opencv_cuda_detection.patch': + '9d7c90a8cdeca24dba41a0d2f11f59ab34a438ed34fa7f4850172848505ecbae'}, {'XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch': '8dcf0f3648f4b3438374ba629a9efa2e5c08eb25ae76ed420513664d21e2246b'}, {'XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch': From bb635813adaecf716c61c72ac083d73e49f84177 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 02:26:55 +0100 Subject: [PATCH 680/793] update MATLAB-Engine v2021a to PyPI package v2021a-9.10.1 --- ...TLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb | 38 +++++++++++++++++++ .../MATLAB-Engine-2021a-GCCcore-10.2.0.eb | 34 ----------------- 2 files changed, 38 insertions(+), 34 deletions(-) create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb delete mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..97c48e8fad3 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'MATLAB-Engine' +_matlab_version = '2021a' +_engine_version = '9.10.1' +version = "%s-%s" % (_matlab_version, _engine_version) + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('MATLAB', _matlab_version, '', SYSTEM), + ('Python', '3.8.6'), +] + +use_pip = True + +exts_list = [ + ('matlabengine', '9.10.1', { + 'modulename': 'matlab.engine', + 'checksums': ['c1610690dbe58ac00e74e8cbb20406208235ede47da7960238e0c2fd3bd496c0'], + }), +] + +sanity_pip_check = True + +# Test that connection with MATLAB can be established successfully +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +# Systems with old glibc (e.g. CentOS7) need to preload shim library +# modluafooter = """ +# setenv("LD_PRELOAD", pathJoin(os.getenv("EBROOTMATLAB"), "bin", "glnxa64", "glibc-2.17_shim.so")) +# """ + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb deleted file mode 100644 index 83a3d5d719c..00000000000 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'MATLAB-Engine' -version = '2021a' - -homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' -description = """The MATLAB Engine API for Python provides a package for Python - to call MATLAB as a computational engine.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -dependencies = [ - ('MATLAB', version, '', SYSTEM), - ('Python', '3.8.6'), -] - -use_pip = False -download_dep_fail = True - -# Since this setup.py does not provide a separate --build-base for the install -# step, both build and install must be performed in a single command. -prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " -buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" - -skipsteps = ['install'] - -# Test that connection with MATLAB can be established successfully -sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] - -sanity_pip_check = True - -options = {'modulename': 'matlab.engine'} - -moduleclass = 'math' From abbb3aa220b6ab59d9720d484cb12aa0774d6ec8 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 02:28:13 +0100 Subject: [PATCH 681/793] update MATLAB-Engine v2021b to PyPI package v2021b-9.11.19 --- ...LAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb | 38 +++++++++++++++++++ .../MATLAB-Engine-2021b-GCCcore-11.2.0.eb | 34 ----------------- 2 files changed, 38 insertions(+), 34 deletions(-) create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb delete mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c7c345f46d5 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'MATLAB-Engine' +_matlab_version = '2021b' +_engine_version = '9.11.19' +version = "%s-%s" % (_matlab_version, _engine_version) + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('MATLAB', _matlab_version, '', SYSTEM), + ('Python', '3.9.6'), +] + +use_pip = True + +exts_list = [ + ('matlabengine', '9.11.19', { + 'modulename': 'matlab.engine', + 'checksums': ['9385a13c27daa18f6cbfbe1669237e86692a51f317775a3f40e9e3d8090c679b'], + }), +] + +sanity_pip_check = True + +# Test that connection with MATLAB can be established successfully +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +# Systems with old glibc (e.g. CentOS7) need to preload shim library +# modluafooter = """ +# setenv("LD_PRELOAD", pathJoin(os.getenv("EBROOTMATLAB"), "bin", "glnxa64", "glibc-2.17_shim.so")) +# """ + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb deleted file mode 100644 index a188c57dcad..00000000000 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'MATLAB-Engine' -version = '2021b' - -homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' -description = """The MATLAB Engine API for Python provides a package for Python - to call MATLAB as a computational engine.""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -dependencies = [ - ('MATLAB', version, '', True), - ('Python', '3.9.6'), -] - -use_pip = False -download_dep_fail = True - -# Since this setup.py does not provide a separate --build-base for the install -# step, both build and install must be performed in a single command. -prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " -buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" - -skipsteps = ['install'] - -# Test that connection with MATLAB can be established successfully -sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] - -sanity_pip_check = True - -options = {'modulename': 'matlab.engine'} - -moduleclass = 'math' From 1b69e4da4ebe89d50fdde47eb3518d14ac80572d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 08:24:15 +0100 Subject: [PATCH 682/793] adding easyconfigs: Meson-0.64.0-GCCcore-12.2.0.eb --- .../m/Meson/Meson-0.64.0-GCCcore-12.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/Meson/Meson-0.64.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.64.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/Meson/Meson-0.64.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..167a5228187 --- /dev/null +++ b/easybuild/easyconfigs/m/Meson/Meson-0.64.0-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'Meson' +version = '0.64.0' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c5e27e091c2a35b9049e152a6535045ebbd057253aeb67856de6ecbb7b917bab'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), # includes required 'wheel' package + ('Ninja', '1.11.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["meson --help"] + +moduleclass = 'tools' From 34b52a6d8a9dfb1a127cf9091d6edac8e56994f9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 16 Nov 2022 12:32:59 +0000 Subject: [PATCH 683/793] adding easyconfigs: ANSYS-2022R2.eb --- easybuild/easyconfigs/a/ANSYS/ANSYS-2022R2.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANSYS/ANSYS-2022R2.eb diff --git a/easybuild/easyconfigs/a/ANSYS/ANSYS-2022R2.eb b/easybuild/easyconfigs/a/ANSYS/ANSYS-2022R2.eb new file mode 100644 index 00000000000..5c94e25f8af --- /dev/null +++ b/easybuild/easyconfigs/a/ANSYS/ANSYS-2022R2.eb @@ -0,0 +1,30 @@ +name = 'ANSYS' +version = '2022R2' + +homepage = 'https://www.ansys.com' +description = """ANSYS simulation software enables organizations to confidently predict + how their products will operate in the real world. We believe that every product is + a promise of something greater. """ + +toolchain = SYSTEM + +download_instructions = 'Manually obtain (ANSYS%(version)s_LINX64_DiskX.iso) from your ANSYS vendor' +# Custom extract command is used since iso sources contain duplicate file. +sources = [ + {'filename': 'ANSYS%(version)s_LINX64_Disk1.iso', 'extract_cmd': '7z x -aos %s'}, + {'filename': 'ANSYS%(version)s_LINX64_Disk2.iso', 'extract_cmd': '7z x -aos %s'}, + {'filename': 'ANSYS%(version)s_LINX64_Disk3.iso', 'extract_cmd': '7z x -aos %s'}, +] +checksums = [ + {'ANSYS2022R2_LINX64_Disk1.iso': '7c9b2a57dd3b87c1dabcd84c913135c83aaac46bf75fbe3fae8da61c85e78198'}, + {'ANSYS2022R2_LINX64_Disk2.iso': '7962ef251e2edb7e999bfb6a857272597973d7ac4c17c2271cfd891347fd452a'}, + {'ANSYS2022R2_LINX64_Disk3.iso': '58d4b72e90a27fe11aee3cd7db251ecd1f80b2353441e7061543c0fc21c14dac'}, +] + +osdependencies = [('p7zip-plugins', 'p7zip-full')] # for extracting iso-files + +# Specify license_server and license_server_port here, or use EB_ANSYS_LICENSE_SERVER and EB_ANSYS_LICENSE_SERVER_PORT +# license_server = "ansys.lic.example.com" +# license_server_port = "1234:5678" + +moduleclass = 'tools' From d431b26b6874c8baec79d10637f28eef402851e8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 16 Nov 2022 15:40:37 +0100 Subject: [PATCH 684/793] adding easyconfigs: IOR-3.3.0-gompi-2022a.eb --- .../i/IOR/IOR-3.3.0-gompi-2022a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb new file mode 100644 index 00000000000..9b3059aa224 --- /dev/null +++ b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Åke Sandgren, HPC2N, Umeå University + +easyblock = 'ConfigureMake' + +name = "IOR" +version = "3.3.0" + +homepage = 'https://github.com/hpc/ior' +description = """ The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, + or HDF5 interfaces. """ + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/hpc/ior/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['41fe66f91aead70f7e53246de68dd194e7ade72070faf696f88efffdcf1bf68b'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Perl', '5.34.1'), +] +dependencies = [ + ('HDF5', '1.12.2'), +] + +configopts = '--with-hdf5 ' +buildopts = 'V=1 ' + +sanity_check_paths = { + 'files': ["bin/ior"], + 'dirs': ["share"] +} + +moduleclass = 'tools' From 4b5e30730dc76f670816a72e2c72017ceeab7685 Mon Sep 17 00:00:00 2001 From: Bart te Lindert Date: Wed, 16 Nov 2022 15:50:27 +0100 Subject: [PATCH 685/793] adding easyconfigs: FreeSurfer-7.3.2-centos7_x86_64.eb --- .../FreeSurfer-7.3.2-centos7_x86_64.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos7_x86_64.eb diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos7_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos7_x86_64.eb new file mode 100644 index 00000000000..56892c77fd0 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos7_x86_64.eb @@ -0,0 +1,33 @@ +name = 'FreeSurfer' +version = '7.3.2' +versionsuffix = '-centos7_x86_64' + +homepage = 'https://surfer.nmr.mgh.harvard.edu/' +description = """FreeSurfer is a set of tools for analysis and visualization +of structural and functional brain imaging data. FreeSurfer contains a fully +automatic structural imaging stream for processing cross sectional and +longitudinal data.""" + +toolchain = SYSTEM + +source_urls = [ + 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', + 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' +] +sources = [ + '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', + 'runtime2014bLinux.tar.gz' +] +checksums = [ + {'freesurfer-linux-centos7_x86_64-7.3.2.tar.gz': + '58518d3ee5abd2e05109208aed2eef145c4e3b994164df8c4e0033c1343b9e56'}, + {'runtime2014bLinux.tar.gz': '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648'}, +] + +postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] + +license_text = """email@example.com +00000 +g1bb3r1sh""" + +moduleclass = 'bio' From 70debb7b60b88734a6f13e6e6e6e4575bc2ed55e Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 16 Nov 2022 14:59:19 +0000 Subject: [PATCH 686/793] adding easyconfigs: cmocean-2.0-foss-2022a.eb --- .../c/cmocean/cmocean-2.0-foss-2022a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb b/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb new file mode 100644 index 00000000000..3531eb02047 --- /dev/null +++ b/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb @@ -0,0 +1,31 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = "PythonBundle" + +name = 'cmocean' +version = '2.0' + +homepage = 'https://github.com/matplotlib/cmocean' +description = """This package contains colormaps for commonly-used +oceanographic variables. Most of the colormaps started from +matplotlib colormaps, but have now been adjusted using the viscm +tool to be perceptually uniform.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['13eea3c8994d8e303e32a2db0b3e686f6edfb41cb21e7b0e663c2b17eea9b03a'], + }), +] + +moduleclass = 'data' From 1f6acfd410de14901f935a58f00c6ff363dc4529 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 16 Nov 2022 15:05:56 +0000 Subject: [PATCH 687/793] Sanity check added --- easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb b/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb index 3531eb02047..452ee96673d 100644 --- a/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb @@ -28,4 +28,9 @@ exts_list = [ }), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + moduleclass = 'data' From e5deb360201cab927d4603083b499a16f4b871b7 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 16 Nov 2022 15:18:07 +0000 Subject: [PATCH 688/793] adding easyconfigs: astropy-5.1.1-foss-2022a.eb --- .../a/astropy/astropy-5.1.1-foss-2022a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/a/astropy/astropy-5.1.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/astropy/astropy-5.1.1-foss-2022a.eb b/easybuild/easyconfigs/a/astropy/astropy-5.1.1-foss-2022a.eb new file mode 100644 index 00000000000..1e3d64025d1 --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-5.1.1-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = "PythonBundle" + +name = 'astropy' +version = '5.1.1' + +homepage = 'https://www.astropy.org/' +description = """The Astropy Project is a community effort to develop a common +core package for Astronomy in Python and foster an ecosystem of interoperable +astronomy packages. + +The Astropy community is committed to supporting diversity and inclusion.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyerfa', '2.0.0.1', { + 'modulename': 'erfa', + 'checksums': ['2fd4637ffe2c1e6ede7482c13f583ba7c73119d78bef90175448ce506a0ede30'], + }), + ('extension-helpers', '1.0.0', { + 'checksums': ['ca1bfac67c79cf4a7a0c09286ce2a24eec31bf17715818d0726318dd0e5050e6'], + }), + (name, version, { + 'checksums': ['ba4bd696af7090fd399b464c704bf27b5633121e461785edc70432606a94bd81'], + }), +] + +moduleclass = 'astro' From d0033ea45c9888ee61dbca3e9bb5cbb632b5ddc6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 16:34:47 +0100 Subject: [PATCH 689/793] adding easyconfigs: intltool-0.51.0-GCCcore-12.2.0.eb --- .../intltool-0.51.0-GCCcore-12.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..68c3f09136f --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' + +homepage = 'https://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +patches = ['intltool-%(version)s_fix-Perl-compat.patch'] +checksums = [ + '67c74d94196b153b774ab9f89b2fa6c6ba79352407037c8c14d5aeb334e959cd', # intltool-0.51.0.tar.gz + 'e839f7228b2b92301831bca88ed0bc7bce5dbf862568f1644642988204903db6', # intltool-0.51.0_fix-Perl-compat.patch +] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Perl', '5.36.0'), +] + +fix_perl_shebang_for = ['bin/intltool-*'] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +sanity_check_commands = ["intltool-merge --help"] + +moduleclass = 'devel' From 6ae319ac98043b85b314fcb44757bfce5ef34628 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 16:36:54 +0100 Subject: [PATCH 690/793] adding easyconfigs: freetype-2.12.1-GCCcore-12.2.0.eb, Brotli-1.0.9-GCCcore-12.2.0.eb --- .../b/Brotli/Brotli-1.0.9-GCCcore-12.2.0.eb | 36 ++++++++++++++++ .../freetype-2.12.1-GCCcore-12.2.0.eb | 43 +++++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.12.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..8056873eb95 --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'Brotli' +version = '1.0.9' + +homepage = 'https://github.com/google/brotli' +description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination + of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio + comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate + but offers more dense compression. +The specification of the Brotli Compressed Data Format is defined in RFC 7932.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/google/brotli/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['Brotli-%(version)s_pc_link_flags.patch'] +checksums = [ + 'f9e8d81d0405ba66d181529af42a3354f838c939095ff99930da6aa9cdf6fe46', # v1.0.9.tar.gz + '1a8498fe5179fa530d5e6da57632a7ca8ee98b462953b9995e3400cdac4c3d7e', # Brotli-1.0.9_pc_link_flags.patch +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT, + 'lib/libbrotlidec-static.a', 'lib/libbrotlienc-static.a'], + 'dirs': [], +} + +sanity_check_commands = ["brotli --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.12.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.12.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..4b7d4298ad1 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.12.1-GCCcore-12.2.0.eb @@ -0,0 +1,43 @@ +name = 'freetype' +version = '2.12.1' + +homepage = 'https://www.freetype.org' + +description = """ + FreeType 2 is a software font engine that is designed to be small, efficient, + highly customizable, and portable while capable of producing high-quality + output (glyph images). It can be used in graphics libraries, display servers, + font conversion tools, text image generation tools, and many other products + as well. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + GNU_SAVANNAH_SOURCE, + SOURCEFORGE_SOURCE, +] +sources = [SOURCE_TAR_GZ] +checksums = ['efe71fd4b8246f1b0b1b9bfca13cfff1c9ad85930340c27df469733bbb620938'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('libpng', '1.6.38'), + ('zlib', '1.2.12'), + ('Brotli', '1.0.9'), +] + +configopts = '--enable-freetype-config --with-harfbuzz=no' + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', + 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +sanity_check_commands = ["freetype-config --help"] + +moduleclass = 'vis' From e7441c854d59e7bc4fbe2d10743688559653681b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 16:37:46 +0100 Subject: [PATCH 691/793] adding easyconfigs: fontconfig-2.14.1-GCCcore-12.2.0.eb, util-linux-2.38.1-GCCcore-12.2.0.eb, gperf-3.1-GCCcore-12.2.0.eb --- .../fontconfig-2.14.1-GCCcore-12.2.0.eb | 40 ++++++++++++++++++ .../g/gperf/gperf-3.1-GCCcore-12.2.0.eb | 32 +++++++++++++++ .../util-linux-2.38.1-GCCcore-12.2.0.eb | 41 +++++++++++++++++++ 3 files changed, 113 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.38.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..6a514ecbd3c --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.1-GCCcore-12.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.14.1' + +homepage = 'https://www.freedesktop.org/wiki/Software/fontconfig/' + +description = """ + Fontconfig is a library designed to provide system-wide font configuration, + customization and application access. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ae480e9ca34382790312ff062c625ec70df94d6d9a9366e2b2b3d525f7f90387'] + +builddependencies = [ + ('binutils', '2.39'), + ('gperf', '3.1'), + ('pkgconf', '1.9.3'), + ('Python', '3.10.8', '-bare'), +] + +dependencies = [ + ('expat', '2.4.9'), + ('freetype', '2.12.1'), + ('util-linux', '2.38.1'), +] + +configopts = '--disable-docs ' + +sanity_check_paths = { + 'files': ['include/fontconfig/fontconfig.h', 'lib/libfontconfig.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..5f019911975 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.1' + +homepage = 'https://www.gnu.org/software/gperf/' +description = """ + GNU gperf is a perfect hash function generator. For a given list of strings, + it produces a hash function and hash table, in form of C or C++ code, for + looking up a value depending on the input string. The hash function is + perfect, which means that the hash table has no collisions, and the hash + table lookup needs a single string comparison only. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['588546b945bba4b70b6a3a616e80b4ab466e3f33024a352fc2198112cdbb3ae2'] + +builddependencies = [ + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [], +} + +sanity_check_commands = ["gperf --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.38.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.38.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..ddc2a4e1286 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.38.1-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.38.1' + +homepage = 'https://www.kernel.org/pub/linux/utils/util-linux' + +description = "Set of Linux utilities" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0820eb8eea90408047e3715424bc6be771417047f683950fecb4bdd2e2cbbc6e'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), +] + +# disable account related utilities (they need OS dependent pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su --disable-rfkill " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' From 4fe7551a558ac201f4797a64a3dd0dbf032eefff Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 16:39:26 +0100 Subject: [PATCH 692/793] replace hardcoded versions for matlabengine extensions --- .../MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb | 2 +- .../MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb index 97c48e8fad3..d559c0538dd 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb @@ -19,7 +19,7 @@ dependencies = [ use_pip = True exts_list = [ - ('matlabengine', '9.10.1', { + ('matlabengine', _engine_version, { 'modulename': 'matlab.engine', 'checksums': ['c1610690dbe58ac00e74e8cbb20406208235ede47da7960238e0c2fd3bd496c0'], }), diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb index c7c345f46d5..d1457326e93 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb @@ -19,7 +19,7 @@ dependencies = [ use_pip = True exts_list = [ - ('matlabengine', '9.11.19', { + ('matlabengine', _engine_version, { 'modulename': 'matlab.engine', 'checksums': ['9385a13c27daa18f6cbfbe1669237e86692a51f317775a3f40e9e3d8090c679b'], }), From 36c48a24e97ca94cef58dacbb5f3aa81cbb59a6b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 16:42:05 +0100 Subject: [PATCH 693/793] adding easyconfigs: X11-20221110-GCCcore-12.2.0.eb --- .../x/X11/X11-20221110-GCCcore-12.2.0.eb | 213 ++++++++++++++++++ 1 file changed, 213 insertions(+) create mode 100644 easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..ea22050d122 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb @@ -0,0 +1,213 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20221110' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', + XORG_DATA_SOURCE + '/xkeyboard-config', + XORG_DATA_SOURCE, +] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('Bison', '3.8.2'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.3'), + ('intltool', '0.51.0'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('fontconfig', '2.14.1'), + ('freetype', '2.12.1'), + ('zlib', '1.2.12'), + ('xorg-macros', '1.19.3'), + ('libpciaccess', '0.17'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + ('libpthread-stubs', '0.4', { # 2017-03-14 + 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], + }), + ('xorgproto', '2022.2', { # 2022-08-11 + 'checksums': ['da351a403d07a7006d7bdc8dcfc14ddc1b588b38fb81adab9989a8eef605757b'], + }), + ('libXau', '1.0.10', { # 2022-08-26 + 'checksums': ['51a54da42475d4572a0b59979ec107c27dacf6c687c2b7b04e5cf989a7c7e60c'], + }), + ('libXdmcp', '1.1.3', { # 2019-03-16 + 'checksums': ['2ef9653d32e09d1bf1b837d0e0311024979653fe755ad3aaada8db1aa6ea180c'], + }), + ('xcb-proto', '1.15.2', { # 2022-06-17 + 'checksums': ['6b1ed9cd7cf35e37913eeecca37e5b85b14903002942b3e332f321335c27a8eb'], + }), + ('libxcb', '1.15', { # 2022-05-03 + 'checksums': ['1cb65df8543a69ec0555ac696123ee386321dfac1964a3da39976c9a05ad724d'], + }), + ('xtrans', '1.4.0', { # 2019-03-16 + 'checksums': ['48ed850ce772fef1b44ca23639b0a57e38884045ed2cbb18ab137ef33ec713f9'], + }), + ('libxkbcommon', '1.4.1', { # 2022-05-21 + 'easyblock': 'MesonNinja', + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['943c07a1e2198026d8102b17270a1f406e4d3d6bbc4ae105b9e1b82d7d136b39'], + 'preconfigopts': '', + 'configopts': '-Denable-wayland=false -Denable-docs=false ', + }), + ('libX11', '1.8.2', { # 2022-11-10 + 'checksums': ['f1bc56187bee0f830e1179ac5068ac93b78c51ace94eb27702ffb2efd116587b'], + }), + ('libXext', '1.3.5', { # 2022-10-29 + 'checksums': ['1a3dcda154f803be0285b46c9338515804b874b5ccc7a2b769ab7fd76f1035bd'], + }), + ('libFS', '1.0.9', { # 2022-08-26 + 'checksums': ['8bc2762f63178905228a28670539badcfa2c8793f7b6ce3f597b7741b932054a'], + }), + ('libICE', '1.0.10', { # 2019-07-14 + 'checksums': ['1116bc64c772fd127a0d0c0ffa2833479905e3d3d8197740b3abd5f292f22d2d'], + }), + ('libSM', '1.2.3', { # 2018-10-10 + 'checksums': ['1e92408417cb6c6c477a8a6104291001a40b3bb56a4a60608fdd9cd2c5a0f320'], + }), + ('libXScrnSaver', '1.2.3', { # 2018-07-05 + 'checksums': ['4f74e7e412144591d8e0616db27f433cfc9f45aae6669c6c4bb03e6bf9be809a'], + }), + ('libXt', '1.2.1', { # 2021-01-24 + 'checksums': ['6da1bfa9dd0ed87430a5ce95b129485086394df308998ebe34d98e378e3dfb33'], + }), + ('libXmu', '1.1.4', { # 2022-10-17 + 'checksums': ['3091d711cdc1d8ea0f545a13b90d1464c3c3ab64778fd121f0d789b277a80289'], + }), + ('libXpm', '3.5.13', { # 2019-12-13 + 'checksums': ['e3dfb0fb8c1f127432f2a498c7856b37ce78a61e8da73f1aab165a73dd97ad00'], + }), + ('libXaw', '1.0.14', { # 2021-03-27 + 'checksums': ['59cfed2712cc80bbfe62dd1aacf24f58d74a76dd08329a922077b134a8d8048f'], + }), + ('libXfixes', '6.0.0', { # 2021-05-11 + 'checksums': ['82045da5625350838390c9440598b90d69c882c324ca92f73af9f0e992cb57c7'], + }), + ('libXcomposite', '0.4.5', { # 2019-03-11 + 'checksums': ['581c7fc0f41a99af38b1c36b9be64bc13ef3f60091cd3f01105bbc7c01617d6c'], + }), + ('libXrender', '0.9.11', { # 2022-10-22 + 'checksums': ['6aec3ca02e4273a8cbabf811ff22106f641438eb194a12c0ae93c7e08474b667'], + }), + ('libXcursor', '1.2.1', { # 2022-04-03 + 'checksums': ['77f96b9ad0a3c422cfa826afabaf1e02b9bfbfc8908c5fa1a45094faad074b98'], + }), + ('libXdamage', '1.1.5', { # 2019-03-11 + 'checksums': ['630ec53abb8c2d6dac5cd9f06c1f73ffb4a3167f8118fdebd77afd639dbc2019'], + }), + ('libfontenc', '1.1.6', { # 2022-08-30 + 'checksums': ['c103543a47ce5c0200fb1867f32df5e754a7c3ef575bf1fe72187117eac22a53'], + }), + ('libXfont', '1.5.4', { # 2017-11-28 + 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], + }), + ('libXfont2', '2.0.6', { # 2022-08-26 + 'checksums': ['a944df7b6837c8fa2067f6a5fc25d89b0acc4011cd0bc085106a03557fb502fc'], + }), + ('libXft', '2.3.6', { # 2022-09-10 + 'checksums': ['b7e59f69e0bbabe9438088775f7e5a7c16a572e58b11f9722519385d38192df5'], + }), + ('libXi', '1.8', { # 2021-09-15 + 'checksums': ['c80fd200a1190e4406bb4cc6958839d9651638cb47fa546a595d4bebcd3b9e2d'], + }), + ('libXinerama', '1.1.5', { # 2022-10-29 + 'checksums': ['2efa855cb42dc620eff3b77700d8655695e09aaa318f791f201fa60afa72b95c'], + }), + ('libXrandr', '1.5.2', { # 2019-03-16 + 'checksums': ['3f10813ab355e7a09f17e147d61b0ce090d898a5ea5b5519acd0ef68675dcf8e'], + }), + ('libXres', '1.2.1', { # 2021-03-31 + 'checksums': ['918fb33c3897b389a1fbb51571c5c04c6b297058df286d8b48faa5af85e88bcc'], + }), + ('libXtst', '1.2.4', { # 2022-09-27 + 'checksums': ['01366506aeb033f6dffca5326af85f670746b0cabbfd092aabefb046cf48c445'], + }), + ('libXv', '1.0.11', { # 2016-10-04 + 'checksums': ['c4112532889b210e21cf05f46f0f2f8354ff7e1b58061e12d7a76c95c0d47bb1'], + }), + ('libXvMC', '1.0.13', { # 2022-03-22 + 'checksums': ['e630b4373af8c67a7c8f07ebe626a1269a613d262d1f737b57231a06f7c34b4e'], + }), + ('libXxf86dga', '1.1.5', { # 2019-03-16 + 'checksums': ['715e2bf5caf6276f0858eb4b11a1aef1a26beeb40dce2942387339da395bef69'], + }), + ('libXxf86vm', '1.1.5', { # 2022-09-27 + 'checksums': ['f3f1c29fef8accb0adbd854900c03c6c42f1804f2bc1e4f3ad7b2e1f3b878128'], + }), + ('libdmx', '1.1.4', { # 2018-05-14 + 'checksums': ['4d05bd5b248c1f46729fa1536b7a5e4d692567327ad41564c36742fb327af925'], + }), + ('libxkbfile', '1.1.1', { # 2022-10-18 + 'checksums': ['87faee6d4873c5631e8bb53e85134084b862185da682de8617f08ca18d82e216'], + }), + ('libxshmfence', '1.3', { # 2018-02-26 + 'checksums': ['7eb3d46ad91bab444f121d475b11b39273142d090f7e9ac43e6a87f4ff5f902c'], + }), + ('xcb-util', '0.4.0', { # 2014-10-15 + 'checksums': ['0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7'], + }), + ('xcb-util-image', '0.4.1', { # 2022-10-18 + 'checksums': ['0ebd4cf809043fdeb4f980d58cdcf2b527035018924f8c14da76d1c81001293b'], + }), + ('xcb-util-keysyms', '0.4.1', { # 2022-10-19 + 'checksums': ['1fa21c0cea3060caee7612b6577c1730da470b88cbdf846fa4e3e0ff78948e54'], + }), + ('xcb-util-renderutil', '0.3.10', { # 2022-10-19 + 'checksums': ['e04143c48e1644c5e074243fa293d88f99005b3c50d1d54358954404e635128a'], + }), + ('xcb-util-wm', '0.4.2', { # 2022-10-19 + 'checksums': ['dcecaaa535802fd57c84cceeff50c64efe7f2326bf752e16d2b77945649c8cd7'], + }), + ('xcb-util-cursor', '0.1.4', { # 2022-10-18 + 'checksums': ['cc8608ebb695742b6cf84712be29b2b66aa5f6768039528794fca0fa283022bf'], + }), + ('xkeyboard-config', '2.37', { # 2022-10-04 + 'easyblock': 'MesonNinja', + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['eb1383a5ac4b6210d7c7302b9d6fab052abdf51c5d2c9b55f1f779997ba68c6c'], + # required to overrule parent preconfigopts that runs autogen.sh if configure script is missing + 'preconfigopts': '', + }), + ('printproto', '1.0.5', { # 2011-01-06 + 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], + }), + ('libXp', '1.0.4', { # 2022-09-12 + 'checksums': ['05e46af1ccb68f1752cca5879774a4fb9bf3b19fe088eb745034956e0c6fadba'], + }), + ('xbitmaps', '1.1.2', { # 2018-03-10 + 'checksums': ['27e700e8ee02c43f7206f4eca8f1953ad15236cac95d7a0f08505c3f7d99c265'], + }), +] + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib/pkgconfig', + 'share/pkgconfig', 'share/X11/xkb'], +} + +moduleclass = 'vis' From 6cf1b4bf4a135e5b20243ba4cfe8f8f954cea413 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 16 Nov 2022 16:12:15 +0000 Subject: [PATCH 694/793] adding easyconfigs: SpaceRanger-2.0.0-GCC-11.2.0.eb --- .../SpaceRanger-2.0.0-GCC-11.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.0.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.0.0-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.0.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..b6aba4be749 --- /dev/null +++ b/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.0.0-GCC-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'Tarball' + +name = 'SpaceRanger' +version = '2.0.0' + +homepage = 'https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger' +description = """ Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output +and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, +perform clustering and gene expression analysis, and place spots in spatial context on the slide image. """ + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +download_instructions = """ +Download sources from homepage, registration required +https://support.10xgenomics.com/spatial-gene-expression/software/downloads/latest +""" + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bdaa784e433c2e3707bed6a868042e954248e97fb4021d7179460a2b3702205c'] + +dependencies = [ + ('bcl2fastq2', '2.20.0'), +] + +allow_prepend_abs_path = True +# prepend reference databases GRCh38 and mm10 to PATH +# modextrapaths = {'PATH': '/path/to/databases/%(namelower)s-%(version)s'} + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['external', 'lib', 'mro'], +} + +sanity_check_commands = ['%(namelower)s -h'] + +moduleclass = 'bio' From 59a818348d8e797c2b498412f5fede03c16ae7bc Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 17:11:14 +0100 Subject: [PATCH 695/793] switch IJulia and MultilevelEstimators to JuliaBundle easyblock --- .../i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb | 14 +------------- ...elEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb | 17 +---------------- 2 files changed, 2 insertions(+), 29 deletions(-) diff --git a/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb b/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb index 54566147c74..06667a1bbf8 100644 --- a/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb +++ b/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'JuliaBundle' name = 'IJulia' version = '1.23.3' @@ -14,12 +14,6 @@ dependencies = [ ('Julia', _julia_ver, '-linux-%s' % ARCH, SYSTEM), ] -exts_defaultclass = 'JuliaPackage' -exts_filter = ("julia -e 'using %(ext_name)s'", "") -exts_default_options = { - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], -} - exts_list = [ ('Parsers', '2.4.2', { 'source_urls': ['https://github.com/JuliaData/Parsers.jl/archive/'], @@ -74,13 +68,7 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['packages'], -} - modextrapaths = { - 'JULIA_DEPOT_PATH': '', 'JUPYTER_PATH': 'jupyter', } diff --git a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb index b26dd65738e..822fe47b647 100644 --- a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'JuliaBundle' name = 'MultilevelEstimators' version = '0.1.0' @@ -15,12 +15,6 @@ dependencies = [ ('Julia', local_julia_ver, '-linux-%s' % ARCH, SYSTEM), ] -exts_defaultclass = 'JuliaPackage' -exts_filter = ("julia -e 'using %(ext_name)s'", "") -exts_default_options = { - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], -} - exts_list = [ ('Preferences', '1.3.0', { 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], @@ -101,13 +95,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['packages/%(name)s'] -} - -modextrapaths = { - 'JULIA_DEPOT_PATH': '', -} - moduleclass = 'lib' From f6b8d3a7a30b02164d0d60654b1412d18a3288b4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 16 Nov 2022 17:44:51 +0100 Subject: [PATCH 696/793] IOR: Drop leftover builddep from old easyconfig. --- easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb index 9b3059aa224..4ddd258e440 100644 --- a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb @@ -18,9 +18,9 @@ sources = [SOURCELOWER_TAR_BZ2] checksums = ['41fe66f91aead70f7e53246de68dd194e7ade72070faf696f88efffdcf1bf68b'] builddependencies = [ - ('Autotools', '20220317'), ('Perl', '5.34.1'), ] + dependencies = [ ('HDF5', '1.12.2'), ] From 4849ec35cc212b948195b1f82eb9e4716b3d0c23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 18:31:41 +0100 Subject: [PATCH 697/793] add missing pyWannier90 dependency for mcu + enhance sanity check --- easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb b/easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb index 5a34c8b03a6..c70eb5db0f6 100644 --- a/easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb +++ b/easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb @@ -19,14 +19,17 @@ dependencies = [ ('SciPy-bundle', '2021.05'), ('matplotlib', '3.4.2'), ('spglib-python', '1.16.1'), + ('pyWannier90', '2021-12-07'), ] -use_pip = True download_dep_fail = True -sanity_pip_check = True +use_pip = True sanity_check_commands = [ "python -c 'from mcu import VASP'", + "python -c 'import mcu.wannier90.pywannier90_vasp'", ] +sanity_pip_check = True + moduleclass = 'lib' From 40bad0fb605e2e69b99a1d12bdc7b59fb63189b6 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 16 Nov 2022 20:45:54 +0000 Subject: [PATCH 698/793] remove unused prebuildopts --- easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb b/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb index 9b019b172c7..456ebc34788 100644 --- a/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb +++ b/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb @@ -40,7 +40,6 @@ exts_list = [ }), (name, version, { 'modulename': 'mpl_toolkits.basemap', - 'prebuildopts': 'GEOS_DIR=$EBROOTGEOS', 'preinstallopts': 'cd packages/%(name)s && GEOS_DIR=$EBROOTGEOS', 'sources': ['v%(version)s.tar.gz'], 'source_urls': ['https://github.com/matplotlib/basemap/archive/'], From a715b34768b61935a0d74e8dc6ec4c96b8313203 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 22:45:24 +0100 Subject: [PATCH 699/793] add build dependency on binutils to MATLAB-Engine v2021a-9.10.1 --- .../MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb index d559c0538dd..f9fc548a6ee 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb @@ -11,6 +11,8 @@ description = """The MATLAB Engine API for Python provides a package for Python toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = [('binutils', '2.35')] + dependencies = [ ('MATLAB', _matlab_version, '', SYSTEM), ('Python', '3.8.6'), From 5b1cfd90607afa5f3f7a31275d9669f8ad6a7850 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 22:46:05 +0100 Subject: [PATCH 700/793] add build dependency on binutils to MATLAB-Engine v2021b-9.11.19 --- .../MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb index d1457326e93..7bbd5629949 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb @@ -11,6 +11,8 @@ description = """The MATLAB Engine API for Python provides a package for Python toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +builddependencies = [('binutils', '2.37')] + dependencies = [ ('MATLAB', _matlab_version, '', SYSTEM), ('Python', '3.9.6'), From 1880305e6208d1c6f1c9fd6736bf455b226ca87d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Nov 2022 09:40:16 +0100 Subject: [PATCH 701/793] using SYSTEM rather than True for CUDA dependency in NAMD easyconfig --- .../easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb index ba107970cf1..d89411f76cc 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb @@ -24,7 +24,7 @@ checksums = [ # support for GCC 8+ on POWER dependencies = [ ('Tcl', '8.6.11'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] builddependencies = [ From 09eacbe4fb9de594bcbd0b5587cd50ef6ce85159 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Nov 2022 10:08:16 +0100 Subject: [PATCH 702/793] simplify 'sources' spec in NAMD 2.14 easyconfig + remove useless comment --- .../easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb index d89411f76cc..eafa0dbcabf 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'usempi': False, 'openmp': False, 'pic': True} source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/946183/'] -sources = [{'filename': 'NAMD_%(version)s_Source.tar.gz'}] +sources = ['NAMD_%(version)s_Source.tar.gz'] patches = [ "%(name)s-%(version)s_Linux-POWER-cuda.patch", "%(name)s-%(version)s-use_system_mremap_decl.patch" @@ -21,7 +21,6 @@ checksums = [ 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch ] -# support for GCC 8+ on POWER dependencies = [ ('Tcl', '8.6.11'), ('CUDA', '11.3.1', '', SYSTEM), From 9885375556349694732e58132ba0e5411bf98b9a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 17 Nov 2022 11:04:14 +0100 Subject: [PATCH 703/793] Add missing cuFFTAdvisor source --- .../x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb index fc96f59b860..f3e9847d3b7 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb @@ -32,6 +32,12 @@ sources = [ 'filename': 'xmippViz-v%(version)s.tar.gz', 'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src', }, + { + 'source_urls': ['https://github.com/DStrelak/cuFFTAdvisor/archive/'], + 'download_filename': '14523b8ca7e2f5474feae49eb5ac8ca1fa25f5cd.tar.gz', + 'filename': 'cuFFTAdvisor-20191010.tar.gz', + 'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src', + }, ] patches = [ '%(name)s-%(version)s_fix_scons_Environent_calls.patch', @@ -50,6 +56,7 @@ checksums = [ {'xmipp-v3.22.07-Helios.tar.gz': 'f62e2729130b63d18e518930dd96a7a5250219e40c155abb78942a0642237ecf'}, {'xmippCore-v3.22.07-Helios.tar.gz': '58e1143626cf807655a4756b165c21578d6f1b1777b43d363a2845d92d0bab8f'}, {'xmippViz-v3.22.07-Helios.tar.gz': 'e1ce2cbbd57d3307d38538b29194a0190d633e5e062685387a6baf0329ad05b3'}, + {'cuFFTAdvisor-20191010.tar.gz': '2d97cc1c9c955fa5bee44eb232d49f25f2c8ad164ea2be754d44c723c613be46'}, {'Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch': '5b59babad5a445ec7315a809509704d2d07232d2a5d180bfb78ebc8007bd0c95'}, {'Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch': From 16045c6c49fc7b7d237e39facdebe7ef016b9b3a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 17 Nov 2022 17:15:22 +0100 Subject: [PATCH 704/793] adding easyconfigs: cdo-bindings-1.5.7-foss-2021b.eb --- .../cdo-bindings-1.5.7-foss-2021b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb b/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb new file mode 100644 index 00000000000..e387e1c022c --- /dev/null +++ b/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'cdo-bindings' +version = '1.5.7' + +homepage = 'https://github.com/Try2Code/cdo-bindings' +description = "Python interface to CDO." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('CDO', '2.0.5'), + ('netcdf4-python', '1.5.8'), + ('xarray', '0.20.1'), # optional +] + +use_pip = True + +exts_list = [ + ('cdo', version, { + 'checksums': ['898c2b0ff97ec494569e5d94302350538efa898d42998bfed76b4f52c6c16f3c'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 2a8ed2478b091d20ffb02aa0242b7594ea7d1717 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 17 Nov 2022 23:32:54 +0100 Subject: [PATCH 705/793] downgrade dependency on netcdf-python from cdo-bindings v1.5.7 --- .../easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb b/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb index e387e1c022c..b3f6ed923ba 100644 --- a/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb +++ b/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ ('Python', '3.9.6'), ('CDO', '2.0.5'), - ('netcdf4-python', '1.5.8'), + ('netcdf4-python', '1.5.7'), ('xarray', '0.20.1'), # optional ] From 26c14ad2227b6a8022cff046833b5cf34a1af51d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 18 Nov 2022 00:41:38 +0100 Subject: [PATCH 706/793] remove default sanity checks from cmocean v2.0 --- easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb b/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb index 452ee96673d..3531eb02047 100644 --- a/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb @@ -28,9 +28,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' From 84bf86d4e5b38adca88f3058f5eb06ca77b325b1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 18 Nov 2022 02:07:59 +0100 Subject: [PATCH 707/793] remove default sanity checks from gsw v3.6.16 --- easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb | 7 ------- 1 file changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb b/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb index aa8438cd21e..b18c6a53181 100644 --- a/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb +++ b/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb @@ -21,22 +21,15 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), - ] use_pip = True sanity_pip_check = True exts_list = [ - (name, version, { 'checksums': ['d24d820c8b43dbf72206cf5e3b0ed800b05aa85ca40afd39c9abd19849714197'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' From 521a6fedbe179e49bf8ca8a79469997f26676345 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 18 Nov 2022 08:54:49 +0100 Subject: [PATCH 708/793] Add missing Authors from previous easyconfigs of IOR. --- easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb index 4ddd258e440..770777c7b5e 100644 --- a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb @@ -1,4 +1,8 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Robert Mijakovic Date: Fri, 18 Nov 2022 10:14:48 +0100 Subject: [PATCH 709/793] Update easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb index 182023f4691..c97a027b5c3 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -34,6 +34,8 @@ dependencies = [ ('cURL', '7.83.0'), ('Szip', '2.1.1'), ('zstd', '1.5.2'), + ('bzip2', '1.0.8'), + ('libxml2', '2.9.13'), ] # make sure both static and shared libs are built From 88fc4eefb4cb7ea38b7578e57f6e7b7a1e5e7504 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 18 Nov 2022 10:36:52 +0100 Subject: [PATCH 710/793] adding easyconfigs: libxml2-python-2.9.13-GCCcore-11.3.0.eb --- .../libxml2-python-2.9.13-GCCcore-11.3.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.13-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.13-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.13-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a63e21ba634 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.13-GCCcore-11.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonPackage' + +name = 'libxml2-python' +version = '2.9.13' + +homepage = 'http://xmlsoft.org/' +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). This is the Python binding.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = ['libxml2-%(version)s.tar.xz'] +patches = [ + 'libxml2-2.9.7_fix-hardcoded-paths.patch', +] +checksums = [ + '276130602d12fe484ecc03447ee5e759d0465558fbc9d6bd144e3745306ebf0e', # libxml2-2.9.13.tar.gz + '3d5651c015fd375d855421983b7d33ffd4af797b7411f46e05cd8c57b210e542', # libxml2-2.9.7_fix-hardcoded-paths.patch +] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('XZ', '5.2.5'), + ('Python', '3.10.4'), + ('libxml2', version), + ('libiconv', '1.17'), +] + +start_dir = 'python' + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'libxml2'} + +moduleclass = 'lib' From b6ee6a570e2700a2ad68cb6034c3f0ba18199815 Mon Sep 17 00:00:00 2001 From: garadar Date: Fri, 18 Nov 2022 10:47:29 +0100 Subject: [PATCH 711/793] Update easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb Co-authored-by: Alex Domingo --- easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb b/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb index f588b3b926d..efcf60ced34 100644 --- a/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb +++ b/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'system', 'version': ''} # source_urls = [PYPI_SOURCE] # Link copy from pypi.org | PYPI_SOURCE is not working -sources = ["https://files.pythonhosted.org/packages/15/0b/fa95a349434f77d8afc775dd999152d7612b6baed52083981ac84eaa41e9/resolos-0.3.5.tar.gz"] +sources = [SOURCE_TAR_GZ] checksums = ['c0fb50e36866fa591f0a7ab3567e9037c97d96f34614e86ee9cad1b62c689de2'] From c41940db6347f79adba9bd48a5306c546c47c1a7 Mon Sep 17 00:00:00 2001 From: garadar Date: Fri, 18 Nov 2022 10:54:33 +0100 Subject: [PATCH 712/793] Update and rename resolos-0.3.5.eb to resolos-0.3.5-GCCcore-11.3.0.eb --- ...os-0.3.5.eb => resolos-0.3.5-GCCcore-11.3.0.eb} | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/r/resolos/{resolos-0.3.5.eb => resolos-0.3.5-GCCcore-11.3.0.eb} (75%) diff --git a/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb similarity index 75% rename from easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb rename to easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb index efcf60ced34..e3cc4db884a 100644 --- a/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb +++ b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb @@ -4,18 +4,26 @@ name = 'resolos' version = '0.3.5' homepage = 'https://gitlab.unige.ch/resolos/resolos' -description = """Resolos is a toolkit written in Python for maintaining reproducible environments for scientific computations. -It's main goal is to enable researchers to easily replicate environments through space (running code on HPC environment) +description = """Resolos is a toolkit written in Python for maintaining reproducible environments +for scientific computations. +It's main goal is to enable researchers to easily replicate environments through space +(running code on HPC environment) + and time (environment preservation for long term archival). For installation and detailed usage, check out the documentation.""" -toolchain = {'name': 'system', 'version': ''} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} # source_urls = [PYPI_SOURCE] # Link copy from pypi.org | PYPI_SOURCE is not working sources = [SOURCE_TAR_GZ] checksums = ['c0fb50e36866fa591f0a7ab3567e9037c97d96f34614e86ee9cad1b62c689de2'] +dependencies = { + ('Python', '3.10.4'), + ('PyYAML', '6.0'), +} + use_pip = True use_pip_for_deps = True From 35f7c584e93f395a9ec79c219b6e57f9d47e82e1 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Fri, 18 Nov 2022 12:07:04 +0100 Subject: [PATCH 713/793] Update easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb index c97a027b5c3..8cec66eec5a 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -39,6 +39,7 @@ dependencies = [ ] # make sure both static and shared libs are built +# and disable "remote" tests that access a unreliable external test server over internet configopts = [ "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", From f951ddcf2b93259bc3a8ecf6a169075421186d90 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 18 Nov 2022 13:56:21 +0100 Subject: [PATCH 714/793] adding easyconfigs: libyaml-0.2.5-GCCcore-12.2.0.eb, PyYAML-6.0-GCCcore-12.2.0.eb --- .../l/libyaml/libyaml-0.2.5-GCCcore-12.2.0.eb | 25 +++++++++++++++++ .../p/PyYAML/PyYAML-6.0-GCCcore-12.2.0.eb | 27 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..6085128a05b --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.2.5' + +homepage = 'https://pyyaml.org/wiki/LibYAML' +description = "LibYAML is a YAML parser and emitter written in C." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://pyyaml.org/download/%(name)s/'] +sources = ['yaml-%(version)s.tar.gz'] +checksums = ['c642ae9b75fee120b2d96c712538bd2cf283228d2337df2cf2988e3c02678ef4'] + +builddependencies = [ + ('binutils', '2.39'), +] + + +sanity_check_paths = { + 'files': ['include/yaml.h', 'lib/libyaml.a', 'lib/libyaml.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..6f216f2874f --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '6.0' + +homepage = 'https://github.com/yaml/pyyaml' +description = "PyYAML is a YAML parser and emitter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['68fb519c14306fec9720a2a5b45bc9f0c8d1b9c72adf45c37baedfcd949c35a2'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('Python', '3.10.8'), + ('libyaml', '0.2.5'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'yaml'} + +moduleclass = 'lib' From ab1b91e436a4ea1e46927f12c90737e6d231577c Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 18 Nov 2022 14:01:30 +0100 Subject: [PATCH 715/793] adding easyconfigs: OpenStackClient-6.0.0-GCCcore-12.2.0.eb --- .../OpenStackClient-6.0.0-GCCcore-12.2.0.eb | 129 ++++++++++++++++++ 1 file changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..4b6ae3f06fe --- /dev/null +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,129 @@ +easyblock = 'PythonBundle' + +name = 'OpenStackClient' +version = '6.0.0' + +homepage = 'https://docs.openstack.org/python-openstackclient/latest/' +description = """OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the +command set for Compute, Identity, Image, Network, Object Store and Block +Storage APIs together in a single shell with a uniform command structure.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +dependencies = [ + ('Python', '3.10.8'), + ('PyYAML', '6.0'), +] +builddependencies = [('binutils', '2.39')] + +exts_default_options = { + 'use_pip': True, +} +exts_list = [ + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('importlib_metadata', '5.0.0', { + 'checksums': ['da31db32b304314d044d3c12c79bd59e307889b287ad12ff387b3500835fc2ab'], + }), + ('cmd2', '2.4.2', { + 'checksums': ['073e555c05853b0f6965f3d03329babdf9e38a5f2cea028e61a64cd7eeb74ad5'], + }), + ('jsonpointer', '2.3', { + 'checksums': ['97cba51526c829282218feb99dab1b1e6bdf8efd1c43dc9d57be093c0d69c99a'], + }), + ('prettytable', '3.5.0', { + 'checksums': ['52f682ba4efe29dccb38ff0fe5bac8a23007d0780ff92a8b85af64bc4fc74d72'], + }), + ('autopage', '0.5.1', { + 'checksums': ['01be3ee61bb714e9090fcc5c10f4cf546c396331c620c6ae50a2321b28ed3199'], + }), + ('stevedore', '4.1.1', { + 'checksums': ['7f8aeb6e3f90f96832c301bff21a7eb5eefbe894c88c506483d355565d88cc1a'], + }), + ('cliff', '4.0.0', { + 'checksums': ['3b0d30e7acf50e3c214a39ee3e66aa2f2b5957e2a1de373e17bba8e98c7501a5'], + }), + ('dogpile.cache', '1.1.8', { + 'checksums': ['d844e8bb638cc4f544a4c89a834dfd36fe935400b71a16cbd744ebdfb720fd4e'], + }), + ('iso8601', '1.1.0', { + 'checksums': ['32811e7b81deee2063ea6d2e94f8819a86d1f3811e49d23623a41fa832bef03f'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('jsonpatch', '1.32', { + 'checksums': ['b6ddfe6c3db30d81a96aaeceb6baf916094ffa23d7dd5fa2c13e13f8b6e600c2'], + }), + ('os-service-types', '1.7.0', { + 'checksums': ['31800299a82239363995b91f1ebf9106ac7758542a1e4ef6dc737a5932878c6c'], + }), + ('keystoneauth1', '5.0.0', { + 'checksums': ['6ebb5f044c9dfd263087a328d51d479947d1ddc90c09daf4191df7dc71334323'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + ('requestsexceptions', '1.4.0', { + 'checksums': ['b095cbc77618f066d459a02b137b020c37da9f46d9b057704019c9f77dba3065'], + }), + ('openstacksdk', '0.102.0', { + 'modulename': 'openstack', + 'checksums': ['b2a18feba79eac2ac3469c8dafe01d4008c8ac30be3a4c6b53275b4f1c6ba2ad'], + }), + ('oslo.i18n', '5.1.0', { + 'modulename': 'oslo_i18n', + 'checksums': ['6bf111a6357d5449640852de4640eae4159b5562bbba4c90febb0034abc095d0'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('debtcollector', '2.5.0', { + 'checksums': ['dc9d1ad3f745c43f4bbedbca30f9ffe8905a8c028c9926e61077847d5ea257ab'], + }), + ('oslo.utils', '6.1.0', { + 'modulename': 'oslo_utils', + 'checksums': ['76bc0108d50aca972b68fec8298e791b5fbcbeb9a51a27c6986b41b0a6a62eeb'], + }), + ('osc-lib', '2.6.2', { + 'checksums': ['879b6c5a142f3294464748ab14adde0cba0a14a5f704a0d840c9e92144489dba'], + }), + ('oslo.serialization', '5.0.0', { + 'modulename': 'oslo_serialization', + 'checksums': ['2845328d0f47dc8a23fed2a82253e90acff0aa731dbd24f379cf8e50e6cc66ba'], + }), + ('rfc3986', '2.0.0', { + 'checksums': ['97aacf9dbd4bfd829baad6e6309fa6573aaf1be3f6fa735c8ab05e46cecb261c'], + }), + ('oslo.config', '9.0.0', { + 'modulename': 'oslo_config', + 'checksums': ['3b6b63c43cf1e09344ba850bcb11d6f2b9201086fbeb0a97a8950e7eac3f2645'], + }), + ('python-novaclient', '18.2.0', { + 'modulename': 'novaclient', + 'checksums': ['185bbf2cafb5f3d761f272e3e184a700cc7ba5cf7d51619065be7f5c4b5b7cf4'], + }), + ('python-keystoneclient', '5.0.1', { + 'modulename': 'keystoneclient', + 'checksums': ['a8bbf671f56c24aa5a37a225b98f2994b82063d73e3486657eb500a33a406d29'], + }), + ('python-cinderclient', '9.1.0', { + 'modulename': 'cinderclient', + 'checksums': ['f9b30af2e6e6e5a126c2c81f35145c5aee70c20955e6dd409919be4d1b87b343'], + }), + ('python-openstackclient', version, { + 'modulename': 'openstackclient', + 'checksums': ['91c3ac12da4b423c16b3917616f84a23e2961e750fce590d409ecc50ee0431ce'], + }), +] + +sanity_pip_check = True +enhance_sanity_check = True +sanity_check_commands = ['openstack -h'] + +sanity_check_paths = { + 'files': ['bin/openstack'], + 'dirs': ["bin", 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' From 4f968721d9f31ad662b58778cf8503c8444e3b3f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 18 Nov 2022 13:45:54 +0000 Subject: [PATCH 716/793] use _ instead of - to simplify package downloads and re-add comment for Python 3.10.8 --- .../p/Python/Python-3.10.8-GCCcore-12.2.0.eb | 40 +++++++------------ 1 file changed, 15 insertions(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb index f0bca199736..59243c2b5dc 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb @@ -78,8 +78,7 @@ exts_list = [ ('toml', '0.10.2', { 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], }), - ('flit-core', '3.8.0', { - 'source_tmpl': 'flit_core-%(version)s.tar.gz', + ('flit_core', '3.8.0', { 'checksums': ['b305b30c99526df5e63d6022dd2310a0a941a187bd3884f4c8ef0418df6c39f3'], }), ('tomli', '2.0.1', { @@ -88,8 +87,7 @@ exts_list = [ ('packaging', '21.3', { 'checksums': ['dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb'], }), - ('setuptools-scm', '7.0.5', { - 'sources': ['setuptools_scm-%(version)s.tar.gz'], + ('setuptools_scm', '7.0.5', { 'checksums': ['031e13af771d6f892b941adb6ea04545bbf91ebc5ce68c78aaf3fff6e1fb4844'], }), ('python-dateutil', '2.8.2', { @@ -130,18 +128,18 @@ exts_list = [ ('cffi', '1.15.1', { 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], }), - ('semantic-version', '2.10.0', { - 'sources': ['semantic_version-%(version)s.tar.gz'], + ('semantic_version', '2.10.0', { 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], }), - ('typing-extensions', '4.4.0', { - 'sources': ['typing_extensions-%(version)s.tar.gz'], + ('typing_extensions', '4.4.0', { 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], }), ('setuptools-rust', '1.5.2', { 'checksums': ['d8daccb14dc0eae1b6b6eb3ecef79675bd37b4065369f79c35393dd5c55652c7'], }), ('cryptography', '38.0.3', { + # avoid that cargo uses $HOME/.cargo, which can lead to build failures if home directory is NFS mounted, + # see https://github.com/rust-lang/cargo/issues/6652 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", 'checksums': ['bfbe6ee19615b07a98b1d2287d6a6073f734735b49ee45b11324d85efc4d5cbd'], }), @@ -188,8 +186,7 @@ exts_list = [ ('zipp', '3.10.0', { 'checksums': ['7a7262fd930bd3e36c50b9a64897aec3fafff3dfdeec9623ae22b40e93f99bb8'], }), - ('importlib-metadata', '5.0.0', { - 'sources': ['importlib_metadata-%(version)s.tar.gz'], + ('importlib_metadata', '5.0.0', { 'checksums': ['da31db32b304314d044d3c12c79bd59e307889b287ad12ff387b3500835fc2ab'], }), ('backports.entry-points-selectable', '1.2.0', { @@ -208,8 +205,7 @@ exts_list = [ ('hatchling', '1.11.1', { 'checksums': ['9f84361f70cf3a7ab9543b0c3ecc64211ed2ba8a606a71eb6a473c1c9b08e1d0'], }), - ('hatch-vcs', '0.2.0', { - 'sources': ['hatch_vcs-%(version)s.tar.gz'], + ('hatch_vcs', '0.2.0', { 'checksums': ['9913d733b34eec9bb0345d0626ca32165a4ad2de15d1ce643c36d09ca908abff'], }), ('platformdirs', '2.5.3', { @@ -221,8 +217,7 @@ exts_list = [ ('pathlib2', '2.3.7.post1', { 'checksums': ['9fe0edad898b83c0c3e199c842b27ed216645d2e177757b2dd67384d4113c641'], }), - ('importlib-resources', '5.10.0', { - 'sources': ['importlib_resources-%(version)s.tar.gz'], + ('importlib_resources', '5.10.0', { 'checksums': ['c01b1b94210d9849f286b86bb51bcea7cd56dde0600d8db721d7b81330711668'], }), ('virtualenv', '20.16.6', { @@ -252,8 +247,7 @@ exts_list = [ ('xlrd', '2.0.1', { 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], }), - ('py-expression-eval', '0.3.14', { - 'sources': ['py_expression_eval-%(version)s.tar.gz'], + ('py_expression_eval', '0.3.14', { 'checksums': ['ea60f9404a18346d5a63854db21c50666dfb4274ae111000165b31c6f8ab93f1'], }), ('tabulate', '0.9.0', { @@ -275,8 +269,7 @@ exts_list = [ 'modulename': 'attr', 'checksums': ['29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6'], }), - ('backports.functools-lru-cache', '1.6.4', { - 'sources': ['backports.functools_lru_cache-%(version)s.tar.gz'], + ('backports.functools_lru_cache', '1.6.4', { 'checksums': ['d5ed2169378b67d3c545e5600d363a923b09c456dab1593914935a68ad478271'], }), ('wcwidth', '0.2.5', { @@ -288,8 +281,7 @@ exts_list = [ ('colorama', '0.4.6', { 'checksums': ['08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44'], }), - ('flit-scm', '1.7.0', { - 'sources': ['flit_scm-%(version)s.tar.gz'], + ('flit_scm', '1.7.0', { 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], }), ('exceptiongroup', '1.0.1', { @@ -377,8 +369,7 @@ exts_list = [ ('zipfile36', '0.1.3', { 'checksums': ['a78a8dddf4fa114f7fe73df76ffcce7538e23433b7a6a96c1c904023f122aead'], }), - ('tomli-w', '1.0.0', { - 'sources': ['tomli_w-%(version)s.tar.gz'], + ('tomli_w', '1.0.0', { 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], }), ('flit', '3.8.0', { @@ -446,7 +437,7 @@ exts_list = [ ('pexpect', '4.8.0', { 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], }), - ('hatch-fancy-pypi-readme', '22.8.0', { + ('hatch_fancy_pypi_readme', '22.8.0', { 'sources': ['hatch_fancy_pypi_readme-%(version)s.tar.gz'], 'checksums': ['da91282ca09601c18aded8e378daf8b578c70214866f0971156ee9bb9ce6c26a'], }), @@ -488,8 +479,7 @@ exts_list = [ ('dulwich', '0.20.50', { 'checksums': ['50a941796b2c675be39be728d540c16b5b7ce77eb9e1b3f855650ece6832d2be'], }), - ('poetry-plugin-export', '1.2.0', { - 'sources': ['poetry_plugin_export-%(version)s.tar.gz'], + ('poetry_plugin_export', '1.2.0', { 'checksums': ['9a1dd42765408931d7831738749022651d43a2968b67c988db1b7a567dfe41ef'], }), ('poetry', '1.2.2', { From cc7a26bef21b44ae8a6ce40df5f02f6b81e23a13 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 18 Nov 2022 14:47:01 +0100 Subject: [PATCH 717/793] update easyconfig OpenStackClient-6.0.0-GCCcore-12.2.0.eb: remove importlib_metadata --- .../o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb index 4b6ae3f06fe..6b695f63279 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb @@ -22,9 +22,6 @@ exts_list = [ ('pyperclip', '1.8.2', { 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], }), - ('importlib_metadata', '5.0.0', { - 'checksums': ['da31db32b304314d044d3c12c79bd59e307889b287ad12ff387b3500835fc2ab'], - }), ('cmd2', '2.4.2', { 'checksums': ['073e555c05853b0f6965f3d03329babdf9e38a5f2cea028e61a64cd7eeb74ad5'], }), From b87080a98c61bf43a3760d02006f9e41f748aba7 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 18 Nov 2022 13:54:01 +0000 Subject: [PATCH 718/793] use SOURCE_WHL / SOURCE_PY3_WHL --- .../p/Python/Python-3.10.8-GCCcore-12.2.0.eb | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb index 59243c2b5dc..2f5d77e3671 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb @@ -385,19 +385,19 @@ exts_list = [ 'checksums': ['9e77e941042ad3a4cc305dcdf2b2dec1aec2fbe3dd9015d2698ad02b173006d1'], }), ('pastel', '0.2.1', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], }), ('crashtest', '0.3.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['300f4b0825f57688b47b6d70c6a31de33512eb2fa1ac614f780939aa0cf91680'], }), ('clikit', '0.6.2', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], }), ('jeepney', '0.8.0', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], }), ('SecretStorage', '3.3.3', { @@ -415,7 +415,7 @@ exts_list = [ 'checksums': ['2ba3d56441ba0637f5f9c096068f67010ac0453f9d0b626de2aa3019353b6431'], }), ('tomlkit', '0.11.6', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['07de26b0d8cfc18f871aec595fda24d95b08fef89d147caa861939f37230bf4b'], }), ('shellingham', '1.5.0', { @@ -431,14 +431,13 @@ exts_list = [ 'checksums': ['a84da4318dd86f870a9447a8c98340aa06216bfc6f2b7bdc4b8766984ae1867c'], }), ('ptyprocess', '0.7.0', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], }), ('pexpect', '4.8.0', { 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], }), ('hatch_fancy_pypi_readme', '22.8.0', { - 'sources': ['hatch_fancy_pypi_readme-%(version)s.tar.gz'], 'checksums': ['da91282ca09601c18aded8e378daf8b578c70214866f0971156ee9bb9ce6c26a'], }), ('jsonschema', '4.17.0', { @@ -454,7 +453,7 @@ exts_list = [ 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], }), ('cleo', '1.0.0a5', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['ff53056589300976e960f75afb792dfbfc9c78dcbb5a448e207a17b643826360'], }), ('cachy', '0.3.0', { From 05cdc1aae7e190ede058643b5d7e0a0afb8494c5 Mon Sep 17 00:00:00 2001 From: Neil Douglas Date: Fri, 18 Nov 2022 14:56:07 +0000 Subject: [PATCH 719/793] adding easyconfigs: Cytoscape-3.9.1-Java-11.eb --- .../c/Cytoscape/Cytoscape-3.9.1-Java-11.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cytoscape/Cytoscape-3.9.1-Java-11.eb diff --git a/easybuild/easyconfigs/c/Cytoscape/Cytoscape-3.9.1-Java-11.eb b/easybuild/easyconfigs/c/Cytoscape/Cytoscape-3.9.1-Java-11.eb new file mode 100644 index 00000000000..3d967783b2c --- /dev/null +++ b/easybuild/easyconfigs/c/Cytoscape/Cytoscape-3.9.1-Java-11.eb @@ -0,0 +1,36 @@ +easyblock = 'Binary' + +name = 'Cytoscape' +version = '3.9.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://cytoscape.org/' +description = """Cytoscape is an open source software platform for visualizing + complex networks and integrating these with any type of attribute data. + A lot of Apps are available for various kinds of problem domains, + including bioinformatics, social network analysis, and semantic web.""" + +toolchain = SYSTEM + +_underscore_version = version.replace('.', '_') + +# https://github.com/cytoscape/cytoscape/releases/download/3.9.1/Cytoscape_3_9_1_unix.sh +source_urls = ['https://github.com/cytoscape/cytoscape/releases/download/3.9.1/'] +sources = ['%%(name)s_%s_unix.sh' % _underscore_version] + +checksums = ['0b20ac377dc01e6b0f7067104c2e463d8f834e50ee19dc302bb101dfcbc342a1'] + +dependencies = [ + ('Java', '11'), +] + +install_cmd = "./%%(name)s_%s_unix.sh -q -dir %%(installdir)s" % _underscore_version + +sanity_check_paths = { + 'files': ['cytoscape.sh', 'Cytoscape'], + 'dirs': ['framework', 'apps', 'sampleData'], +} + +sanity_check_commands = ["%(namelower)s.sh --help"] + +moduleclass = 'bio' From 6cad70bc4ac115d05608737b4ee703af68fafe41 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 20:20:26 +0000 Subject: [PATCH 720/793] Correct sanity-check-command added --- easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb b/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb index d1f4c2ad3a1..cfd3b1b4d0f 100644 --- a/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb +++ b/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb @@ -35,4 +35,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['KITEx |grep "^Starting program..."'] + moduleclass = 'chem' From e5fad376f9c3ea85eb9cb08d0942e6b13445a32f Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 20:26:46 +0000 Subject: [PATCH 721/793] tqdm removed --- .../easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb b/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb index 4459e4473f3..12bc9138bfa 100644 --- a/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb @@ -20,7 +20,6 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), - ('tqdm', '4.64.0'), ] use_pip = True From 2cd36bf71be4edfea029b23106457aee2d71b0f4 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 20:45:23 +0000 Subject: [PATCH 722/793] entrypoints added to close PR #16651 --- easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb index ff8bb790e8f..8c6c042e34d 100644 --- a/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb +++ b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb @@ -19,6 +19,9 @@ use_pip = True sanity_pip_check = True exts_list = [ + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), ('asciitree', '0.3.3', { 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], }), From bf57a8625d1298cc3d1db2999b240ccfd0f52526 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 20:52:53 +0000 Subject: [PATCH 723/793] dask version changed to 2022.10.0 --- easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb index aeac427c9c5..fbdcdebc32d 100644 --- a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('MITgcmutils', '0.1.2'), - ('dask', '2022.10.2'), + ('dask', '2022.10.0'), ] use_pip = True From 7755da5e2cbe6cd064f3467fb3667de518de4a29 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 20:57:32 +0000 Subject: [PATCH 724/793] dask version changed to 2022.10.0 --- easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb index d73a95fced8..55ff2f1d94f 100644 --- a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), - ('dask', '2022.10.2'), + ('dask', '2022.10.0'), ] use_pip = True From f89845cb8f9044ba73ebdb72acdc296830407741 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 21:10:01 +0000 Subject: [PATCH 725/793] adding easyconfigs: xarray-2022.9.0-foss-2022a.eb --- .../x/xarray/xarray-2022.9.0-foss-2022a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/x/xarray/xarray-2022.9.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/x/xarray/xarray-2022.9.0-foss-2022a.eb b/easybuild/easyconfigs/x/xarray/xarray-2022.9.0-foss-2022a.eb new file mode 100644 index 00000000000..5d3d2e2cf28 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-2022.9.0-foss-2022a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'xarray' +version = '2022.9.0' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], + }), +] + +moduleclass = 'data' From c738921011e77e1ab6057d34302597d89bc7fd22 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 21:38:43 +0000 Subject: [PATCH 726/793] entrypoint dependency removed --- easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb index 8c6c042e34d..b04ea6aea02 100644 --- a/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb +++ b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb @@ -12,7 +12,6 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), - ('entrypoints', '0.4'), ] use_pip = True From ad2331ea10c39203802a22ebcb30c78e261f543a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Nov 2022 08:44:45 +0100 Subject: [PATCH 727/793] add scDblFinder extension to Bioconductor 3.15 --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 43c53a70184..118a0158da3 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1098,6 +1098,9 @@ exts_list = [ ('ROntoTools', '2.24.0', { 'checksums': ['dec7ec0d6d709fbdb44d595d776fc462420957e5c23c7bd6d2d63f5a44df04dd'], }), + ('scDblFinder', '1.10.0', { + 'checksums': ['c0834495a342c6467d64dc899ba5913354ea5d53037c9be95e639950db6e2478'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From f3facbd38a67d9d047cddd06a6e2e7dee1f62f30 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 21 Nov 2022 10:28:02 +0100 Subject: [PATCH 728/793] adding easyconfigs: APR-1.7.0-GCCcore-11.3.0.eb, APR-util-1.6.1-GCCcore-11.3.0.eb --- .../APR-util/APR-util-1.6.1-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ .../a/APR/APR-1.7.0-GCCcore-11.3.0.eb | 22 +++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..52ae17f084c --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'APR-util' +version = '1.6.1' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b65e40713da57d004123b6319828be7f1273fbc6490e145874ee1177e112c459'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('APR', '1.7.0'), + ('SQLite', '3.38.3'), + ('expat', '2.4.8'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..200453bcb54 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-11.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'APR' +version = '1.7.0' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['48e9dbf45ae3fdc7b491259ffb6ccf7d63049ffacbc1c0977cced095e4c2d5a2'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' From 3e01282dd85ef34dd215ffe5652c3f3accac5523 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 21 Nov 2022 10:28:27 +0100 Subject: [PATCH 729/793] adding easyconfigs: Serf-1.3.9-GCCcore-11.3.0.eb --- .../s/Serf/Serf-1.3.9-GCCcore-11.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..41c4515fadd --- /dev/null +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'SCons' +name = 'Serf' +version = '1.3.9' + +homepage = 'https://serf.apache.org/' +description = """The serf library is a high performance C-based HTTP client library + built upon the Apache Portable Runtime (APR) library""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Serf-%(version)s_python3_scons.patch'] +checksums = [ + '549c2d21c577a8a9c0450facb5cca809f26591f048e466552240947bdf7a87cc', # serf-1.3.9.tar.bz2 + 'db401893bfb464ddcf369b543cacb9a165a21f8ff9bf1a819e4b61550bb9d3d0', # Serf-1.3.9_python3_scons.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('Python', '3.10.4'), + ('SCons', '4.4.0'), +] + +dependencies = [ + ('APR', '1.7.0'), + ('APR-util', '1.6.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +buildopts = "APR=$EBROOTAPR/bin/apr-1-config APU=$EBROOTAPRMINUTIL/bin/apu-1-config" + +sanity_check_paths = { + 'files': ['include/serf-1/serf.h'] + + ['lib/libserf-1.%s' % x for x in ['a', 'so']], + 'dirs': [], +} + +moduleclass = 'tools' From 057dca5363ed71ef4b156c4925a39e890644a0b8 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 21 Nov 2022 12:13:20 +0200 Subject: [PATCH 730/793] fix source_urls --- .../c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb index c4b1c45f09f..805ff73105f 100644 --- a/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb @@ -46,7 +46,9 @@ exts_list = [ 'checksums': ['76f8fef59cf2061dbd849bbce4fe49bdd820884385004b0ca59136ac3db129e4'], }), (name, version, { - 'checksums': ['3a2cdd4dc2d8b4832fa132a0bd1102f86c38f6865d7f119018404069d35984b2'], + 'source_urls': ['https://github.com/hpcaitech/ColossalAI/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['e0975cd9a0860a2d00d1f725baaee3652e2f601724968628d8750021ef483320'], }), ] From 5fe59c9f66198ca47bc7f8569596fe8b5681ecda Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 21 Nov 2022 12:14:46 +0200 Subject: [PATCH 731/793] fix dllogger checksum --- .../o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb index 52743c921ac..9eec3b5f807 100644 --- a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb @@ -71,7 +71,7 @@ exts_list = [ ('dllogger', version, { 'source_urls': ['https://github.com/NVIDIA/dllogger/archive/refs/tags/'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['43e5e3c3acf891dfe6151f7d869f3ad2424772fe57fd8dcb0a45bad06de93bf7'], + 'checksums': ['abae2b2ac73b9e176fa87144bf6c2048ddd3dae8e7002d6d5a270bc7e4da6b4d'], }), (name, version, { 'source_urls': ['https://github.com/aqlaboratory/openfold/archive/refs/tags/'], From 4dfba82a0fc56d09f89ddcdb886d833b907946d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Nov 2022 12:37:06 +0100 Subject: [PATCH 732/793] use same patches for netcdf4-python 1.6.1 in foss/intel easyconfigs --- .../n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb index 60eb9cd8eef..d5d6084f968 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb @@ -24,13 +24,18 @@ exts_list = [ 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], }), (name, version, { - 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'patches': [ + 'netcdf4-python-1.1.8-avoid-diskless-test.patch', + 'netcdf4-python-1.6.1_relax_tolerance_compression_test.patch', + ], 'source_tmpl': 'netCDF4-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], 'checksums': [ 'ba8dc5d65293a99f1afb8c2acf588d903fdfdc1963a62545b677fa2734262a78', # netCDF4-1.6.1.tar.gz # netcdf4-python-1.1.8-avoid-diskless-test.patch 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + # netcdf4-python-1.6.1_relax_tolerance_compression_test.patch + '64d192a5d1e3e00af78f053da78f5a35015fa713c7f97b10b622be6a44347166', ], }), ] From 0dcbf4e8f71e4b7b28bd9598918cfd8c04c19376 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 21 Nov 2022 13:36:55 +0100 Subject: [PATCH 733/793] adding easyconfigs: OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb --- .../OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..5d2f680ca42 --- /dev/null +++ b/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'OmegaFold' +version = '1.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/HeliXonProtein/OmegaFold' +description = """OmegaFold: High-resolution de novo Structure Prediction from Primary Sequence""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', '-CUDA-%(cudaver)s'), + ('Biopython', '1.79'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'preinstallopts': """sed -i '/^setup(/a \ version="%(version)s",' setup.py && """, + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/HeliXonProtein/OmegaFold/archive/'], + 'checksums': ['ab3b48fe7721539b6943b49cdbafc9799e15b4425a324cc25daf15a24e3f9e37'], + }), +] + +sanity_check_paths = { + 'files': ['bin/omegafold'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/omegafold'], +} + +sanity_check_commands = [ + "omegafold --help", +] + +moduleclass = 'bio' From 92a83bf682fbc93dfc2b4b103440f6aad2ac9ef8 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 21 Nov 2022 14:28:42 +0100 Subject: [PATCH 734/793] use PythonBundle with resolos v0.3.5 --- .../r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb index e3cc4db884a..efe3f01dcbc 100644 --- a/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb @@ -1,36 +1,36 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'resolos' version = '0.3.5' homepage = 'https://gitlab.unige.ch/resolos/resolos' description = """Resolos is a toolkit written in Python for maintaining reproducible environments -for scientific computations. -It's main goal is to enable researchers to easily replicate environments through space -(running code on HPC environment) - +for scientific computations. It's main goal is to enable researchers to easily +replicate environments through space (running code on HPC environment) and time (environment preservation for long term archival). For installation and detailed usage, check out the documentation.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -# source_urls = [PYPI_SOURCE] -# Link copy from pypi.org | PYPI_SOURCE is not working -sources = [SOURCE_TAR_GZ] -checksums = ['c0fb50e36866fa591f0a7ab3567e9037c97d96f34614e86ee9cad1b62c689de2'] - dependencies = { ('Python', '3.10.4'), ('PyYAML', '6.0'), } - use_pip = True -use_pip_for_deps = True -moduleclass = 'data' + +exts_list = [ + (name, version, { + 'checksums': ['c0fb50e36866fa591f0a7ab3567e9037c97d96f34614e86ee9cad1b62c689de2'], + }), +] + +sanity_pip_check = True sanity_check_commands = ["r3s info"] sanity_check_paths = { 'files': ["bin/r3s"], - 'dirs': [] + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } + +moduleclass = 'tools' From 9b5627504dcf2de5ba8caf1976e32804aaf69f30 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 21 Nov 2022 14:56:11 +0100 Subject: [PATCH 735/793] use SYSTEM global in flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb --- .../f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb index 1ad8d95623e..7223c3f1260 100644 --- a/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb @@ -10,7 +10,7 @@ description = "A very simple framework for state-of-the-art NLP" toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('PyTorch', '1.10.0', versionsuffix), ('tqdm', '4.61.2'), From 675a7ec13b0a7b359ce47aa491da28e71d126af1 Mon Sep 17 00:00:00 2001 From: garadar Date: Mon, 21 Nov 2022 15:29:06 +0100 Subject: [PATCH 736/793] Update easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb Co-authored-by: Alex Domingo --- easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb index efe3f01dcbc..7aaeaad8e10 100644 --- a/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb @@ -12,6 +12,8 @@ For installation and detailed usage, check out the documentation.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +builddependencies = [('binutils', '2.38')] + dependencies = { ('Python', '3.10.4'), ('PyYAML', '6.0'), From 97e7e854b4affd0d73ecc8dcb1bc18b8e6393497 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Nov 2022 16:49:51 +0100 Subject: [PATCH 737/793] add missing extensions to easyconfig for R-bundle-Bioconductor v3.15 with foss/2021b --- ...bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb index 9c7b01b9137..b6ac8e83c45 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb @@ -1090,6 +1090,21 @@ exts_list = [ ('SPOTlight', '1.0.0', { 'checksums': ['f6baf718e468292960884a1aacdf8295f0864d771f5eb0f2088fb9a1bc00dcc0'], }), + ('CGHcall', '2.58.0', { + 'checksums': ['c5e86b9234685462b7330c85b91ca648a801a76c99f3e98cd509ac47ee8afae2'], + }), + ('QDNAseq', '1.32.0', { + 'checksums': ['75bbde9b6cc55cd6a47b9f466358033a180b480def2144abdcc93a2a8e066668'], + }), + ('HiCcompare', '1.18.0', { + 'checksums': ['b9320fa7a9f10832e2ac7ade0245f85ac4c2c26edef2580078888f5e1050ee2d'], + }), + ('ROntoTools', '2.24.0', { + 'checksums': ['dec7ec0d6d709fbdb44d595d776fc462420957e5c23c7bd6d2d63f5a44df04dd'], + }), + ('scDblFinder', '1.10.0', { + 'checksums': ['c0834495a342c6467d64dc899ba5913354ea5d53037c9be95e639950db6e2478'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 3c66bade085902d638af6a6e73852c496697d445 Mon Sep 17 00:00:00 2001 From: garadar Date: Mon, 21 Nov 2022 16:57:17 +0100 Subject: [PATCH 738/793] Update easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb Co-authored-by: Alex Domingo --- .../r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb index 7aaeaad8e10..4a7708038c7 100644 --- a/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb @@ -22,6 +22,19 @@ dependencies = { use_pip = True exts_list = [ + ('click-log', '0.4.0', { + 'checksums': ['3970f8570ac54491237bcdb3d8ab5e3eef6c057df29f8c3d1151a51a9c23b975'], + }), + ('conda-pack', '0.6.0', { + 'checksums': ['615f41353fdc8793b0edb55702212273f17e40b43cc2c17493430e9c66d9f0b3'], + }), + ('semver', '2.13.0', { + 'checksums': ['fa0fe2722ee1c3f57eac478820c3a5ae2f624af8264cbdf9000c980ff7f75e3f'], + }), + ('PyJWT', '2.6.0', { + 'modulename': 'jwt', + 'checksums': ['69285c7e31fc44f68a1feb309e948e0df53259d579295e6cfe2b1792329f05fd'], + }), (name, version, { 'checksums': ['c0fb50e36866fa591f0a7ab3567e9037c97d96f34614e86ee9cad1b62c689de2'], }), From 048d1168850897b96d49c05f63752d4bd731dacf Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 21 Nov 2022 21:28:45 +0100 Subject: [PATCH 739/793] add comment for missing version --- .../o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb index 5d2f680ca42..0008cde884d 100644 --- a/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb @@ -19,9 +19,10 @@ dependencies = [ use_pip = True sanity_pip_check = True +# add missing version for OmegaFold exts_list = [ (name, version, { - 'preinstallopts': """sed -i '/^setup(/a \ version="%(version)s",' setup.py && """, + 'preinstallopts': """sed -i '/^setup(/a \ version="%(version)s",' setup.py && """, # noqa: W605 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/HeliXonProtein/OmegaFold/archive/'], 'checksums': ['ab3b48fe7721539b6943b49cdbafc9799e15b4425a324cc25daf15a24e3f9e37'], From 010536c00c9d1afb9459a581c594c3c4c278dedf Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 21 Nov 2022 22:00:45 +0100 Subject: [PATCH 740/793] update pyproj version for Cartopy 0.20.3 --- easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb index f8c63257d0f..436e9a24ca9 100644 --- a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb @@ -16,7 +16,7 @@ dependencies = [ ('GDAL', '3.5.0'), ('GEOS', '3.10.3'), ('matplotlib', '3.5.2'), - ('pyproj', '3.3.1'), + ('pyproj', '3.4.0'), ('SciPy-bundle', '2022.05'), ('Shapely', '1.8.2'), ('lxml', '4.9.1'), From d9d7c82f7c936623f56403625c806f84917962ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Nov 2022 17:23:13 +0100 Subject: [PATCH 741/793] stick to older PyQt-builder in easyconfig for PyQt5 5.15.5, so that 'pip check' passes --- easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb index 594f66926cc..11986d88534 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb @@ -50,10 +50,10 @@ components = [ 'use_pip': True, 'options': {'modulename': 'PyQt5.sip'}, }), - ('PyQt-builder', '1.14.0', { + ('PyQt-builder', '1.11.0', { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], - 'checksums': ['6755931c6d2f8940553e0334d10c933ce5cc18b64425e94fda1accf4ff774f59'], + 'checksums': ['40f6df88c00e6aa9ac9a8bc5688f9fe2a4bd56c06cdb0a0b00ce8955ec34ffe5'], 'start_dir': 'PyQt-builder-%(version)s', 'use_pip': True, }), @@ -97,6 +97,7 @@ sanity_check_commands = [ "pyuic5 --help", "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", + "pip check", ] modextrapaths = { From 497ee827e02fd25aae30206316b44b04461a26be Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 22 Nov 2022 17:32:56 +0000 Subject: [PATCH 742/793] xarray added as dependency instead of extension --- easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb index fbdcdebc32d..c8a25756118 100644 --- a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb @@ -16,6 +16,7 @@ dependencies = [ ('Python', '3.10.4'), ('MITgcmutils', '0.1.2'), ('dask', '2022.10.0'), + ('xarray', '2022.9.0'), ] use_pip = True @@ -25,9 +26,6 @@ exts_list = [ ('cachetools', '5.2.0', { 'checksums': ['6a94c6402995a99c3970cc7e4884bb60b4a8639938157eeed436098bf9831757'], }), - ('xarray', '2022.9.0', { - 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], - }), (name, version, { 'checksums': ['7dda45fdf6182a859f5c441cd5928a7c99d41c8bcea9fccf471b7011791b1131'], }), From 0d413469b3877fad7783bff87ba2fe9f10a22b67 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 22 Nov 2022 18:24:09 +0000 Subject: [PATCH 743/793] xarray added as dependency instead of extension --- .../easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb index 55ff2f1d94f..b81f3b84574 100644 --- a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb @@ -14,19 +14,16 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('dask', '2022.10.0'), + ('xarray', '2022.9.0'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('xarray', '2022.9.0', { - 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], - }), ('xgcm', '0.8.0', { 'checksums': ['99e7e2fc9268fb13827f8849dbae279eaaa4960d51872d62bc38293605b0215f'], }), - (name, version, { 'checksums': ['8c684ecdfe03bade171e17f5ae6bedd422e51db6faffed0303e1839051d40614'], }), From 27d802f112e033736cceb2688ef41162e673aae6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Nov 2022 20:20:50 +0100 Subject: [PATCH 744/793] avoid using empty string in sanity_check_paths in MONAI easyconfigs --- .../easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb | 2 +- easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb index bd6d8765a06..c4ae75df709 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb @@ -44,7 +44,7 @@ sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'" sanity_check_paths = { 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], - 'dirs': [''], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb index 0d272341e2c..0314fc871d4 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb @@ -42,7 +42,7 @@ sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'" sanity_check_paths = { 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], - 'dirs': [''], + 'dirs': [], } moduleclass = 'vis' From b8bed9f936c7067b63bc49aa7bca17c574f3cba7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Nov 2022 22:46:18 +0100 Subject: [PATCH 745/793] avoid hardcoding OpenJPEG version in preinstallopts in imagecodecs easyconfig --- .../i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb index 2a32ac22f2e..284a8b29cb8 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb @@ -63,7 +63,7 @@ exts_list = [ }), (name, version, { 'extract_cmd': "tar -xvf %s && find . -type f -print0 | xargs -0 dos2unix", - 'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-2.4/:$CPATH && ", + 'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-%s/:$CPATH && " % local_openjpeg_maj_min, 'sources': ['%(name)s-%(version)s.tar.gz'], 'checksums': ['04d5757d8fd7819844b0f8d9eed05025dca4962f280d0010b42c7c9c993fe371'], }), From a8cf06cf7f9db89b306bf07aba66a5e5a84425eb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Nov 2022 00:31:32 +0100 Subject: [PATCH 746/793] downgrade dependency of oceanspy v0.2.0 on xarray to v2022.6.0 --- easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb index b81f3b84574..ac13454ba89 100644 --- a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('dask', '2022.10.0'), - ('xarray', '2022.9.0'), + ('xarray', '2022.6.0'), ] use_pip = True From 0a9d01452b248f18dda7d527ed5be70e5733c5de Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Nov 2022 00:32:43 +0100 Subject: [PATCH 747/793] downgrade dependency of xmitgcm v0.5.2 on xarray to v2022.6.0 --- easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb index c8a25756118..cf4cebe8ec1 100644 --- a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.10.4'), ('MITgcmutils', '0.1.2'), ('dask', '2022.10.0'), - ('xarray', '2022.9.0'), + ('xarray', '2022.6.0'), ] use_pip = True From 0ae557bd93cf3e13fe872f03288dfe6c2a560439 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 10:52:35 +0100 Subject: [PATCH 748/793] adding easyconfigs: nodejs-18.12.1-GCCcore-12.2.0.eb --- .../n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..46b6a0c4ae4 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '18.12.1' # LTS on 2022-11-22 +local_libversion = '108' + +homepage = 'https://nodejs.org' +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://nodejs.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] +checksums = ['ba8174dda00d5b90943f37c6a180a1d37c861d91e04a4cb38dc1c0c74981c186'] + +builddependencies = [ + ('binutils', '2.39'), + ('Python', '3.10.8', '-bare'), +] + +configopts = [ + '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library + '--shared --with-intl=none', # Build libnode.so in a second run +] + +# Link libv8 libs to libnode +postinstallcmds = [ + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), +] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s' % SHLIB_EXT, 'lib/libv8.%s' % SHLIB_EXT], + 'dirs': ['lib/node_modules', 'include/node'] +} + +sanity_check_commands = ["node --help"] + +moduleclass = 'lang' From a3c4da77a27192f4369b8e83391b990a75b358b5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Nov 2022 11:31:59 +0100 Subject: [PATCH 749/793] adding easyconfigs: Boost.MPI-1.79.0-gompi-2022a.eb --- .../Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb new file mode 100644 index 00000000000..be6c179e528 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'EB_Boost' + +name = 'Boost.MPI' +version = '1.79.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['273f1be93238a068aba4f9735a4a2b003019af067b9c183ed227780b8f36062c'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), + ('XZ', '5.2.5'), + ('ICU', '71.1'), +] + +configopts = '--without-libraries=python' + +boost_mpi = True +tagged_layout = True + +moduleclass = 'devel' From 811ef35e395c75580ddfeec617d0cbaac2650231 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Nov 2022 12:40:15 +0100 Subject: [PATCH 750/793] prefix custom parameters with local in nodejs --- .../n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb | 18 +++++++++--------- .../n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb | 18 +++++++++--------- .../n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 18 +++++++++--------- 3 files changed, 27 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb index bf1db1aa052..866799bfdea 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'nodejs' version = '14.17.0' # LTS on 2021-06-03 -_libversion = '83' +local_libversion = '83' homepage = 'https://nodejs.org' description = """Node.js is a platform built on Chrome's JavaScript runtime @@ -37,24 +37,24 @@ dependencies = [ ] # Use ICU and OpenSSL from EasyBuild -_common_configopts = "--with-intl=system-icu --shared-openssl " +local_common_configopts = "--with-intl=system-icu --shared-openssl " configopts = [ - _common_configopts, # Static build - '--shared %s' % _common_configopts, # Build libnode.so in a second run + local_common_configopts, # Static build + '--shared %s' % local_common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode -_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] -_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in _extra_sonames] -_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, _libversion) +local_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +local_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in local_extra_sonames] +local_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, local_libversion) postinstallcmds = [ - "cd %%(installdir)s/lib && ln -s %s %s" % (_libnode_real, x) for x in _extra_libs + "cd %%(installdir)s/lib && ln -s %s %s" % (local_libnode_real, x) for x in local_extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [_libnode_real] + _extra_libs], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [local_libnode_real] + local_extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb index a6fe9b552ba..6be4d509878 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'nodejs' version = '14.17.6' # LTS on 2020-08-31 -_libversion = '83' +local_libversion = '83' homepage = 'https://nodejs.org' description = """Node.js is a platform built on Chrome's JavaScript runtime @@ -27,24 +27,24 @@ dependencies = [ ] # Use ICU and OpenSSL from EasyBuild -_common_configopts = "--with-intl=system-icu --shared-openssl " +local_common_configopts = "--with-intl=system-icu --shared-openssl " configopts = [ - _common_configopts, # Static build - '--shared %s' % _common_configopts, # Build libnode.so in a second run + local_common_configopts, # Static build + '--shared %s' % local_common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode -_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] -_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in _extra_sonames] -_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, _libversion) +local_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +local_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in local_extra_sonames] +local_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, local_libversion) postinstallcmds = [ - "cd %%(installdir)s/lib && ln -s %s %s" % (_libnode_real, x) for x in _extra_libs + "cd %%(installdir)s/lib && ln -s %s %s" % (local_libnode_real, x) for x in local_extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [_libnode_real] + _extra_libs], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [local_libnode_real] + local_extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb index bcd9c8dded1..117331f1af8 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'nodejs' version = '16.15.1' # LTS on 2022-06-12 -_libversion = '93' +local_libversion = '93' homepage = 'https://nodejs.org' description = """Node.js is a platform built on Chrome's JavaScript runtime @@ -27,24 +27,24 @@ dependencies = [ ] # Use ICU and OpenSSL from EasyBuild -_common_configopts = "--with-intl=system-icu --shared-openssl " +local_common_configopts = "--with-intl=system-icu --shared-openssl " configopts = [ - _common_configopts, # Static build - '--shared %s' % _common_configopts, # Build libnode.so in a second run + local_common_configopts, # Static build + '--shared %s' % local_common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode -_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] -_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in _extra_sonames] -_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, _libversion) +local_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +local_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in local_extra_sonames] +local_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, local_libversion) postinstallcmds = [ - "cd %%(installdir)s/lib && ln -s %s %s" % (_libnode_real, x) for x in _extra_libs + "cd %%(installdir)s/lib && ln -s %s %s" % (local_libnode_real, x) for x in local_extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [_libnode_real] + _extra_libs], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [local_libnode_real] + local_extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } From d8364b3d5b9b06d6057c7e9de380ebb80a93ab00 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Wed, 23 Nov 2022 12:55:10 +0100 Subject: [PATCH 751/793] adding easyconfigs: GLM-0.9.9.8-GCCcore-11.3.0.eb --- .../g/GLM/GLM-0.9.9.8-GCCcore-11.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..22d687ed0f4 --- /dev/null +++ b/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'GLM' +version = '0.9.9.8' + +homepage = 'https://github.com/g-truc/glm' +description = """ +OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics +software based on the OpenGL Shading Language (GLSL) specifications.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/g-truc/glm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + 'GLM-0.9.9.8_fix_missing_install.patch', +] +checksums = [ + '7d508ab72cb5d43227a3711420f06ff99b0a0cb63ee2f93631b162bfe1fe9592', # 0.9.9.8.tar.gz + '1cc199f9d66679b0b5e9a9fbe20bca0d9b15760fa172ca8759dd15bab35802ca', # GLM-0.9.9.8_fix_missing_install.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/glm/gtc', 'include/glm/gtx'], +} + +moduleclass = 'lib' From acff80f03c68708109802872b0db1993a9964020 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 23 Nov 2022 12:05:06 +0000 Subject: [PATCH 752/793] adding easyconfigs: libspatialindex-1.9.3-GCCcore-11.3.0.eb --- .../libspatialindex-1.9.3-GCCcore-11.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..445496497a1 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'libspatialindex' +version = '1.9.3' + +homepage = 'https://libspatialindex.org' +description = """C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/libspatialindex/libspatialindex/releases/download/%(version)s/'] +sources = ['spatialindex-src-%(version)s.tar.gz'] +checksums = ['47d8779e32477b330e46b62fb7e62cb812caee5d8e684c35cb635a42a749f3fc'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['lib/libspatialindex.%s' % SHLIB_EXT], + 'dirs': ['include/spatialindex'], +} + +moduleclass = 'lib' From 46b4c405d06e84d3fb1e72bed94dc5082e123311 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 14:30:41 +0100 Subject: [PATCH 753/793] use proper dependencies for ICU and OpenSSL for nodejs 18.12.1 --- .../i/ICU/ICU-72.1-GCCcore-12.2.0.eb | 29 +++++++++++++++++++ .../n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb | 23 ++++++++++----- 2 files changed, 45 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/i/ICU/ICU-72.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/i/ICU/ICU-72.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/ICU/ICU-72.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..9b141a4671d --- /dev/null +++ b/easybuild/easyconfigs/i/ICU/ICU-72.1-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ICU' +version = '72.1' + +homepage = 'https://icu.unicode.org' +description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization + support for software applications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] +sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] +checksums = ['a2d2d38217092a7ed56635e34467f92f976b370e20182ad325edea6681a71d68'] + +builddependencies = [ + ('binutils', '2.39'), + ('Python', '3.10.8', '-bare'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['lib/libicu%s.%s' % (x, SHLIB_EXT) for x in ['data', 'i18n', 'io', 'test', 'tu', 'uc']], + 'dirs': ['bin', 'include/unicode', 'share/icu', 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb index 46b6a0c4ae4..2ea5d3c974f 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb @@ -21,21 +21,30 @@ builddependencies = [ ('Python', '3.10.8', '-bare'), ] +dependencies = [ + ('ICU', '72.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +# Use ICU and OpenSSL from EasyBuild +local_common_configopts = "--with-intl=system-icu --shared-openssl " + configopts = [ - '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library - '--shared --with-intl=none', # Build libnode.so in a second run + local_common_configopts, # Static build + '--shared %s' % local_common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode +local_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +local_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in local_extra_sonames] +local_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, local_libversion) + postinstallcmds = [ - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s %s %s" % (local_libnode_real, x) for x in local_extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s' % SHLIB_EXT, 'lib/libv8.%s' % SHLIB_EXT], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [local_libnode_real] + local_extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } From 6361e43ad12699fc7afaed695b7cc9d8a5c3f780 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 15:30:58 +0100 Subject: [PATCH 754/793] adding easyconfigs: LLVM-15.0.5-GCCcore-12.2.0.eb --- .../l/LLVM/LLVM-15.0.5-GCCcore-12.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-15.0.5-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-15.0.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-15.0.5-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..fad97fede29 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-15.0.5-GCCcore-12.2.0.eb @@ -0,0 +1,46 @@ +name = 'LLVM' +version = '15.0.5' + +homepage = "https://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'cstd': 'gnu++11', 'pic': True} + +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'cmake-%(version)s.src.tar.xz', +] +checksums = [ + {'llvm-15.0.5.src.tar.xz': '4428688b567ab1c9911aa9e13cb44c9bc1b14431713c14de491e10369f2b0370'}, + {'cmake-15.0.5.src.tar.xz': '61a9757f2fb7dd4c992522732531eb58b2bb031a2ca68848ff1cfda1fc07b7b3'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('Python', '3.10.8'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +sanity_check_commands = ["llvm-ar --help"] + +moduleclass = 'compiler' From 09e832fc190757d9ce10f0e701ca6e9c0b521790 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Dvo=C5=99=C3=A1=C4=8Dek=20Josef?= Date: Wed, 23 Nov 2022 17:26:33 +0100 Subject: [PATCH 755/793] adding easyconfigs: libconfig-1.7.3-GCCcore-11.2.0.eb --- .../libconfig-1.7.3-GCCcore-11.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..4cf46abac37 --- /dev/null +++ b/easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libconfig' +version = '1.7.3' + +homepage = 'https://hyperrealm.github.io/libconfig' +description = "Libconfig is a simple library for processing structured configuration files" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://hyperrealm.github.io/libconfig/dist/'] +sources = [SOURCE_TAR_GZ] +checksums = ['545166d6cac037744381d1e9cc5a5405094e7bfad16a411699bcff40bbb31ee7'] + +builddependencies = [ + ('binutils', '2.37'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] + +sanity_check_paths = { + 'files': ['include/libconfig.h', 'include/libconfig.h++', 'lib/libconfig.a', 'lib/libconfig++.a', + 'lib/libconfig.%s' % SHLIB_EXT, 'lib/libconfig++.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' From ce2947aead4d9ae74e80445e06f913db4c6168f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 22:44:22 +0100 Subject: [PATCH 756/793] adding easyconfigs: zstd-1.5.2-GCCcore-12.2.0.eb, gzip-1.12-GCCcore-12.2.0.eb, lz4-1.9.4-GCCcore-12.2.0.eb --- .../g/gzip/gzip-1.12-GCCcore-12.2.0.eb | 29 +++++++++++++ .../l/lz4/lz4-1.9.4-GCCcore-12.2.0.eb | 30 ++++++++++++++ .../z/zstd/zstd-1.5.2-GCCcore-12.2.0.eb | 41 +++++++++++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/z/zstd/zstd-1.5.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..22956fb64c7 --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'gzip' +version = '1.12' + +homepage = 'https://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['gzip-1.12_fix-gnulib-strndup-redeclaration.patch'] +checksums = [ + '5b4fb14d38314e09f2fc8a1c510e7cd540a3ea0e3eb9b0420046b82c3bf41085', # gzip-1.12.tar.gz + # gzip-1.12_fix-gnulib-strndup-redeclaration.patch + '9c67e3e88848f7ff1f19f29d87f286bac1cc8f027f7eea9bcaf53883b95032e4', +] + +builddependencies = [('binutils', '2.39')] + +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..6f3f81b768d --- /dev/null +++ b/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'lz4' +version = '1.9.4' + +homepage = 'https://lz4.github.io/lz4/' +description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. + It features an extremely fast decoder, with speed in multiple GB/s per core.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['0b0e3aa07c8c063ddf40b082bdf7e37a1562bda40a0ff5272957f3e987e0e54b'] + +builddependencies = [('binutils', '2.39')] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/lz4", "lib/liblz4.%s" % SHLIB_EXT, "include/lz4.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zstd/zstd-1.5.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/z/zstd/zstd-1.5.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7176db3c09e --- /dev/null +++ b/easybuild/easyconfigs/z/zstd/zstd-1.5.2-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'zstd' +version = '1.5.2' + +homepage = 'https://facebook.github.io/zstd' +description = """Zstandard is a real-time compression algorithm, providing high compression ratios. + It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. + It also offers a special mode for small data, called dictionary compression, and can create dictionaries + from any sample set.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'facebook' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f7de13462f7a82c29ab865820149e778cbfe01087b3a55b5332707abf9db4a6e'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('gzip', '1.12'), + ('XZ', '5.2.7'), + ('lz4', '1.9.4'), +] + +skipsteps = ['configure'] + +runtest = 'check' + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ["bin/zstd", "lib/libzstd.%s" % SHLIB_EXT, "include/zstd.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' From 6266613ac52a07184c8d2b51c1fa352fabdcf366 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 22:46:43 +0100 Subject: [PATCH 757/793] {vis}[GCCcore/12.2.0] Mesa v22.2.4, Mako v1.2.4, libglvnd v1.6.0, libdrm v2.4.114, libunwind v1.6.2 --- .../l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb | 32 +++++++++ .../libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb | 33 +++++++++ .../libunwind-1.6.2-GCCcore-12.2.0.eb | 32 +++++++++ .../m/Mako/Mako-1.2.4-GCCcore-12.2.0.eb | 29 ++++++++ .../m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb | 69 +++++++++++++++++++ 5 files changed, 195 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..613ec59df25 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'libdrm' +version = '2.4.114' + +homepage = 'https://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['3049cf843a47d12e5eeefbc3be3496d782fa09f42346bf0b7defe3d1e598d026'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), +] +dependencies = [('X11', '20221110')] + +# installing manpages requires an extra build dependency (docbook xsl) +configopts = '-Dman-pages=false' + +sanity_check_paths = { + 'files': ['lib/libdrm.%s' % SHLIB_EXT, 'include/libdrm/drm.h'], + 'dirs': ['include', 'lib'], +} + + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b953d44c572 --- /dev/null +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'libglvnd' +version = '1.6.0' + +homepage = 'https://gitlab.freedesktop.org/glvnd/libglvnd' +description = "libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://gitlab.freedesktop.org/glvnd/libglvnd/-/archive/v%(version)s/'] +sources = ['libglvnd-v%(version)s.tar.gz'] +checksums = ['33b8b993adf47a21bc1c46bcf970927edeb9884390d5b09b1aed051d600c0b2f'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), +] + +dependencies = [('X11', '20221110')] + +# Let EGL find system-installed vendor files in /etc/glvnd/egl_vendor.d etc. +allow_prepend_abs_path = True +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "/etc/glvnd/egl_vendor.d:/usr/share/glvnd/egl_vendor.d"} + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['EGL', 'GL', 'GLX', 'OpenGL']], + 'dirs': ['include/%s' % x for x in ['EGL', 'GL', 'GLES', 'GLES2', 'GLES3', 'glvnd', 'KHR']] + ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..5e849e316cd --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.6.2' + +homepage = 'https://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4a6aec666991fb45d0889c44aede8ad6eb108071c3554fcdff671f9c94794976'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('XZ', '5.2.7'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fno-common" && ' + +sanity_check_paths = { + 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..5aaa05828b2 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.2.4' + +homepage = 'https://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d60a3903dc3bb01a18ad6a89cdbe2e4eadc69c0bc8ef1e3773ba53d44c3f7a34'] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +builddependencies = [('binutils', '2.39')] + +dependencies = [('Python', '3.10.8')] + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ["mako-render --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f59d911be6a --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb @@ -0,0 +1,69 @@ +# This is a Mesa using software rendering via Gallium-DRI and libglvnd +# - libglvnd can dynamically choose between system-installed NVidia +# libGLX/libEGL or the software renderers provided by this Mesa +# - EGL is available +# +# Software renderers enabled (swr deprecated as of v22): +# - llvmpipe: uses LLVM for JIT code generation (multi-threaded) +# - softpipe: a reference Gallium driver +# Default renderer is llvmpipe. To use softpipe, set the environment +# variable GALLIUM_DRIVER=softpipe + +name = 'Mesa' +version = '22.2.4' + +homepage = 'https://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', +] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['65d76b53ca5c7b46019e0e8e5b414de45d2fecd3fcd71707f6c3bc7691c9f7ab'] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('pkgconf', '1.9.3'), + ('Mako', '1.2.4'), + ('libxml2', '2.10.3'), + ('expat', '2.4.9'), + ('gettext', '0.21.1'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('zstd', '1.5.2'), + ('libdrm', '2.4.114'), + ('libglvnd', '1.6.0'), + ('libunwind', '1.6.2'), + ('LLVM', '15.0.5'), + ('X11', '20221110'), +] + +configopts = "-Dplatforms=x11 -Dosmesa=true -Ddri-drivers='' -Dvulkan-drivers='' " +configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" + +# Easybuild will automatically add appropriate Gallium drivers for the processor architecture of the host +# If you need a different configuration, it possible to override those values by setting your own configopts +# configopts += " -Dgallium-drivers=swrast" + +# symlink indirect to mesa GLX, similar to Debian, see +# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881789 +# This helps in certain X forwarding situations (e.g. XQuartz) +postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] + +# Tells libglvnd where to find EGL libraries +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} + +moduleclass = 'vis' From 8338bf7b0d8e45eb8a6155dae9792dc14be1f10d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 22:52:50 +0100 Subject: [PATCH 758/793] use 'disabled' to skip installation of man pages for libdrm 2.4.114 --- easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb index 613ec59df25..40a3653b38d 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [('X11', '20221110')] # installing manpages requires an extra build dependency (docbook xsl) -configopts = '-Dman-pages=false' +configopts = '-Dman-pages=disabled' sanity_check_paths = { 'files': ['lib/libdrm.%s' % SHLIB_EXT, 'include/libdrm/drm.h'], From 205429ecc30c39fab6171fe430898c5d73a1a925 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 22:54:14 +0100 Subject: [PATCH 759/793] fix checksum for libglvnd 1.6.0 --- .../easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb index b953d44c572..6e95158d902 100644 --- a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} source_urls = ['https://gitlab.freedesktop.org/glvnd/libglvnd/-/archive/v%(version)s/'] sources = ['libglvnd-v%(version)s.tar.gz'] -checksums = ['33b8b993adf47a21bc1c46bcf970927edeb9884390d5b09b1aed051d600c0b2f'] +checksums = ['efc756ffd24b24059e1c53677a9d57b4b237b00a01c54a6f1611e1e51661d70c'] builddependencies = [ ('binutils', '2.39'), From 0dc8178599b7c7d388169d5db7797275ba873a9c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 23:05:33 +0100 Subject: [PATCH 760/793] adding easyconfigs: libGLU-9.0.2-GCCcore-12.2.0.eb --- .../l/libGLU/libGLU-9.0.2-GCCcore-12.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2a35c328e4b --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.2' + +homepage = 'https://mesa.freedesktop.org/archive/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://mesa.freedesktop.org/archive/glu/'] +sources = ['glu-%(version)s.tar.gz'] +checksums = ['24effdfb952453cc00e275e1c82ca9787506aba0282145fff054498e60e19a65'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Mesa', '22.2.4'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From ea2ea8b366a92933d652ae53987e948b85f64687 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 23:22:08 +0100 Subject: [PATCH 761/793] {lib}[GCCcore/12.2.0] libjpeg-turbo v2.1.4, NASM v2.15.05 --- .../libjpeg-turbo-2.1.4-GCCcore-12.2.0.eb | 42 +++++++++++++++++++ .../n/NASM/NASM-2.15.05-GCCcore-12.2.0.eb | 25 +++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0117bb716bf --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.4-GCCcore-12.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'libjpeg-turbo' +version = '2.1.4' + +homepage = 'https://sourceforge.net/projects/libjpeg-turbo/' + +description = """ + libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to + accelerate baseline JPEG compression and decompression. libjpeg is a library + that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d3ed26a1131a13686dfca4935e520eb7c90ae76fbc45d98bb50a8dc86230342b'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + +dependencies = [ + ('NASM', '2.15.05'), +] + +configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', + 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', + 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', + 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e4fa39b554e --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.15.05' + +homepage = 'https://www.nasm.us/' + +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['3c4b8339e5ab54b1bcb2316101f8985a5da50a3f9e504d43fa6f35668bee2fd0'] + +builddependencies = [ + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' From 8cdfede4b48a9bd320ece80e54808ae9ed538224 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 23:24:56 +0100 Subject: [PATCH 762/793] adding easyconfigs: double-conversion-3.2.1-GCCcore-12.2.0.eb --- .../double-conversion-3.2.1-GCCcore-12.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d3221353d9f --- /dev/null +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.1-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'double-conversion' +version = '3.2.1' + +homepage = 'https://github.com/google/double-conversion' +description = "Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/google/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e40d236343cad807e83d192265f139481c51fc83a1c49e406ac6ce0a0ba7cd35'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +separate_build_dir = True + +build_type = 'Release' + +# Build static lib, static lib with -fPIC and shared lib +configopts = [ + '', + '-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_STATIC_LIBRARY_SUFFIX_CXX=_pic.a', + '-DBUILD_SHARED_LIBS=ON' +] + +sanity_check_paths = { + 'files': ['include/double-conversion/%s.h' % h for h in ['bignum', 'cached-powers', 'diy-fp', 'double-conversion', + 'fast-dtoa', 'fixed-dtoa', 'ieee', 'strtod', 'utils']] + + ['lib/libdouble-conversion.%s' % e for e in ['a', SHLIB_EXT]] + ['lib/libdouble-conversion_pic.a'], + 'dirs': [], +} + +moduleclass = 'lib' From d0d8e02b7a4101b871dfe52484c14b546f85384c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 23:27:06 +0100 Subject: [PATCH 763/793] adding easyconfigs: cairo-1.17.4-GCCcore-12.2.0.eb, GLib-2.75.0-GCCcore-12.2.0.eb, pixman-0.42.2-GCCcore-12.2.0.eb, PCRE2-10.40-GCCcore-12.2.0.eb --- .../c/cairo/cairo-1.17.4-GCCcore-12.2.0.eb | 49 +++++++++++++++++ .../g/GLib/GLib-2.75.0-GCCcore-12.2.0.eb | 52 +++++++++++++++++++ .../p/PCRE2/PCRE2-10.40-GCCcore-12.2.0.eb | 28 ++++++++++ .../p/pixman/pixman-0.42.2-GCCcore-12.2.0.eb | 28 ++++++++++ 4 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.17.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.75.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/PCRE2/PCRE2-10.40-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.17.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.17.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a9661b33bce --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.17.4-GCCcore-12.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.17.4' + +homepage = 'https://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [ + 'https://cairographics.org/releases/', + 'https://cairographics.org/snapshots/' +] +sources = [SOURCE_TAR_XZ] +checksums = ['74b24c1ed436bbe87499179a3b27c43f4143b8676d8ad237a6fa787401959705'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), + ('libpng', '1.6.38'), + ('freetype', '2.12.1'), + ('pixman', '0.42.2'), + ('expat', '2.4.9'), + ('GLib', '2.75.0'), + ('X11', '20221110'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT, + 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.75.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.75.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0390a9a2e54 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.75.0-GCCcore-12.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'MesonNinja' + +name = 'GLib' +version = '2.75.0' + +homepage = 'https://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['6dde8e55cc4a2c83d96797120b08bcffb5f645b2e212164ae22d63c40e0e6360'] + +builddependencies = [ + # Python is required for building against GLib, at least when + # gdbus-codegen or one of the other python scripts are used. + # Since Meson 0.50 and later are Python >=3.5 only we can't build + # Python specific versions of GLib that uses Python 2.x + # thus Python should not be a runtime dependency for GLib. + # Packages that use GLib should either have an explicit + # (build)dependency on Python or it will use the system version + # EasyBuild itself uses. + ('Python', '3.10.8'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('libffi', '3.4.4'), + ('gettext', '0.21.1'), + ('libxml2', '2.10.3'), + ('PCRE2', '10.40'), + ('util-linux', '2.38.1'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--buildtype=release --default-library=both " + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.40-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.40-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7aed3007b9f --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.40-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE2' +version = '10.40' + +homepage = 'https://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ded42661cab30ada2e72ebff9e725e745b4b16ce831993635136f2ef86177724'] + +builddependencies = [('binutils', '2.39')] + +configopts = "--enable-shared --enable-jit --enable-pcre2-16 --enable-unicode" + +sanity_check_paths = { + 'files': ["bin/pcre2-config", "bin/pcre2grep", "bin/pcre2test", "lib/libpcre2-8.a", "lib/libpcre2-16.a"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..17b7e5b6432 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'pixman' +version = '0.42.2' + +homepage = 'http://www.pixman.org/' +description = """ + Pixman is a low-level software library for pixel manipulation, providing + features such as image compositing and trapezoid rasterization. Important + users of pixman are the cairo graphics library and the X server. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ea1480efada2fd948bc75366f7c349e1c96d3297d09a3fe62626e38e234a625e'] + +builddependencies = [ + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From d6999f0e4958a0ce6afed3d64824c0659ea0405a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 23:41:12 +0100 Subject: [PATCH 764/793] adding easyconfigs: NSS-3.85-GCCcore-12.2.0.eb, NSPR-4.35-GCCcore-12.2.0.eb --- .../n/NSPR/NSPR-4.35-GCCcore-12.2.0.eb | 30 +++++++++ .../n/NSS/NSS-3.85-GCCcore-12.2.0.eb | 61 +++++++++++++++++++ 2 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/n/NSS/NSS-3.85-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..1795b557f16 --- /dev/null +++ b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'NSPR' +version = '4.35' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR' +description = """Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level + and libc-like functions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://ftp.mozilla.org/pub/nspr/releases/v%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7ea3297ea5969b5d25a5dd8d47f2443cda88e9ee746301f6e1e1426f8a6abc8f'] + +builddependencies = [('binutils', '2.39')] + +configopts = "--disable-debug --enable-optimize --enable-64bit" + +sanity_check_paths = { + 'files': ['bin/nspr-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplc%(version_major)s.a', 'lib/libplc%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplds%(version_major)s.a', 'lib/libplds%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/nspr.pc'], + 'dirs': ['include/nspr'], +} + +sanity_check_commands = ["nspr-config --version"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.85-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.85-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e0d91d152f0 --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.85-GCCcore-12.2.0.eb @@ -0,0 +1,61 @@ +easyblock = 'MakeCp' + +name = 'NSS' +version = '3.85' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS' +description = """Network Security Services (NSS) is a set of libraries designed to support cross-platform development + of security-enabled client and server applications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_major)s_%(version_minor)s_RTM/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'NSS-3.39_pkgconfig.patch', + 'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch', +] +checksums = [ + {'nss-3.85.tar.gz': 'afd9d64510b1154debbd6cab3571e9ff64a3373898e03483e4c85cdada13d297'}, + {'NSS-3.39_pkgconfig.patch': '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774'}, + {'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch': + '15768297c5dd6918132af281531afcfe3e358f45a00bc2655d20a6cbe4310a9b'}, +] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('NSPR', '4.35'), + ('zlib', '1.2.12'), +] + +# building in parallel fails +parallel = 1 + +# disable use of -Werror to work around compilation errors with newer glibc versions, +# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 +buildopts = "NSS_ENABLE_WERROR=0 " +# fix for not being able to find header files +buildopts += 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +# fix c standard causing missing functions +buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' +# also install pkgconfig file (see patch) +buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -" +# optional testsuite (takes a long time) +# buildopts += " && cd %(builddir)s/%(namelower)s-%(version)s/%(namelower)s/tests && BUILD_OPT=1 USE_64=1 ./all.sh " + +files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] + +sanity_check_paths = { + 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/nss'], +} + +sanity_check_commands = [ + "multinit --help", + "nss-config --version", +] + +modextrapaths = {'CPATH': 'include/nss'} + +moduleclass = 'lib' From cbf1e6db9570125f7566c5ddb35445cc9c588fd5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 23:29:04 +0100 Subject: [PATCH 765/793] {vis}[GCCcore/12.2.0] HarfBuzz v5.3.1, GObject-Introspection v1.74.0 --- ...ect-Introspection-1.74.0-GCCcore-12.2.0.eb | 44 +++++++++++++++++++ .../HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.2.0.eb | 38 ++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.74.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.74.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.74.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f4d572664a7 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.74.0-GCCcore-12.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'GObject-Introspection' +version = '1.74.0' + +homepage = 'https://gi.readthedocs.io/en/latest/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['347b3a719e68ba4c69ff2d57ee2689233ea8c07fc492205e573386779e42d653'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('cairo', '1.17.4'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('GLib', '2.75.0'), + ('libffi', '3.4.4'), + ('util-linux', '2.38.1'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.' + SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e39adfe0f43 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '5.3.1' + +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'harfbuzz' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['77c8c903f4539b050a6d3a5be79705c7ccf7b1cb66d68152a651486e261edbd2'] + +builddependencies = [ + ('binutils', '2.39'), + ('GObject-Introspection', '1.74.0'), + ('pkgconf', '1.9.3'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('GLib', '2.75.0'), + ('ICU', '72.1'), + ('cairo', '1.17.4'), + ('freetype', '2.12.1'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' From dce9c8a5771b6bf09e4c5f6d13cd479151df907c Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Thu, 24 Nov 2022 12:07:53 +0100 Subject: [PATCH 766/793] adding easyconfigs: OpenImageIO-2.3.17.0-GCC-11.3.0.eb --- .../OpenImageIO-2.3.17.0-GCC-11.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..30ccd8238c3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'OpenImageIO' +version = '2.3.17.0' + +homepage = 'https://openimageio.org/' +description = """OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, + and applications.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/OpenImageIO/oiio/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['22d38347b40659d218fcafcadc9258d3f6eda0be02029b11969361c9a6fa9f5c'] +#patches = ['oiio-tiff.patch'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('git', '2.36.0', '-nodocs'), +] +dependencies = [ + ('Boost', '1.79.0'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('OpenEXR', '3.1.5'), + ('freetype', '2.12.1'), + ('zlib', '1.2.12'), +] + +separate_build_dir = True + +configopts = '-DSTOP_ON_WARNING=OFF -DUSE_PYTHON=OFF' + +sanity_check_paths = { + 'files': ['bin/oiiotool', 'lib/libOpenImageIO.%s' % SHLIB_EXT, 'lib/libOpenImageIO_Util.%s' % SHLIB_EXT], + 'dirs': ['include/OpenImageIO', 'share'], +} + +moduleclass = 'lib' + From 77e4bcb0d05710fdd2ce697b4401a71269815b07 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Thu, 24 Nov 2022 13:35:07 +0100 Subject: [PATCH 767/793] Fix style errors --- .../o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb index 30ccd8238c3..9b762b8294b 100644 --- a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb @@ -12,7 +12,6 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/OpenImageIO/oiio/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] checksums = ['22d38347b40659d218fcafcadc9258d3f6eda0be02029b11969361c9a6fa9f5c'] -#patches = ['oiio-tiff.patch'] builddependencies = [ ('CMake', '3.23.1'), @@ -38,4 +37,3 @@ sanity_check_paths = { } moduleclass = 'lib' - From e1ea5df5ee45f8f4336002f90a11c0d8e272f478 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Thu, 24 Nov 2022 16:43:37 +0000 Subject: [PATCH 768/793] Make sure VTK finds the specified Python --- easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb | 1 + easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2021a.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb index b4161f95eaf..c92d21af64b 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb @@ -54,6 +54,7 @@ configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " # Python configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' # Other configopts += "-DVTK_USE_MPI=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2021a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2021a.eb index b6987d9bb81..c2ca95e963f 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2021a.eb @@ -49,6 +49,7 @@ configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " # Python configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' # Other configopts += "-DVTK_USE_MPI=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" From 1218b03af4935fcb966673a092aa13cc8b103f45 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Nov 2022 22:36:31 +0100 Subject: [PATCH 769/793] make test_pr_sanity_check_paths aware of JuliaBundle --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 374e82ddb0c..82f50ce177d 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1092,9 +1092,9 @@ def test_pr_sanity_check_paths(self): """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" # some generic easyblocks already have a decent customised sanity_check_paths, - # including CMakePythonPackage, GoPackage, PythonBundle & PythonPackage; + # including CMakePythonPackage, GoPackage, JuliaBundle, PythonBundle & PythonPackage; # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check. - whitelist = ['BuildEnv', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage', 'ModuleRC', + whitelist = ['BuildEnv', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage', 'JuliaBundle', 'ModuleRC', 'PythonBundle', 'PythonPackage', 'Toolchain'] # Bundles of dependencies without files of their own # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, From dd920df794a7221b7ef157295397b3a4a28341e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Nov 2022 15:22:08 +0100 Subject: [PATCH 770/793] add HGNChelper extension to R 4.2.1 --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index e3da8a7d9fa..3e4080c1ebf 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3364,6 +3364,9 @@ exts_list = [ ('LMERConvenienceFunctions', '3.0', { 'checksums': ['eb430de9fbf836173f716960d60afc2de91de7f986471f406c3ca9027142e849'], }), + ('HGNChelper', '0.8.1', { + 'checksums': ['aa3f0b3a8691ed93d63bec8f36d2954c6fcfd0b8b3efc705379248544c999363'], + }), ] moduleclass = 'lang' From 5644eb72a00df067560a8e4bce84f05f30cbd10e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 25 Nov 2022 15:43:49 +0100 Subject: [PATCH 771/793] adding easyconfigs: cuTENSOR-1.6.1.5-CUDA-11.7.0.eb --- .../cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.7.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.7.0.eb new file mode 100644 index 00000000000..32caad1f155 --- /dev/null +++ b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.7.0.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'cuTENSOR' +local_shortver = '1.6.1' +version = local_shortver + '.5' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/cutensor' +description = """The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, + reduction and elementwise operations.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cutensor/redist/libcutensor/linux-x86_64/'] +sources = ['libcutensor-linux-x86_64-%(version)s-archive.tar.xz'] +checksums = ['793b425c30ffd423c4f3a2e94acaf4fcb6752264aa73b74695a002dd2fe94b1a'] + +local_cudamajver = '11' +dependencies = [('CUDA', local_cudamajver + '.7.0')] + +sanity_check_paths = { + 'files': ['include/cutensor.h', 'include/cutensor/types.h', + 'lib/%s/libcutensor.%s' % (local_cudamajver, SHLIB_EXT), + 'lib/%s/libcutensor_static.a' % local_cudamajver], + 'dirs': [], +} + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib/%s' % local_cudamajver], + 'LIBRARY_PATH': ['lib/%s' % local_cudamajver], +} + +moduleclass = 'lib' From ec57679185f46c6c2bee9b441810b158d57791bd Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Fri, 25 Nov 2022 17:10:22 +0000 Subject: [PATCH 772/793] adding easyconfigs: Fiji-2.9.0-Java-8.eb --- .../easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb b/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb new file mode 100644 index 00000000000..a0253523720 --- /dev/null +++ b/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb @@ -0,0 +1,49 @@ +easyblock = 'PackedBinary' + +name = 'Fiji' +version = '2.9.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://fiji.sc' +description = """Fiji is an image processing package—a 'batteries-included' distribution of + ImageJ, bundling a lot of plugins which facilitate scientific image analysis. +This release is based on ImageJ-2.1.0 and Fiji-2.1.1""" + +toolchain = SYSTEM + +source_urls = ['https://downloads.imagej.net/fiji/releases/%(version)s/'] +sources = ['fiji-%(version)s-nojre.zip'] +checksums = ['970fb80cf2a4fe8bfcecc2cc9a8617b9ab28f19fbe229ea6ae2f7f42674c8a42'] + +dependencies = [('Java', '8', '', SYSTEM)] + +postinstallcmds = [ + # Remove binaries for other platforms + 'rm %(installdir)s/{ImageJ-win32.exe,ImageJ-win64.exe}', + # Enable any update site (edit existing site with same parameters to enable it) + # Full list at https://imagej.github.io/list-of-update-sites/ + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ImageScience"' + ' https://sites.imagej.net/ImageScience/', + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "3D ImageJ Suite"' + ' https://sites.imagej.net/Tboudier/', + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ilastik"' + ' https://sites.imagej.net/Ilastik/', + # Add a new update site + # '%(installdir)s/ImageJ-linux64 --headless --update add-update-site "New Name"' + # ' https://site.url/NewName/', + # Update the installation + '%(installdir)s/ImageJ-linux64 --headless --update update', +] + +sanity_check_paths = { + 'files': ['ImageJ-linux64'], + 'dirs': [], +} + +modloadmsg = """ +Additional plugins can be installed in your $HOME/.plugins folder or requested to user support +Use ImageJ/Fiji in headless mode in your scripts with the command `ImageJ-linux64 --headless` +More information at https://imagej.net/Headless +""" + +moduleclass = 'vis' From 876bdb05adbbcc76565a20fa2d19fe24b079919c Mon Sep 17 00:00:00 2001 From: easybuild Date: Fri, 25 Nov 2022 22:31:59 +0100 Subject: [PATCH 773/793] adding easyconfigs: Vim-9.0.0950-GCCcore-11.3.0.eb --- .../v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb b/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..cde4ee8d056 --- /dev/null +++ b/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +# Last contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 + +easyblock = 'ConfigureMake' + +name = 'Vim' +version = '9.0.0950' + +homepage = 'http://www.vim.org' +description = """ Vim is an advanced text editor that seeks to provide the power + of the de-facto Unix editor 'Vi', with a more complete feature set. """ + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/vim/vim/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c53542fbec58362c3a5ed60a0fe5aa219ef49cd15d9545311ec0f6d1f03e2fdd'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('Perl', '5.34.1'), + ('PCRE', '8.45') +] + +configopts = '--with-features=huge --enable-python3interp=yes --enable-perlinterp=yes' + +sanity_check_paths = { + 'files': ['bin/vim', 'bin/vimtutor', 'bin/xxd'], + 'dirs': ['bin', 'share'], +} + +moduleclass = 'tools' From 59bcc0d5b70753a1a32b229456caedecfdf6873c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Krop=C3=A1=C4=8Dek?= <77022965+anselmicz@users.noreply.github.com> Date: Fri, 25 Nov 2022 22:37:13 +0100 Subject: [PATCH 774/793] Update Vim-9.0.0950-GCCcore-11.3.0.eb Add basic sanity check. --- easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb b/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb index cde4ee8d056..3ebc9ac6bd5 100644 --- a/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb @@ -31,4 +31,6 @@ sanity_check_paths = { 'dirs': ['bin', 'share'], } +sanity_check_commands = ['vim --version'] + moduleclass = 'tools' From 818c6bc1011f6f78b799ef90ce9a1ddda106c1be Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 26 Nov 2022 17:00:55 +0100 Subject: [PATCH 775/793] adding easyconfigs: PyBerny-0.6.3-foss-2022a.eb --- .../p/PyBerny/PyBerny-0.6.3-foss-2022a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2022a.eb b/easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2022a.eb new file mode 100644 index 00000000000..1d3ffa473d1 --- /dev/null +++ b/easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2022a.eb @@ -0,0 +1,38 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'PyBerny' +version = '0.6.3' + +homepage = 'https://github.com/jhrmnn/pyberny' +description = """PyBerny is an optimizer of molecular geometries with respect to the total energy, +using nuclear gradient information.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True + +exts_list = [ + ('pyberny', version, { + 'modulename': 'berny', + 'checksums': ['b4bd9d3d2d58261e8f1d91b8204cc563617044d4b9daf6aae8feee31893cb336'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/berny'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["berny -h"] + +moduleclass = 'chem' From 74bba6153408a470a0aa939c6f12d7e49fbacada Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 26 Nov 2022 17:01:47 +0100 Subject: [PATCH 776/793] adding easyconfigs: NECI-20220711-foss-2022a.eb --- .../n/NECI/NECI-20220711-foss-2022a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/n/NECI/NECI-20220711-foss-2022a.eb diff --git a/easybuild/easyconfigs/n/NECI/NECI-20220711-foss-2022a.eb b/easybuild/easyconfigs/n/NECI/NECI-20220711-foss-2022a.eb new file mode 100644 index 00000000000..71c70f8ab4a --- /dev/null +++ b/easybuild/easyconfigs/n/NECI/NECI-20220711-foss-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMakeCp' +name = 'NECI' +version = '20220711' +_commit = 'd7a9e87ed6a4a29479dc25fbf36a7bb556c3f5a3' + +homepage = 'https://github.com/ghb24/NECI_STABLE' +description = """Standalone NECI codebase designed for FCIQMC and other stochastic quantum +chemistry methods.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +sources = [{ + 'git_config': { + 'url': 'https://github.com/ghb24', + 'repo_name': 'NECI_STABLE', + 'recursive': True, + 'commit': _commit, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +dependencies = [ + ('HDF5', '1.12.2'), +] + +# enable support for HDF5 +configopts = "-DENABLE_HDF5=ON" + +test_cmd = 'ctest' +runtest = '-j' + +files_to_copy = ['bin', 'lib', (['modules'], 'include')] + +_binaries = ['dneci', 'kdneci', 'kmneci', 'kneci', 'mneci', 'neci'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + ['lib/lib%s.a' % x for x in _binaries], + 'dirs': ['include'], +} + +moduleclass = 'chem' From fc26d3c11c5baeae5915e91165fb90fc8c79da53 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 20 Oct 2022 16:54:02 +0200 Subject: [PATCH 777/793] adding easyconfigs: PyTorch-1.12.1-foss-2021a.eb, PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb --- .../PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 129 ++++++++ .../p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 115 +++++++ ...2.1_fix-TestCudaFuser.test_unary_ops.patch | 26 ++ ...PyTorch-1.12.1_fix-TestTorch.test_to.patch | 21 ++ ...ch-1.12.1_fix-cuda-gcc-version-check.patch | 79 +++++ ...x-use-after-free-in-tensorpipe-agent.patch | 24 ++ .../PyTorch-1.12.1_fix-vsx-loadu.patch | 109 ++++++ .../PyTorch-1.12.1_fix-vsx-vector-funcs.patch | 310 ++++++++++++++++++ ...2.1_increase-test-adadelta-tolerance.patch | 22 ++ ...h-1.12.1_increase-tolerance-test_ops.patch | 27 ++ .../PyTorch-1.12.1_no-cuda-stubs-rpath.patch | 159 +++++++++ ...skip-ao-sparsity-test-without-fbgemm.patch | 26 ++ ...yTorch-1.12.1_skip-failing-grad-test.patch | 51 +++ 13 files changed, 1098 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestTorch.test_to.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-cuda-gcc-version-check.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-loadu.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-vector-funcs.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-test-adadelta-tolerance.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-tolerance-test_ops.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_no-cuda-stubs-rpath.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..564c7ada0c8 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,129 @@ +name = 'PyTorch' +version = '1.12.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch', + 'PyTorch-1.12.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.12.1_skip-failing-grad-test.patch', +] +checksums = [ + '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch + 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch + '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', + '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch + # PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d', + 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2', # PyTorch-1.12.1_fix-vsx-vector-funcs.patch + '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2', # PyTorch-1.12.1_fix-vsx-loadu.patch + # PyTorch-1.12.1_increase-test-adadelta-tolerance.patch + '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695', + # PyTorch-1.12.1_increase-tolerance-test_ops.patch + '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb', + '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch + # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch + 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', + 'b24442e38e42ab62c340c84d9daaebd9f5a893ba8434338b97fcff6bba9ff24f', # PyTorch-1.12.1_skip-failing-grad-test.patch +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.20.1'), + ('hypothesis', '6.13.1'), +] + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.9.5'), + ('protobuf', '3.17.3'), + ('protobuf-python', '3.17.3'), + ('pybind11', '2.6.2'), + ('SciPy-bundle', '2021.05'), + ('typing-extensions', '3.10.0.0'), + ('PyYAML', '5.4.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.3.2'), + ('Pillow', '8.2.0'), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), + ('magma', '2.6.1', '-CUDA-%(cudaver)s'), + ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), + ('expecttest', '0.1.3'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6'] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +# The readelf sanity check command can be taken out once the TestRPATH test from +# https://github.com/pytorch/pytorch/pull/87593 is accepted, since it is then checked as part of the PyTorch test suite +local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT +sanity_check_commands = [ + "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, +] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb new file mode 100644 index 00000000000..cd38c8b8e9c --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -0,0 +1,115 @@ +name = 'PyTorch' +version = '1.12.1' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch', + 'PyTorch-1.12.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.12.1_skip-failing-grad-test.patch', +] +checksums = [ + '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch + 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch + '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', + '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch + # PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d', + 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2', # PyTorch-1.12.1_fix-vsx-vector-funcs.patch + '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2', # PyTorch-1.12.1_fix-vsx-loadu.patch + # PyTorch-1.12.1_increase-test-adadelta-tolerance.patch + '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695', + # PyTorch-1.12.1_increase-tolerance-test_ops.patch + '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb', + '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch + # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch + 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', + 'b24442e38e42ab62c340c84d9daaebd9f5a893ba8434338b97fcff6bba9ff24f', # PyTorch-1.12.1_skip-failing-grad-test.patch +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.20.1'), + ('hypothesis', '6.13.1'), +] + +dependencies = [ + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.9.5'), + ('protobuf', '3.17.3'), + ('protobuf-python', '3.17.3'), + ('pybind11', '2.6.2'), + ('SciPy-bundle', '2021.05'), + ('typing-extensions', '3.10.0.0'), + ('PyYAML', '5.4.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.3.2'), + ('Pillow', '8.2.0'), + ('expecttest', '0.1.3'), +] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch new file mode 100644 index 00000000000..28a8238fb30 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch @@ -0,0 +1,26 @@ +Fix test failure with a commit contained in https://github.com/pytorch/pytorch/pull/78244 + +From fade8da55e60a118c5595378896d34b862b2fcc3 Mon Sep 17 00:00:00 2001 +From: "S. Song" <41357537+shmsong@users.noreply.github.com> +Date: Mon, 23 May 2022 16:41:01 -0700 +Subject: [PATCH] patch python test for bfloat16 (#1724) + +* patch python test +--- + test/test_jit_cuda_fuser.py | 5 +++-- + 1 file changed, 3 insertions(+), 2 deletions(-) + +diff --git a/test/test_jit_cuda_fuser.py b/test/test_jit_cuda_fuser.py +index 48dd8a4659f1..324a758ff713 100644 +--- a/test/test_jit_cuda_fuser.py ++++ b/test/test_jit_cuda_fuser.py +@@ -598,7 +598,9 @@ def t(x: torch.Tensor, y: torch.Tensor): + # bfloat16 kernels instead of eager mode + # implementation, since mismatch in cast + # adds excessive noise. +- o = t(x.to(torch.float64), y.to(torch.float64)).to(torch.bfloat16) ++ o = t(x.to(torch.float64), y.to(torch.float64)) ++ if o.dtype.is_floating_point: ++ o = o.to(torch.bfloat16) + else: + o = t(x, y) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestTorch.test_to.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestTorch.test_to.patch new file mode 100644 index 00000000000..8d78d655b5b --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestTorch.test_to.patch @@ -0,0 +1,21 @@ +A bug in PyTorch makes sparse Tensors report the wrong device making the test fail +when using multiple GPUs. +Fixed in 1.13 by https://github.com/pytorch/pytorch/pull/85240 + +Here change the test to only run the check with the default CUDA device. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_torch.py b/test/test_torch.py +index 0c9c00984c..99285b20dc 100644 +--- a/test/test_torch.py ++++ b/test/test_torch.py +@@ -7687,7 +7687,7 @@ tensor([[[1.+1.j, 1.+1.j, 1.+1.j, ..., 1.+1.j, 1.+1.j, 1.+1.j], + + if torch.cuda.is_available(): + for non_blocking in [True, False]: +- for cuda in ['cuda', 'cuda:0' if torch.cuda.device_count() == 1 else 'cuda:1']: ++ for cuda in ['cuda']: + b = torch.tensor(5., device=cuda) + test_copy_behavior(b, non_blocking) + self.assertEqual(b.device, b.to(cuda, non_blocking=non_blocking).device) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-cuda-gcc-version-check.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-cuda-gcc-version-check.patch new file mode 100644 index 00000000000..def8bc857bc --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-cuda-gcc-version-check.patch @@ -0,0 +1,79 @@ +Update CUDA <-> compiler version compatibility matrix +See https://github.com/pytorch/pytorch/pull/86360 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/utils/cpp_extension.py b/torch/utils/cpp_extension.py +index aed4fd5004..fca125ce26 100644 +--- a/torch/utils/cpp_extension.py ++++ b/torch/utils/cpp_extension.py +@@ -48,20 +48,30 @@ MINIMUM_MSVC_VERSION = (19, 0, 24215) + # The following values were taken from the following GitHub gist that + # summarizes the minimum valid major versions of g++/clang++ for each supported + # CUDA version: https://gist.github.com/ax3l/9489132 ++# Or from include/crt/host_config.h in the CUDA SDK ++# The second value is the exclusive(!) upper bound, i.e. min <= version < max + CUDA_GCC_VERSIONS = { +- '10.2': (MINIMUM_GCC_VERSION, (8, 0, 0)), +- '11.1': (MINIMUM_GCC_VERSION, (10, 0, 0)), +- '11.2': (MINIMUM_GCC_VERSION, (10, 0, 0)), +- '11.3': (MINIMUM_GCC_VERSION, (10, 0, 0)), +- '11.4': ((6, 0, 0), (10, 0, 0)) ++ '10.2': (MINIMUM_GCC_VERSION, (9, 0)), ++ '11.0': (MINIMUM_GCC_VERSION, (10, 0)), ++ '11.1': (MINIMUM_GCC_VERSION, (11, 0)), ++ '11.2': (MINIMUM_GCC_VERSION, (11, 0)), ++ '11.3': (MINIMUM_GCC_VERSION, (11, 0)), ++ '11.4': ((6, 0, 0), (12, 0)), ++ '11.5': ((6, 0, 0), (12, 0)), ++ '11.6': ((6, 0, 0), (12, 0)), ++ '11.7': ((6, 0, 0), (12, 0)), + } + ++MINIMUM_CLANG_VERSION = (3, 3, 0), + CUDA_CLANG_VERSIONS = { +- '10.2': ((3, 3, 0), (8, 0, 0)), +- '11.1': ((6, 0, 0), (10, 0, 0)), +- '11.2': ((6, 0, 0), (10, 0, 0)), +- '11.3': ((6, 0, 0), (10, 0, 0)), +- '11.4': ((6, 0, 0), (10, 0, 0)) ++ '10.2': (MINIMUM_CLANG_VERSION, (9, 0)), ++ '11.1': (MINIMUM_CLANG_VERSION, (11, 0)), ++ '11.2': (MINIMUM_CLANG_VERSION, (12, 0)), ++ '11.3': (MINIMUM_CLANG_VERSION, (12, 0)), ++ '11.4': (MINIMUM_CLANG_VERSION, (13, 0)), ++ '11.5': (MINIMUM_CLANG_VERSION, (13, 0)), ++ '11.6': (MINIMUM_CLANG_VERSION, (14, 0)), ++ '11.7': (MINIMUM_CLANG_VERSION, (14, 0)), + } + + +@@ -819,12 +829,11 @@ class BuildExtension(build_ext, object): + if cuda_str_version not in cuda_compiler_bounds: + warnings.warn(f'There are no {compiler_name} version bounds defined for CUDA version {cuda_str_version}') + else: +- min_compiler_version, max_compiler_version = cuda_compiler_bounds[cuda_str_version] ++ min_compiler_version, max_excl_compiler_version = cuda_compiler_bounds[cuda_str_version] + min_compiler_version_str = '.'.join(map(str, min_compiler_version)) +- max_compiler_version_str = '.'.join(map(str, max_compiler_version)) ++ max_excl_compiler_version_str = '.'.join(map(str, max_excl_compiler_version)) + +- version_bound_str = f'>={min_compiler_version_str}' +- version_bound_str = f'{version_bound_str}, <={max_compiler_version_str}' ++ version_bound_str = f'>={min_compiler_version_str}, <{max_excl_compiler_version_str}' + + if compiler_version < TorchVersion(min_compiler_version_str): + raise RuntimeError( +@@ -832,10 +841,10 @@ class BuildExtension(build_ext, object): + f'than the minimum required version by CUDA {cuda_str_version} ({min_compiler_version_str}). ' + f'Please make sure to use an adequate version of {compiler_name} ({version_bound_str}).' + ) +- elif compiler_version > TorchVersion(max_compiler_version_str): ++ elif compiler_version >= TorchVersion(max_excl_compiler_version_str): + raise RuntimeError( + f'The current installed version of {compiler_name} ({compiler_version}) is greater ' +- f'than the maximum required version by CUDA {cuda_str_version} ({max_compiler_version_str}). ' ++ f'than the maximum required version by CUDA {cuda_str_version}. ' + f'Please make sure to use an adequate version of {compiler_name} ({version_bound_str}).' + ) + else: diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch new file mode 100644 index 00000000000..e0f64391792 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch @@ -0,0 +1,24 @@ +Fix an invalid usage of `erase` leading to a use after free. +See https://github.com/pytorch/pytorch/issues/87359 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/csrc/distributed/rpc/tensorpipe_agent.cpp b/torch/csrc/distributed/rpc/tensorpipe_agent.cpp +index 39935febe6..c160d1c771 100644 +--- a/torch/csrc/distributed/rpc/tensorpipe_agent.cpp ++++ b/torch/csrc/distributed/rpc/tensorpipe_agent.cpp +@@ -1261,9 +1261,11 @@ void TensorPipeAgent::updateGroupMembership( + workerNameToInfo_.erase(name); + workerNameToURL_.erase(name); + +- for (const auto& it : reverseDeviceMaps_) { +- if (reverseDeviceMaps.find(it.first) == reverseDeviceMaps.end()) { +- reverseDeviceMaps_.erase(it.first); ++ for(auto iter = reverseDeviceMaps_.begin(); iter != reverseDeviceMaps_.end(); ) { ++ if (reverseDeviceMaps.find(iter->first) == reverseDeviceMaps.end()) { ++ iter = reverseDeviceMaps_.erase(iter); ++ } else { ++ ++iter; + } + } + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-loadu.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-loadu.patch new file mode 100644 index 00000000000..839c6567bb2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-loadu.patch @@ -0,0 +1,109 @@ +Fix access to unitialized memory resulting in e.g. failures in TestNNDeviceTypeCPU.test_groupnorm_nhwc_cpu_float32 +See https://github.com/pytorch/pytorch/issues/32502 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h +index cb8bb78597..f5084f2101 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h +@@ -142,7 +142,7 @@ class Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return { +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +index 8445a31fb3..b4e35acfb4 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +@@ -196,7 +196,7 @@ class Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return { +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h +index c53b7c792e..810e79ebfe 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h +@@ -171,7 +171,7 @@ class Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +index 0267c40e1e..1a6aec7dbe 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +@@ -180,7 +180,7 @@ class Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h +index 464a13c9f5..7c300c8087 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h +@@ -269,7 +269,7 @@ class Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h +index 6ef6147447..c98ab6215e 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h +@@ -199,7 +199,7 @@ class Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h +index c0f1146d9d..a4171026a2 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h +@@ -148,7 +148,7 @@ class Vectorized { + (vint64)vec_vsx_ld(offset16, dptr)}; + } + +- __at_align__ double tmp_values[size()]; ++ __at_align__ double tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return { +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint32_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint32_vsx.h +index c3cec14a5b..a85730c9a6 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint32_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint32_vsx.h +@@ -81,7 +81,7 @@ struct Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-vector-funcs.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-vector-funcs.patch new file mode 100644 index 00000000000..56a02bdac0e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-vector-funcs.patch @@ -0,0 +1,310 @@ +That code fails for large values such as sin(1e20) producing inf. +See https://github.com/pytorch/pytorch/issues/85978 +and https://github.com/pytorch/pytorch/pull/86453 +Use the Sleef functions similar to the double variants. + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +index 77cf3695ab912..8fe6cc25f0ee9 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +@@ -256,29 +256,29 @@ class Vectorized { + } + + Vectorized C10_ALWAYS_INLINE acos() const { +- return {Sleef_acosf4_u10vsx(_vec0), Sleef_acosf4_u10vsx(_vec1)}; ++ return {Sleef_acosf4_u10vsx(_vec0), Sleef_acosf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE asin() const { +- return {Sleef_asinf4_u10vsx(_vec0), Sleef_asinf4_u10vsx(_vec1)}; ++ return {Sleef_asinf4_u10vsx(_vec0), Sleef_asinf4_u10vsx(_vec1)}; + } + Vectorized atan() const { +- return {Sleef_atanf4_u10vsx(_vec0), Sleef_atanf4_u10vsx(_vec1)}; ++ return {Sleef_atanf4_u10vsx(_vec0), Sleef_atanf4_u10vsx(_vec1)}; + } + Vectorized atan2(const Vectorized& b) const { +- return {Sleef_atan2f4_u10vsx(_vec0, b._vec0), Sleef_atan2f4_u10vsx(_vec1, b._vec1)}; ++ return {Sleef_atan2f4_u10vsx(_vec0, b._vec0), Sleef_atan2f4_u10vsx(_vec1, b._vec1)}; + } + Vectorized copysign(const Vectorized &sign) const { + return {Sleef_copysignf4_vsx(_vec0, sign._vec0), Sleef_copysignf4_vsx(_vec1, sign._vec1)}; + } + Vectorized lgamma() const { +- return {Sleef_lgammaf4_u10vsx(_vec0), Sleef_lgammaf4_u10vsx(_vec1)}; ++ return {Sleef_lgammaf4_u10vsx(_vec0), Sleef_lgammaf4_u10vsx(_vec1)}; + } + Vectorized erf() const { +- return {Sleef_erff4_u10vsx(_vec0), Sleef_erff4_u10vsx(_vec1)}; ++ return {Sleef_erff4_u10vsx(_vec0), Sleef_erff4_u10vsx(_vec1)}; + } + + Vectorized erfc() const { +- return {Sleef_erfcf4_u15vsx(_vec0), Sleef_erfcf4_u15vsx(_vec1)}; ++ return {Sleef_erfcf4_u15vsx(_vec0), Sleef_erfcf4_u15vsx(_vec1)}; + } + + Vectorized erfinv() const { +@@ -301,133 +301,32 @@ class Vectorized { + } + + Vectorized C10_ALWAYS_INLINE exp() const { +- // implementation logic from avx_mathfun with some modifications from sleef +- // Express e**x = e**g 2**n +- /// = e**g e**( n loge(2) ) +- /// = e**( g + n loge(2) ) +- // +- auto tmp_x = *this; +- auto fx = (tmp_x * log2e_inv).round(); +- +- auto x = fx.madd(negln2f_hi, tmp_x); +- x = fx.madd(negln2f_lo, x); +- auto z = x * x; +- auto y = x.madd(exp_p0, exp_p1); +- y = y.madd(x, exp_p2); +- y = y.madd(x, exp_p3); +- y = y.madd(x, exp_p4); +- y = y.madd(x, exp_p5); +- y = y.madd(z, x) + one; +- +- // vm_pow2n 2^n +- vint32 imm0 = vec_signed(fx._vec0); +- vint32 imm1 = vec_signed(fx._vec1); +- // this pow2n logic is from Sleef code +- vint32 imm00 = imm0 >> 1; //>>1 +- vint32 imm01 = imm1 >> 1; +- vint32 imm10 = imm0 - imm00; +- vint32 imm11 = imm1 - imm01; +- imm00 = (imm00 + v0x7f) << vu_23; +- imm01 = (imm01 + v0x7f) << vu_23; +- imm10 = (imm10 + v0x7f) << vu_23; +- imm11 = (imm11 + v0x7f) << vu_23; +- // treat imm as float vector without conversion +- +- y._vec0 = (y._vec0 * (vfloat32)imm00) * (vfloat32)imm10; +- y._vec1 = (y._vec1 * (vfloat32)imm01) * (vfloat32)imm11; +- // boundary check +- auto tmp = blendv(y, v_inf, (Vectorized(exp_hi) <= tmp_x)); +- y = blendv(tmp, zero, (tmp_x < Vectorized(exp_lo))); +- +- return y; ++ return {Sleef_expf4_u10vsx(_vec0), Sleef_expf4_u10vsx(_vec1)}; + } + Vectorized expm1() const { +- return exp() - one; ++ return {Sleef_expm1f4_u10vsx(_vec0), Sleef_expm1f4_u10vsx(_vec1)}; + } + + Vectorized C10_ALWAYS_INLINE log() const { + return {Sleef_logf4_u10vsx(_vec0), Sleef_logf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE log10() const { +- return {Sleef_log10f4_u10vsx(_vec0), Sleef_log10f4_u10vsx(_vec1)}; ++ return {Sleef_log10f4_u10vsx(_vec0), Sleef_log10f4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE log1p() const { +- return {Sleef_log1pf4_u10vsx(_vec0), Sleef_log1pf4_u10vsx(_vec1)}; ++ return {Sleef_log1pf4_u10vsx(_vec0), Sleef_log1pf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE log2() const { +- return {Sleef_log2f4_u10vsx(_vec0), Sleef_log2f4_u10vsx(_vec1)}; ++ return {Sleef_log2f4_u10vsx(_vec0), Sleef_log2f4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE ceil() const { + return {vec_ceil(_vec0), vec_ceil(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE cos() const { +- // take the absolute value +- auto x = abs(); +- // extract the sign bit (upper one) +- auto sign_bit = (*this) & sign_mask; +- // scale by 4/Pi +- auto y = x * _4div_pi; +- // store the integer part of y in mm0 +- // j=(j+1) & (~1) (see the cephes sources) +- vint32 imm0 = (vec_signed(y._vec0) + vi_1) & vi_inv1; +- vint32 imm1 = (vec_signed(y._vec1) + vi_1) & vi_inv1; +- y._vec0 = vec_float(imm0); +- y._vec1 = vec_float(imm1); +- +- imm0 = imm0 - vi_2; +- imm1 = imm1 - vi_2; +- Vectorized poly_mask; +- // get the swap sign flag +- vint32 tmp0 = vec_and(vec_nand(imm0, imm0), vi_4); +- vint32 tmp1 = vec_and(vec_nand(imm1, imm1), vi_4); +- sign_bit._vecb0 = (vbool32)vec_sl(tmp0, vu_29); +- sign_bit._vecb1 = (vbool32)vec_sl(tmp1, vu_29); +- // get the polynom selection mask +- // there is one polynom for 0 <= x <= Pi / 4 +- // and another one for Pi / 4 < x <= Pi / 2 +- // Both branches will be computed. +- +- poly_mask._vecb0 = (vbool32)vec_cmpeq((imm0 & vi_2), vi_0); +- poly_mask._vecb1 = (vbool32)vec_cmpeq((imm1 & vi_2), vi_0); +- +- // The magic pass: "Extended precision modular arithmetic" +- // x = ((x - y * DP1) - y * DP2) - y * DP3; +- x = y.madd(minus_cephes_dp1, x); +- x = y.madd(minus_cephes_dp2, x); +- x = y.madd(minus_cephes_dp3, x); +- +- // Evaluate the first polynom (0 <= x <= Pi/4) +- auto z = x * x; +- y = z.madd(coscof_p0, coscof_p1); +- y = y.madd(z, coscof_p2); +- y = y * z * z; +- y = y - z * half + one; +- +- // Evaluate the second polynom (Pi/4 <= x <= 0) +- auto y_2 = z.madd(sincof_p0, sincof_p1); +- y_2 = y_2.madd(z, sincof_p2); +- y_2 = y_2 * z; +- y_2 = y_2.madd(x, x); +- +- // select the correct result from the two polynoms +- y = blendv(y, y_2, poly_mask); +- // update the sign +- y = y ^ sign_bit; +- +- return y; ++ return {Sleef_cosf4_u10vsx(_vec0), Sleef_cosf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE cosh() const { +- // cosh = 1/2 * (e^x + e^-x) +- auto x = abs(); +- auto e_x = x.exp(); +- auto ret = (e_x + Vectorized(one) / e_x) * half; +- // inf and nan checks +-#if 0 +- ret = blendv(ret, v_inf, x >= vf_89); +- ret = blendv(ret, v_inf, ret.isnan()); +- ret = blendv(ret, v_nan, this->isnan()); +-#endif +- return ret; ++ return {Sleef_coshf4_u10vsx(_vec0), Sleef_coshf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE floor() const { + return {vec_floor(_vec0), vec_floor(_vec1)}; +@@ -440,97 +339,16 @@ class Vectorized { + return {vec_round(_vec0), vec_round(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE sin() const { +- // take the absolute value and xtract sign +- auto x = abs(); +- auto sign_bit = (*this) & sign_mask; +- +- // scale by 4/Pi +- auto y = x * _4div_pi; +- // store the integer part of y in mm0 +- +- // j=(j+1) & (~1) (see the cephes sources) +- vint32 imm0 = (vec_signed(y._vec0) + vi_1) & vi_inv1; +- vint32 imm1 = (vec_signed(y._vec1) + vi_1) & vi_inv1; +- y._vec0 = vec_float(imm0); +- y._vec1 = vec_float(imm1); +- // get the swap sign flag +- Vectorized swap_sign_bit, poly_mask; +- swap_sign_bit._vecb0 = (vbool32)vec_sl(imm0 & vi_4, vu_29); +- swap_sign_bit._vecb1 = (vbool32)vec_sl(imm1 & vi_4, vu_29); +- // get the polynom selection mask +- // there is one polynom for 0 <= x <= Pi/4 +- // and another one for Pi/4 C10_ALWAYS_INLINE sinh() const { +- auto temp_abs = abs(); +- // get exponent +- auto ret = temp_abs.exp(); +- auto recp = Vectorized(half) / ret; +- auto v = ret * half - recp; +- // extract the sign bit (upper one) +- auto sign_bit = (*this) & sign_mask; +- auto z = temp_abs * temp_abs; +- auto y = z.madd(p0, p1); +- y = y.madd(z, p2); +- y = (y * z).madd(temp_abs, temp_abs); +- // check and select +- auto result = blendv(y, v, temp_abs > one); +- return result | sign_bit; ++ return {Sleef_sinhf4_u10vsx(_vec0), Sleef_sinhf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE tan() const { +- return {Sleef_tanf4_u10vsx(_vec0), Sleef_tanf4_u10vsx(_vec1)}; ++ return {Sleef_tanf4_u10vsx(_vec0), Sleef_tanf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE tanh() const { +- auto x = *this; +- auto vabs = abs(); +- // get exponent +- auto exp2x = (vabs + vabs).exp(); +- auto vv = Vectorized(one) - Vectorized(two) / (exp2x + one); +- // extract the sign bit (upper one) +- auto sign_bit = (*this) & sign_mask; +- auto z = vabs * vabs; +- auto y = z.madd(tanh_p0, tanh_p1); +- auto tmp = y.madd(z, tanh_p2); +- y = z.madd(tmp, tanh_p3); +- tmp = y.madd(z, tanh_p4); +- y = tmp * z; +- tmp = y.madd(x, x); +- // add sign +- vv = vv | sign_bit; +- // check and select +- auto sel_mask = vabs >= tanh_0p625; +- auto max_mask = vabs > tanh_half_max; +- auto max_ret = sign_bit ^ one; +- return blendv(blendv(tmp, vv, sel_mask), max_ret, max_mask); ++ return {Sleef_tanhf4_u10vsx(_vec0), Sleef_tanhf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE trunc() const { + return {vec_trunc(_vec0), vec_trunc(_vec1)}; +@@ -555,15 +373,15 @@ class Vectorized { + } + + Vectorized fmod(const Vectorized& b) const { +- return {Sleef_fmodf4_vsx(_vec0, b._vec0),Sleef_fmodf4_vsx(_vec1, b._vec1)}; ++ return {Sleef_fmodf4_vsx(_vec0, b._vec0),Sleef_fmodf4_vsx(_vec1, b._vec1)}; + } + + Vectorized hypot(const Vectorized& b) const { +- return {Sleef_hypotf4_u05vsx(_vec0, b._vec0), Sleef_hypotf4_u05vsx(_vec1, b._vec1)}; ++ return {Sleef_hypotf4_u05vsx(_vec0, b._vec0), Sleef_hypotf4_u05vsx(_vec1, b._vec1)}; + } + + Vectorized nextafter(const Vectorized& b) const { +- return {Sleef_nextafterf4_vsx(_vec0, b._vec0), Sleef_nextafterf4_vsx(_vec1, b._vec1)}; ++ return {Sleef_nextafterf4_vsx(_vec0, b._vec0), Sleef_nextafterf4_vsx(_vec1, b._vec1)}; + } + + Vectorized igamma(const Vectorized& x) const { diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-test-adadelta-tolerance.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-test-adadelta-tolerance.patch new file mode 100644 index 00000000000..6455052773f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-test-adadelta-tolerance.patch @@ -0,0 +1,22 @@ +TestOptim.test_adadelta fails on some systems with +> Mismatched elements: 1 / 50 (2.0%) +> Greatest absolute difference: 0.0012711584568023682 at index (1, 3) (up to 1e-05 allowed) +> Greatest relative difference: 0.005316456816424191 at index (1, 3) (up to 0.004 allowed) +This is possibly related to the CUDA driver version. See also https://github.com/pytorch/pytorch/issues/51992 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_optim.py b/test/test_optim.py +index 6d587b4b35..32e5dbcc2f 100644 +--- a/test/test_optim.py ++++ b/test/test_optim.py +@@ -621,7 +621,8 @@ class TestOptim(TestCase): + # ROCm precision is too low to pass this test + def test_adadelta(self): + # Handles https://github.com/pytorch/pytorch/issues/69698 +- self.rel_tol = 4e-3 ++ self.precision = 2e-3 ++ self.rel_tol = 1e-2 + for optimizer in [optim.Adadelta, optim_mt.Adadelta]: + self._test_basic_cases( + lambda weight, bias, maximize: optimizer([weight, bias], maximize=maximize), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-tolerance-test_ops.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-tolerance-test_ops.patch new file mode 100644 index 00000000000..9a728ce288d --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-tolerance-test_ops.patch @@ -0,0 +1,27 @@ +`test_out` may fail due to slightly different values caused by different order of matrizes in SGEMM: + +> Mismatched elements: 1 / 50 (2.0%) +> Greatest absolute difference: 1.430511474609375e-05 at index (4, 5) (up to 1e-05 allowed) +> Greatest relative difference: 4.65393206065873e-06 at index (4, 5) (up to 1.3e-06 allowed) + +See https://github.com/pytorch/pytorch/pull/86365 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py +index 00eb3f7f09..d97505ffb6 100644 +--- a/torch/testing/_internal/common_methods_invocations.py ++++ b/torch/testing/_internal/common_methods_invocations.py +@@ -9984,7 +9984,11 @@ op_db: List[OpInfo] = [ + DecorateInfo( + toleranceOverride({torch.float32: tol(atol=1.3e-05, rtol=1.3e-05), + torch.complex64: tol(atol=1e-05, rtol=1.2e-03)}), +- 'TestCommon', 'test_reference_testing')], ++ 'TestCommon', 'test_reference_testing'), ++ DecorateInfo( ++ toleranceOverride({torch.float32: tol(atol=1.5e-05, rtol=1e-05)}), ++ 'TestCommon', 'test_out'), ++ ], + skips=( + # NVIDIA only assures that bfloat16 is supported by bmm if SM >= 5.3 + DecorateInfo(unittest.skip("Skipped!"), 'TestCommon', 'test_dtypes', device_type='cuda', active_if=not SM53OrLater), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_no-cuda-stubs-rpath.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_no-cuda-stubs-rpath.patch new file mode 100644 index 00000000000..60e09456182 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_no-cuda-stubs-rpath.patch @@ -0,0 +1,159 @@ +# PyTorch's CMAKE configuration by default sets RUNPATH on libraries if they link other libraries +# that are outside the build tree, which is done because of the CMAKE config on +# https://github.com/pytorch/pytorch/blob/v1.10.0/cmake/Dependencies.cmake#L10. +# This provides problems, since the cuda stubs library path then also gets added to the RUNPATH. +# As a result, at runtime, the stub version of things like libcuda.so.1 gets picked up, instead of the real drivers +# See https://github.com/easybuilders/easybuild-easyconfigs/issues/14359 +# This line https://github.com/pytorch/pytorch/blob/v1.10.0/cmake/Dependencies.cmake#L16 +# Makes sure that any path that is linked, is also added to the RUNPATH. +# This has been reported upstream in https://github.com/pytorch/pytorch/issues/35418 +# and a fix was attempted in https://github.com/pytorch/pytorch/pull/37737 but it was reverted +# +# This EasyBuild patch changes behavior for the libraries that were failing, i.e. the ones in this list: +# https://github.com/easybuilders/easybuild-easyconfigs/issues/14359#issuecomment-970479904 +# This is done by setting INSTALL_RPATH_USE_LINK_PATH to false, and instead, specifying the RPATH +# explicitely by defining INSTALL_RPATH, but only adding directories that do not match to the "stubs" regex +# +# Original patch: Caspar van Leeuwen +# Updated: Alexander Grund (TU Dresden) +# +# See https://github.com/pytorch/pytorch/pull/87593 + +diff --git a/caffe2/CMakeLists.txt b/caffe2/CMakeLists.txt +index 328210c978..f06ee0bb4e 100644 +--- a/caffe2/CMakeLists.txt ++++ b/caffe2/CMakeLists.txt +@@ -643,13 +643,12 @@ if(NOT INTERN_BUILD_MOBILE OR NOT BUILD_CAFFE2_MOBILE) + if(USE_CUDA) + list(APPEND Caffe2_GPU_CU_SRCS ${Caffe2_GPU_HIP_JIT_FUSERS_SRCS}) + add_library(caffe2_nvrtc SHARED ${ATen_NVRTC_STUB_SRCS}) ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(caffe2_nvrtc ${CUDA_NVRTC} ${CUDA_CUDA_LIB} ${CUDA_NVRTC_LIB}) + if(MSVC) + # Delay load nvcuda.dll so we can import torch compiled with cuda on a CPU-only machine +- set(DELAY_LOAD_FLAGS "-DELAYLOAD:nvcuda.dll;delayimp.lib") +- else() +- set(DELAY_LOAD_FLAGS "") ++ target_link_libraries(caffe2_nvrtc "-DELAYLOAD:nvcuda.dll;delayimp.lib") + endif() +- target_link_libraries(caffe2_nvrtc ${CUDA_NVRTC} ${CUDA_CUDA_LIB} ${CUDA_NVRTC_LIB} ${DELAY_LOAD_FLAGS}) + target_include_directories(caffe2_nvrtc PRIVATE ${CUDA_INCLUDE_DIRS}) + install(TARGETS caffe2_nvrtc DESTINATION "${TORCH_INSTALL_LIB_DIR}") + if(USE_NCCL) +diff --git a/cmake/LinkCudaLibraries.cmake b/cmake/LinkCudaLibraries.cmake +new file mode 100644 +index 0000000000..a24583bff4 +--- /dev/null ++++ b/cmake/LinkCudaLibraries.cmake +@@ -0,0 +1,33 @@ ++# Link CUDA libraries to the given target, i.e.: `target_link_libraries(target )` ++# ++# Additionally makes sure CUDA stub libs don't end up being in RPath ++# ++# Example: link_cuda_libraries(mytarget PRIVATE ${CUDA_LIBRARIES}) ++function(link_cuda_libraries target) ++ set(libs ${ARGN}) ++ set(install_rpath "") ++ set(filtered FALSE) ++ foreach(lib IN LISTS libs) ++ # CUDA stub libs are in form /prefix/lib/stubs/libcuda.so ++ # So extract the name of the parent folder, to check against "stubs" ++ # And the parent path which we need to add to the INSTALL_RPATH for non-stubs ++ get_filename_component(parent_path "${lib}" DIRECTORY) ++ get_filename_component(parent_name "${parent_path}" NAME) ++ if(parent_name STREQUAL "stubs") ++ message(STATUS "Filtering ${lib} from being set in ${target}'s RPATH, " ++ "because it appears to point to the CUDA stubs directory.") ++ set(filtered TRUE) ++ elseif(parent_path) ++ list(APPEND install_rpath ${parent_path}) ++ endif() ++ endforeach() ++ ++ # Regular link command ++ target_link_libraries(${target} ${scope} ${libs}) ++ # Manually set INSTALL_RPATH when there were any stub libs ++ if(filtered) ++ list(REMOVE_DUPLICATES install_rpath) ++ set_target_properties(${target} PROPERTIES INSTALL_RPATH_USE_LINK_PATH FALSE) ++ set_target_properties(${target} PROPERTIES INSTALL_RPATH "${install_rpath}") ++ endif() ++endfunction() +diff --git a/test/cpp/api/CMakeLists.txt b/test/cpp/api/CMakeLists.txt +index 373895a0ce..19868221cb 100644 +--- a/test/cpp/api/CMakeLists.txt ++++ b/test/cpp/api/CMakeLists.txt +@@ -58,7 +58,8 @@ if(NOT MSVC) + endif() + + if(USE_CUDA) +- target_link_libraries(test_api PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_api PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/dist_autograd/CMakeLists.txt b/test/cpp/dist_autograd/CMakeLists.txt +index 9969c63e16..356ba5be55 100644 +--- a/test/cpp/dist_autograd/CMakeLists.txt ++++ b/test/cpp/dist_autograd/CMakeLists.txt +@@ -10,7 +10,8 @@ if(USE_DISTRIBUTED AND NOT WIN32) + target_link_libraries(test_dist_autograd PRIVATE torch gtest) + + if(USE_CUDA) +- target_link_libraries(test_dist_autograd PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_dist_autograd PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/jit/CMakeLists.txt b/test/cpp/jit/CMakeLists.txt +index 60b43b81fc..57cd4422f8 100644 +--- a/test/cpp/jit/CMakeLists.txt ++++ b/test/cpp/jit/CMakeLists.txt +@@ -136,7 +137,8 @@ if(LINUX) + endif() + + if(USE_CUDA) +- target_link_libraries(test_jit PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_jit PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/rpc/CMakeLists.txt b/test/cpp/rpc/CMakeLists.txt +index 3997f8753e..21fddbc645 100644 +--- a/test/cpp/rpc/CMakeLists.txt ++++ b/test/cpp/rpc/CMakeLists.txt +@@ -33,7 +33,8 @@ target_include_directories( + target_link_libraries(test_cpp_rpc PRIVATE ${TORCH_RPC_TEST_DEPENDENCY_LIBS}) + + if(USE_CUDA) +- target_link_libraries(test_cpp_rpc PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_cpp_rpc PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/tensorexpr/CMakeLists.txt b/test/cpp/tensorexpr/CMakeLists.txt +index 7dff70630d..ecb8300549 100644 +--- a/test/cpp/tensorexpr/CMakeLists.txt ++++ b/test/cpp/tensorexpr/CMakeLists.txt +@@ -57,14 +57,15 @@ if(USE_PTHREADPOOL) + target_link_libraries(test_tensorexpr PRIVATE pthreadpool_interface) + endif() + if(USE_CUDA) +- target_link_libraries(test_tensorexpr PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_tensorexpr PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} + ${TORCH_CUDA_LIBRARIES}) + target_compile_definitions(test_tensorexpr PRIVATE USE_CUDA) + +- target_link_libraries(tutorial_tensorexpr PRIVATE ++ link_cuda_libraries(tutorial_tensorexpr PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch new file mode 100644 index 00000000000..6b2fb265395 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch @@ -0,0 +1,26 @@ +Those tests (from test_ao_sparsity) require FBGEMM which may not be available. +So add the skip decorator. +See https://github.com/pytorch/pytorch/issues/87364 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/ao/sparsity/test_composability.py b/test/ao/sparsity/test_composability.py +index b44c885507..b7d35343c0 100644 +--- a/test/ao/sparsity/test_composability.py ++++ b/test/ao/sparsity/test_composability.py +@@ -9,6 +9,7 @@ import torch.ao.quantization as tq + from torch import nn + from torch.ao import sparsity + from torch.testing._internal.common_utils import TestCase ++from torch.testing._internal.common_quantization import skipIfNoFBGEMM + + logging.basicConfig( + format="%(asctime)s - %(name)s - %(levelname)s - %(message)s", level=logging.INFO +@@ -23,6 +24,7 @@ sparse_defaults = { + # This series of tests are to check the composability goals for sparsity and quantization. Namely + # that performing quantization and sparsity model manipulations in various orderings + # does not cause problems ++@skipIfNoFBGEMM + class TestComposability(TestCase): + def _get_model_and_sparsifier_and_sparse_config(self, qconfig=None): + model = nn.Sequential( diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch new file mode 100644 index 00000000000..b515d8dd432 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch @@ -0,0 +1,51 @@ +Test test_fn_grad_linalg_det_singular_cpu_complex128 in test_ops_gradients fails not only on Windows, +so extend the skip marker introduced in https://github.com/pytorch/pytorch/pull/69827 + +test_forward_mode_AD_norm_inf_cpu_complex128 in test_ops_gradients fails due to NaNs. +Might be fixed by https://github.com/pytorch/pytorch/pull/80082 where a part of the changes +come from with additional skip for that test similar to other complex128 skips. + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py +index 00eb3f7f09..8d009cf280 100644 +--- a/torch/testing/_internal/common_methods_invocations.py ++++ b/torch/testing/_internal/common_methods_invocations.py +@@ -9729,11 +9729,11 @@ op_db: List[OpInfo] = [ + dtypesIfCUDA=all_types_and_complex_and(torch.bool, torch.half, torch.bfloat16, torch.chalf), + skips=( + # Inplace abs doesn't support complex inputs +- DecorateInfo(unittest.expectedFailure, 'TestGradients', ++ DecorateInfo(unittest.skip("In-place abs not supported for complex tensors"), 'TestGradients', + 'test_inplace_grad', dtypes=(torch.cdouble,)), +- DecorateInfo(unittest.expectedFailure, 'TestGradients', ++ DecorateInfo(unittest.skip("In-place abs not supported for complex tensors"), 'TestGradients', + 'test_inplace_gradgrad', dtypes=(torch.cdouble,)), +- DecorateInfo(unittest.expectedFailure, 'TestGradients', ++ DecorateInfo(unittest.skip("In-place abs not supported for complex tensors"), 'TestGradients', + 'test_inplace_forward_mode_AD', dtypes=(torch.cdouble,)), + DecorateInfo(unittest.skip("Skipped!"), 'TestUnaryUfuncs', 'test_reference_numerics_extremal', + device_type='cpu', dtypes=[torch.cfloat, torch.cdouble]), +@@ -11559,7 +11559,7 @@ op_db: List[OpInfo] = [ + skips=( + # These tests started breaking after touching the SVD. + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_grad', device_type='cpu', +- dtypes=(torch.complex128,), active_if=IS_WINDOWS), ++ dtypes=(torch.complex128,)), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_gradgrad'), + # dtypes are tested in the suite above, no need to repeat it for singular + DecorateInfo(unittest.skip("Skipped!"), 'TestCommon', 'test_dtypes'), +@@ -17230,6 +17230,13 @@ op_db: List[OpInfo] = [ + device_type="cpu", + dtypes=(torch.complex128,), + ), ++ DecorateInfo( ++ unittest.skip("NaNs in analytical jacobian!"), ++ "TestGradients", ++ "test_forward_mode_AD", ++ device_type="cpu", ++ dtypes=(torch.complex128,), ++ ), + DecorateInfo(unittest.expectedFailure, 'TestGradients', 'test_fn_fwgrad_bwgrad', + dtypes=[torch.complex128]), + # AssertionError: RuntimeError not raised : Expected RuntimeError when doing an unsafe cast from a result From a51c4dcc20707b75971d9ae9df434a89c85677fd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 27 Oct 2022 13:46:48 +0200 Subject: [PATCH 778/793] Remove test which times out --- .../p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index 564c7ada0c8..5c8c7675ce6 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -25,6 +25,7 @@ patches = [ 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', @@ -59,6 +60,8 @@ checksums = [ # PyTorch-1.11.0_increase-distributed-test-timeout.patch '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.11.1_skip-test_init_from_local_shards.patch + '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch From d720a6809955020093c01b5d221fb5d6d994786d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 22 Nov 2022 15:58:48 +0100 Subject: [PATCH 779/793] Patch failure on older CUDA drivers --- .../PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 5 +-- .../p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 5 +-- ...h-1.12.1_fix-test_cpp_extensions_jit.patch | 31 +++++++++++++++++++ 3 files changed, 37 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index 5c8c7675ce6..ae0cff605da 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -14,7 +14,6 @@ sources = ['%(namelower)s-v%(version)s.tar.gz'] patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', - 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', 'PyTorch-1.10.0_fix-test-model_dump.patch', @@ -27,6 +26,7 @@ patches = [ 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', @@ -42,7 +42,6 @@ checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch - '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch # PyTorch-1.10.0_fix-kineto-crash.patch 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch @@ -64,6 +63,8 @@ checksums = [ '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index cd38c8b8e9c..cb1f43fa095 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -13,7 +13,6 @@ sources = ['%(namelower)s-v%(version)s.tar.gz'] patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', - 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', 'PyTorch-1.10.0_fix-test-model_dump.patch', @@ -25,6 +24,7 @@ patches = [ 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', @@ -40,7 +40,6 @@ checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch - '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch # PyTorch-1.10.0_fix-kineto-crash.patch 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch @@ -60,6 +59,8 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch new file mode 100644 index 00000000000..38dcd0c2eb6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch @@ -0,0 +1,31 @@ +When the CUDA Toolkit (compiler...) is to new or to old for the GPU or the GPU driver +this test may fail. +See https://github.com/pytorch/pytorch/pull/89495 + +diff --git a/test/test_cpp_extensions_jit.py b/test/test_cpp_extensions_jit.py +index 2ead8d32ca179..dd350823ffef9 100644 +--- a/test/test_cpp_extensions_jit.py ++++ b/test/test_cpp_extensions_jit.py +@@ -200,7 +200,21 @@ def test_jit_cuda_archflags(self): + archflags["5.0;6.0+PTX;7.0;7.5"] = (['50', '60', '70', '75'], ['60']) + + for flags, expected in archflags.items(): +- self._run_jit_cuda_archflags(flags, expected) ++ try: ++ self._run_jit_cuda_archflags(flags, expected) ++ except RuntimeError as e: ++ # Using the device default (empty flags) may fail if the device is newer than the CUDA compiler ++ # This raises a RuntimeError with a specific message which we explictely ignore here ++ if not flags and "Error building" in str(e): ++ pass ++ else: ++ raise ++ try: ++ torch.cuda.synchronize() ++ except RuntimeError: ++ # Ignore any error, e.g. unsupported PTX code on current device ++ # to avoid errors from here leaking into other tests ++ pass + + @unittest.skipIf(not TEST_CUDNN, "CuDNN not found") + def test_jit_cudnn_extension(self): From f223ac3773b440849fe8a6c428780287e0aa75db Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 25 Nov 2022 10:36:58 +0100 Subject: [PATCH 780/793] Skip test which may succeed --- .../PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 2 +- .../p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 2 +- ...yTorch-1.12.1_skip-failing-grad-test.patch | 21 +++++++++++++++++++ 3 files changed, 23 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index ae0cff605da..e8cea51ff73 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -79,7 +79,7 @@ checksums = [ '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', - 'b24442e38e42ab62c340c84d9daaebd9f5a893ba8434338b97fcff6bba9ff24f', # PyTorch-1.12.1_skip-failing-grad-test.patch + '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index cb1f43fa095..bb39edb055d 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -75,7 +75,7 @@ checksums = [ '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', - 'b24442e38e42ab62c340c84d9daaebd9f5a893ba8434338b97fcff6bba9ff24f', # PyTorch-1.12.1_skip-failing-grad-test.patch + '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch index b515d8dd432..a79bc9a7a5e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch @@ -5,6 +5,9 @@ test_forward_mode_AD_norm_inf_cpu_complex128 in test_ops_gradients fails due to Might be fixed by https://github.com/pytorch/pytorch/pull/80082 where a part of the changes come from with additional skip for that test similar to other complex128 skips. +Also skip test_forward_mode_AD_nn_functional_max_unpool2d_cpu_float64 & test_forward_mode_AD_nn_functional_max_unpool3d_cpu_float64 +which may unexpectably succeed. + Author: Alexander Grund (TU Dresden) diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py @@ -35,6 +38,24 @@ index 00eb3f7f09..8d009cf280 100644 DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_gradgrad'), # dtypes are tested in the suite above, no need to repeat it for singular DecorateInfo(unittest.skip("Skipped!"), 'TestCommon', 'test_dtypes'), +@@ -13447,7 +13447,7 @@ op_db: List[OpInfo] = [ + # and if there are several indices pointing to the same memory, + # gradcheck is oblivious about that and cannot perturb them all at once + # (see sample_inputs_max_unpool_grad to find out more). +- DecorateInfo(unittest.expectedFailure, 'TestGradients', 'test_forward_mode_AD'), ++ DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_forward_mode_AD'), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_gradgrad'), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_grad'), + )), +@@ -13481,7 +13481,7 @@ op_db: List[OpInfo] = [ + # and if there are several indices pointing to the same memory, + # gradcheck is oblivious about that and cannot perturb them all at once + # (see sample_inputs_max_unpool_grad to find out more). +- DecorateInfo(unittest.expectedFailure, 'TestGradients', 'test_forward_mode_AD'), ++ DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_forward_mode_AD'), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_gradgrad'), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_grad'), + )), @@ -17230,6 +17230,13 @@ op_db: List[OpInfo] = [ device_type="cpu", dtypes=(torch.complex128,), From 6e3c238b82abe35f249701a69ca6f53c558e2038 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 25 Nov 2022 11:12:42 +0100 Subject: [PATCH 781/793] Skip c10d test which times out --- .../PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 3 +++ .../p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 3 +++ ...skip-test_round_robin_create_destroy.patch | 26 +++++++++++++++++++ 3 files changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index e8cea51ff73..f81fea585ec 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -37,6 +37,7 @@ patches = [ 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', 'PyTorch-1.12.1_skip-failing-grad-test.patch', + 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', ] checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz @@ -80,6 +81,8 @@ checksums = [ # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch + # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch + '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index bb39edb055d..ab67d74f854 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -35,6 +35,7 @@ patches = [ 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', 'PyTorch-1.12.1_skip-failing-grad-test.patch', + 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', ] checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz @@ -76,6 +77,8 @@ checksums = [ # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch + # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch + '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch new file mode 100644 index 00000000000..f8e01a445db --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch @@ -0,0 +1,26 @@ +test_round_robin_create_destroy of distributed/test_c10d_gloo may run into timeouts. +So simply skip the on all OS (not only on Windows), the existing skip marker suggest that this is OK. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributed/test_c10d_gloo.py b/test/distributed/test_c10d_gloo.py +index e49d65ea33d..b4fb75a1b11 100644 +--- a/test/distributed/test_c10d_gloo.py ++++ b/test/distributed/test_c10d_gloo.py +@@ -10,6 +10,7 @@ import sys + import tempfile + from functools import reduce + from itertools import groupby ++from unittest import skip + + import torch + import torch.distributed as c10d +@@ -1438,7 +1439,7 @@ class ProcessGroupGlooTest(MultiProcessTestCase): + pg.broadcast(tensor, root=0).wait() + self.assertEqual(torch.full([100, 100], 0.0), tensor) + +- @skip_if_win32() ++ @skip("Occasionally times out") + @requires_gloo() + def test_round_robin_create_destroy(self): + store = c10d.FileStore(self.file_name, self.world_size) From ec03d0c0bd8b8bddaf3ff85655be03efe494d17a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 25 Nov 2022 16:32:16 +0100 Subject: [PATCH 782/793] Fix test failures on 1 GPU --- .../PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 2 + .../p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 2 + .../PyTorch-1.12.1_fix-skip-decorators.patch | 118 ++++++++++++++++++ 3 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index f81fea585ec..03c04cd2a9e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -26,6 +26,7 @@ patches = [ 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', @@ -64,6 +65,7 @@ checksums = [ '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + '32fc722f5f93b9a89b10809c2b38718de9c847a96ffdd540d2c71eae154e4201', # PyTorch-1.12.1_fix-skip-decorators.patch # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index ab67d74f854..7fd464b8dd2 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -24,6 +24,7 @@ patches = [ 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', @@ -60,6 +61,7 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + '32fc722f5f93b9a89b10809c2b38718de9c847a96ffdd540d2c71eae154e4201', # PyTorch-1.12.1_fix-skip-decorators.patch # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch new file mode 100644 index 00000000000..8300d0d5086 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch @@ -0,0 +1,118 @@ +The decorators are implemented to run when the function is called which is after +the test `setup` method spawned subprocesses which may use NCCL to sync failing when there are +not enough GPUs available. +So replace the custom code by calls to the `unittest` skip decorators. +See https://github.com/pytorch/pytorch/pull/89750 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_distributed.py b/torch/testing/_internal/common_distributed.py +index 8baf7d03d9f..3dc922ee923 100644 +--- a/torch/testing/_internal/common_distributed.py ++++ b/torch/testing/_internal/common_distributed.py +@@ -124,46 +124,11 @@ def skip_if_odd_worldsize(func): + return wrapper + + def require_n_gpus_for_nccl_backend(n, backend): +- def decorator(func): +- @wraps(func) +- def wrapper(*args, **kwargs): +- if backend == "nccl" and torch.cuda.device_count() < n: +- sys.exit(TEST_SKIPS[f"multi-gpu-{n}"].exit_code) +- else: +- return func(*args, **kwargs) +- +- return wrapper +- +- return decorator ++ return skip_if_lt_x_gpu(n) if backend == "nccl" else unittest.skipIf(False, None) + + + def skip_if_lt_x_gpu(x): +- def decorator(func): +- @wraps(func) +- def wrapper(*args, **kwargs): +- if torch.cuda.is_available() and torch.cuda.device_count() >= x: +- return func(*args, **kwargs) +- sys.exit(TEST_SKIPS[f"multi-gpu-{x}"].exit_code) +- +- return wrapper +- +- return decorator +- +- +-# This decorator helps avoiding initializing cuda while testing other backends +-def nccl_skip_if_lt_x_gpu(backend, x): +- def decorator(func): +- @wraps(func) +- def wrapper(*args, **kwargs): +- if backend != "nccl": +- return func(*args, **kwargs) +- if torch.cuda.is_available() and torch.cuda.device_count() >= x: +- return func(*args, **kwargs) +- sys.exit(TEST_SKIPS[f"multi-gpu-{x}"].exit_code) +- +- return wrapper +- +- return decorator ++ return unittest.skipIf(torch.cuda.device_count() < x, TEST_SKIPS[f"multi-gpu-{x}"].message) + + + def verify_ddp_error_logged(model_DDP, err_substr): +diff --git a/torch/testing/_internal/distributed/distributed_test.py b/torch/testing/_internal/distributed/distributed_test.py +index 1414a0376b1..1f6b00e6edf 100644 +--- a/torch/testing/_internal/distributed/distributed_test.py ++++ b/torch/testing/_internal/distributed/distributed_test.py +@@ -56,7 +56,6 @@ from torch.testing._internal.common_distributed import ( + skip_if_small_worldsize, + skip_if_odd_worldsize, + skip_if_lt_x_gpu, +- nccl_skip_if_lt_x_gpu, + skip_if_no_gpu, + require_n_gpus_for_nccl_backend, + requires_nccl_version, +@@ -4604,7 +4603,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(BACKEND, 2) + def test_accumulate_gradients_no_sync(self): + """ + Runs _test_accumulate_gradients_no_sync using default inputs +@@ -4615,7 +4614,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(BACKEND, 2) + def test_accumulate_gradients_no_sync_grad_is_view(self): + """ + Runs _test_accumulate_gradients_no_sync using default inputs +@@ -4626,7 +4625,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(BACKEND, 2) + def test_accumulate_gradients_no_sync_allreduce_hook(self): + """ + Runs multiple iterations on _test_accumulate_gradients_no_sync +@@ -4654,7 +4653,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(BACKEND, 2) + def test_accumulate_gradients_no_sync_allreduce_with_then_hook(self): + """ + Runs multiple iterations on _test_accumulate_gradients_no_sync using allreduce +@@ -4688,7 +4687,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(BACKEND, 2) + def test_get_future(self): + def mult(fut): + return [t * 3 for t in fut.wait()] From d159a5a3c98487a79900be700b9e49b1468b9449 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 28 Nov 2022 13:27:16 +0100 Subject: [PATCH 783/793] Fix test failures on 1 GPU --- .../p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 2 +- .../easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 2 +- .../p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch | 10 +++++----- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index 03c04cd2a9e..9778d40af76 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -65,7 +65,7 @@ checksums = [ '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', - '32fc722f5f93b9a89b10809c2b38718de9c847a96ffdd540d2c71eae154e4201', # PyTorch-1.12.1_fix-skip-decorators.patch + 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index 7fd464b8dd2..4417c0cacee 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -61,7 +61,7 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', - '32fc722f5f93b9a89b10809c2b38718de9c847a96ffdd540d2c71eae154e4201', # PyTorch-1.12.1_fix-skip-decorators.patch + 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch index 8300d0d5086..0fbe044ff32 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch @@ -76,7 +76,7 @@ index 1414a0376b1..1f6b00e6edf 100644 "get_future is only supported on mpi, nccl and gloo", ) - @nccl_skip_if_lt_x_gpu(BACKEND, 2) -+ @require_n_gpus_for_nccl_backend(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) def test_accumulate_gradients_no_sync(self): """ Runs _test_accumulate_gradients_no_sync using default inputs @@ -85,7 +85,7 @@ index 1414a0376b1..1f6b00e6edf 100644 "get_future is only supported on mpi, nccl and gloo", ) - @nccl_skip_if_lt_x_gpu(BACKEND, 2) -+ @require_n_gpus_for_nccl_backend(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) def test_accumulate_gradients_no_sync_grad_is_view(self): """ Runs _test_accumulate_gradients_no_sync using default inputs @@ -94,7 +94,7 @@ index 1414a0376b1..1f6b00e6edf 100644 "get_future is only supported on mpi, nccl and gloo", ) - @nccl_skip_if_lt_x_gpu(BACKEND, 2) -+ @require_n_gpus_for_nccl_backend(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) def test_accumulate_gradients_no_sync_allreduce_hook(self): """ Runs multiple iterations on _test_accumulate_gradients_no_sync @@ -103,7 +103,7 @@ index 1414a0376b1..1f6b00e6edf 100644 "get_future is only supported on mpi, nccl and gloo", ) - @nccl_skip_if_lt_x_gpu(BACKEND, 2) -+ @require_n_gpus_for_nccl_backend(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) def test_accumulate_gradients_no_sync_allreduce_with_then_hook(self): """ Runs multiple iterations on _test_accumulate_gradients_no_sync using allreduce @@ -112,7 +112,7 @@ index 1414a0376b1..1f6b00e6edf 100644 "get_future is only supported on mpi, nccl and gloo", ) - @nccl_skip_if_lt_x_gpu(BACKEND, 2) -+ @require_n_gpus_for_nccl_backend(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) def test_get_future(self): def mult(fut): return [t * 3 for t in fut.wait()] From 1d3e6ac7b0c5015794e4d36e30c360665a1021e3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 28 Nov 2022 14:23:57 +0100 Subject: [PATCH 784/793] Cancel old GithubAction runs --- .github/workflows/linting.yml | 5 +++++ .github/workflows/unit_tests.yml | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 6346d959773..d7482ec3f7d 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,5 +1,10 @@ name: Static Analysis on: [push, pull_request] + +concurrency: + group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}} + cancel-in-progress: true + jobs: python-linting: runs-on: ubuntu-20.04 diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 1a8e16547f5..620535115d9 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -1,5 +1,10 @@ name: easyconfigs unit tests on: [push, pull_request] + +concurrency: + group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}} + cancel-in-progress: true + jobs: test-suite: runs-on: ubuntu-20.04 From abd1f7187f7c4174fe2795f1ba5755ba05ec80fb Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Mon, 28 Nov 2022 15:36:00 +0100 Subject: [PATCH 785/793] adding easyconfigs: phonopy-2.16.3-foss-2022a.eb --- .../p/phonopy/phonopy-2.16.3-foss-2022a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb new file mode 100644 index 00000000000..d06fecee5a2 --- /dev/null +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'phonopy' +version = '2.16.3' + +homepage = 'https://atztogo.github.io/phonopy/' +description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['c536d355156626f26e5d5fd158b03e10c4a13c461d6a02a26b05e3b6311b9d79'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # for numpy + ('matplotlib', '3.5.2'), + ('PyYAML', '6.0'), + ('h5py', '3.7.0'), + ('spglib-python', '2.0.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/phonopy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["phonopy --help"] + +sanity_pip_check = True + +moduleclass = 'lib' From d22f33188db10e850b2a14fd6bd60c6d276d1872 Mon Sep 17 00:00:00 2001 From: easybuild Date: Mon, 28 Nov 2022 20:41:41 +0100 Subject: [PATCH 786/793] add MAD support --- easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb index 3216a7a24e7..c1e324f3ce3 100644 --- a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb @@ -1,7 +1,5 @@ -# Institution: IT4Innovations National Supercomputing Center, Czech Republic -# Author: Jakub Kropacek -# License: GPLv3 -# Year: 2022 +# Contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 easyblock = 'ConfigureMake' @@ -23,6 +21,7 @@ builddependencies = [('binutils', '2.38')] dependencies = [ ('FLAC', '1.3.4'), ('LAME', '3.100'), + ('libmad', '0.15.1b'), ('libvorbis', '1.3.7'), ('FFmpeg', '5.0.1'), ] @@ -33,6 +32,4 @@ sanity_check_paths = { 'dirs': ['bin', 'include', 'lib', 'lib/pkgconfig', 'share/man'], } -sanity_check_commands = ['sox --help'] - moduleclass = 'data' From f797f9a82d82cf1c87303126f57b534b3e6d2805 Mon Sep 17 00:00:00 2001 From: easybuild Date: Mon, 28 Nov 2022 20:44:14 +0100 Subject: [PATCH 787/793] return sanity check --- easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb index c1e324f3ce3..b009ef44f7f 100644 --- a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb @@ -32,4 +32,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include', 'lib', 'lib/pkgconfig', 'share/man'], } +sanity_check_commands = ['sox --help'] + moduleclass = 'data' From 6017f5bad23ca3a12b701954950f165c2434c508 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 29 Nov 2022 13:41:46 +0100 Subject: [PATCH 788/793] adding easyconfigs: memtester-4.5.1-GCCcore-11.3.0.eb --- .../memtester-4.5.1-GCCcore-11.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7812a2d4fed --- /dev/null +++ b/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'memtester' +version = '4.5.1' + +homepage = 'https://pyropus.ca./software/memtester/' +description = 'A userspace utility for testing the memory subsystem for faults' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://pyropus.ca./software/memtester/old-versions/'] +sources = [SOURCE_TAR_GZ] +checksums = ['1c5fc2382576c084b314cfd334d127a66c20bd63892cac9f445bc1d8b4ca5a47'] + +builddependencies = [ + ('binutils', '2.38'), +] + +files_to_copy = [(['memtester'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/memtester'], + 'dirs': [] +} + +moduleclass = 'tools' From 6ebd52a7d602583625c3d66174a45b3570f819ac Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 29 Nov 2022 14:27:11 +0100 Subject: [PATCH 789/793] Switch to ubuntu mirror --- .../m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb index 7812a2d4fed..06490ea807a 100644 --- a/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb @@ -8,10 +8,13 @@ description = 'A userspace utility for testing the memory subsystem for faults' toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['https://pyropus.ca./software/memtester/old-versions/'] -sources = [SOURCE_TAR_GZ] +# Using ubuntu source mirror due to problematic URL redirects +source_urls = ['http://archive.ubuntu.com/ubuntu/pool/universe/m/memtester/'] +sources = ['memtester_%(version)s.orig.tar.gz'] checksums = ['1c5fc2382576c084b314cfd334d127a66c20bd63892cac9f445bc1d8b4ca5a47'] +insecure_download = True + builddependencies = [ ('binutils', '2.38'), ] From de50989c691cdacbe189538fc89f2da383419702 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 29 Nov 2022 15:27:52 +0100 Subject: [PATCH 790/793] Remove faulty variable --- .../easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb index 06490ea807a..901ab911bea 100644 --- a/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb @@ -13,8 +13,6 @@ source_urls = ['http://archive.ubuntu.com/ubuntu/pool/universe/m/memtester/'] sources = ['memtester_%(version)s.orig.tar.gz'] checksums = ['1c5fc2382576c084b314cfd334d127a66c20bd63892cac9f445bc1d8b4ca5a47'] -insecure_download = True - builddependencies = [ ('binutils', '2.38'), ] From 544b780cd6af10c2bd48d07ff0f16c13fcdaa2ef Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 25 Oct 2022 12:59:43 +0200 Subject: [PATCH 791/793] adding easyconfigs: PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb, PyTorch-1.12.1-foss-2022a.eb and patches: PyTorch-1.12.1_fix-test_wishart_log_prob.patch, PyTorch-1.12.1_python-3.10-annotation-fix.patch, PyTorch-1.12.1_python-3.10-compat.patch, PyTorch-1.12.1_remove-flaky-test-in-testnn.patch --- .../PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb | 148 ++++++++++++++++++ .../p/PyTorch/PyTorch-1.12.1-foss-2022a.eb | 133 ++++++++++++++++ ...rch-1.12.1_fix-test_wishart_log_prob.patch | 36 +++++ ...ch-1.12.1_python-3.10-annotation-fix.patch | 69 ++++++++ .../PyTorch-1.12.1_python-3.10-compat.patch | 115 ++++++++++++++ ...h-1.12.1_remove-flaky-test-in-testnn.patch | 22 +++ 6 files changed, 523 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_wishart_log_prob.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-annotation-fix.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-compat.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_remove-flaky-test-in-testnn.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..7f1ab7e67f8 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,148 @@ +name = 'PyTorch' +version = '1.12.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-test_wishart_log_prob.patch', + 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch', + 'PyTorch-1.12.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.12.1_python-3.10-annotation-fix.patch', + 'PyTorch-1.12.1_python-3.10-compat.patch', + 'PyTorch-1.12.1_remove-flaky-test-in-testnn.patch', + 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.12.1_skip-failing-grad-test.patch', + 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', +] +checksums = [ + '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch + 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch + # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', + # PyTorch-1.12.1_fix-test_wishart_log_prob.patch + 'cf475ae6e6234b96c8d1bf917597c5176c94b3ccd940b72f2e1cd0c979580f45', + # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch + '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', + '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch + # PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d', + 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2', # PyTorch-1.12.1_fix-vsx-vector-funcs.patch + '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2', # PyTorch-1.12.1_fix-vsx-loadu.patch + # PyTorch-1.12.1_increase-test-adadelta-tolerance.patch + '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695', + # PyTorch-1.12.1_increase-tolerance-test_ops.patch + '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb', + '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch + # PyTorch-1.12.1_python-3.10-annotation-fix.patch + '11e168fd429d9e156fc79dd806b08125f3640651ad9998abd810446b2ed0c2d7', + '81402420a878b40f824778f0333fbec6504325a6a1b06a22749c4cac3eaccf67', # PyTorch-1.12.1_python-3.10-compat.patch + # PyTorch-1.12.1_remove-flaky-test-in-testnn.patch + 'e81b678e354dd137c0d6d974605cdedbf672096fdbdf567c347bc2fbfc73471d', + # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch + 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', + '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch + # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch + '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d', +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.23.1'), + ('hypothesis', '6.46.7'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.10.4'), + ('protobuf', '3.19.4'), + ('protobuf-python', '3.19.4'), + ('pybind11', '2.9.2'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.4.2'), + ('Pillow', '9.1.1'), + ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', SYSTEM), + ('magma', '2.6.2', '-CUDA-%(cudaver)s'), + ('NCCL', '2.12.12', '-CUDA-%(cudaver)s'), + ('expecttest', '0.1.3'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6'] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375 + 'distributions/test_constraints', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +# The readelf sanity check command can be taken out once the TestRPATH test from +# https://github.com/pytorch/pytorch/pull/87593 is accepted, since it is then checked as part of the PyTorch test suite +local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT +sanity_check_commands = [ + "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, +] + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb new file mode 100644 index 00000000000..c31da630572 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb @@ -0,0 +1,133 @@ +name = 'PyTorch' +version = '1.12.1' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-test_wishart_log_prob.patch', + 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch', + 'PyTorch-1.12.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.12.1_python-3.10-annotation-fix.patch', + 'PyTorch-1.12.1_python-3.10-compat.patch', + 'PyTorch-1.12.1_remove-flaky-test-in-testnn.patch', + 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.12.1_skip-failing-grad-test.patch', + 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', +] +checksums = [ + '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch + 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch + # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', + # PyTorch-1.12.1_fix-test_wishart_log_prob.patch + 'cf475ae6e6234b96c8d1bf917597c5176c94b3ccd940b72f2e1cd0c979580f45', + # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch + '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', + '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch + # PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d', + 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2', # PyTorch-1.12.1_fix-vsx-vector-funcs.patch + '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2', # PyTorch-1.12.1_fix-vsx-loadu.patch + # PyTorch-1.12.1_increase-test-adadelta-tolerance.patch + '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695', + # PyTorch-1.12.1_increase-tolerance-test_ops.patch + '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb', + '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch + # PyTorch-1.12.1_python-3.10-annotation-fix.patch + '11e168fd429d9e156fc79dd806b08125f3640651ad9998abd810446b2ed0c2d7', + '81402420a878b40f824778f0333fbec6504325a6a1b06a22749c4cac3eaccf67', # PyTorch-1.12.1_python-3.10-compat.patch + # PyTorch-1.12.1_remove-flaky-test-in-testnn.patch + 'e81b678e354dd137c0d6d974605cdedbf672096fdbdf567c347bc2fbfc73471d', + # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch + 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', + '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch + # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch + '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d', +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.23.1'), + ('hypothesis', '6.46.7'), +] + +dependencies = [ + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.10.4'), + ('protobuf', '3.19.4'), + ('protobuf-python', '3.19.4'), + ('pybind11', '2.9.2'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.4.2'), + ('Pillow', '9.1.1'), + ('expecttest', '0.1.3'), +] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375 + 'distributions/test_constraints', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_wishart_log_prob.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_wishart_log_prob.patch new file mode 100644 index 00000000000..c801b4ca53f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_wishart_log_prob.patch @@ -0,0 +1,36 @@ +Fix a TestDistributions.test_wishart_log_prob failure in test_distributions +See https://github.com/pytorch/pytorch/pull/87977 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributions/test_distributions.py b/test/distributions/test_distributions.py +index 127018516e123..219eacf4790b0 100644 +--- a/test/distributions/test_distributions.py ++++ b/test/distributions/test_distributions.py +@@ -2036,7 +2036,7 @@ def test_lowrank_multivariate_normal_log_prob(self): + unbatched_prob = torch.stack([dist_unbatched[i].log_prob(x[:, i]) for i in range(5)]).t() + + self.assertEqual(batched_prob.shape, unbatched_prob.shape) +- self.assertEqual(0.0, (batched_prob - unbatched_prob).abs().max(), atol=1e-3, rtol=0) ++ self.assertEqual(batched_prob, unbatched_prob, atol=1e-3, rtol=0) + + @unittest.skipIf(not TEST_NUMPY, "NumPy not found") + def test_lowrank_multivariate_normal_sample(self): +@@ -2176,7 +2176,7 @@ def test_multivariate_normal_log_prob(self): + unbatched_prob = torch.stack([dist_unbatched[i].log_prob(x[:, i]) for i in range(5)]).t() + + self.assertEqual(batched_prob.shape, unbatched_prob.shape) +- self.assertEqual(0.0, (batched_prob - unbatched_prob).abs().max(), atol=1e-3, rtol=0) ++ self.assertEqual(batched_prob, unbatched_prob, atol=1e-3, rtol=0) + + @unittest.skipIf(not TEST_NUMPY, "NumPy not found") + def test_multivariate_normal_sample(self): +@@ -2331,7 +2331,7 @@ def test_wishart_log_prob(self): + unbatched_prob = torch.stack([dist_unbatched[i].log_prob(x[:, i]) for i in range(5)]).t() + + self.assertEqual(batched_prob.shape, unbatched_prob.shape) +- self.assertEqual(0.0, (batched_prob - unbatched_prob).abs().max(), atol=1e-3, rtol=0) ++ self.assertEqual(batched_prob, unbatched_prob, atol=1e-3, rtol=0) + + @unittest.skipIf(not TEST_NUMPY, "NumPy not found") + def test_wishart_sample(self): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-annotation-fix.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-annotation-fix.patch new file mode 100644 index 00000000000..61f04d40743 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-annotation-fix.patch @@ -0,0 +1,69 @@ +Handle change of type annotation handling in Python 3.10 in the JIT module. +Fixes failures in e.g. test_jit. + +From https://github.com/pytorch/pytorch/pull/81334 & https://github.com/pytorch/pytorch/pull/81506 +Backport: Alexander Grund (TU Dresden) + +diff --git a/torch/_jit_internal.py b/torch/_jit_internal.py +index 3c067d5c1c5..2cc3dba89b4 100644 +--- a/torch/_jit_internal.py ++++ b/torch/_jit_internal.py +@@ -1059,11 +1059,19 @@ def _get_named_tuple_properties(obj): + if field in obj._field_defaults] + else: + defaults = [] ++ # In 3.10 recommended way to get annotations is to call `inspect.get_annotations` function ++ # Also, annotations from base class are not inherited so they need to be queried explicitly ++ if sys.version_info[:2] < (3, 10): ++ obj_annotations = getattr(obj, '__annotations__', {}) ++ else: ++ obj_annotations = inspect.get_annotations(obj) ++ if len(obj_annotations) == 0 and hasattr(obj, "__base__"): ++ obj_annotations = inspect.get_annotations(obj.__base__) ++ + annotations = [] +- has_annotations = hasattr(obj, '__annotations__') + for field in obj._fields: +- if has_annotations and field in obj.__annotations__: +- the_type = torch.jit.annotations.ann_to_type(obj.__annotations__[field], fake_range()) ++ if field in obj_annotations: ++ the_type = torch.jit.annotations.ann_to_type(obj_annotations[field], fake_range()) + annotations.append(the_type) + else: + annotations.append(torch._C.TensorType.getInferred()) +diff --git a/torch/jit/_recursive.py b/torch/jit/_recursive.py +index 8175d14fe5d..aa36a4561d4 100644 +--- a/torch/jit/_recursive.py ++++ b/torch/jit/_recursive.py +@@ -5,6 +5,7 @@ import collections + import textwrap + import functools + import warnings ++import sys + from typing import Dict, List, Set, Type + + import torch._jit_internal as _jit_internal +@@ -134,7 +135,22 @@ def infer_concrete_type_builder(nn_module, share_types=True): + if isinstance(nn_module, (torch.nn.ParameterDict)): + concrete_type_builder.set_parameter_dict() + +- class_annotations = getattr(nn_module, '__annotations__', {}) ++ def get_annotations(obj): ++ if sys.version_info < (3, 10): ++ return getattr(obj, '__annotations__', {}) ++ # In Python-3.10+ it is recommended to use inspect.get_annotations ++ # See https://docs.python.org/3.10/howto/annotations.html ++ # But also, in 3.10 annotations from base class are not inherited ++ # by unannotated derived one, so they must be manually extracted ++ annotations = inspect.get_annotations(obj) ++ if len(annotations) > 0: ++ return annotations ++ cls = obj if isinstance(obj, type) else type(obj) ++ if len(cls.__bases__) == 0: ++ return {} ++ return inspect.get_annotations(cls.__bases__[0]) ++ ++ class_annotations = get_annotations(nn_module) + if isinstance(nn_module, (torch.ao.quantization.QuantWrapper)): + class_annotations = {} + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-compat.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-compat.patch new file mode 100644 index 00000000000..957a31669b0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-compat.patch @@ -0,0 +1,115 @@ +Fixes some compatibility issues with Python 3.10 + +Most notably conversion from float to long which avoids: + TypeError: 'float' object cannot be interpreted as an integer +Also some test failures in test_fx & test_jit due to differences in Python 3.10. + +From https://github.com/pytorch/pytorch/pull/82329 +Backported: Alexander Grund (TU Dresden) + +diff --git a/test/jit/test_hash.py b/test/jit/test_hash.py +index cb1c1544b10..2ca1e9cda0a 100644 +--- a/test/jit/test_hash.py ++++ b/test/jit/test_hash.py +@@ -75,7 +75,10 @@ class TestHash(JitTestCase): + self.checkScript(fn, (1.2345, float("inf"))) + self.checkScript(fn, (float("inf"), float("inf"))) + self.checkScript(fn, (1.2345, float('nan'))) +- self.checkScript(fn, (float("nan"), float("nan"))) ++ if sys.version_info < (3, 10): ++ # Hash of two nans are not guaranteed to be equal. From https://docs.python.org/3/whatsnew/3.10.html : ++ # Hashes of NaN values of both float type and decimal.Decimal type now depend on object identity. ++ self.checkScript(fn, (float("nan"), float("nan"))) + self.checkScript(fn, (float("nan"), float("inf"))) + + def test_hash_int(self): +diff --git a/test/test_fx.py b/test/test_fx.py +index 625614d29a8..307b629cab3 100644 +--- a/test/test_fx.py ++++ b/test/test_fx.py +@@ -3280,6 +3280,7 @@ class TestFX(JitTestCase): + .run(scripted.code) + + @unittest.skipIf(IS_WINDOWS, "Python Windows bug? https://bugs.python.org/issue45108") ++ @unittest.skipIf(sys.version_info >= (3, 10), "Does not work on Python-3.10") + def test_assert(self): + def f(x): + assert x > 1 +@@ -4017,7 +4018,7 @@ class TestFunctionalTracing(JitTestCase): + + def functional_test(self): + if func_name in self.UNTRACEABLE_FUNCTIONALS_PY38 and \ +- sys.version_info >= (3, 8) and sys.version_info < (3, 10): ++ sys.version_info >= (3, 8) and sys.version_info < (3, 11): + exc, err = self.UNTRACEABLE_FUNCTIONALS_PY38[func_name] + with self.assertRaisesRegex(exc, err): + symbolic_trace(fn) +diff --git a/test/test_jit.py b/test/test_jit.py +index 7dbae135a9a..ea436482a55 100644 +--- a/test/test_jit.py ++++ b/test/test_jit.py +@@ -7450,6 +7450,9 @@ a") + # tensor from empty list is type float in python and annotated type in torchscript + if "annotate" in li and "dtype" not in option: + continue ++ # Skip unsigned tensor initializaton for signed values on 3.10 ++ if sys.version_info[:2] >= (3, 10) and "torch.uint8" in option and "-" in li: ++ continue + code = tensor_template.format(list_create=li, tensor_op=op, options=option) + scope = {} + exec(code, globals(), scope) +diff --git a/torch/csrc/utils/python_scalars.h b/torch/csrc/utils/python_scalars.h +index 7f454bdff82..7df0662fa2c 100644 +--- a/torch/csrc/utils/python_scalars.h ++++ b/torch/csrc/utils/python_scalars.h +@@ -1,6 +1,7 @@ + #pragma once + + #include ++#include + #include + + #include +@@ -8,13 +9,37 @@ + + namespace torch { namespace utils { + ++template ++inline T unpackIntegral(PyObject* obj, const char* type) { ++#if PY_VERSION_HEX >= 0x030a00f0 ++ // In Python-3.10 floats can no longer be silently converted to integers ++ // Keep backward compatible behavior for now ++ if (PyFloat_Check(obj)) { ++ return c10::checked_convert(THPUtils_unpackDouble(obj), type); ++ } ++ return c10::checked_convert(THPUtils_unpackLong(obj), type); ++#else ++ return static_cast(THPUtils_unpackLong(obj)); ++#endif ++} ++ + inline void store_scalar(void* data, at::ScalarType scalarType, PyObject* obj) { + switch (scalarType) { +- case at::kByte: *(uint8_t*)data = (uint8_t)THPUtils_unpackLong(obj); break; +- case at::kChar: *(int8_t*)data = (int8_t)THPUtils_unpackLong(obj); break; +- case at::kShort: *(int16_t*)data = (int16_t)THPUtils_unpackLong(obj); break; +- case at::kInt: *(int32_t*)data = (int32_t)THPUtils_unpackLong(obj); break; +- case at::kLong: *(int64_t*)data = THPUtils_unpackLong(obj); break; ++ case at::kByte: ++ *(uint8_t*)data = unpackIntegral(obj, "uint8"); ++ break; ++ case at::kChar: ++ *(int8_t*)data = unpackIntegral(obj, "int8"); ++ break; ++ case at::kShort: ++ *(int16_t*)data = unpackIntegral(obj, "int16"); ++ break; ++ case at::kInt: ++ *(int32_t*)data = unpackIntegral(obj, "int32"); ++ break; ++ case at::kLong: ++ *(int64_t*)data = unpackIntegral(obj, "int64"); ++ break; + case at::kHalf: + *(at::Half*)data = at::convert(THPUtils_unpackDouble(obj)); + break; diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_remove-flaky-test-in-testnn.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_remove-flaky-test-in-testnn.patch new file mode 100644 index 00000000000..31d44fb01d1 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_remove-flaky-test-in-testnn.patch @@ -0,0 +1,22 @@ +This test is flaky when run with the type float16. +I.e. TestNNDeviceTypeCPU.test_embedding_bag_device_cpu_int32_int32_float16 & + TestNNDeviceTypeCPU.test_embedding_bag_device_cpu_int64_int64_float16 +fail. +See https://github.com/pytorch/pytorch/issues/86638 +So remove the half precision test. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_nn.py b/test/test_nn.py +index aad884ebd4f..b514f72a3e9 100644 +--- a/test/test_nn.py ++++ b/test/test_nn.py +@@ -18236,7 +18236,7 @@ class TestNNDeviceType(NNTestCase): + self.assertRaises(RuntimeError, lambda: es(input.view(-1), offset)) + + @skipMeta +- @dtypes(*itertools.product((torch.int, torch.long), (torch.int, torch.long), (torch.float, torch.double, torch.half))) ++ @dtypes(*itertools.product((torch.int, torch.long), (torch.int, torch.long), (torch.float, torch.double))) + def test_embedding_bag_device(self, device, dtypes): + self._test_EmbeddingBag(device, 'sum', False, wdtype=dtypes[2], dtype=dtypes[0], odtype=dtypes[1]) + self._test_EmbeddingBag(device, 'mean', False, wdtype=dtypes[2], dtype=dtypes[0], odtype=dtypes[1]) From 7bcc8094ce3db34b1457f35102f1900eccff975a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 30 Nov 2022 10:27:37 +0100 Subject: [PATCH 792/793] adding easyconfigs: GlobalArrays-5.8.2-intel-2022a.eb --- .../GlobalArrays-5.8.2-intel-2022a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb new file mode 100644 index 00000000000..4af8e53447d --- /dev/null +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'GlobalArrays' +version = '5.8.2' + +homepage = 'https://hpc.pnl.gov/globalarrays' +description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/GlobalArrays/ga/releases/download/'] +sources = ['v%(version)s/ga-%(version)s.tar.gz'] + +configopts = ' --with-mpi --enable-i8' +configopts += ' --with-blas8="-L$MLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' +configopts += ' --with-scalapack8="L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' +configopts += '-lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"' + +# select armci network as (Comex) MPI-1 two-sided +configopts += ' --with-mpi-ts' + +sanity_check_paths = { + 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', + 'lib/libcomex.a', 'lib/libga.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 93fddda86a3291b8dc66f36dfedfe34283b1145d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 30 Nov 2022 10:52:04 +0100 Subject: [PATCH 793/793] add missing checksums --- .../easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb index 4af8e53447d..435986d2ef9 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb @@ -11,6 +11,7 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/GlobalArrays/ga/releases/download/'] sources = ['v%(version)s/ga-%(version)s.tar.gz'] +checksums = ['51599e4abfe36f05cecfaffa33be19efbe9e9fa42d035fd3f866469b663c22a2'] configopts = ' --with-mpi --enable-i8' configopts += ' --with-blas8="-L$MLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"'