Merge tag 'v2020.4' into release-2020-fda

GROMACS version 2020.4
HITS-MBM · Oct 29, 2020 · 4b57905 · 4b57905
2 parents 912d4c5 + 4266b0b
commit 4b57905
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Showing 68 changed files with 1,208 additions and 459 deletions.
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -37,13 +37,10 @@ stages:
   # Deploy stage for release builds
   - release-deploy
 
-default:
-  tags:
-    - k8s-scilifelab
-
 include:
   # Mix-in helper job definitions of general utility.
   - local: '/admin/gitlab-ci/global.gitlab-ci.yml'
+  - local: '/admin/gitlab-ci/rules.gitlab-ci.yml'
   # gmxapi Python package.
   - local: '/admin/gitlab-ci/python-gmxapi.gitlab-ci.yml'
   # Further API validation and usability of sample gmxapi extension package.

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -404,7 +404,7 @@ check_cxx_source_compiles("int main(){ return __builtin_clz(1);}"   HAVE_BUILTIN
 check_cxx_source_compiles("int main(){ return __builtin_clzll(1);}" HAVE_BUILTIN_CLZLL)
 if(MSVC)
     check_cxx_source_compiles("#include <intrin.h>\n int main(){unsigned long r;unsigned long i=1;_BitScanReverse(&r,i);return r;}" HAVE_BITSCANREVERSE)
-    check_cxx_source_compiles("#include <intrin.h>\n int main(){unsigned long r;unsigned __int64 i=1;_BitScanReverse(&r,i);return r;}" HAVE_BITSCANREVERSE64)
+    check_cxx_source_compiles("#include <intrin.h>\n int main(){unsigned long r;unsigned __int64 i=1;_BitScanReverse64(&r,i);return r;}" HAVE_BITSCANREVERSE64)
 elseif(CMAKE_CXX_COMPILER_ID MATCHES "XL")
     check_cxx_source_compiles("int main(){ return __cntlz4(1);}" HAVE_CNTLZ4)
     check_cxx_source_compiles("int main(){ return __cntlz8(1);}" HAVE_CNTLZ8)

diff --git a/admin/gitlab-ci/archive.gitlab-ci.yml b/admin/gitlab-ci/archive.gitlab-ci.yml
@@ -7,16 +7,14 @@ prepare-release-version:
   cache: {}
   # Docker image uploaded to dockerhub by user eriklindahl
   # TODO: Get DockerFile for admin/dockerfiles
-  image: biophysics/gcc-gromacs
+  image: gromacs/ci-docs-llvm:2020
   stage: configure-build
-
   variables:
     KUBERNETES_CPU_LIMIT: 1
     KUBERNETES_CPU_REQUEST: 1
-    KUBERNETES_MEMORY_LIMIT: 2Gi
+    KUBERNETES_MEMORY_REQUEST: 2Gi
   script:
     - cmake -P cmake/gmxVersionInfo.cmake &> version.json
-
   artifacts:
     paths:
       - version.json
@@ -27,18 +25,26 @@ prepare-release-version:
 regressiontests:prepare:
   extends:
     - .variables:default
-    - .rules:merge-requests
+    - .rules:merge-and-post-merge-acceptance
   cache: {}
-  image: biophysics/gcc-gromacs
+  image: gromacs/ci-docs-llvm:2020
   stage: configure-build
-
   variables:
     KUBERNETES_CPU_LIMIT: 1
     KUBERNETES_CPU_REQUEST: 1
-    KUBERNETES_MEMORY_LIMIT: 2Gi
+    KUBERNETES_MEMORY_REQUEST: 2Gi
   # Always clone the default version for this branch, master in this case
   script:
     - export REGTESTBRANCH=release-2020
+    - if [[ ! -z $REGRESSIONTESTBRANCH ]] ; then
+      export REGTESTBRANCH=$REGRESSIONTESTBRANCH ;
+      echo "Using $REGTESTBRANCH instead of default" ;
+      fi
+    - export CHECKOUTCOMMIT=FETCH_HEAD
+    - if [[ ! -z $REGRESSIONTESTCOMMIT ]] ; then
+      export CHECKOUTCOMMIT=$REGRESSIONTESTCOMMIT ;
+      echo "Using $CHECKOUTCOMMIT instead of head of $REGTESTBRANCH" ;
+      fi
     - if [[ ! -d regressiontests ]] ; then
         mkdir regressiontests ;
         cd regressiontests ;
@@ -47,7 +53,7 @@ regressiontests:prepare:
       fi
     - cd regressiontests
     - git fetch https://gitlab.com/gromacs/gromacs-regressiontests.git $REGTESTBRANCH
-    - git checkout -qf FETCH_HEAD
+    - git checkout -qf $CHECKOUTCOMMIT
     - git clean -ffdxq
     - git gc
     - git archive -o gmx-regressiontests.tar.gz --prefix regressiontests/ -9 HEAD
@@ -65,13 +71,12 @@ regressiontests:package:
   cache: {}
   # Docker image uploaded to dockerhub by user eriklindahl
   # TODO: Get DockerFile for admin/dockerfiles
-  image: biophysics/gcc-gromacs
+  image: gromacs/ci-docs-llvm:2020
   stage: release-package
-
   variables:
     KUBERNETES_CPU_LIMIT: 1
     KUBERNETES_CPU_REQUEST: 1
-    KUBERNETES_MEMORY_LIMIT: 2Gi
+    KUBERNETES_MEMORY_REQUEST: 2Gi
   needs:
     - job: prepare-release-version
   script:
@@ -144,7 +149,7 @@ archive:configure:release:
   variables:
     KUBERNETES_CPU_LIMIT: 4
     KUBERNETES_CPU_REQUEST: 2
-    KUBERNETES_MEMORY_LIMIT: 4Gi
+    KUBERNETES_MEMORY_REQUEST: 4Gi
   script:
     - rm -rf gromacs*tar.gz
     - cd $BUILD_DIR
@@ -203,7 +208,7 @@ archive:package:
     BUILD_DIR: build-package
 
 release-verify:
-  image: biophysics/gcc-gromacs
+  image: gromacs/ci-docs-llvm:2020
   stage: release-verify
   extends:
     - .variables:default
@@ -213,7 +218,7 @@ release-verify:
   variables:
     KUBERNETES_CPU_LIMIT: 1
     KUBERNETES_CPU_REQUEST: 1
-    KUBERNETES_MEMORY_LIMIT: 2Gi
+    KUBERNETES_MEMORY_REQUEST: 2Gi
   script:
     - VERSION=`cat version.json |
       python3 -c "import json,sys; print(json.load(sys.stdin)['version'])"`

diff --git a/admin/gitlab-ci/documentation.gitlab-ci.yml b/admin/gitlab-ci/documentation.gitlab-ci.yml
@@ -12,9 +12,8 @@
   variables:
     KUBERNETES_CPU_LIMIT: 1
     KUBERNETES_CPU_REQUEST: 1
-    KUBERNETES_MEMORY_LIMIT: 2Gi
+    KUBERNETES_MEMORY_REQUEST: 2Gi
     CMAKE_COMPILER_SCRIPT: "-DCMAKE_C_COMPILER=clang-7 -DCMAKE_CXX_COMPILER=clang++-7"
-    CMAKE_EXTRA_OPTIONS: ""
     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=OFF"
     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
@@ -79,9 +78,8 @@
   variables:
     KUBERNETES_CPU_LIMIT: 1
     KUBERNETES_CPU_REQUEST: 1
-    KUBERNETES_MEMORY_LIMIT: 2Gi
+    KUBERNETES_MEMORY_REQUEST: 2Gi
     CMAKE_COMPILER_SCRIPT: "-DCMAKE_C_COMPILER=clang-7 -DCMAKE_CXX_COMPILER=clang++-7"
-    CMAKE_EXTRA_OPTIONS: ""
     CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=None"
     CMAKE_MPI_OPTIONS: "-DGMX_THREAD_MPI=ON"
     CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
@@ -178,7 +176,6 @@ docs:configure:
   extends:
     - .docs:configure
     - .rules:basic-push
-  tags: []
   variables:
     BUILD_DIR: build-docs
     CMAKE_EXTRA_OPTIONS: -DGMX_BUILD_HELP=on -DGMX_BUILD_MANUAL=on
@@ -206,7 +203,6 @@ docs:build:
     - .before_script:default
     - .rules:basic-push
   stage: documentation
-  tags: []
   needs:
     - job: docs:configure
   variables:
@@ -231,7 +227,7 @@ docs:build:
   variables:
     KUBERNETES_CPU_LIMIT: 4
     KUBERNETES_CPU_REQUEST: 2
-    KUBERNETES_MEMORY_LIMIT: 4Gi
+    KUBERNETES_MEMORY_REQUEST: 4Gi
   script:
     - cd $BUILD_DIR
     - cmake --build . --target manual -- -j4 | tee docs/manual/all-output.log
@@ -263,7 +259,6 @@ webpage:build:
     - .webpage:build
     - .rules:basic-push
   stage: post-test
-  tags: []
   needs:
     - job: docs:build
     - job: check-source
@@ -276,6 +271,8 @@ webpage:configure:
     - .docs:configure:release
     - .rules:nightly-only-for-release
   cache: {}
+  tags:
+    - k8s-scilifelab
   dependencies:
     - archive:package
     - regressiontests:package
@@ -293,6 +290,8 @@ webpage:dependencies:
     - .before_script:default
     - .rules:nightly-only-for-release
   stage: release-build
+  tags:
+    - k8s-scilifelab
   needs:
     - job: webpage:configure
   variables:
@@ -302,9 +301,11 @@ webpage:build:release:
   extends:
     - .webpage:build
     - .rules:nightly-only-for-release
+  stage: release-prepare-deploy
+  tags:
+    - k8s-scilifelab
   dependencies:
     - webpage:dependencies
     - webpage:configure
-  stage: release-prepare-deploy
   variables:
     BUILD_DIR: release-doc-builds
diff --git a/admin/gitlab-ci/global.gitlab-ci.yml b/admin/gitlab-ci/global.gitlab-ci.yml
@@ -1,19 +1,24 @@
 # Mix-in job definitions.
+# The (hidden) job definitions in this file are available to the regular job
+# definitions in other files because this file is first in the *include* list
+# in the root `.gitlab-ci.yml` file.
 
 # Centralized definitions of common job parameter values.
+# Parameters with many optional configurations may be in separate files.
+# Refer to the Infrastructure section of the GROMACS Developer Guide.
 
 .variables:default:
   variables:
     KUBERNETES_CPU_LIMIT: 8
     KUBERNETES_CPU_REQUEST: 4
+    KUBERNETES_MEMORY_REQUEST: 4Gi
     KUBERNETES_MEMORY_LIMIT: 8Gi
     KUBERNETES_EXTENDED_RESOURCE_NAME: ""
     KUBERNETES_EXTENDED_RESOURCE_LIMIT: 0
     CACHE_FALLBACK_KEY: "$CI_JOB_NAME-$CI_JOB_STAGE-release-2020"
     BUILD_DIR: build
     INSTALL_DIR: install
-    CMAKE_GMXAPI_OPTIONS: "-DGMX_PYTHON_PACKAGE=OFF"
-# TODO: Get these from updated Docker images.
+    CMAKE_GMXAPI_OPTIONS: ""
 
 # Our generic before_script to install dependencies and prepare the ccache directory.
 .before_script:default:
@@ -22,113 +27,6 @@
     - export CCACHE_BASEDIR=${PWD}
     - export CCACHE_DIR=${PWD}/ccache
 
-# Jobs that run for new commits and pipelines triggered by schedules or
-# through the web interface, unless GROMACS_RELEASE is set. Excluded from
-# extra pipelines generated by merge request events.
-# Includes non-gromacs projects. Note that jobs using this rule are
-# eligible to run on non-gromacs project infrastructure, and should therefore
-# override the default *tag* parameter to exclude tags specific to the GROMACS
-# GitLab Runner infrastructure. I.e. in the job definition, set `tags: []`
-.rules:basic-push:
-  rules:
-    - if: '$GROMACS_RELEASE'
-      when: never
-    - if: '$CI_PIPELINE_SOURCE == "web"'
-      when: always
-    - if: '$CI_PIPELINE_SOURCE == "push"'
-      when: always
-    - if: '$CI_PIPELINE_SOURCE == "schedule"'
-      when: always
-    - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
-      when: never
-
-# Jobs that run for merge requests and schedules, but not when GROMACS_RELEASE
-# is set. Excludes non-gromacs projects.
-.rules:merge-requests:
-  rules:
-    - if: '$CI_PROJECT_NAMESPACE != "gromacs"'
-      when: never
-    - if: '$GROMACS_RELEASE'
-      when: never
-    - if: '$CI_PIPELINE_SOURCE == "web"'
-      when: always
-    - if: '$CI_PIPELINE_SOURCE == "push"'
-      when: never
-    - if: '$CI_PIPELINE_SOURCE == "schedule"'
-      when: always
-    - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
-      when: always
-
-# Jobs that run for merge requests and schedules for branch `master`,
-# but not when GROMACS_RELEASE is set.
-# Excludes non-gromacs projects.
-.rules:merge-requests:master:
-  rules:
-    - if: '$CI_PROJECT_NAMESPACE != "gromacs"'
-      when: never
-    - if: '$GROMACS_RELEASE'
-      when: never
-    # This rule catches "push" and other events in branches other than `master`
-    # but allows merge_request_events for merge requests targeting master.
-    # This rule is before "web" so the web interface won't include jobs that can't succeed
-    # (and would not ordinarily be run). Such jobs are hard to identify in a way that is
-    # sufficiently general for a global rules definition.
-    # If extra coverage is needed through a web-triggered job in merge request branches,
-    # we could provide an additional short-circuiting rule based on an environment variable
-    # to be provided through the web interface.
-    - if: '$CI_MERGE_REQUEST_TARGET_BRANCH_NAME != "master" && $CI_COMMIT_REF_NAME != "master"'
-      when: never
-    - if: '$CI_PIPELINE_SOURCE == "web"'
-      when: always
-    - if: '$CI_PIPELINE_SOURCE == "schedule"'
-      when: always
-    - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
-      when: always
-
-# Jobs that run for merge requests and schedules for branch `release-2020`,
-# but not when GROMACS_RELEASE is set.
-# Excludes non-gromacs projects.
-.rules:merge-requests:release-2020:
-  rules:
-    - if: '$CI_PROJECT_NAMESPACE != "gromacs"'
-      when: never
-    - if: '$GROMACS_RELEASE'
-      when: never
-    - if: '$CI_PIPELINE_SOURCE == "web"'
-      when: always
-    # This next rule catches "push" and other events in branches other than `release-2020`
-    # but allows merge_request_events for merge requests targeting `release-2020`.
-    - if: '$CI_MERGE_REQUEST_TARGET_BRANCH_NAME != "release-2020" && $CI_COMMIT_REF_NAME != "release-2020"'
-      when: never
-    - if: '$CI_PIPELINE_SOURCE == "schedule"'
-      when: always
-    - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
-      when: always
-
-# Rule to run a job only in nightly release-preparation pipelines.
-# Checks if the GROMACS_RELEASE variable was set (typically through the GitLab web interface).
-# Excludes merge_requests and non-gromacs projects.
-# TODO: Update to *rules* syntax.
-.rules:nightly-only-for-release:
-  rules:
-    - if: '$CI_PROJECT_NAMESPACE != "gromacs"'
-      when: never
-    - if: '$GROMACS_RELEASE && $CI_PIPELINE_SOURCE == "web"'
-      when: always
-    - if: '$GROMACS_RELEASE && $CI_PIPELINE_SOURCE == "schedule"'
-      when: always
-
-# Jobs that run on schedules, but not for merge requests or when GROMACS_RELEASE
-# is set. Excludes non-gromacs projects.
-.rules:nightly-not-for-release:
-  rules:
-    - if: '$CI_PROJECT_NAMESPACE != "gromacs"'
-      when: never
-    - if: '$GROMACS_RELEASE'
-      when: never
-    - if: '$CI_PIPELINE_SOURCE == "web" || $CI_PIPELINE_SOURCE == "schedule"'
-      when: always
-
 # Behavioral templates
 
 # Use a persistent compiler cache to speed up rebuilds for a single job.