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ChangeLog
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======================================================================
Originator:Chris Fischer
Date: 6-25-2018
Tag: cime5.7.0
Answer Changes: None
Tests: scripts_regression_tests
xmllint of env_mach_specific.xml
Dependencies:
Brief Summary:
- Merge in changes from maint-5.6(CESM release) branch.
- Fix issue with e3sm mali file archiving.
- Config compiler parser fix.
- XSD definitions did not match implementation.
- config_compilers.xml updates from e3sm.
- Fix minor issue with recent non-local PR.
- Allow users to go up through the setup phase on non-local machines.
- e3sm st_archive fix for ESP.
- Import fixes and updates from e3sm.
- Update e3sm to compilers v2.
- Maint 5.6 merge to master.
- Add the allow_error flag to schema.
- Fix weird whitespace.
- Improve robustness of compare-two tests.
- Fix find_circular_dependency.py.
- Maint 5.6 merge to master.
- Jgfouca/branch for acme split 2018 05 18.
- Add commas to output using --value.
- Multisubmit tests were not resubmitting.
- New script to add additional metadata for stat ensemble test.
- Fix formatting issue.
- Update iyear for 2000 runs.
- Merge branch 'master' of github.com:ESMCI/cime.
- Add grid neede for cime standalone testing.
- Updated the wrappers for the ESMF mapping tools to work on NCAR machines.
User interface changes:
- New --non-local flag for create_test/create_newcase.
PR summary: git log --oneline --first-parent [previous_tag]..master
6ceaf73 Merge pull request #2690 from ESMCI/maint-5.6
aeaac31 Merge pull request #2683 from jedwards4b/e3sm_st_archive_fix
b78593b Merge pull request #2671 from jedwards4b/config_compiler_test
58a5e43 Merge pull request #2670 from ESMCI/jgfouca/fix_directive_selection
95fe393 config_compilers.xml updates from e3sm
4888867 Fix minor issue with recent non-local PR
43a6812 Merge pull request #2665 from ESMCI/jgfouca/allow_non_local_machine_setup
8a2f9d5 Merge pull request #2663 from jedwards4b/e3sm_st_archive
22ab62b Merge pull request #2661 from ESMCI/jgfouca/fix_e3sm_compilers
18f23fc Merge pull request #2655 from ESMCI/jgfouca/update_e3sm_to_compilersv2
c1eff51 Merge pull request #2657 from ESMCI/maint-5.6
6b01d3b Merge pull request #2654 from jedwards4b/validate_allow_error
8e4054b Fix weird whitespace
ed9d13b Merge pull request #2635 from ESMCI/jgfouca/preemptively_add_compare_pend
3d65363 Merge pull request #2630 from gold2718/fix_circular
5dd50b1 Merge pull request #2627 from ESMCI/maint-5.6
6933518 Merge pull request #2613 from ESMCI/jgfouca/branch-for-acme-split-2018-05-18
2e997e0 Merge pull request #2607 from jedwards4b/xmlquery_multivalue
f1d501f Merge pull request #2600 from jedwards4b/test_issues
5c256ec Merge pull request #2582 from jedwards4b/stattest_add_metadata
8ce38a4 fix formatting issue
6c53cfc Merge pull request #2594 from jedwards4b/orb_iyear_2000
c04da3c Merge branch 'master' of github.com:ESMCI/cime
166a40c these grids are needed for cime standalone testing
7cef855 Merge pull request #2589 from mnlevy1981/mlevy/mapping_on_geyser
Modified files: git diff --name-status [previous_tag]
M .gitignore
M config/cesm/config_archive.xml
M config/cesm/config_files.xml
M config/cesm/config_grids.xml
M config/cesm/machines/config_batch.xml
M config/cesm/machines/config_compilers.xml
M config/cesm/machines/config_machines.xml
M config/cesm/machines/template.case.run
M config/cesm/machines/template.case.test
M config/cesm/machines/template.st_archive
M config/e3sm/allactive/config_pesall.xml
M config/e3sm/machines/config_batch.xml
M config/e3sm/machines/config_compilers.xml
M config/e3sm/machines/config_machines.xml
M config/e3sm/machines/template.st_archive
M config/xml_schemas/config_batch.xsd
M config/xml_schemas/config_machines.xsd
M config/xml_schemas/testlist.xsd
M doc/Makefile
M doc/README
D doc/source/README
M doc/source/conf.py
M doc/source/users_guide/building-a-case.rst
A doc/source/users_guide/cime-change-namelist.rst
A doc/source/users_guide/cime-dir.rst
M doc/source/users_guide/cloning-a-case.rst
M doc/source/users_guide/compsets.rst
M doc/source/users_guide/create-a-case.rst
M doc/source/users_guide/grids.rst
M doc/source/users_guide/index.rst
M doc/source/users_guide/introduction-and-overview.rst
M doc/source/users_guide/machine.rst
M doc/source/users_guide/pes-threads.rst
M doc/source/users_guide/porting-cime.rst
M doc/source/users_guide/running-a-case.rst
M doc/source/users_guide/setting-up-a-case.rst
M doc/source/users_guide/testing.rst
M doc/source/users_guide/timers.rst
M doc/source/users_guide/troubleshooting.rst
M doc/source/users_guide/unit_testing.rst
D doc/source/users_guide/use_cases/basics-a-basic-example.rst
D doc/source/users_guide/use_cases/basics-setting-up-a-branch-or-hybrid-run.rst
D doc/source/users_guide/use_cases/cesm-nml.rst
D doc/source/users_guide/use_cases/datamod-nml.rst
D doc/source/users_guide/use_cases/driver-nml.rst
D doc/source/users_guide/use_cases/namelist-gen.rst
D doc/source/users_guide/use_cases/use-cases.rst
A doc/source/users_guide/workflows.rst
M doc/tools_autodoc.cfg
M doc/tools_autodoc.py
M scripts/Tools/Makefile
M scripts/Tools/xmlquery
M scripts/create_newcase
M scripts/create_test
M scripts/fortran_unit_testing/run_tests.py
M scripts/lib/CIME/BuildTools/macrowriterbase.py
M scripts/lib/CIME/BuildTools/possiblevalues.py
M scripts/lib/CIME/Servers/gftp.py
M scripts/lib/CIME/SystemTests/pet.py
M scripts/lib/CIME/SystemTests/system_tests_common.py
M scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M scripts/lib/CIME/XML/compilerblock.py
M scripts/lib/CIME/XML/compilers.py
M scripts/lib/CIME/XML/env_base.py
M scripts/lib/CIME/XML/env_batch.py
M scripts/lib/CIME/XML/env_mach_specific.py
M scripts/lib/CIME/XML/grids.py
M scripts/lib/CIME/XML/machines.py
M scripts/lib/CIME/bless_test_results.py
M scripts/lib/CIME/case/case.py
M scripts/lib/CIME/case/case_setup.py
M scripts/lib/CIME/case/case_st_archive.py
M scripts/lib/CIME/case/case_submit.py
M scripts/lib/CIME/case/check_input_data.py
M scripts/lib/CIME/compare_namelists.py
M scripts/lib/CIME/test_scheduler.py
M scripts/lib/CIME/test_status.py
M scripts/lib/CIME/tests/SystemTests/test_system_tests_compare_two.py
M scripts/lib/CIME/utils.py
M scripts/lib/CIME/wait_for_tests.py
D scripts/manage_pes
M scripts/tests/scripts_regression_tests.py
M src/build_scripts/buildlib.csm_share
M src/components/data_comps/datm/datm_comp_mod.F90
M src/components/data_comps/datm/mct/atm_comp_mct.F90
M src/drivers/mct/cime_config/config_component.xml
M src/drivers/mct/cime_config/config_component_e3sm.xml
M src/drivers/mct/cime_config/namelist_definition_drv.xml
M src/drivers/mct/cime_config/testdefs/testlist_drv.xml
M src/externals/pio1/pio/box_rearrange.F90.in
M src/externals/pio1/pio/pio_support.F90
M src/externals/pio1/pio/piolib_mod.F90
M tools/mapping/check_maps/README
M tools/mapping/check_maps/check_map.sh
M tools/mapping/check_maps/src/ESMF_RegridWeightGenCheck.F90
M tools/mapping/check_maps/src/Makefile
M tools/mapping/gen_domain_files/src/.gitignore
M tools/mapping/gen_domain_files/src/Makefile
A tools/mapping/gen_mapping_files/.gitignore
M tools/mapping/gen_mapping_files/README
M tools/mapping/gen_mapping_files/gen_ESMF_mapping_file/.gitignore
M tools/mapping/gen_mapping_files/gen_ESMF_mapping_file/README
M tools/mapping/gen_mapping_files/gen_ESMF_mapping_file/create_ESMF_map.sh
D tools/mapping/gen_mapping_files/gen_ESMF_mapping_file/regridbatch.yellowstone.sh
M tools/mapping/gen_mapping_files/gen_cesm_maps.sh
M tools/mapping/gen_mapping_files/runoff_to_ocn/.gitignore
M tools/mapping/gen_mapping_files/runoff_to_ocn/src/Makefile
M tools/mapping/map_field/.gitignore
M tools/mapping/map_field/README
M tools/mapping/map_field/src/Makefile
M tools/statistical_ensemble_test/README
A tools/statistical_ensemble_test/addmetadata.sh
A tools/statistical_ensemble_test/ensemble.py
A tools/statistical_ensemble_test/pyCECT/.gitignore
A tools/statistical_ensemble_test/pyCECT/EET.py
M tools/statistical_ensemble_test/pyCECT/LICENSE.txt
M tools/statistical_ensemble_test/pyCECT/README_pyCECT.rst
M tools/statistical_ensemble_test/pyCECT/README_pyEnsSum.rst
M tools/statistical_ensemble_test/pyCECT/ens_excluded_varlist.json
A tools/statistical_ensemble_test/pyCECT/ens_sub.pbs
M tools/statistical_ensemble_test/pyCECT/ens_sub.sh
A tools/statistical_ensemble_test/pyCECT/exclude_empty.json
A tools/statistical_ensemble_test/pyCECT/included_varlist.json
M tools/statistical_ensemble_test/pyCECT/pyCECT.py
M tools/statistical_ensemble_test/pyCECT/pyEnsLib.py
M tools/statistical_ensemble_test/pyCECT/pyEnsSum.py
M tools/statistical_ensemble_test/pyCECT/pyEnsSumPop.py
A tools/statistical_ensemble_test/single_run.py
M tools/utils/find_circular_dependency.py
======================================================================
=======
Originator: Chris Fischer
Date: 7-13-2018
Tag: cime5.6.10
Answer Changes: None
Tests: hand test
code_checker on create_newcase; manually checked create_newcase --help
ERS_Ln9.f19_g17.X.hobart_intel , ERS_Ln9.f19_g17.X.hobart_gnu,
ERS_Ln9.f19_g17.X.hobart_nag
Dependencies:
Brief Summary:
- Add scripts/Tools/archive_metadata to CIME for use in CESM cases only.
- Change DIN_LOC_ROOT_CLMFORC for new glade setup on cheyenne.
- Make docs more consistent.
- cprnc compiler updates for hobart.
User interface changes:
- archive_metadata --help stand_alone script.
PR summary: git log --oneline --first-parent [previous_tag]..master
9f4377c Merge pull request #2715 from bertinia/maint-5.6_archive_metadata
ef2f2e4 Merge pull request #2714 from ekluzek/newgladedinlocclmfrc
154b475 Merge pull request #2693 from billsacks/make_docs_more_consistent
631869c Merge pull request #2709 from ESMCI/fischer/hobart_cprnc
Modified files: git diff --name-status [previous_tag]
M config/cesm/machines/config_machines.xml
M doc/source/users_guide/create-a-case.rst
A scripts/Tools/archive_metadata
M scripts/create_newcase
M scripts/lib/CIME/case/case.py
M scripts/lib/CIME/utils.py
======================================================================
======================================================================
Originator: Chris Fiscehr
Date: 7-5-2018
Tag: cime5.6.9
Answer Changes: None
Tests: prealpha on edison, cori-haswell, cori-knl
scripts_regression_tests, ect-uf on bluewaters
Dependencies:
Brief Summary:
- Maint-5.6 nersc update.
- Maint-5.6 hobart update.
- Fix issue with rebuilding csm_share.
- Bluewaters update.
- Edit and cleanup parts of CCS users guide.
- Change -v to --env for theta.
- Fix unittest.
- Tryagain with tput code.
- ww3 data staging fix.
- Fix refcase logiv.
- Add and clarify pieces that describe adding a test to the prebeta testing.
- Archive test refinement.
User interface changes:
- --test becomes --test-all and --test-case is added
PR summary: git log --oneline --first-parent [previous_tag]..master
3ee8b07 Merge pull request #2697 from jedwards4b/maint-5.6-nersc-update
b76c449 Merge pull request #2701 from jedwards4b/maint-5.6-hobart-update
34677a4 Merge pull request #2684 from jedwards4b/improve_shared_build_performance
57c8924 Merge pull request #2675 from jedwards4b/bluewaters_update
3a5281d Merge pull request #2662 from ESMCI/rljacob/doc/ug1-read
f8cc2a7 Merge pull request #2666 from jedwards4b/theta_fix
2e9973f fix unittest
49f59b6 tryagain with tput code
0819198 Merge branch 'ww3_data_staging' into maint-5.6
7478f2f Merge branch 'fix_refcase_logic' into maint-5.6
cd64838 Merge pull request #2647 from ESMCI/fischer/augment_testing_doc
3016427 Merge pull request #2656 from jedwards4b/archive_test_refinement
Modified files: git diff --name-status [previous_tag]
M config/cesm/machines/config_batch.xml
M config/cesm/machines/config_compilers.xml
M config/cesm/machines/config_machines.xml
M config/cesm/machines/template.st_archive
M config/e3sm/machines/template.st_archive
M config/xml_schemas/config_machines.xsd
M config/xml_schemas/testlist.xsd
M doc/source/users_guide/building-a-case.rst
M doc/source/users_guide/cime-change-namelist.rst
A doc/source/users_guide/cime-dir.rst
M doc/source/users_guide/compsets.rst
M doc/source/users_guide/create-a-case.rst
M doc/source/users_guide/index.rst
M doc/source/users_guide/introduction-and-overview.rst
M doc/source/users_guide/pes-threads.rst
M doc/source/users_guide/running-a-case.rst
M doc/source/users_guide/setting-up-a-case.rst
M doc/source/users_guide/testing.rst
M scripts/Tools/Makefile
M scripts/Tools/preview_run
M scripts/lib/CIME/SystemTests/system_tests_common.py
M scripts/lib/CIME/XML/env_batch.py
M scripts/lib/CIME/case/case.py
M scripts/lib/CIME/case/case_st_archive.py
M scripts/lib/CIME/case/case_submit.py
M scripts/lib/CIME/case/check_input_data.py
M scripts/lib/CIME/test_scheduler.py
M scripts/lib/CIME/test_status.py
M scripts/lib/CIME/tests/SystemTests/test_system_tests_compare_two.py
M scripts/tests/scripts_regression_tests.py
M src/build_scripts/buildlib.csm_share
======================================================================
======================================================================
Originator: Chris Fischer
Date: 5-14-2018
Tag: cime5.6.7
Answer Changes: None
Tests: scripts_regression_tests, xmlquery --listall --file env_run.xml
Dependencies:
Brief Summary:
- xmlquery fix.
- Fixes an issue when selecting mpilib on cheyenne.
- Fixed some print format bugs left over from the string rewrite of a year ago.
- Documentation updates, including major updates to --help for scripts.
- Need to append config files.
- Get model_version working.
- Adds T85_T85_mg17 grid.
- Correct spelling of protocol.
User interface changes:
PR summary: git log --oneline --first-parent [previous_tag]..master
5a54b88 Merge pull request #2588 from jedwards4b/xmlquery_fix
0b07cb5 Merge pull request #2591 from jedwards4b/configure_mpilib
5f4c8e4 Merge pull request #2586 from gold2718/pelayout_fixes
6ebcd23 Merge pull request #2585 from ESMCI/mvertens/documentation_updates
940e29c need this to append config files
72a1cf6 Merge pull request #2579 from ekluzek/clm50r1/cime5.6.3
b86853d Merge pull request #2575 from jedwards4b/newgrid
fcebaad Merge pull request #2571 from jedwards4b/misspelling_protocol
Modified files: git diff --name-status [previous_tag]
M config/cesm/config_grids.xml
M config/cesm/config_inputdata.xml
M config/e3sm/config_inputdata.xml
M config/xml_schemas/config_inputdata.xsd
M doc/source/conf.py
M doc/source/users_guide/building-a-case.rst
M doc/source/users_guide/cime-config.rst
M doc/source/users_guide/cloning-a-case.rst
M doc/source/users_guide/porting-cime.rst
M doc/source/users_guide/running-a-case.rst
M doc/source/users_guide/testing.rst
M scripts/Tools/case.build
M scripts/Tools/case.cmpgen_namelists
M scripts/Tools/case.qstatus
M scripts/Tools/case.setup
M scripts/Tools/case.submit
M scripts/Tools/check_case
M scripts/Tools/check_input_data
M scripts/Tools/pelayout
M scripts/Tools/preview_namelists
M scripts/Tools/preview_run
M scripts/Tools/xmlchange
M scripts/Tools/xmlquery
M scripts/create_clone
M scripts/create_newcase
M scripts/create_test
M scripts/lib/CIME/Servers/ftp.py
M scripts/lib/CIME/Servers/gftp.py
M scripts/lib/CIME/Servers/svn.py
M scripts/lib/CIME/Servers/wget.py
M scripts/lib/CIME/XML/generic_xml.py
M scripts/lib/CIME/XML/inputdata.py
M scripts/lib/CIME/case/check_input_data.py
M scripts/lib/CIME/utils.py
M scripts/query_config
M scripts/query_testlists
M src/drivers/mct/cime_config/namelist_definition_drv.xml
M tools/configure
======================================================================
======================================================================
Originator: Chris Fischer
Date: 5-02-2018
Tag: cime5.6.3
Answer Changes: None
Tests:
Dependencies:
Brief Summary:
- Fix config write of logical.
User interface changes:
PR summary: git log --oneline --first-parent [previous_tag]..master
974839b fix config write of logical
Modified files: git diff --name-status [previous_tag]
M scripts/Tools/case.submit
======================================================================
======================================================================
Originator: Chris Fischer
Date: 5-01-2018
Tag: cime5.6.2
Answer Changes: None
Tests: load_balancing_test.py
hand tested create_newcase --case foo --compset QSC6 --res f19_f19_mg17
Dependencies:
Brief Summary:
- Refine distinction of E vs Q compset.
- Update load balance tool.
User interface changes:
PR summary: git log --oneline --first-parent [previous_tag]..master
b2a19cd Merge pull request #2525 from jedwards4b/better_distinguish_compset_Q_from_E
28b8634 Merge pull request #2520 from ESMCI/sarich/update-loadbalancingtool
Modified files: git diff --name-status [previous_tag]
M scripts/lib/CIME/case/case.py
M tools/load_balancing_tool/load_balancing_submit.py
M tools/load_balancing_tool/tests/load_balancing_test.py
======================================================================
======================================================================
Originator: Chris Fischer
Date: 5-01-2018
Tag: cime5.6.1
Answer Changes: None, PR #2195 has roundoff for code not currently used.
Tests: scripts_regression_tests, code_checker, by-hand
Dependencies:
Brief Summary:
- Refine cheyenne retry method.
- Save submit options for resubmit.
- Need schema description for NODE_FAIL_REGEX.
- Use nodefail code for cheyenne.
- Make st_archive handle DART's restart history files.
- Check input logic fix.
- Only check for rundir if not a test.
- Jgfouca/branch for acme split 2018-04-26.
- Correct equations of the form **(1/3) to be **(1.0_R8/3.0_R8) to evaluate correctly.
- Remove debug print statements.
- Revert change to cheyenne mpt.
- Remove manage_testlist.
- Testreporter fix.
- Match entire string for XML attribute selectors for env_mach_specific.
- Fix undefined variable in some circumstances.
- wait_for_tests needs to upload case2 logs if there are some
- Another fix for testreporter.py.
User interface changes:
- manage_testlist was removed.
- Changes to matching behavior in env_mach_specific.
- New option to wait_for_tests.
PR summary: git log --oneline --first-parent [previous_tag]..master
5af0e02 Merge pull request #2516 from jedwards4b/refine_retry
5e8a173 Merge pull request #2518 from jedwards4b/save_submit_options
1d7a27d need schema description for NODE_FAIL_REGEX
879249b Merge pull request #2509 from jedwards4b/cheyenne_nodefail
40cf173 Merge pull request #2491 from kdraeder/dart_rh_files
988eff2 Merge pull request #2501 from jedwards4b/check_input_logic_fix
7ee7a0d Merge pull request #2508 from jedwards4b/test_init_fix
fbe0814 Merge pull request #2505 from ESMCI/jgfouca/branch-for-acme-split-2018-04-26
8977e55 Merge pull request #2195 from jedwards4b/diurnal_atmocn_flux_bugfix
4e489b7 remove debug print statements
438e1f0 revert change to cheyenne mpt
2e0ba3b Merge pull request #2503 from ESMCI/fischer/rm_manage_testlist
cf19590 Merge pull request #2502 from ESMCI/fischer/testreporter_fix
1a7dac9 Merge pull request #2499 from ESMCI/jgfouca/match_entire_string
71be68f Fix undefined variable in some circumstances
6673d6a Merge pull request #2498 from ESMCI/jgfouca/wait_for_tests_case2
8360ddc Merge pull request #2494 from ESMCI/fischer/test_reporter
Modified files: git diff --name-status [previous_tag]
M config/cesm/config_archive.xml
M config/cesm/machines/config_machines.xml
M config/e3sm/allactive/config_compsets.xml
M config/e3sm/allactive/config_pesall.xml
M config/e3sm/config_archive.xml
M config/e3sm/config_files.xml
M config/e3sm/config_grids.xml
M config/e3sm/config_inputdata.xml
M config/e3sm/machines/Depends.titan.pgi
M config/e3sm/machines/config_batch.xml
M config/e3sm/machines/config_compilers.xml
M config/e3sm/machines/config_machines.xml
M config/e3sm/testmods_dirs/allactive/v1cmip6/user_nl_cam
M config/e3sm/tests.py
A config/e3sm/usermods_dirs/README
D config/e3sm/usermods_dirs/b1850/shell_commands
D config/e3sm/usermods_dirs/b1850_cism/include_user_mods
D config/e3sm/usermods_dirs/b1850_cism/user_nl_cism
M config/xml_schemas/config_machines.xsd
M doc/source/users_guide/testing.rst
M scripts/Tools/case.submit
M scripts/Tools/jenkins_generic_job
M scripts/Tools/wait_for_tests
M scripts/lib/CIME/XML/env_batch.py
M scripts/lib/CIME/XML/env_mach_specific.py
M scripts/lib/CIME/XML/test_reporter.py
M scripts/lib/CIME/build.py
M scripts/lib/CIME/case/case_run.py
M scripts/lib/CIME/case/case_st_archive.py
M scripts/lib/CIME/case/case_submit.py
M scripts/lib/CIME/case/check_input_data.py
M scripts/lib/CIME/wait_for_tests.py
M scripts/lib/get_tests.py
D scripts/manage_testlists
M src/drivers/mct/cime_config/config_component.xml
M src/drivers/mct/cime_config/config_component_e3sm.xml
M src/drivers/mct/main/cime_comp_mod.F90
M src/share/util/shr_flux_mod.F90
======================================================================
======================================================================
Originator: Chris Fischer
Date: 4-19-2018
Tag: cime5.6.0
Answer Changes: None
Tests: scripts_regression_tests
Dependencies:
Brief Summary:
- Don't access data servers if no data is needed.
- Add a test of the st_archive capability.
- Improve help message for resubmitting to dash.
- Simple compare improvement.
- Force the NODEFAIL test to run on the cheyenne regular queue.
- Download refcase from servers for hybrid.
- Add a warning if an unsupported testlist.xml is encountered.
- Replace TOTALPES with total_tasks.
- Fix massive misuse of TOTALPES for mpi -np all across e3sm.
- Fix test_scheduler's computation of procs needed for a test.
- Transition CIME to using a custom util for copying files.
- Minor fix to help msgs for options for e3sm mgmt tools.
User interface changes:
- case.st_archive now has a --test option.
PR summary: git log --oneline --first-parent [previous_tag]..master
0cd58a7 Merge pull request #2489 from jedwards4b/nodatanoserver
aeb0f47 Merge pull request #2470 from jedwards4b/st_archive_test
f1c2759 Improve help message for resubmitting to dash
afc640c Merge pull request #2487 from jedwards4b/simple_compare_improvement
9410812 Merge pull request #2486 from jedwards4b/nodefail_fix
d3c73b7 Merge pull request #2481 from jedwards4b/cid_decesm
b0afec2 Merge pull request #2482 from jedwards4b/testlist_format
3874d08 replace TOTALPES with total_tasks
28265be Fix massive misuse of TOTALPES for mpi -np all across e3sm
9344b16 Merge pull request #2479 from ESMCI/jgfouca/fix_test_sched_procs_needed
f48c994 Merge pull request #2475 from ESMCI/jgfouca/safer_copy
adae0ae Minor fix to help msgs for options for e3sm mgmt tools
Modified files: git diff --name-status [previous_tag]
M config/cesm/config_archive.xml
M config/cesm/machines/config_machines.xml
M config/cesm/machines/template.st_archive
M config/e3sm/config_archive.xml
M config/e3sm/machines/config_machines.xml
M config/e3sm/machines/template.st_archive
M config/xml_schemas/config_archive.xsd
M scripts/Tools/e3sm_cime_merge
M scripts/Tools/e3sm_cime_split
M scripts/lib/CIME/BuildTools/configure.py
M scripts/lib/CIME/Servers/ftp.py
M scripts/lib/CIME/Servers/gftp.py
M scripts/lib/CIME/Servers/svn.py
M scripts/lib/CIME/Servers/wget.py
M scripts/lib/CIME/SystemTests/eri.py
M scripts/lib/CIME/SystemTests/err.py
M scripts/lib/CIME/SystemTests/system_tests_common.py
M scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M scripts/lib/CIME/XML/archive.py
A scripts/lib/CIME/XML/archive_base.py
M scripts/lib/CIME/XML/env_archive.py
M scripts/lib/CIME/XML/env_batch.py
M scripts/lib/CIME/XML/generic_xml.py
M scripts/lib/CIME/XML/testlist.py
M scripts/lib/CIME/build.py
M scripts/lib/CIME/case/case.py
M scripts/lib/CIME/case/case_clone.py
M scripts/lib/CIME/case/case_cmpgen_namelists.py
M scripts/lib/CIME/case/case_run.py
M scripts/lib/CIME/case/case_setup.py
M scripts/lib/CIME/case/case_st_archive.py
M scripts/lib/CIME/case/check_input_data.py
M scripts/lib/CIME/case/preview_namelists.py
M scripts/lib/CIME/get_timing.py
M scripts/lib/CIME/hist_utils.py
M scripts/lib/CIME/locked_files.py
M scripts/lib/CIME/simple_compare.py
M scripts/lib/CIME/test_scheduler.py
M scripts/lib/CIME/user_mod_support.py
M scripts/lib/CIME/utils.py
M scripts/lib/CIME/wait_for_tests.py
M scripts/lib/jenkins_generic_job.py
M scripts/tests/scripts_regression_tests.py
M src/drivers/mct/cime_config/config_archive.xml
M src/drivers/mct/cime_config/namelist_definition_drv.xml
======================================================================
======================================================================
Originator: Chris Fischer
Date: 4-17-2018
Tag: cime5.4.0-alpha.30
Answer Changes: None
Tests: scripts_regression_tests, code checker
Dependencies:
Brief Summary:
- Change the CESM inputdata server precedence order to gridftp, svn, ftp, wget.
- Fix totalpes to properly include threads.
- Refactor BUILD_THREADED case value.
User interface changes:
- New FORCE_BUILD_THREADED.
PR summary: git log --oneline --first-parent [previous_tag]..master
9af0120 Merge pull request #2477 from ESMCI/fischer/gftp_svn_ftp
d556876 Merge pull request #2465 from jedwards4b/fix_totalpes
ed78b14 Merge pull request #2466 from ESMCI/jgfouca/refactor_build_threaded
Modified files: git diff --name-status [previous_tag]
M config/cesm/config_inputdata.xml
M config/cesm/machines/config_batch.xml
M config/config_tests.xml
M scripts/Tools/Makefile
M scripts/create_test
M scripts/fortran_unit_testing/run_tests.py
M scripts/lib/CIME/case/case.py
M scripts/lib/CIME/case/case_setup.py
M scripts/lib/CIME/hist_utils.py
M scripts/lib/CIME/test_utils.py
M scripts/manage_pes
M scripts/manage_testlists
M scripts/tests/scripts_regression_tests.py
M src/build_scripts/buildlib.gptl
M src/build_scripts/buildlib.pio
M src/drivers/mct/cime_config/config_component.xml
======================================================================
======================================================================
Originator: Chris Fischer
Date: 4-13-2018
Tag: cime5.4.0-alpha.29
Answer Changes: None
Tests: scripts_regression_tests
code_checker, testing by hand
Dependencies:
Brief Summary:
- Fix variable initialization.
- Add model doi url to seq_infodata and to cpl history global attributes.
- Remove the LOGDIR variable and stop copying logs back to the case directory.
- Fix env_mach_specific.sh file when module init is None.
- Support renamed glimmer-cism directory; add README files to SourceMods directories.
- Add f10_f10_mg37 grid.
- Update casename restrictions.
- Update statistical ensemble test for new verison of CESM.
- Add PEM test to cime developer.
- Add inputdata servers for grid ftp, ftp, and wget.
- Use --no-logging in call to checkout_externals.
- Add support for stampede2-skx and stampede2-knl at TACC.
- split_test_py
- Merge commit '20e3277dd143e4058ffa0ef610180c199cbb6ea1'
- E3SM split.
- PEA and PEM need to call case_setup for case2.
- Revert small piece of #2299.
- Fixes the potential leak reported by address sanitizer in PIO.
- Reorganize Users Guide part 1 and 2 content.
User interface changes:
PR summary: git log --oneline --first-parent [previous_tag]..master
057e8a5 fix variable initialization
4913315 Merge pull request #2468 from ESMCI/mvertens/model_doi_url
37985f4 Merge pull request #2461 from jedwards4b/remove_logdir
f1f498f Merge pull request #2464 from ESMCI/jgfouca/never_source_none
b16ec34 Merge pull request #2462 from billsacks/rename_glimmer_cism_v2
0cead4e Merge pull request #2463 from ESMCI/fischer/f10_f10_mg37
08e05e2 Merge pull request #2460 from jedwards4b/update_casename_restrictions
578a7ab Merge pull request #2447 from allibco/master
356cec0 Merge pull request #2449 from ESMCI/jgfouca/add_pem_test_to_cimedev
a1d7814 Merge pull request #2439 from jedwards4b/addgridftp
0126382 Merge pull request #2444 from billsacks/manic_no_logging
dd58d01 Merge pull request #2440 from ESMCI/fischer/stampede2
9febe47 Merge branch 'jgfouca/split_test_py'
35a70fc Merge commit '20e3277dd143e4058ffa0ef610180c199cbb6ea1'
b06a755 Merge pull request #2433 from ESMCI/jgfouca/branch-for-acme-split-2018-04-09
f18bc36 Merge pull request #2437 from jedwards4b/fixpeaandpem
826c8ec Merge pull request #2434 from ESMCI/jgfouca/minor_seq_comm_mct_revert
35ce6f1 Merge pull request #2432 from ESMCI/mfdeakin-sandia/fix_pio_reported_leak
67088a3 Merge pull request #2407 from ESMCI/rljacob/docs/reorg-ug
Modified files: git diff --name-status [previous_tag]
M config/cesm/config_grids.xml
M config/cesm/config_inputdata.xml
M config/cesm/machines/config_batch.xml
M config/cesm/machines/config_compilers.xml
M config/cesm/machines/config_machines.xml
M config/e3sm/allactive/config_compsets.xml
M config/e3sm/allactive/config_pesall.xml
M config/e3sm/config_archive.xml
M config/e3sm/config_files.xml
A config/e3sm/machines/Depends.summit.ibm
A config/e3sm/machines/Depends.theta.intel
M config/e3sm/machines/config_batch.xml
M config/e3sm/machines/config_compilers.xml
M config/e3sm/machines/config_machines.xml
D config/e3sm/testmods_dirs/allactive/cam/cosplite/user_nl_cam
D config/e3sm/testmods_dirs/allactive/cam/cosplite/xmlchange_cmnds
D config/e3sm/testmods_dirs/allactive/cam/cosplite_nhtfrq5/user_nl_cam
D config/e3sm/testmods_dirs/allactive/cam/cosplite_nhtfrq5/xmlchange_cmnds
D config/e3sm/testmods_dirs/allactive/cam/outfrq9s/user_nl_cam
D config/e3sm/testmods_dirs/allactive/cam/outfrq9s/user_nl_clm
D config/e3sm/testmods_dirs/allactive/cam/outfrq9s/xmlchange_cmnds
D config/e3sm/testmods_dirs/allactive/cam/rtm_null/xmlchange_cmnds
D config/e3sm/testmods_dirs/allactive/clm/betr/xmlchange_cmnds
D config/e3sm/testmods_dirs/allactive/clm/bgcexp/user_nl_clm
D config/e3sm/testmods_dirs/allactive/clm/bgcexp/xmlchange_cmnds
D config/e3sm/testmods_dirs/allactive/clm/bgcinterface/user_nl_clm
D config/e3sm/testmods_dirs/allactive/clm/eca/user_nl_clm
D config/e3sm/testmods_dirs/allactive/clm/fates/user_nl_clm
D config/e3sm/testmods_dirs/allactive/clm/rd/user_nl_clm
D config/e3sm/testmods_dirs/allactive/clm/vst/user_nl_clm
D config/e3sm/testmods_dirs/allactive/drv/y100k
D config/e3sm/testmods_dirs/allactive/force_netcdf_pio/xmlchange_cmnds
A config/e3sm/testmods_dirs/allactive/v1cmip6/shell_commands
D config/e3sm/testmods_dirs/allactive/v1cmip6/xmlchange_cmnds
A config/e3sm/tests.py
M config/xml_schemas/config_inputdata.xsd
M doc/source/index.rst
D doc/source/users_guide/adding-cases.rst
D doc/source/users_guide/case-basics.rst
A doc/source/users_guide/cime-config.rst
M doc/source/users_guide/cime-internals.rst
A doc/source/users_guide/compsets.rst
M doc/source/users_guide/create-a-case.rst
D doc/source/users_guide/creating-new-compsets.rst
D doc/source/users_guide/customizing-a-case.rst
A doc/source/users_guide/grids.rst
M doc/source/users_guide/index.rst
A doc/source/users_guide/machine.rst
D doc/source/users_guide/optimizing-processor-layout.rst
A doc/source/users_guide/pes-threads.rst
M doc/source/users_guide/porting-cime.rst
M doc/source/users_guide/running-a-case.rst
M doc/source/users_guide/testing.rst
A doc/source/users_guide/timers.rst
M doc/source/users_guide/use_cases/basics-a-basic-example.rst
D doc/source/users_guide/use_cases/basics-mpi-example.rst
A doc/source/users_guide/use_cases/cesm-nml.rst
A doc/source/users_guide/use_cases/datamod-nml.rst
A doc/source/users_guide/use_cases/driver-nml.rst
A doc/source/users_guide/use_cases/namelist-gen.rst
M doc/source/users_guide/use_cases/use-cases.rst
M scripts/Tools/Makefile
M scripts/Tools/list_e3sm_tests
D scripts/Tools/update_e3sm_tests
M scripts/create_test
M scripts/lib/CIME/Servers/__init__.py
M scripts/lib/CIME/Servers/ftp.py
A scripts/lib/CIME/Servers/gftp.py
M scripts/lib/CIME/SystemTests/pea.py
M scripts/lib/CIME/SystemTests/pem.py
M scripts/lib/CIME/XML/env_mach_specific.py
M scripts/lib/CIME/build.py
M scripts/lib/CIME/case/case.py
M scripts/lib/CIME/case/case_clone.py
M scripts/lib/CIME/case/case_run.py
M scripts/lib/CIME/case/check_input_data.py
M scripts/lib/CIME/hist_utils.py
M scripts/lib/CIME/provenance.py
M scripts/lib/CIME/test_scheduler.py
M scripts/lib/CIME/utils.py
A scripts/lib/get_tests.py
D scripts/lib/update_e3sm_tests.py
M scripts/tests/scripts_regression_tests.py
M src/drivers/mct/cime_config/config_component.xml
M src/drivers/mct/cime_config/config_component_cesm.xml
M src/drivers/mct/cime_config/config_component_e3sm.xml
M src/drivers/mct/cime_config/namelist_definition_drv.xml
M src/drivers/mct/main/seq_hist_mod.F90
M src/drivers/mct/main/seq_io_mod.F90
M src/drivers/mct/shr/seq_comm_mct.F90
M src/drivers/mct/shr/seq_infodata_mod.F90
M src/externals/pio1/pio/piodarray.F90.in
M src/share/timing/ChangeLog
M src/share/timing/gptl.h
M src/share/timing/private.h
M tools/statistical_ensemble_test/README
M tools/statistical_ensemble_test/ensemble.sh
M tools/statistical_ensemble_test/single_run.sh
======================================================================
======================================================================
Originator: Chris Fischer
Date: 4-06-2018
Tag: cime5.4.0-alpha.28
Answer Changes: None
Tests: ERI.f09_g17.B1850.cheyenne_intel.allactive-defaultio
scripts_regression_tests.py
code_checker
Dependencies:
Brief Summary:
- py3 fix
- Fix for ERI test.
- More fixes for archiver and tests.
- cime_bisect improvements.
- ERS and ERI tests need skip_pnl=False.
- More fixes related to cesm testing.
- CESM test fixes.
- Refactor crucial run_sub_or_cmd method.
- Restore shell batch capability.
User interface changes:
- New custom script option.
PR summary: git log --oneline --first-parent [previous_tag]..master
35fd3d1 py3 fix
6c6d3b5 Merge pull request #2429 from jedwards4b/eri_fix
83ef1ba Merge pull request #2426 from jedwards4b/archiver_and_test_fixes
58f020d Merge pull request #2425 from ESMCI/jgfouca/cime_bisect_improvements
3c3fdeb Merge pull request #2424 from jedwards4b/cesm_sta_fixes
603d5da Merge pull request #2423 from jedwards4b/cesm_sta_fixes
fc83e87 Merge pull request #2422 from jedwards4b/cesm_sta_fixes
7602f4b Merge pull request #2420 from ESMCI/jgfouca/refactor_run_sub_or_cmd
d9e3cdf Merge pull request #2419 from ESMCI/jgfouca/restore_shell_batch
Modified files: git diff --name-status [previous_tag]
M config/cesm/config_archive.xml
M scripts/Tools/cime_bisect
M scripts/Tools/mkSrcfiles
M scripts/lib/CIME/SystemTests/eri.py
M scripts/lib/CIME/SystemTests/erp.py
M scripts/lib/CIME/SystemTests/ers.py
M scripts/lib/CIME/SystemTests/irt.py
M scripts/lib/CIME/SystemTests/nck.py
M scripts/lib/CIME/SystemTests/seq.py
M scripts/lib/CIME/SystemTests/system_tests_common.py
M scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M scripts/lib/CIME/XML/env_batch.py
M scripts/lib/CIME/build.py
M scripts/lib/CIME/case/case_run.py
M scripts/lib/CIME/case/case_setup.py
M scripts/lib/CIME/case/case_st_archive.py
M scripts/lib/CIME/test_scheduler.py
M scripts/lib/CIME/utils.py
M src/drivers/mct/cime_config/config_archive.xml
M src/share/util/shr_scam_mod.F90
======================================================================
======================================================================
Originator: Chris Fischer
Date: 4-03-2018
Tag: cime5.4.0-alpha.27
Answer Changes: None
Tests:
Dependencies:
Brief Summary:
- Avoid encode error.
User interface changes:
PR summary: git log --oneline --first-parent [previous_tag]..master
018c8e9 avoid encode error
Modified files: git diff --name-status [previous_tag]
M scripts/lib/CIME/test_scheduler.py
======================================================================
======================================================================
Originator: Chris Fischer
Date: 4-02-2018
Tag: cime5.4.0-alpha.26
Answer Changes: None
Tests: scripts_regression_tests
high-res couple runs on Theta and Cori-KNL
./create_test cime_developer on hobart
hand testing
e3sm_developer
code_checker
Dependencies:
Brief Summary:
- Remove the run_e3sm testing scripts from the CIME repo.
- Fix pylint
- Update hobart queue limits.
- Allow env vars to be unresolved.
- Add mosart restart history to archive list.
- Improve cprnc build.
- External script handling.
- Update MPI message tags in coupler-component exchanges.
- Always downscale walltime for tests.
- st_archive the DART restart history files.
- Do not make unnecessary env_batch jobs or batch job scripts.
- Add unofficial support for shell version of case.run batch script.
- Remove test mod from cime_developer PET test.
- Only set and check glcrun_avg_alarm if glc_prognostic is true.
- Branch for acme split 2018-03-27.
- Allow case_diff to work on cases that are not tests.
- Locals method did not work in py3, using getattr instead works in both.
- env_mach_specific was coded to always try to combine module operations.
Instead, it should only do that for "module" module systems.
- Rearrange case subdirectory.
- Remove text 'ccsm' and 'cesm' and replace appropriately.
- Add comment.
- Permit IOErrors as well as OSErrors when trying to copy crpnc log.
- Update MCT to 2.10rc2.
- Make case tools part of the Case object.
- Cleanup acme -> e3sm references in rst documentation.
- Add an A and X compset test to aux_cime_baselines.
- Compare two case setup.
- Remove old pointclm directory.
- Update key concepts documentation.
- Fix skip-pnl for tests.
- Order e3sm test list by runtime.
- Update to newer version of cprnc on hobart.
- Support full matching restrictions for batch directives.
- Ignore files beginning in test_.
- More updates to e3sm cime mgmt.
- Rename and reorg upper level contents.
- Move example of query_config to introduction.
- Add switch to list of module actions that cannot be batched.
- Improve create_test error message.
- Allow custom batch directive prefixes.
- Provide infrastructure to allow single column model to run with SE dycore.
- Branch for acme split 2018-03-13.
- Add better output to cime mgmt tool.
- Add stack size modifier to hobart.
- Add ability to xmlquery derived attributes.
- Modify regex for hobart to work on compute nodes.
- Make sure to clean repo before doing cime updates.
- st archive/encapsulate datetime.
- lawrencium machine cesm entries.
- Add a CONTRIBUTING file welcoming contributions and giving some brief guidance.
- Documentation updates for user customization.
- Fix XML errors in config_archive for E3SM.
- Implement improvements to st_archive regular expressions.
- Remove the run_e3sm testing scripts from the CIME repo.
User interface changes:
- env_archive.xml
- .case.run.sh file generated for E3SM.
- New selectors allowed for batch directives.
- Source code files beginning in test_ will be ignored in build.
- New prefix attribute available for batch directives.
- xmlquery will now accept derived attributes.
- Users may run on lawrencium lr3/lr2.
- In env_archive.xml.
PR summary: git log --oneline --first-parent [previous_tag]..master
de9dc73 Merge pull request #2418 from ESMCI/mfdeakin-sandia/rm_run_e3sm_testing
e9e89bc Fix pylint
150db63 Merge pull request #2362 from mnlevy1981/cesm/hobart_updates
bf467f3 Merge pull request #2412 from jedwards4b/allow_unresolved_envvars
6605d4d add mosart restart history to archive list
6652100 Merge pull request #2417 from jedwards4b/cprnc_build
ed4130b Merge pull request #2413 from jedwards4b/external_script_handling
020fd34 Merge pull request #2397 from ESMCI/azamat/update-msgtag-in-cpl-comp-exchanges
43bfaef Merge pull request #2410 from ESMCI/jgfouca/downscale_walltime_force_queue
8799abc Merge pull request #2415 from kdraeder/dart_rest_hist
7d9c9c5 Merge pull request #2405 from ESMCI/jgfouca/cleanup_envbatch_and_batch_scripts
74696ed Merge pull request #2386 from ESMCI/jgfouca/e3sm_bash_batch
5539ece Remove test mod from cime_developer PET test
39fd78e Merge pull request #2404 from billsacks/glcrun_avg_alarm
356fda0 Merge pull request #2406 from ESMCI/jgfouca/branch-for-acme-split-2018-03-27
19675f9 Merge pull request #2398 from ESMCI/jgfouca/fix_case_diff_newcase