update modules and PE layouts for cori-knl and cori-haswell #1222
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Go ahead and merge this to next. |
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I tried, but I got: |
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@ndkeen you lost the race; you'll need to reset --hard to origin/next and re-try the merge. |
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and to be sure, a "git fetch" before the "git reset --hard origin/next" |
ndkeen
added a commit
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Jan 17, 2017
Update modules and PE layouts for cori (haswell and KNL) Does not pass all of the acme_developer tests yet.
ndkeen
added a commit
that referenced
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Jan 21, 2017
A few additional changes to getting Cori (haswell and KNL nodes) to work. Not all of the tests pass yet.
rljacob
pushed a commit
that referenced
this pull request
Feb 27, 2017
A few additional changes to getting Cori (haswell and KNL nodes) to work. Not all of the tests pass yet.
rljacob
added a commit
that referenced
this pull request
Mar 7, 2017
215e459 Merge pull request #1182 from jedwards4b/config_archive_split
441136f fix pylint problems
46e7d99 Revert "Revert "add --mpilib option to create_test"" Not sure how the first revert got there This reverts commit 6bb7d0b3492e6fa3ed3ff24bb29badc3e0bf6583.
33dcf97 break up config_archive into component specific files
6bb7d0b Revert "add --mpilib option to create_test"
9f45612 Update ChangeLog
fd200f6 Merge pull request #1181 from ESMCI/agsalin/add_S_case_test
d33e6a2 Merge pull request #1180 from jedwards4b/create_test_mpilib_option
d210e0b Merge pull request #1159 from bertinia/master
dc74164 Add S-case test to cime_developers
5efd5b7 update to resolve problem with merge and PR #1159
9d25fcf Merge branch 'bertinia-master' Fix for conflict with ESMCI master and PR #1159
9ac175a Merge branch 'master' of https://github.com/ESMCI/cime into bertinia-master
42acfd4 add --mpilib option to create_test
ad5ff79 Merge pull request #1172 from ESMCI/mvertens/pop_python_namelist
4ab605f Merge pull request #1177 from jedwards4b/pio1_bld_fixes
2f1b3b8 make sure pio1 finds netcdf4
9c2a499 Tweak ChangeLog text
933b92e Update ChangeLog for cime5.2.0-alpha.25
bac0ce7 Merge pull request #1174 from jedwards4b/compiler_backout
cc6a1c2 back out pgi and gnu compilers on yellowstone
cf6e97f revert intel compiler change on yellowstone
646cc2f Update ChangeLog for cime5.2.0-alpha.24
980a6b8 Merge pull request #1167 from fischer-ncar/drip_annual_changes_test_fix
4d88e2a Add for_testing_allow_non_annual_changes = .true. to fix a testing issue with clm. Also remove SMS_D.f09_g16.B1850.yellowstone_intel since we also have a ERS_D.f09_g16.B1850.yellowstone_intel test.
c452564 updating
3e3a73f Revert "update case_lt_archive python implimentation"
e8929e2 Merge pull request #1165 from ESMCI/jayeshkrishna/cond_incl_make_undefine
fac6377 Conditionally use undefine in Makefile for backward compatibility
9554cce Merge pull request #1160 from jedwards4b/get_timing_correction
642cc32 Merge pull request #1164 from billsacks/unit_tests_local
b657cd0 Bring back setting of -D<env>OS</env>
89354ea add back whitespace, improve case.build output
143972d update case_lt_archive python implimentation
a886a17 Changes needed to get unit tests to build on my Mac
efcdb3d remove cam version requirement from ccsm_bgc setting
1f7694c Nothing to do is a dumb thing to write
e630446 more timing file fixes
b19a1de Merge remote-tracking branch 'upstream/master'
d8e92cb remove cime_config/cesm/allactive from CIME and replace it with an external
d3262cb correction to get_timing output, updates for cheyenne and yellowstone
938e9b0 Merge pull request #1157 from billsacks/unit_test_parallel
3929369 Merge pull request #1149 from jedwards4b/correct_path_query_for_testlistxml
9b1630f Merge pull request #1152 from jedwards4b/pio_bld_fix
f3cb2ac Updating master
032f57a change from allactive to drv testlist for testing
db95da1 Merge pull request #1151 from ESMCI/agsalin/gitignore
20d7e17 Build unit tests in debug mode by default
eafcfe1 Get circle_area CTest-based test passing
06f81c7 Enable parallel builds of the unit tests, controlled by --make-j argument.
88a3b27 Change recommended unit testing command to be shell independent
c447cc2 pass correct args to cmake
2394b9e replace hard coded path with query of config_files.xml
b19c3b5 replace hard coded path with query of config_files.xml
43040e0 gitignore: add buildnmlc
c80c65c Merge pull request #1145 from billsacks/unit_test_cleanup
bdd9518 Suggest creating a temporary directory for the unit test build
4746c74 Change build-type default back to CESM_DEBUG rather than CIME_DEBUG
2821dd5 Bring back a commented-out line in the circle_area CMakeLists.txt
4f2ec39 Add comment
e8d8c67 fix pylint issue
cd50668 changes to get pop namelists working with user_nl_pop changes
7ef40c0 Merge pull request #1140 from jedwards4b/cleanbld_refactor
1497e80 fix issues with tests
fa5ed4c update README.unit_testing;
00b7038 revert to rmtree for clean-all option
3782eb0 response to review
4a5076c get clean working for tests
b610338 refactor clean bld
bd3fc66 Merge pull request #1135 from jedwards4b/unit_test_refactor
a731c7e Tweak the pylint fixes for plot_gradient
534aade Merge branch 'jgfouca/allow_arbitrary_batch_args' (PR #1137)
5c88b36 No longer need to specify PAPI_LIB - this must be picked up implicitly now
fb1707e Merge remote-tracking branch 'jedwards4b/unit_test_refactor' into unit_test_refactor
9ed4097 better cleanup after testing
f06f9bc cleanup after testing
9394134 fix cime unit tests, all tests now pass on yellowstone
d4f0b39 use correct word
df34102 Document that --use-openmp is now needed
85931b7 Fix documentation to refer to CIME_utils rather than CESM_utils
2064822 Rename CMAKE_MODULE_DIRECTORY to CIME_CMAKE_MODULE_DIRECTORY
d0a1616 Merge pull request #1136 from ESMCI/jgfouca/handle_batch_errors_better
69ed15e Add support to case.submit for sending arbitrary arguments to the batch submission cmd
9a1f703 Better handling of exceptions in batch code
a867fb3 fix pio1 build
15f0257 more cleanup
342659a still working on tests
6d1e898 cleanup pylint issues
0021f0a add unit_test tool test to scripts_regression_tests.py
04ae9f2 some tests are working now
f5c6476 just commit to rebase
732547f use pio2 cmake tools
5c2dd68 update toplevel CMakeList
766552a getting close
f725e31 baby steps
00f113e begin to refactor
26cd982 Merge pull request #1131 from bertinia/master
26dd1e2 Merge pull request #1126 from ESMCI/jgfouca/bless_test_update
98c0ff1 Merge pull request #1127 from ESMCI/jgfouca/namelist_allow_star
b47ccce Fix config_archive.xml and case_st_archive.py
a51fb8c Merge pull request #1128 from ESMCI/jgfouca/xmlquery_partial_match
505410b Changes based on reviews
253a3a0 xmlquery: allow partial match of variable name
02df5c4 Allow star to appear in namelists
77cf83e Merge branch 'worleyph/timing/non-null-terminated_string_support_fix' into master (PR #895)
b10ffcb Update to bless_test_results
21ea438 Merge pull request #1122 from gold2718/DAEfix
7248aef Merge branch 'jgfouca/acme5.1_to_esmci_try2' (PR #1123)
bf458af Sync up with old jgfouca/5.1_integration
4cd5a94 Merge branch 'maint-cime5.1' into jgfouca/acme5.1_to_esmci_try2
3ad0cf6 Merge branch 'rljacob/split-cime51-5' into maint-cime5.1
62116a2 Added more re-run cleanup to set CONTINUE_RUN back to FALSE.
69627c8 Hotfix for minor whitespace issue in exception text
2456b56 Merge pull request #1110 from ESMCI/jgfouca/fixes_to_recent_new_tests
18734f3 Merge pull request #1104 from jedwards4b/tested_msg
95386c9 change message wording
64aea96 Disable PRE.f19_f19.ADESP test, it's far too expension
23b2ef4 Couple fixes to recent PR.
11e30d6 Merge pull request #1109 from gold2718/TimeMgrFix
e84d7f2 Restore interfaces used by active components
67fd4aa change from ERROR to STOP
e367fb4 Merge pull request #1098 from ESMCI/mfdeakin-sandia/map_field_build
8d110fd Merge branch 'mfdeakin-sandia/map_field_build' of github.com:ESMCI/cime into mfdeakin-sandia/map_field_build
277a3c5 update INSTALL doc
b1af290 Merge branch 'mfdeakin-sandia/map_field_build' of github.com:ESMCI/cime into mfdeakin-sandia/map_field_build
68d1d91 Fix typo in config_machines.xml and it's associated entry in config_compilers.xml
a499612 update Makefiles to match config_compilers change
825e43e autofind CIME_MODEL, fix issue with CPPDEFS
ff4f207 Merge pull request #1095 from gold2718/DAdesp
81fd416 Clean directory before running to avoid issues with multiple run calls.
aa1c548 Changes requested in PR review
cdbd4ce only count tests in prealpha prebeta or aux_* categories
a93184d Merge pull request #1097 from jedwards4b/tie_timers_to_xml
86c0bf2 Merge branch 'mfdeakin-sandia/map_field_build' of github.com:ESMCI/cime into mfdeakin-sandia/map_field_build
a63600d Move 'CPPDEFS += -DLINUX' from the Makefile to <compilers OS='LINUX'> block so that it's a part of Macros.make
f91bf1d Attempt at fixing Macros.make for building map_field
0816471 update netcdf on cheyenne
e0bb5f6 fix typo in xml
7f61116 change args to match
e8404fd update create_newcase --mach to --machine to match create_test
86bb24a reconnect timer level and depth to xml variables
9e20e45 Merge branch 'DAdesp' of github.com:gold2718/cime into DAdesp Forgot to pull changes from repo
0fb525c Addressed most PR comments by @jedwards4b
618f515 Merge pull request #1092 from mgduda/esmf_timemgr/i8_interval_division
654504c Merge pull request #1094 from ESMCI/jgfouca/err_resub_fix
167a7ca pylint comment change for pelayout
6ebb452 ERR XML settings need CONTINUE_RUN=FALSE
5a92de2 Fix pylint issues
025a9d9 Create data ESP component and add pause/resume to driver Create DESP model and test compset (ADESP) Added PAUSE options to driver XML Removed unused public interfaces: public :: seq_timemgr_restartAlarmSetOff ! Turn off restart alarm public :: seq_timemgr_runAlarmSetOff ! Turn off run alarm public :: seq_timemgr_historyAlarmSetOff ! Turn off history alarm public :: seq_timemgr_stopAlarmIsOn ! Is a stop alarm ringing public :: seq_timemgr_runAlarmIsOn ! Is a run alarm ringing public :: seq_timemgr_historyAlarmIsOn ! Is a history alarm ringing Replace CASE with TEST in testname documentation for create_test Cleanup error output for adding timers Added new test, PRE, to test pause/resume
0c6398f Merge branch 'mfdeakin-sandia/map_field_build' of github.com:ESMCI/cime into mfdeakin-sandia/map_field_build
03822a9 Move 'CPPDEFS += -DLINUX' from the Makefile to <compilers OS='LINUX'> block so that it's a part of Macros.make
8f3c188 Attempt at fixing Macros.make for building map_field
fc7e808 Move 'CPPDEFS += -DLINUX' from the Makefile to <compilers OS='LINUX'> block so that it's a part of Macros.make
1472b8d Add homme.log to TestStatus.log for HOMME test
f56a446 Merge pull request #1090 from jedwards4b/lt_archive_issues
656670e Add ESMF_TimeIntervalProdI8 routine to multiply a time interval by an 8-byte int
c9bcfe4 fix issues with lt_archive
ccd1e96 Merge pull request #1082 from jedwards4b/addback_mask_grid
81f08e1 Merge pull request #1081 from jedwards4b/fix_no_nesting_fail
efd958d add back the mask grid dropped in v2 but used by components
ccd67d9 fix expect statement for directive nesting error
1d083cc fix pylint issue
9e2764c Merge pull request #1080 from jedwards4b/config_compilers_conformity
1be8831 revert to $ENV style in config_compilers
59ab0ca remove incorrect comment
c92ce35 add tests for new syntax
79fbb8b fix regression tests
e13ffae update config_compilers to use $ENV{} $SHELL{} and ${} syntax
b559f27 Cleanup config_grids.xml to remove duplicate entries and fix discrepancies.
ccb7c22 Revert "Change over acme env usage to correct syntax"
ce2dbab Merge pull request #1077 from jedwards4b/update_changelog
8175e43 updates to template and ChangeLog
09da9a2 fix documentation error
6dfa124 Attempt at fixing Macros.make for building map_field
7ee5f68 update changelog
feb28f3 Merge pull request #1076 from ESMCI/mvertens/fix_clm_usrdat
853da02 Merge pull request #1069 from jtruesdal/cime_plus_defs
3fb0130 fixed #1075
38cc009 Merge pull request #1068 from jedwards4b/test_fixes
dd32465 updating pop defaults for cesm
077100f update cime_developer tests to catch this problem
0e0cde9 refactor tests to catch this problem
c088e09 fix names in lock
7318d40 backout machines changes for testing, will move to seperate PR
bbd8ba7 restore filenames reversed
d179cac fix for ers and err, cp env_mach_pes for pfs, no sharedlibroot for single test
3d0965a Merge pull request #1062 from ESMCI/mvertens/tfreeze_option
834ed3e made the input namelist variable tfreeze_option either acme or cesm settable in terms of defaults
f0d4fe6 Merge branch 'jonbob/mpas/new_mpas_grids_V3' (PR #1240)
19a104d Change over acme env usage to correct syntax
29aac9b Merge branch 'yinghuilu/cice/fix952' (PR #1196)
8d92fa0 Merge pull request #1048 from jedwards4b/depends_file_precidence
1e3008f Merge pull request #1054 from ESMCI/jgfouca/fix_eri_resub
5de3b4d Merge pull request #1055 from ESMCI/jgfouca/add_support_for_shell_in_XML
dfc7cdf add f19_g16_r01 grid
4d144d7 Add access to shell in XML files
a532692 Fix ERI resubmission
19cca33 Script changes to support new MPAS v3 grids.
a32a28c remove duplicate in config_grids.xml
9321f45 Merge branch 'azamat/mira/default-pio-stride' (PR #1242)
e94ae3c Fix PIO stride at Mira+Cetus to 128 to avoid OOM errors
f659d2d Merge branch 'azamat/machfiles/homme-on-anvil' (PR #1119)
c46e8f0 Merge branch 'ACME-Climate/jgfouca/cime/perf_data_fixes' (PR #1201)
441aba9 Change depends file precidence
c11093d Update Blues and Anvil machine files for HOMME
18479ce Merge pull request #1039 from ESMCI/jgfouca/lock_env_batch
3a84a6e Merge pull request #1046 from jedwards4b/some_log_issues
49b1e4a Update ACME batch configs, do not lock env_batch.xml
d4a6945 add test case directory to log info output
2d4dfb1 add create_test command line to README.case
0489798 Fix Z_FullSystemTests on batch machines
3dba187 Update Anvil Intel compiler to v17
20f5614 Lock env_mach.xml file
742c8dc Merge pull request #1036 from ESMCI/jgfouca/fix_resubmission_of_some_testcases
49a7de6 fix pylint issue
7c3edd9 Merge branch 'azamat/anvil/improve-defaults' (PR #1225)
03948a3 Update defaults
2a2fc7f rename corip1 as cori-haswell and cori-knl
2a1d924 Merge branch 'azamat/cetus/fix-runjob-settings' (PR #1229)
d7b370a Update default PEs on Cetus
b3ca367 When all PEs fit in one node, request at least one node
b572ed4 Make Cetus build settings identical as Mira's
d20cfd1 Fix pylint warning
23072b4 Fix syslog_jobid path name
3062ea4 Better solution for getting the jobid into slurm output files
85cd34f Revert "Add timestamp to output_error_path"
5211b4d Add timestamp to output_error_path
167c8c1 Change gzip utility function to preserve timestamps of original file
c47bf26 Address additional feedback for PR.
c592938 Fixes based on review
1aa8242 Fixes to provenance/timing saving
aa5b443 Merge branch 'ndk/machinefiles/cori-haswell-knl' (PR #1222)
3e5e93d Fix submission of ERS and ERR tests.
289e39e Merge pull request #1034 from ESMCI/jgfouca/better_support_for_custom_input_files
a0796d8 Only flag an error if they try to download the file
4b2c22b check_input_data: better support for custom input files
869f904 Merge pull request #1025 from ESMCI/jgfouca/more_create_test_force_pecount_chgs
df10e41 Minor changes.
25de83b update ChangeLog
b344d31 Minor adjustments to calculations of cores_per_task
5b52add remove flag from cori PBS
33d74c3 Merge pull request #1030 from jedwards4b/fix_drive_namelist_issue
83a388d fix drv namelist issue
9f707da update ChangeLog
4309786 Simplify library paths
cf59a6b Adjustments to TOTAL_CORES and cores_per_task
281625a Merge pull request #1028 from jedwards4b/science_support_field
924f00d Changes to allow for the HOMME test to pass for cori-haswell and cori-knl. Add "module load zlib" and use this library. Add custom srun flags temporarily Remove old corip1 config file
8f50f07 fix typos
fce60ef add science_support field to xml
3fff2cc Adding default F-case PE layouts for Anvil
1aef6ab fix issue in create_newcase
82bcfc3 add science_support field
476f87a Fixes non-BFB issue with F-compsets when threading is used
63b6046 Refactor implementation of forcing procs/threads in create_test
5b97dc5 Make Mira and Cetus Depends files identical
efc4c2a Merge pull request #1024 from jedwards4b/create_clone_cime_output_root
d0fc04c add cime-output-root option to create_clone
7a64201 Merge pull request #1022 from jedwards4b/yellowstone_gnu_serial_build_issue
ca192f9 SCC was not being defined in Macros.make
5bc9040 Make Mira and Cetus PE calculations identical
eee0cd5 Fix PE calculation for Cobalt
e3ea27e Merge pull request #1018 from jedwards4b/config_batch_schema
178ca8e add schema for config_files
8aaff27 add compsets schema to config_files.
5b6c249 add config_compsets schema
95cda1d fix issue in testlist schema
6dacf08 fix path
1ab88b0 add NAMELIST_DEFINITION_FILE to config files
6da3bd6 add BATCH_SPEC_FILE to config_files.xml update code to read and use schema files
6432695 add schema for config_batch.xml
269751c Merge pull request #1016 from ESMCI/jgfouca/create_test_force_pecount
2082b26 Merge pull request #1015 from ESMCI/jgfouca/fix_z_full_system_test_race_cond
b5af1b5 Updating Anvil defaults
5436f3b create_test: Add --force-procs and --force-threads options
868b9a5 ERS and ERR also do not re-run successfully
e3d2010 Fix race condition in Z_FullSystemTests test re-runs
329b53e Fixes non-BFB issue with F-compsets when threading is used
d281b24 Merge pull request #1013 from jedwards4b/config_machines_template
64dee72 Merge pull request #1012 from ESMCI/mfdeakin-sandia/no_invalid_characters_fortran
d59a558 Add a fully documented template for the config_machines file
79cea1b Update PE layouts for edison. Add -z muldefs to link line for edison. Remove machine hopper.
b516ae0 Initialize strings in structures in the structure declaration
66526fa Paranoia about preinitializing strings, think it's all of them
054e60e update modules and PE layouts for cori-knl and cori-haswell
61a6a49 Merge pull request #1007 from ESMCI/mvertens/split_drv_config_component
2876a10 Preinitialize strings to blank before using them to try and fix #1000
e44e727 Merge pull request #1011 from jedwards4b/costpes_correction
0b6b6d5 added DRV_THREADING,SAVE_TIING,SAVE_TIMING_DIR,BFBFLAG to config_component_[acme|cesm].xml
6158dd9 update ChangeLog
99bef30 improved evaluation of cost_pes
244804f Merge pull request #1010 from jedwards4b/pea_test_fix
8081074 Merge pull request #1009 from fischer-ncar/testlist_tuning
7d3f3eb Update CESM testlist. Increase wall clock times for some yellowstone tests. Remove test that's too large for hobart. Fix grid names.
6d92e59 make sure netcdf is used when totattasks=1
7f376ef Merge remote-tracking branch 'upstream/master'
1629d33 Merge pull request #1008 from jedwards4b/machine_updates
d179d98 Merge branch 'cheyenne_updates' into machine_updates
e369668 updates for cori
e1660bb update compiler and fix pbs dependancy bug
c0d83a6 Merge pull request #1005 from jedwards4b/add_overrides_for_pes
0e30690 additional fixes for branch
c8f131e create new additional model specific config_component_[acme|cesm].xml that has compset dependent attributes
f971fbc add schema for config_pes.xml and add overrides section to that file
c4ff567 add an overrides section to config_pes.xml
c782486 Merge branch 'azamat/mpas/scratch-file-io' (PR #1110)
9e57a5c update changelog
658e7e2 Merge pull request #1004 from jedwards4b/first_cheyenne_port
76a9b42 change comment
cbb1124 port to cheyenne
77cae9b Merge pull request #1003 from ESMCI/jgfouca/print_job_id
8fc9f80 Always print jobid unless --silent
dc71c08 update ChangeLog
bf8dc8c Merge pull request #1001 from jedwards4b/backout_982
f71821e backout PR 982
993a170 Merge pull request #998 from jedwards4b/config_machines_schema
0606129 update documentation
05980d1 add documentation to config_machines.xsd
52c7fbf turn pio timing on by default
6f2cf78 move PIO settings to correct location
ff1ff02 clean up acme config_machines.xml
d57e9e1 add schema for config_machines.xml
1a40caa cesm machines validates
e966685 Change cron_script to always submit to dashboard.
116e114 add a schema for config_machines.xml
870953d correction to ChangeLog
f7ec9c9 update ChangeLog
61015da Merge pull request #997 from jedwards4b/nersc_updates
cfe3b86 Merge pull request #996 from jedwards4b/ERI_test_fix
dfa1635 some updates for nersc systems
d21d726 make sure log directory exists
d112fef Merge pull request #984 from ESMCI/mvertens/add_cime_model_attribute
801a5ff Merge pull request #995 from ESMCI/jgfouca/add_run_env_txt
8efa7f1 Merge pull request #994 from ESMCI/jgfouca/fix_append_status_exc
c32b882 Add run_environment.txt output for all runs of CIME.
ee7977f Make sure to convert exception to string before appending to status
3758cbd Merge pull request #993 from ESMCI/jgfouca/ensure_threadpool_threads_are_closed
f6a4086 Merge pull request #988 from ESMCI/jgfouca/add_machine_to_tests
950927e Merge pull request #986 from ESMCI/jgfouca/reduce_case_setup_calls
5dc3666 Ensure thread pool threads for code_checker are closed upon exit
3e0fcf8 Merge pull request #987 from ESMCI/jgfouca/memleak_not_impact_case_test_success
527185f Minor fixes, comment update
83eb0f3 Merge pull request #989 from ESMCI/jgfouca/improve_msgs_from_nl_cmpgen
62cf600 Add back cron_script from pre-CIME5 ACME.
7abe68e Merge pull request #991 from jedwards4b/netcdf_build_fix
a11981e Change case_test to return success based on run_phase only
1f0250b update error message
48a55a8 update error message
252fdfc NETCDF include path is needed by all components
f8b6015 Add NLCOMP tag, say which files failed
684c801 Add CIME_MACHINE env variable
a184ecb Add support for --machine to scripts_regression_tests
37d2fa9 added test to ensure that cesm and acme attributes were working correctly for X compset and CPL_SEQ_OPTION
9130e4b Presence of a memleak should not impact case.test success
36ef260 Reduce redundant case setups
0374167 Add expect statement for jobid search
9fd6719 added cime_model attribute to all value entries that had compset attribute matches
297076d Merge pull request #982 from jtruesdal/cime_plus_119defaults
a3d3009 new cesm defaults - 1hr pop cpl, Robert Filtering, new grid files for EBM, mushy ice
96acbbf update ChangeLog
00ac7a6 Merge pull request #978 from ESMCI/mfdeakin-sandia/Separate_NetCDF_C_Fortran
9e84e54 Merge pull request #981 from fischer-ncar/testlist_upates
434cb98 Simplify logic for determining whether to check for NetCDF information. Also fix driver name after verifying with info statements
651b2cb Fix model name for building the coupled acme and cesm
dfc75c1 Use a cleaner method to detect if we're building PIO or the coupled model. Also explicitly link to both netcdff and netcdf
d8139d0 Update tests, remove IOP, update stampede configuration
ff5c949 Merge remote-tracking branch 'upstream/master'
0207191 Add more robust checks for conditions on NETCDF_SEPARATE. Also link to the NetCDF C library on Skybridge
ad02138 Merge pull request #977 from ESMCI/jgfouca/get_sandia_climate_machine_working
6e3353a sandia-srn-sems was missing compiler block
193de2a Fix case.build --clean for CESM using the same fix as the previous fix commit
6719870 Merge branch 'mfdeakin-sandia/Separate_NetCDF_C_Fortran' of github.com:ESMCI/cime into mfdeakin-sandia/Separate_NetCDF_C_Fortran
9d324cd Fix case.build --clean by raising an error when the NetCDF library isn't defined only when building PIO or ACME
d1eda0f Fix PIO1 builds for CESM using the same fix as the previous commit
745919a Fix building PIO1 on Edison - always use , not
fb4eb37 Add support to the CESM makefile for separate NetCDF C and Fortran installations Tested on Skybridge with an A compset, need to verify on Edison Change CESM config_compilers.xml skybridge entry to not rely on nf-config which isn't available for all modules
1ecb96e Minor cleanups: Remove some information printing Remove superfluous check for the definition of NETCDF_SEPARATE Change Skybridge ACME config back to using the single NetCDF install
19a15d6 Merge pull request #974 from ESMCI/jgfouca/significant_code_checker_refactor
32aac5b Fix for case when NETCDF_PATH is defined in the users environment. Not robust - it'd probably be better to undefine variables not specified by the compiler/machine xml
0cc002a Significant refactor of code_checker and related tests
421b173 Merge pull request #971 from ESMCI/jgfouca/minor_refactor_of_namelists
42bd1b5 Allow flexible spacing methods
408d3e2 Better support of multiply operation, other refactors
156a3fb update ChangeLog
7ba7124 Merge pull request #969 from ESMCI/jgfouca/shared_area_context
893bb03 Merge pull request #970 from jedwards4b/1x1_grid_fix
4583c0a explicitly set rof grid to null for this single column cases
762f1e0 Add SharedArea context manager
8dd6e98 Merge pull request #968 from ESMCI/jgfouca/fix_pelayout_pylint_issues
2fff644 Merge pull request #967 from jedwards4b/pio_namelist_fix
de6c95e Fix pelayout pylint issues
ebe3e43 Merge pull request #966 from ESMCI/fischer/cime5.2.0-alpha.13.bhist
6d493bc cleanup, change args to da script
c286dae fix for buildnml issue
e0f9f2f initialize and check pio vars in case_setup
de35e5b Fix git describe errors on some platforms
bc654b0 Fix cesm configuration for building on Skybridge
493380e Update changelog
306b342 Fix ChangeLog
0abba7d Fix merge conflicts for cime_config/cesm/allactive/config_compsets.xml cime_config/cesm/allactive/testlist_allactive.xml
2bba07d Another minor fix for the makefile. Also fix the SLIBS variable on Skybridge
47efa8e update ChangeLog
01bf497 Merge pull request #957 from gold2718/pelayout
444fa41 Merge pull request #965 from ESMCI/mvertens/nmlgen_update2
cba21bd fix pylint issue
d6c68f3 Work on supporting separate NETCDF_C_PATH and NETCDF_FORTRAN_PATH defines instead of just a conglomerate NETCDF_PATH for pio Add test configuration lines to Skybridge's entry in config_compilers.xml Makefile cleanup
575ba31 reverted add_default changes back to original set_value
7faf48d fixed startdate setting
d418428 fixed typo
fe6f915 fixed pylint problems
3f77665 a few more bugfixes
7484f29 fixes for dealing with skipped groups correctly
bc19a79 added attribute to add_default to ignore_abs_path
cd2e9c6 more cleanup updates for performance optimization
955214b fixed rebasing problem
880de69 fixed pylint errors
86a177c fixed problems with drv_flds_in refactor
771ac08 fixed pylint problems
a488388 updates to new interfaces for nmlgen
fb47fde more cleanup for performance optimization
eba840b changes to permit performance optimization
7e4203c first set of performance updates - in validation step
34b5866 fix pylint issue
5bf83db Merge pull request #964 from ESMCI/mvertens/nmlgen_updates
a8ba7fc Merge pull request #963 from jedwards4b/comp_classes_cleanup
1df1b57 removed hack that is no longer needed
27fe222 fixed doc tests for new uncompressed list format
24db0e9 changes to speed up buildnml for data models
602490f removed unused variable
7d498a4 quick hack to give env objects access to the comp_classes
b70bc64 expanded get_value interface in entry_id to add an optional node argument
f14d413 more updates and fixes for removing compression in namelist
7b6bf8e updates for performances and bugfixes
78697b6 Fix pnetcdf module for pgi on hobart. Update BHIST compset names.
fc70a7f Merge pull request #960 from ESMCI/jgfouca/fix_tprof_setting_in_buildnml
1e68418 cleanup whitespace changes
fbc515d fix indentation
861d956 fix issue with lookups
8eb87ed clean up components code
19b1871 Fix bug in setting up tprof namelist vals.
e43ff82 Merge pull request #959 from billsacks/cism4km_new_grid
359c2eb Restored mysteriously disappearing return statement
df3d603 Added --header and --no-header options
908781d Fixed bug with complex layouts
85e18ec Improved documentation and implemented options to change layouts
fdf5c5d Fix machine config for edison.
1497546 Point to new glc -> ocn runoff mapping files
41234d8 Implemented pelayout tool for viewing PE layouts
d44810b Point to new lnd <-> glc mapping files for redefined CISM 4km grid
9ae308e Merge pull request #952 from jedwards4b/minor_tuning
75a8e46 Fix pnetcdf module for pgi on hobart. Update BHIST compset names.
31361e3 Merge branch 'minor_tuning' of github.com:jedwards4b/cime into minor_tuning
9476917 update README
5292e9b more issues from laramie
4cfc084 add sort to xmlquery, fix a test
d3a3d85 clean up Makefile and scripts_regression_tests
d3d90ab Merge pull request #944 from ESMCI/mvertens/remove_clm40_compsets
195d71c Merge pull request #951 from ESMCI/jgfouca/fix_single_submit
271c92d Detect the NETCDFF_PATH environment variable in the makefile. If it exists, set the CMake arguments for it
cadd8d5 Fix single submit.
9c99fe4 Allow for suite-specific test walltimes in ACME
518e5a2 Merge pull request #948 from jedwards4b/build_improvements
7ac1343 response to review
be917a0 set sharedlibroot as subdirectory of outputroot (instead of testroot)
e097f2c build gptl prior to mct
2494f7b Merge pull request #932 from jedwards4b/refactor_xml_compvars
2172903 removed clm40 compsets from allactive compsets and tests
13610bb Merge branch 'jgfouca/machine_files/redsky_updates' into master (PR #1193)
f3feb78 Merge branch 'mt5555/homme/removeFVM'
7f8995e Update redsky configuration
56e8537 response to review
193219e fix pylint issues
50baad2 change DRV on comp_classes to CPL
3fdd621 fixes after rebase
be1db99 pylint cleanup and testing fixes
b32a3cf finish pio vars
ffdb514 add more pio vars
fe3f631 better approach
fd9601c more cleanup
6df92f9 add PIO_TYPENAME, rearrange code
5e15389 add more fields
200a75a fix pylint issues
e63d8c8 handle mpi-serial, cleanup
7669b43 NTASKS working
be2f946 update changelog
cb79f75 Merge pull request #941 from jedwards4b/alpha05b_fixes
f3c871d add -v back, fix output of xmlquery for logicals
46470d6 Merge branch 'jgfouca/titan_env_fix' into master (PR #1175)
7f36442 Only do titan pgiacc fix for ACME
5df5855 logicals need to return string type
a268a0d fix nag build issue
d75c214 fix mpi-serial issue on yellowstone
c87142e Merge pull request #939 from jedwards4b/fix_cmake_srt
340367b set default timer depth limit to 2
99264c9 cleanup
b370b60 remove unused macro
90a486e ctest now calls scripts_regression_tests instead of unittest.main
bce83f4 Changing pgi_acc to pgiacc in config_machines.xml
b69a50f compare_test_results: Support ACME's $compiler/$name baseline scheme
7e800c3 Merge pull request #936 from ESMCI/mvertens/dlnd_nmlbugfix
f2b6717 fixed typo
60baa24 changes for getting cesm prognostic components to work correctly with python buildnml, buildlib and new configure_xxx.py
7c696b5 Special case for titan and pgiacc
c10ff81 Adjust default walltimes for sandia HPCs
88412af Merge pull request #930 from jedwards4b/xlmquery_refactor
79455a5 add valid_values and type
f845fab fix indentation issue
0de957f fix indentation issue
9cbbc34 update ChangeLog, fix for cori-haswell
6840d9b Merge pull request #931 from ESMCI/jgfouca/use_umask_for_check_input
42676f9 Merge pull request #933 from ESMCI/mvertens/datm_nmlbugfix
5ec175b explicitly add pylint tests
d7285f7 bug fixes that appeared in the datm_udpates PR
4a2a905 check_input_data: Use umask before svn export
fb18a59 fix issue in scripts_regression_tests, breakdown tests by class for ctest in list_tests
5d6dcab rebase and resolve conflict
f03b43e add full option
07df7a8 update xmlquery testing
0c3470e progress on env_batch variables
aa5050e listall working
78b9ed6 fix get_groups
944bcea more progres
0d83047 add support for listall
3b817c9 add description option
fdf9b58 rearranging code
731c093 Merge pull request #929 from ESMCI/jgfouca/fixes_to_J_TestCreateNewcase
aeadaa5 Be much more clear about using cls vs self
1ce9d5e update ChangeLog
f881c99 Merge pull request #928 from jedwards4b/clm_bld_fix
eccb58d Merge pull request #923 from ESMCI/mvertens/datm_updates
a01ac6a fix include paths
51fb758 fix clm shared bld issue
8173e4c Merge pull request #926 from ESMCI/jgfouca/minor_fix_for_acme_tests
d49e7d9 Merge pull request #927 from ESMCI/jgfouca/fix_skybridge_env
b651ae4 Fix hdf5 serial version on skybrdige
e56f0d8 Fix bug in negation of test_suite for acme tests
753afa6 Update melvin gcc to 5.3.0
14c52ef Merge pull request #924 from ESMCI/jgfouca/fix_bless_test_test_for_cesm
e5d0b4b bless_test_results: make namelist blessing compatible for both models
4edd850 Merge remote-tracking branch 'remotes/origin/mvertens/datm_updates' into mvertens/datm_updates
3b6a861 updated regular expression handling
5e05c06 Renaming Depends.titan.pgi_acc to Depends.titan.pgiacc
b657765 Merge pull request #921 from billsacks/query_testlists_error
ff4c081 fixed 5x5_amazon grid name
3010661 set domainfile to null if CPLHISTForcingForOcnIce mode
802ef25 Merge remote-tracking branch 'esmci/mvertens/datm_updates' into mvertens/datm_updates
4eaaefe Fix pgiacc environment for titan
69ce49a bless_test_results: hot fix to support acme baseline naming
38a3ce2 Hotfix for anvil SAVE_TIMING_DIR
a92dd7c removed DEBUG comment
6244802 fixed bug for numa_IA grid
9eec70d refactored namelist_definition_datm.xml by using regular expressions for matches in nmlgen rather than exact matches
635df6d Merge pull request #919 from jedwards4b/clone_fix
72836f0 Merge pull request #920 from ESMCI/jgfouca/fix_bless_regr_test
f1bddbc Fix for Q_TestBlessTestResults do not wait for namelist-only
5c932df Merge pull request #915 from ESMCI/mvertens/python_namelists
52131e8 Merge pull request #914 from ESMCI/remove_pesetuphist
acadec7 Merge pull request #912 from ESMCI/starchive_bugfix
9f80be7 Merge pull request #918 from mnlevy1981/runoff/remove_src_mask
1120d0c Merge branch 'rljacob/cime/cime5-upgrade' (PR #1169)
d592ba7 pylint cleanup
0e59da7 improve cleanup
43945f8 fix create_clone and add tests to scripts_regression_tests
f3bd0ba runoff src mask = 1 globally
119d969 Change skybridge and redsky envs to be exact match to cime2
891fff6 fixed iradsw for GECO spinup
cd09234 fixed issue #916
29341b8 added comment
d8fc3b6 Give a meaningful error message when query_testlists can't find anything
b07ec81 For titan, don't put numa_node on aprun for pgi
64f03b2 added T42 domain
3fe48c6 added T42 domain
85dc29a added T42 domain
9400ac4 removed PESetupHist backup directory
a9abeba removed verbose output in create_namelists - this is a big cleanup in the output and makes it much more understandable, the output can be obtained in debug mode
1c49362 data components only output in debug mode - cleanup in output
ad30dcd bug fixes for new grids specfication
2fe35ca Merge pull request #913 from ESMCI/remove_docs
23fe061 reverted to original buildnml scripts
ba64359 removed doc directory that is not longer needed - since all documentation is now on esmci wiki
46213ff short term archiving bugfix
5817ede Merge pull request #909 from jedwards4b/laramie_port2
21ba5b9 Merge pull request #906 from ESMCI/jayeshkrishna/conflict-resolve-br/santos/quote-timing
e28ecc4 Merge pull request #911 from gold2718/fixFCD
3f8b623 Fix for Depends with multiple spaces between filenames
8d0cc0f removed call to create_namelists for the case of tests
9a5203b cleaned up TestStatus.log and put in bug fixes for new pythonization of cesm buildnml for active components
3d6e665 put in capability to have unsorted namelists be written out
483efec updated xmlchange to head of master
80b0c86 changes needed for cice pythonization of buildlib and buildnml
9e17508 first set of fixes to address #826
a4c078f Update CIME5 config_grids w ocean cavities
8ba1236 Set CO2_PPMV value for ACME AV1C-04P2 compset
04d30bb Replace ERP_Ln3.ne30_oEC.A_WCYCL2000 with ERP_Ld3.ne30_oEC.A_WCYCL2000
d202c78 Revert "Switch to using several config_pes.xml files"
e89ca40 Switch skybridge and redsky back to openmpi-1.6
9e0e29f Unshare sharedlibs, fix bug in machines.py
ec5924e more laramie updates
3b25b50 Merge pull request #898 from jedwards4b/compilers1_fix
703dfcc Merge pull request #891 from fvitt/compsets_cime5.2.0-alpha.7
60669c1 Merge branch 'santos/quote-timing' into jayeshkrishna/conflict-resolve-br/santos/quote-timing
36fc024 Switch to using several config_pes.xml files
298963e update 3 config_pes files after testing
9fe9a76 fix name in config_compilers for acme
3bc12f0 fix Macros file name
e0eb0eb force compilers version 2 for regression testing
90912e0 Merge branch 'rljacob/cime/cime5-upgrade' of github.com:ACME-Climate/ACME into rljacob/cime/cime5-upgrade
d9d0147 removed print statements for debugging
7c24b95 removed print statement
aa8e1ca Add entry for coupled cases on anvil in config_pes
f5c3f15 Set up the ACME coupled config_pes.xml
c6fa9da Make sure glc_do_dynglacier is true for MPASLI
de4699e Update ChangeLog to correct original description of the problem
0095ff9 Merge pull request #828 from jedwards4b/config_build
c088677 always code_check file if full path provided
a1a46fe MP_MPILIB over defined
c940582 updates for cori-knl
d042b1c changes for cori-knl
c925d41 fix include file name
bec57d1 remove whitespace difference
be40065 fix issue in mct configure
886720f update for NAG
0195917 save this change for another PR
7de9f18 rename corip1 cori-haswell
0414f47 update for theta
d39d236 file cleanup
f117402 rearrange some files
a4e0e0c fix unit tests
999ca40 fix tests
450c6e3 merge build into compilers
b450b10 move into CIME
44d1d2d improve configure program flow
311f78a mv build to BuildTools
cc0b9ba restructuring code
364b3cc Revert "Cleanup duplicate PE layouts"
995ba58 Cleanup duplicate PE layouts
604f247 Prioritize machine matching over grid,compset,size in PE matching
9a20827 Replace strncpy and snprintf where applied to non-null-term. strings
3f14453 Update Mira compiler to the latest version
70b8252 Merge pull request #886 from ESMCI/jgfouca/minor_fix_to_bless_tests
ae81376 Another minor naming change to provenance file
691cf5a Minor rename of showq file
c616a69 Added numa node computation and creation of aprun options for Titan
66a1bad Replace execution place holder string with path; Titan/aprun specific
525788d Replaced aprun option with "aprun" variable, value computed in task_maker
27f716c Increase Anvil default stack size for threaded runs
edd70a1 Add namelist capability to compare_test_results, add tests
0df8f4e Change NTHRDS_ESP default to 1
a7240d0 Remove PFS test
1aef408 Added option for printing mpirun command
0a74631 Make bless_test_results more robust by providing full path to create_test run_cmd
38635ee Merge pull request #885 from jedwards4b/xmlchange_div_by_zero
99baa5a prevent division by 0
ff23f9a Merge pull request #825 from ESMCI/ndk/machines/cori-haswell4
3c8ceaa Merge pull request #880 from jedwards4b/buildnml_fix
08cecc5 raise error if file is python
bafc903 trap on perl buildnml
f61a8c5 Correct pe layout for MPASLISIA case
fce75f0 Merge pull request #879 from jedwards4b/buildnml_without_run_cmd
69748cb fix pylint issues, extend pylint coverage
6d63d47 convert buildnml scripts to callable modules
d209769 load_source working
35f3822 first attempt
e3a7623 ACME use driver_cpl config_pes for X,A,S cases
70ae92f Merge pull request #875 from jedwards4b/fix_clone_and_format_issues
e6c06fa fix an issue with cloning and format
7e155a5 Move long-running atm test to acme_integration
8f2b190 Debug, check for existing directory
2862060 Avoid misspelling, define filename once
9aea3c0 Copy additional file into caseroot/Tools if exists
c55e1f8 Give problems 5 hours on skybridge
391c215 Merge pull request #846 from jedwards4b/module_load_error_message
561ce10 Add intel support to climate
fe792b7 fix tab issue again
ff0e7cf make sure we get errors from module load
9ed873f Merge pull request #844 from jedwards4b/debug_attribute_fix
3ec818c Merge pull request #833 from mvertens/klindsay_spinup3
cc16b84 the comma was causing debug to be set incorrectly
909565d Fixes DATM_CLMNCEP_YR_END for 20TR compset
a420cc6 Merge pull request #840 from jtruesdal/cime_plus_marblmod
82cc763 Change DRV_THREADING default to TRUE
cc1d036 Fix typo in provenance.py
365eee1 Set SAVE_TIMING default to TRUE
ab48984 Add timing variables and update defaults
37889ec remove cvmixlib creation now done in pop
13ba9e4 update ChangeLog
826b0f7 Merge pull request #831 from jedwards4b/remove_ccsm_baseline
ea774b7 Merge pull request #836 from jedwards4b/pylint_and_xmlchange_fixes
f6c34b0 Merge pull request #835 from fischer-ncar/stampede_and_testfix
7991922 Update support for stampede. Change ERR_N3 tests to NCK_N3 tests. Removed blank spaces from testlist_allactive.xml.
57d16eb report errors if xmlchange or xmlquery is given bad input
31c7d2f Fix log reporting for sharedlib builds
0452cd6 add error check in xmlquery
c9e9359 add an error message if var not found
5575267 fixed bug in wrong setting of prescribed aerosols for G compsets
ef4feb2 fixed problem with rebasing error
1a3ac33 Merge pull request #832 from mvertens/ww3fixes
cd64444 changes need for getting ww3 to have branch capabilities
f3e1d1e Adjustments to building/running on KNL
7755f64 one more
e40fa5a replace CCSM_BASELINE with BASELINE_ROOT
69ca9cf take out the --cpu_binding=cores flag to srun for now, while we try to get the "correct" value to the -c arg of srun. Currently setting -c 2 for cori-haswell and -c 4 for cori-knl.
37e6e14 Changes to get tests building/running with cori-haswell. Some changes to modules for edison. Some changes to build/run on cori-knl
e767f7b Another HOMME fix
acc888c Fix CCSM_BASELINE again
3074eea Change homme to use BASELINE_ROOT instead of CCSM_BASELINE
4892641 Changes to build/run on cori-haswell. Stubs got cori-knl.
46e8f1d Merge pull request #813 from gold2718/addTool
11093f2 Renamed file to utils directory and added a main function
2cc6268 More updates for 20TR compset
b4783ba added files back in that were mistakenly deleted
52d6b9d Make infra work with ACME-style testmods
50387fb fixed more ocean spinup issues
13b349c put in latest changes from Keith - particularly to get drof and datm to set domain to stream for CPLHISTForcingForOcnIce
f145731 changes needed for geco test for Keith
579e193 first test using changes now runs
e331d89 changes for creating forcing files for ocn/ice spinup
a2ce180 reverted prep_ocn_mod.F90 to esmci/master - changes not relevant
672d2cb first pass for putting in klindsay's changes
62fb6dd Make clm not a sharedlib for ACME
26534bd Keep MPAS SCRATCH files open during init, run and finalization
4c6b57b Merge pull request #812 from ESMCI/mfdeakin-sandia/SystemTestsCompareTwo/NOC
f35d4b7 Merge pull request #823 from ESMCI/jgfouca/fix_bless_tests_results
64dd303 bless_test_results: Fix a couple mistakes in interactive code
a51ebd1 Fix mistake in create_test
18b8796 remove fvm code from I/O routines
5b86c49 Merge pull request #814 from jedwards4b/config_grids2
da9ef7f Merge branch 'jgfouca/copy_balwinder_constance' (PR #820)
5bff500 Correct layout for titan and low-res wcycl
21393f8 Merge pull request #809 from ESMCI/ndk/machines/cori-haswell
2cf2160 Merge pull request #808 from ESMCI/sarich/fix-config_pes_converter
746d9df Updates machine files for PNNL's constance machine for ACME
d95f3af fix that darn tab
920edef Merge pull request #817 from ESMCI/singhbalwinder/machines/constance-mach-files-maint-cime5.1
b472bc3 Updates machine files for PNNL's constance machine for ACME
f791a8e response to review, removed RUN STATUS and replaced testsavetimings
6398013 remove debug comment, fix tab
f9675c1 cleanup pylint issues
72b34fc fixed short term archiving bug for multiple instances
34d8c85 only check schema if version > 1.0
b5cba8f fixed problems for TG compsets
039f4df uncomment mapping file
ed2dc6e rearrange for more code reuse
3f0c546 domain path should only be used if provided
381bf66 make schema check generic
5b97fda fix indents and xml spaces
24e4356 code cleanup
ccbfee9 rearrange a little
d8cbaff new grids schema
34382c1 Revert changes to this file back to original per request by Rob Jacob
f4f3b94 New tool to find circular dependencies in a Depends file.
b94d051 Remove NOC test
d4a0c7e Restore auto-addition of compiler to baseline_name
a5b523b Temporary revert of env changes on melvin and climate
685a84c Merge pull request #811 from ESMCI/jgfouca/skip_single_submit_unless_skybridge
c4226a7 Skip single-submit test unless on skybridge
18102e7 Fix env settings for sandia climate machine
eda093f Add back support for 20TR time period
5794829 Add support for compsets with 20TR in datm
98bad8c Add help string to allactive config_compsets
adf1e26 Remove a duplicate entry from config_pesall.xmo
03b8302 Correct CCSM_CO2_PPMV setting for waccm and cam-chem compsets
6a74fa3 Change CMPASO_NYF compset name back
2245f67 Allow for building/running on cori-haswell (basically same as corip1, but renaming) and some stubs for cori-knl.
34aa9fa Update config_pesall.xml with missing configs.
6a1f94c Update config_components for ACME
bbe10e1 clean up code a little
4f1c95c change cime4 references to cime5
ab64f25 config_pes_converter automatically fixes bad xml comments from cime2 file
5d4e743 Fix 2 mpasli items in config files
27950c1 Change shr_orb_cosz calculation back to cime2
f154398 Change compset names in tests to match new ones
9264e62 Merge pull request #799 from jedwards4b/make_dependancy_fix
7656437 Merge pull request #751 from ESMCI/jayeshkrishna/update_anvil_max_tasks_36
1af4177 Merge remote-tracking branch 'upstream/master'
6b6ac15 fix an issue with clm bld dependancies
864c77b Remove unsupported waccm and chemistry compsets and modify test list accordingly
4aff1cc update ChangeLog
151b965 Merge pull request #795 from jedwards4b/laramie_update3
d70623a pnetcdf module still broken
26ceb2c readd pnetcdf
d0f417c pnetcdf module fixed
36d218c Merge pull request #755 from ESMCI/jgfouca/handle_timeout_in_teststatus
20f2ca2 Merge pull request #777 from bertinia/st_archive
a38b0f4 update for PR #777 to more completely check restart files and remove doc/images
221ee7a remove doc/images
a336573 Merge pull request #788 from billsacks/compare_test_results_maintain_comment
19bdc1e Merge pull request #790 from jedwards4b/laramie_update2
b975026 add images for wiki documentation
40540cb move logger message outside of try block for case_st_archive.py add image file subdirectory to docs for wiki documentation.
a4b82e3 updates for laramie
180ee86 Print the comment from comparison if it's a brief one-liner
125d819 Delete nav-cesm-ug.png
7c362ba Delete cplug-02.1-figx1.jpg
b85a8c8 Add CIME Users Guide image
4bd6f83 Add image file for Coupler User's Guide documentation
0ead034 updates for laramie port
0f7f1fe make logger output debug instead of warn Fixes #783
d1dd00d Be sure to terminate children upon receiving a signal
01fa586 Merge pull request #780 from fischer-ncar/stampede_update
091a405 Updates to config_machines.xml to fix builds on stampede
47978b1 Merge remote-tracking branch 'upstream/master'
00ad619 Merge pull request #778 from jedwards4b/erio_fix
b87c52a fix erio test,and a minor format change for cray compiler
45bdde9 Merge pull request #775 from jedwards4b/cori_port2a
10d6383 fix needed for erio test
8a81b1b port to corip1
c595180 Handle additional signals, better exception message
952ce71 port to cori
8e075c9 rework to support derived variables
a56fd3c Merge pull request #764 from jedwards4b/buildexe_fix
48d0d60 Merge pull request #769 from jedwards4b/pio_netcdf4_detect_fix
9814832 detect netcdf4 correctly in pio1
f60e3cd straighten out postional argument mess
081dab4 Merge pull request #765 from jedwards4b/caseroot_file_fix
c81f4a6 fix mixed up positional args
6e9eb60 Merge pull request #762 from billsacks/rename_xmlchange_cmnds
61f4ba0 only put caseroot file in bld and run dirs
8c8c457 build exe in correct location
fc91c86 Merge pull request #758 from mnlevy1981/user_mod_fix4
825fb0d Add actual file name to log message
b9aec4c Add log message about deprecated xmlchange_cmnds
68125e2 Merge pull request #760 from bertinia/st_archive
0799a66 minor bug fix to restart pattern match for datm suffix
044e3ab Combine shell_commands and xmlchange_cmnds
9a4e934 Rename xmlchange_cmnds files to shell_commands
20605f6 Add comment explaining why loop is reversed
84c9cbe Merge pull request #752 from billsacks/cism2_default
78b70d7 Merge pull request #730 from ESMCI/azamat/machines/theta
2f6b396 Merge pull request #759 from ESMCI/jgfouca/check_scripts_using_GMAKE
2914889 minor bug fix to restart pattern match for datm suffix
19e3efb Ensure all of CIME is using the GMAKE case setting
5ef1543 Another possible fix to #756
e78ae82 Better handling of timeouts for case.test
c33b8e1 Update anvil's MAX_TASKS/PES_PER_NODE to occupy all cores
4a50948 Merge pull request #748 from billsacks/compare_test_results_output
9f2c652 Return a non-zero error code if there are diffs
1b4c722 update Changelog
02e5635 Merge pull request #749 from fischer-ncar/testreporter_fixes
31f578c Bug fixes for test reporter and update wall clocks for long tests.
8eb9544 Merge remote-tracking branch 'upstream/master' into testreporter_fixes
98e689f Bug fixes for test reporter and update wall clocks for long tests.
82ab32a Merge pull request #747 from ESMCI/jgfouca/wait_for_create_tests
8a49eb7 Merge pull request #746 from jedwards4b/laramie_update
64115e1 Merge pull request #725 from jedwards4b/cpl_rest_read_fix
77a7a17 add a little documentation
2c1f3fe need to add MPI_SHEPHERD=true for fake tests on laramie
740f3aa Fix scripts_regression_tests for new output format
470ca7d remove EXEROOT and BLDDIR from machine definition
e1c1883 Add some documentation
65693e6 Convert CESMSCRATCHROOT to CIME_OUTPUT_ROOT
caf6a05 Build-in support for waiting for create_test
d4c9811 Allow optional output_suffix in summarize_cprnc_diffs
0fa63a9 Merge pull request #745 from ESMCI/jgfouca/erio_test
9ece311 Add new ERIO test type.
f9d196e Put detailed comments in log file rather than stdout
17dd09d Give cprnc.out files a unique name
8eb7ae3 Add baseline_root to the log file
783edab correct for total nodes < 1
488c079 Change reporting for compare_test_results
c6e1b35 Always exit with a 0 status from compare_test_results
90f1b9a continue work on port
3acee39 add aprun fix for using less than full node of tasks
099f028 CESM machine updates for Theta
e9e11ca If TOTALPES is less than PES_PER_NODE, set PES_PER_NODE to TOTALPES
77b0ad9 Initial port to ALCF Theta machine
df92be7 Merge pull request #743 from ESMCI/jgfouca/fix_regr_test
6f00066 Merge pull request #735 from billsacks/copy_user_nl_to_multiinst
c2e85e1 Fix regression namelist regression test
ecc022d remove unused variables
94fcfa2 Merge pull request #739 from jedwards4b/add_output_root_option
24bdc90 Merge pull request #742 from jedwards4b/pea_test_fix
f0ec12f Just apply user_mods in create_newcase; remove unneeded multiinst code
ff977d3 Merge pull request #736 from jedwards4b/build_improvements
3dbe959 update for acme
8410e95 response to review
469b769 move case.load_env up in case.setup, make sure pnetcdf is not loaded when building mpi-serial builds
645ebba Merge branch 'master' into copy_user_nl_to_multiinst
e3431e0 Merge pull request #727 from jedwards4b/user_mod_fix2
912caed add CASEROOT file to bld and run directories
2ef4bc1 update user defined template for cesm
bda3c01 further cleanup
64eded0 rename CESMSCRATCHROOT to CIME_OUTPUT_ROOT, add cli
6edc721 fix bad argument to clm build
ed44be8 Merge pull request #623 from ESMCI/jayeshkrishna/machinefiles/add_Anvil
9d855d1 improve output on build errors
9d85e90 Revert "remove testmods application from case.setup, remove check for duplication of entries in user_nl files"
0f31ddf Copy user_nl_foo from the case directory to the multi-instance version
de38a26 remove testmods application from case.setup, remove check for duplication of entries in user_nl files
df524a6 fix pylint issue
7bf81e8 try again
67eefee get unique list of dirs
0732c4c update ChangeLog
f210c86 Merge pull request #733 from jedwards4b/xmlchange_revert
a0d1557 backout change to xmlchange (needed by external components)
213c37c Change allactive compsets to use CISM2 rather than CISM1 by default
4ecde62 Do not turn on cpl hist output in CISM cases
f4acb96 Merge pull request #729 from ESMCI/jgfouca/fix_namelist_cmpgen
a9e887c Merge pull request #722 from ESMCI/jgfouca/misc_changes
09d761f Merge pull request #731 from billsacks/fix_eri_and_erp
51192b7 Merge pull request #709 from ESMCI/jgfouca/fix_anl_workstations
8efc834 hardcode pnetcdf path for now
b25c7fe Don't assume . is in PATH.
a79cf81 cpl restart read should only happen on cpl tasks
80253cd Ensure that ERP halves tasks and threads for all components
43c761d Remove BUILD_THREADED for ERI and DAE tests
c55e505 trim include directories list so that each is only added once
ce3572f Change sleep in cleanup. Minor fixes to code_checker so it can run standalone
6098bde Merge pull request #721 from jedwards4b/lt_archive_queue
0f1bbc1 change lt_archive queue to caldera, add sleep in scripts_regression_tests
6ecb119 update changelog
4c406d8 Merge pull request #717 from jedwards4b/shr_scam_fix
5c52d8b update documentation
216d864 Merge pull request #711 from jedwards4b/erp_test_fix
da1ce6f Merge pull request #715 from billsacks/indent_cs_status
cb231c5 Merge pull request #713 from jedwards4b/user_mods_include_fix
ed27808 Merge pull request #680 from billsacks/summarize_cprnc_suffix
edf6ac3 fixes issue #704
5fc549d Merge pull request #716 from ESMCI/revert-705-scam_fix
5fb3265 Revert "fix for issue #704"
0d7f609 restructure to reduce code
9557764 Add indentation in cs.status output
61e3c47 response to review
83939b7 fix issue with recursive include of user mods
141e28a Merge pull request #705 from jedwards4b/scam_fix
f31677b erp test needs create_namelist in case.setup
753c42e create_namelists when case.setup is run in testmode
27722c8 Change env settings from use of bash to use of environment
b609fcc resolve merge conflict
43ef805 Merge branch 'pylint_cleanup_Tools'
d53d9b8 move python path settings into pylint so that code_checker can be run without mods
dc01576 response to review
16e1c04 Merge pull request #707 from jedwards4b/env_mach_specific_bug_fix
3569a19 more cleanup
b6a2808 xmlchange cleanup
f29ab4b fix indentation error
af9f697 more cleanup
b111a7e cleanup of Tools directory
883e199 more cleanup
b7761ea begin cleanup of Tools
2d129ba Merge branch 'jgfouca/changes_to_env_mach_spec_env' (PR #701)
114f39b Merge branch 'master' into jgfouca/changes_to_env_mach_spec_env
849dfce fix for issue #704
d7acfef update ChangeLog
cf82013 Merge pull request #697 from jedwards4b/sharedlib_build_installs_to_case
76dc62c fix rebase issue
dd9e936 remove unneeded copy
c7a46f6 need to create include directory
684e846 change copy method for mpi-serial files
0f69fa1 fix issues with mpi-serial build and install
f1085b0 fix merge issue
e6ffa16 add comment on sharedpath
52401ae update acme side
83ea569 install sharedlib builds to individual case to avoid conflict
d766617 Merge pull request #689 from ESMCI/jgfouca/optimize_preview_namelists
db1d397 Changes to handling of environment_variables
f6e3e14 Merge pull request #699 from jedwards4b/code_checker_fix
5342abf fix issue with pylint
f7b98c4 Merge branch 'master' into jgfouca/optimize_preview_namelists
f317808 Merge pull request #696 from jedwards4b/jgfouca/optimize_preview_namelists
d6a27fa need to create_namelists in build
e9202d5 Merge pull request #693 from jedwards4b/pio_build_update
bab357e Merge pull request #694 from cacraigucar/geotrace_cime
eff82fc reorganize
2825d34 response to review
39110ea add limited buildnml back to build.py
3ed3929 add new buildlib.pio script to acme
04b6f10 fix issue with unresolved var in env settings
7665b99 Changes to support DATM in isotopes
435de61 Merge pull request #681 from billsacks/irrig_as_fraction_cime5
080af4c mv buildlib.pio to python, add smarts
c3e3974 Fix preview_namelists, add test for preview_namelists
52c3cac Change do_namelists to cmpgen_namelists, add missing tool
94bb46a Major refactor to handling of namelists
5ffd940 Merge pull request #688 from jedwards4b/pio_workaround_removed
c3e73fa remove workaround, now done in scripts
57a7a7f Merge pull request #686 from mnlevy1981/mlevy/bugfix/runoff-update-take2
071f341 Group similar calls together
a8cb7d2 Bugfix for failing C compset DEBUG tests
943199b Merge remote-tracking branch 'cesmdev/master' into geotrace_cime
1239bd2 Merge pull request #683 from billsacks/always_print_provenance
04c4afe add extra newline
0cd148d Print provenance info from main function, rather than in a 'test'
001fa3d Merge pull request #682 from billsacks/print_cime_model
df1fcac Merge pull request #679 from billsacks/fix_fortran_unit_tests
0a13ef4 In addition to printing the commit, print the current cime_model
9d24c28 add warning for version not found
8d68524 fix issue causing fail when not in CIME_MODEL structure
23acbc7 Get fortran unit tests passing
8a2953a Delete trailing whitespace
b06306e summarize_cprnc_diffs uses .nc.cprnc.out rather than .base.cprnc.out
d3b2cfb Merge pull request #678 from ESMCI/jgfouca/make_regr_tests_more_portable
801533e Make all cime test suites use P1 instead of mpi-serial.
f90b4bc update ChangeLog
5f9299d Merge branch 'jgfouca/make_pea_work_without_mpi_serial' (PR #647)
edb5a25 Merge pull request #640 from mvertens/build-namelist2
41b0e92 fix issue in test
405663f merge to head of master, resolve conflicts
7a8a247 Merge pull request #677 from jedwards4b/set_walltime_for_queue_option
0065904 Merge pull request #676 from jedwards4b/MODEL_VERSION_IN_CASE
14447b4 fix pylint issue
e7e3029 fix issue 675
0f8596b clean up xml version code
5edbe51 clean up xml version code
6e1c6d1 move this to case configure
9994647 Merge pull request #674 from ESMCI/jgfouca/improve_test_status_documentation
0822fed add host model version to case information
df53174 Improve test status documentation
e65a578 Merge pull request #673 from ESMCI/jgfouca/create_test_enhancements
68567bf Enhance use_existing capability for create_test, add test
7fbd5a2 Merge remote-tracking branch 'jedwards/build-namelist2' into build-namelist2
2ca20b1 Initial change to use SystemTestsCompareTwo for NOC tests
4dab377 remove obsolete documentation
90884a0 fix issues in acme config_grids.xml file
2e26413 response to self review
6612ed8 Merge remote-tracking branch 'jedwards/build-namelist2' into build-namelist2
f785358 Merge pull request #670 from ESMCI/jgfouca/code_checker_too_verbose
3e7b796 Merge pull request #652 from fischer-ncar/testlist_wallclock
45cad1a expand pylint testing and fix issues
4899ac8 code_checker: don't be so verbose in debug mode
3fffa7f more pylint cleanup
de8ce42 Merge pull request #668 from ESMCI/jgfouca/remove_support_for_cimeroot_env_var
9028e81 Add cimeroot env setting back to standard_script_setup
580e552 out of date, unit tests are now in scripts
deaf2c5 fixes found in testing xml schema
951a460 Remove CIMEROOT from cesm batch.xml
a21286b Remove support for user setting CIMEROOT.
9af04a2 remove tabs from data model namelist_definition files
a87817a fix issue with single_column setting
b6789d4 Merge pull request #664 from ESMCI/jayeshkrishna/machinefiles/anlworkstation_lib_ver_updates
2e2feb6 remove drydep_list valid_values, add better message for invalid values
54d7be0 port changes to pio2
ce183a7 Merge remote-tracking branch 'jedwards/build-namelist2' into build-namelist2
eb6ef04 Merge pull request #661 from billsacks/test_status_cleanup
f1b7e44 Merge pull request #660 from ESMCI/mfdeakin-sandia/SystemTestsCompareTwo/PEM
57a6789 Remove unneeded imports, fixes pylint issues
9ccec99 Remove _common_setup from pem by moving variables to config_tests.xml
681e6b4 do not fail if drydep_inparm not found
0d6e22e fix drv_flds_in, clean up
2cee122 Minor cleanup and documentation
105445b Move options to cime_config/config_tests.xml
b0d48e5 Merge pull request #658 from jedwards4b/pbs_problem_fix
a8b9bcc Make certain to use integer division for computing the new number of tasks
44d6a17 Remove unneeded import
c724e3b Remove second case_setup call left in
0329207 Remove _pem_first_phase and _pem_second_phase; use SystemTestsCompareTwo instead Move use of case_setup with reset=True to PEM
43f1480 Fixed issue with HIST_OPTION and HIST_N not being set correctly due to dependency on unset environment variables
7ac9c1a Merge remote-tracking branch 'jedwards/build-namelist2' into build-namelist2
9991c86 fix version check info
58644f0 Start of conversion of PEM tests to SystemTestsCompareTwo Currently only sets up the environment files correctly (I'm in the process of verifying this, but a diff of) system_tests_compare_two now resets the setup for case 2 after it's been setup; this allows case 2 to modify env_mach_pes
fb9afe4 some pbs systems want the directives first
471aa3c cleanup pylint issues
82fd542 works with A case
e28f698 git rid of defaults
d2408d6 removed namelist-defaults object
1a2e8a7 merge to build-namelist2
67a381d driver buildnml working
9a18528 cleanup namelist_definition
d8f7322 cleanup namelist_definition
d81ea0d change modify_in_xml
8f4d479 split entry_id schema for namelist xml validation
3082912 Merge pull request #654 from jedwards4b/thread_count_fix
5c383de Update wallclocks in testlist_allactive.xml
8c9c2d3 Merge remote-tracking branch 'upstream/master'
880ae14 Merge pull request #648 from ESMCI/jgfouca/improve_compare_test_status_entries
51f2b75 fix problem getting thread_count
0776377 Merge pull request #649 from jedwards4b/get_values_rename
a448815 fixed attributes by making atm_grid lower case
7645def removed char* references in namelist_definition_xxx.xml files
dfadcf3 progress
2ccd7ee changes to schema for all namelist definition files
af6263c fixed bug for AIAF
721ec62 bug fixes
6c9f213 incorporated more streamlined approached for adding defaults via scanning the namelist_definition file for all entries and automatically adding them
e3ef21a now looping over all possible default values in namelist_definition_drv.xml - significantly shortened driver buildnml
cacafc1 fixed doctest issue
322e01b fixed more bugs necessary to run prealpha and prebeta aux tests
e11dac7 updates to fix numerous bugs
734d748 updates to fix numerous bugs
dd12c06 added new required method get_case_root
d47676c incorporated changes to have all build-namelist occur in python for driver and all data models
5c37c1f apply get_values to COMP_CLASSES xml variable
e62f89e rename get_values to get_full_records
82a0e2b fixed attributes by making atm_grid lower case
2ff833f Separate baseline and non-baseline compare phases
68c19a3 removed char* references in namelist_definition_xxx.xml files
2a73760 PEA should not always fail on machines without mpi-serial
82ba881 Merge remote-tracking branch 'jedwards/build-namelist3' into build-namelist3
1de7d37 progress
ce63e7a Merge pull request #645 from jedwards4b/xsd_improved_format
62374e8 Merge pull request #644 from ESMCI/jgfouca/internal_diff_fail
b1022d1 Ensure that internal (non-baseline) test diffs cause the test to FAIL
da6a246 improved format for entry_id schema file
42c726a changes to schema for all namelist definition files
d973cf2 Merge pull request #642 from ESMCI/jgfouca/improve_test_sched_msg
f5ed87d Improve test_scheduler runphase message for batch systems
67e8b38 Merge pull request #641 from jedwards4b/add_xsd_and_test_xml
23a8cf5 Merge pull request #639 from ESMCI/jgfouca/pend_refactor
fe767fb Change TEST_PENDING_STATUS to TEST_PEND_STATUS
d794942 change log messages to debug
e3344a1 all config_component.xml files now validate
f63b831 fixed bug for AIAF
8cb1f9b bug fixes
2fc0952 Refactor TestStatus
692e957 Merge pull request #637 from billsacks/query_testlists_show_options_v2
016b356 add and test schema for config_component xml files
275f21d incorporated more streamlined approached for adding defaults via scanning the namelist_definition file for all entries and automatically adding them
77b9ad6 Align comments and options better
49d0a5c Show comment and (optionally) options in query_testlists
2f8fc63 resolve merge conflict
38fc267 change testlist format to match
ad90d5a rework options in test data hash, move machine independent options out one level
18b2a44 remove debug stateements
8e415b6 correction to option path
42cc67f fix issue with options level
8c6363e response to review
56b6436 undo unintended change
e86b409 undo testing change
13f8a90 add memleak_tolerance variable for tests
b80e839 Merge pull request #634 from billsacks/list_tests
aa3d539 Merge branch 'master' of github.com:ESMCI/cime
019f523 Merge pull request #636 from ESMCI/jgfouca/update_sandia_envs
f397f1a Fix pylint issues
3bd480a Update sandia machines to use SEMS smart modules
094f438 Merge pull request #635 from jedwards4b/cobalt_walltimemax_fix
3b64f3a Merge branch 'master' of github.com:ESMCI/cime
edecd05 Merge pull request #619 from jedwards4b/cprnc_cmake_update
bc65a81 Merge pull request #633 from jedwards4b/create_test_fix
fa05f41 response to review
d0b3b45 fix walltime max specification for mira/cetus
b58cfd4 Merge branch 'master' of github.com:ESMCI/cime
7296701 now looping over all possible default values in namelist_definition_drv.xml - significantly shortened driver buildnml
91cc6b6 Merge pull request #632 from Katetc/master
df5a955 add INCOMPLETE_PHASE
e98556f fixed doctest issue
218f1b0 st_archive should use config_files.xml additional sanity check for CIMEROOT
858c466 Merge commit '45c1c327749d755ec9ded868a5e2ecf688949f31' into list_tests
ef47d25 Add --list option to query_testlists
19c4e62 remove incorrect comment
8ab062b Properly include extra_args in test of query_testlists
eb706b9 Add --count option to query_testlists
b244dce More fixes for spaces in compiler names
a7275e3 fixed more bugs necessary to run prealpha and prebeta aux tests
41a5a8a Update to fix errors about not enough comp tasks for io tasks
60160ef Add a smoke integration test for query_testlists
2640468 Merge pull request #1 from ESMCI/master
674a0d1 remove logic to resolve from env
363e013 warn if variable is resolved from env
8365444 Merge pull request #597 from billsacks/archive_cism_initial_hist
f7d80da Minor cleanup
0ecdd23 Get logger set up correctly
e74e0ab fix logic of env logicals
0c33bc0 cleanup erp test for nag
45c1c32 Merge pull request #622 from ESMCI/jgfou…
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0f241db response to comments 1007a7a cannot predetermin ndims here 99ef07d Merge pull request #1241 from NCAR/free_new_allocs 29ed162 free recently allocated vars fbc3584 Merge pull request #1239 from NCAR/dontuse_nc_max 63dee3d Merge pull request #1240 from NCAR/limitto2GiB 64f2492 limit to 2GiB due to romio bug 29aee05 dont use NC_MAX values d831ad3 Merge pull request #1231 from mgduda/mpi_type_fix e996bdb Merge pull request #1222 from NCAR/ejh_autoconf_logging 426af22 Partial fix for incorrect type of 'mpi_type' in pioc_support.c 7eb724f added enable-logging option to autotools build git-subtree-dir: src/externals/pio2 git-subtree-split: 0f241db88cfee1912a2769a052dba0d2d79f83d5
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A few additional changes to getting Cori (haswell and KNL nodes) to work. Not all of the tests pass yet.
jgfouca
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Mar 14, 2018
A few additional changes to getting Cori (haswell and KNL nodes) to work. Not all of the tests pass yet.
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A few additional changes to getting Cori (haswell and KNL nodes) to work.
Not all of the tests pass yet.
Fixes #1004