Update CIME to 5.2.0 #1300

rljacob · 2017-03-07T18:33:49Z

Update CIME to version 5.2 after it has received all of the ACME 5.1 changes.

New in CIME5.2
Some system test refactoring for improved reuse of tests
Single test no longer has external SHAREDLIBROOT setting
New flag in create_clone --cime-output-root to support cloning across user
Add runtime env to provenance output.
Add schema files for config_batch, config_compsets, config_machines, config_pes xml files.
Add model dependent config_component_$model.xml files for driver
Change several xml variables of the form XXX_COMP to variables of the
form XXX with values for each COMP. NOTE: Perl scripts in component models can no
longer read these COMP variables directely - they must now use xmlquery.
Build gptl prior to MCT. Performance improvements in buildnml
Critical namelist bug fix for datm, Refactor xmlquery tool
Fix bless_test_results, move config_build to config_compilers.
Refactor config_grids.xml refactor,Fix pea test, testreporter fixes
Remove CCSM_BASELINE variable - replaced with BASELINE_ROOT
Add error checks in xmlquery and xmlchange
Improved build logging, --output-root option, fix issues with user_mods,
Fix for ERP tests, Fix for testmods recursion, pylint testing extended
Change when preview_namelists is run, first in case.build and less frequently overall
Change where sharedlib builds are installed to avoid conflicts in builds
Convert the driver and data model build namelist scripts to python,
add xml schema checks for config_component and namelist_definition files
Better TestStatus for incomplete tests.
Allow separate liquid and solid runoff mapping files from land ice.

Fixes #1245
Fixes #1227
Fixes #1210
Fixes #1177
Fixes #916

[BFB]

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…

Merge commit '83634512187f89f012c73f3e42e0a1c1dd0b3ab8' into rljacob/cime/uptocime5.2.0 Bring in cime5.2.0 with a git subtree merge --squash Most conflicts for .py files resolved by using cime5.2.0 version. Conflicts: cime/cime_config/acme/allactive/config_pes.xml cime/cime_config/acme/allactive/config_pesall.xml cime/cime_config/acme/allactive/testmods_dirs/cam/outfrq9s/shell_commands cime/cime_config/acme/allactive/testmods_dirs/cam/outfrq9s/xmlchange_cmnds cime/cime_config/acme/allactive/testmods_dirs/force_netcdf_pio/shell_commands cime/cime_config/acme/allactive/testmods_dirs/force_netcdf_pio/xmlchange_cmnds cime/cime_config/acme/config_grids.xml cime/cime_config/acme/machines/Makefile cime/cime_config/acme/machines/config_batch.xml cime/cime_config/acme/machines/config_build.xml cime/cime_config/acme/machines/config_compilers.xml cime/cime_config/acme/machines/config_machines.xml cime/cime_config/acme/testmods_dirs/allactive/cam/outfrq9s/xmlchange_cmnds cime/cime_config/acme/testmods_dirs/allactive/force_netcdf_pio/xmlchange_cmnds cime/components/data_comps/datm/cime_config/config_component.xml cime/components/data_comps/dlnd/cime_config/config_component.xml cime/driver_cpl/cime_config/buildnml cime/driver_cpl/cime_config/config_component.xml cime/scripts/Tools/taskmaker cime/utils/python/CIME/SystemTests/homme.py cime/utils/python/CIME/XML/machines.py cime/utils/python/CIME/XML/pes.py cime/utils/python/CIME/bless_test_results.py cime/utils/python/CIME/build.py cime/utils/python/CIME/compare_test_results.py cime/utils/python/CIME/provenance.py cime/utils/python/CIME/task_maker.py cime/utils/python/CIME/test_scheduler.py cime/utils/python/CIME/utils.py cime/utils/python/update_acme_tests.py

ACME is still using the older algorithm in shr_orb_cosz so restore that.

Conflicts: cime/utils/python/update_acme_tests.py

…rce_netcdf_pio working

Change all instances of ROF2OCN_RMAPNAME to pairs of ROF2OCN_ICE_RMAPNAME and ROF2OCN_LIQ_RMAPNAME. The same mapfile is used for both.

Get HOMME test working again

Apparently too much of our build infrastructure cannot handle it.

Update config files with the results of resolving conlicts after a merge of rljacob/uptocime5.2 to next. modified: ../config_grids.xml modified: config_batch.xml modified: config_machines.xml

Add ARCHIVE_SPEC_FILE entry to config_files.xml. Needed for the new splitting of the archive configs.

Otherwise, the appended e-6 later will result in an invalid number.

Make sure OCN_NCPL is still 1 for A cases which now have SLND instead of DLND%NULL. Keeps BFB compared to 5.1 A cases.

Update acme's main config_archive.xml to version 2.0 remove data model entries. replace dart with esp.

This commit updates all 3 MPAS submodules to include an MPAS Makefile change that supports CIME5.2. Specifically, it brings in this MPAS framework commit: commit 2a73060 Author: James Foucar <[email protected]> Date: Fri Feb 17 11:41:29 2017 -0700 Fix incompatibilities with CIME 5.2 New submodule hashes are: mpas-o: 117b541 mpas-cice: a09734c mpasli: a73c64c

rljacob · 2017-03-08T00:33:57Z

This PR was extensively reviewed in its old version (PR #1261) and fixes from that branch were cherry picked on to this one and verified to still work.

testing by hand: A cases and low WCYCL are still BFB.
MPAS LISIO builds and runs.

rljacob · 2017-03-08T00:40:24Z

Merged to next.

The A case was slightly redefined to use SLND instead of DLND. That by itself won't change answers but config settings that were keying "DLND" need to now use "SLND". This commit should allow A-cases to be BFB with 5.1 baselines.

Second merge of this branch to add a fix for A-cases

This reverts commit a9a41eb. Perl syntax looks like typos

Update CIME to version 5.2 after it has received all of the ACME 5.1 changes. New in CIME5.2 Some system test refactoring for improved reuse of tests Single test no longer has external SHAREDLIBROOT setting New flag in create_clone --cime-output-root to support cloning across user Add runtime env to provenance output. Add schema files for config_batch, config_compsets, config_machines, config_pes xml files. Add model dependent config_component_$model.xml files for driver Change several xml variables of the form XXX_COMP to variables of the form XXX with values for each COMP. NOTE: Perl scripts in component models can no longer read these COMP variables directely - they must now use xmlquery. Build gptl prior to MCT. Performance improvements in buildnml Critical namelist bug fix for datm, Refactor xmlquery tool Fix bless_test_results, move config_build to config_compilers. Refactor config_grids.xml refactor,Fix pea test, testreporter fixes Remove CCSM_BASELINE variable - replaced with BASELINE_ROOT Add error checks in xmlquery and xmlchange Improved build logging, --output-root option, fix issues with user_mods, Fix for ERP tests, Fix for testmods recursion, pylint testing extended Change when preview_namelists is run, first in case.build and less frequently overall Change where sharedlib builds are installed to avoid conflicts in builds Convert the driver and data model build namelist scripts to python, add xml schema checks for config_component and namelist_definition files Better TestStatus for incomplete tests. Allow separate liquid and solid runoff mapping files from land ice. [BFB] * rljacob/cime/uptocime5.2.0: (26 commits) Revert "Fix typo in clm buildnml" ACME must do a namelist-gen at case.setup Fix typo in clm buildnml Get HOMME working again Add more SLND-based settings for A-cases. Update MPAS submodules to be CIME5.2-compatible Update main config_archive Restore OCN_NCPL for A cases Ensure CCSM_CO2_PPMV comes in as a floating point Add ARCHIVE_SPEC_FILE entry Update configs after conflict resolution Fix for clm buildnml script Disable sharing of sharedlib in ACME Fix whitespace error in ACME Makefile Get HOMME test working again Change ROF2OCN_RMAPNAME to LIQ and ICE RMAPNAME Progress getting MPAS to work with 5.2 Fix a couple places that were using the outdated 'CCSM_COMPSET' entry Need uppercase boolean strings More fixes to get SMS_Ly3.1x1_smallvilleIA.ICLM45CNCROP.melvin_gnu.force_netcdf_pio working ...

Set a default value for esmf_logging

6f0afaa Merge pull request #1496 from NCAR/ejh_next_version 67253c0 changed versions 7f1ae08 changed versions bc7091a changed versions 539b7ea Merge pull request #1495 from NCAR/ejh_release b323420 merged changes from master 12bee91 Merge pull request #1493 from NCAR/ejh_docs_fix 7942185 changed version numbers 7f16cf0 fixed fortran decomp docs ae8b174 Merge pull request #1491 from NCAR/ejh_logging 337d32a fix error handling b6522c4 now pio_init_logging() checks are returns error codes c2d8426 now pio_init_logging() checks are returns error codes a2897a0 now pio_init_logging() checks are returns error codes 2af631f Merge pull request #1489 from NCAR/ejh_mpe 9924038 whitespace cleanup bab1c80 added MPE to test_perf2.c 513190a Merge pull request #1486 from NCAR/ejh_isolate_gptl 0cc7164 no longer delete docs directory a8412c2 isolating GPTL calls 4f814ad Merge pull request #1481 from NCAR/ejh_cleanup_2 e0b1d8a fixing CDF5 issue 7b54b3e cleanup of comments in pio_types.F90 03a2580 more cleanup for pio_types.F90 826de45 more cleanup for pio_types.F90 e4cada7 starting to clean up pio_types.F90 0bf6599 Merge pull request #1479 from NCAR/ejh_cleanup 31a3ca0 whitespace cleanup de73965 fixed problem attempting to remove docs directory 96bc111 Merge pull request #1476 from NCAR/ejh_even_more_docs_2 e5190c8 Merge branch 'master' into ejh_even_more_docs_2 cf2c4a7 Merge pull request #1475 from NCAR/ejh_even_more_docs 6a239a4 Merge branch 'master' into ejh_even_more_docs f754949 Merge pull request #1472 from jedwards4b/jedwards/strnlen_fix c77ceac Merge branch 'master' into jedwards/strnlen_fix c370336 removed unneeded prototype for removed function 4b7a1fa putting vard functions in appropriate place in docs df1218b separated put functions into category by var/vara/var1/vars/vard for documentation 030e7d4 response to review 6de0e94 separated get functions into category by var/vara/var1/vars/vard for documentation 42a43de removed unused functions 2d3528b Merge pull request #1470 from NCAR/ejh_vard_functions 5aeae4e clean up daac77e redo cmake change e69191d fix warning in intel19 strnlen implicit 4819d30 adding tests for void * versions of vard functions e49c2b9 added rest of netcdf-4 atomic types b7aad13 adding more netcdf-4 atomic types to test f213355 adding netcdf-4 UBYTE type to test d83ca72 starting to add netcdf-4 atomic type tests f85ff96 test development 6618962 test development 341d753 moving iotype for loop f5b5d56 moving iotype for loop e98dff3 more tests, fixing char type bc03efa adding more testing, fixing some type stuff 44030a2 starting to add netcdf4 types 86f8a17 adding types 9f2a33a adding types 586b09c cleanup 8114b34 cleanup b6ea1d4 working on vard test 328afad working on vard test 2ec36c71 adding vard testing aa26496 disallow type conversion in vard reads (for now) b280e4a disallow type conversion in vard writes (for now) 9f84247 trying to fix cmake build f33f309 further work on vard functions c2a24fb more work on vard functions ee5c7ed starting to add vard functions f96b039 Merge pull request #1466 from NCAR/ejh_new_free_iosystem ac9612b Merge branch 'master' into ejh_new_free_iosystem 56cd15b Merge pull request #1468 from NCAR/ejh_memcheck_removal 3a4af14 removed home-rolled memory checking code d392ff9 changed examples to PIOc_free_iosystem() 9132d9f changed tests to PIOc_free_iosystem() f3840b4 documentation changes de57f08 moving function code for PIOc_free_iosystem() 5b652fb added PIOc_free_iosystem() ba3e18d Merge pull request #1465 from NCAR/ejh_doc_diagrams 8f79b6e fixed diagram in Makefile.am 76de3e1 more diagrams 6112687 adding diagrams, fixing diagrams 9b921fe more documentation improvements 09feb0e Merge pull request #1464 from NCAR/ejh_more_docs_6 9b12c1c gettng closer! e901b40 more documentation changes 866608a more documentation changes 7ba0816 Merge pull request #1462 from NCAR/ejh_more_docs_4 ce207c5 Merge branch 'master' into ejh_more_docs_4 bb52636 more doc work fe7b080 Merge pull request #1460 from NCAR/ejh_more_docs_3 f608641 moved more defgroups to beginning of file 9bccea5 moved defgroups to top of file 9f327b3 more documentation changes fe90e61 more docs work ad98a0b more docs work d282ec2 more docs work 1a1925d more docs work 54db8b2 more documentation work f9faae9 Merge pull request #1458 from NCAR/ejh_more_docs 5167124 more fortran doc changes f1b72e1 fortran documentation changes 8cc123f fortran documentation cleanup 7cffdfd Merge pull request #1454 from NCAR/ejh_even_more_docs 3765d09 more changes 81b60cc more documentation changes 0dc2f14 adding breif descriptions to defgroups 48702cd Merge pull request #1452 from NCAR/ejh_more_docs_2 9932f6e clean up error handling page f598b73 added iosystem.txt 1465335 Merge pull request #1451 from NCAR/ejh_more_docs 8b24763 adding users_guide.txt 37144d9 more documentation changes 11f4828 more documentation work 54c4530 documentation work e48b9f9 Merge pull request #1450 from NCAR/ejh_doc_images a7a576a added image 35561dd centralized COPYRIGHT notice b03bee5 adding images directory 281cf23 Merge pull request #1449 from NCAR/ejh_no_more_docs_folder 4fa0e85 removed docs cb379e9 Merge pull request #1448 from NCAR/ejh_check_developer_docs_in_travis 7e9209f changed --enable-docs to --enable-developer-docs 167d331 Merge pull request #1447 from NCAR/ejh_try_3 5188bc5 documentation fix for --enable-developer-docs abb1339 Merge pull request #1446 from NCAR/ejh_again ad5f1f1 added graphviz, working on fortranfree format thing 9be9905 moved more deprecated tags, working on fortranfree format thing 1949bb9 moved deprecated tag 4f9327e map f90 to FortranFree for doxygen cfc738d map f90 to FortranFree for doxygen 332199d added doxygen 4ee91b5 now building doc 61667d2 trying to find netcdf.inc 025e7aa trusty does not let me install libnetcdff-dev 66fa92d switched back to trusty 893b9f0 adding libnetcdff-dev to travis 473c69a turning off cmake build of examples/f03 3491e45 switched to xenial dist f833104 change to trigger CI 08d0dbc Merge pull request #1445 from NCAR/ejh_test 09f7a51 fixed Makefile.am in doc/source 548170d change to trigger CI 74153a0 finished separating C API from Fortran API d28b7aa more C API documentation 828cc91 more C API documentation 31ec493 C file operations df2524b starting separate manual for C/Fortran e2a58a2 change to trigger CI 04234a4 Merge pull request #1441 from NCAR/ejh_docs_8 fafbaea Merge branch 'master' into ejh_docs_8 56c19ba Merge pull request #1440 from NCAR/ejh_docs_7 bb15b50 cause make check to build documentation and check for warnings 22ebc9f fixed last of dixygen warnings, now documentation build fails if there are warnings 2103f65 Merge branch 'master' into ejh_docs_7 6b4dcc2 fixed documentation error c6a2a3e merged ejh_docs_7 561eb3d preprocessing F90 files for doxygen 615e4c8 more documentation fixes b5e97d5 more documentation fixes 29cac1e Merge pull request #1439 from NCAR/ejh_docs_6 cd4b080 Merge branch 'master' into ejh_docs_6 2c20802 Merge pull request #1438 from NCAR/ejh_docs_5 596ee10 more documentation fixes 6dd156c merged ejh_docs_5 298090c Merge pull request #1435 from NCAR/ejh_docs_4 d6acd33 more documentation fixes 05e3081 more documentation improvements 26b530f added --enable-developer-docs option to configure dc60db6 last of doxygen warnings for C library 527b999 documentation fixes 52ac338 Merge pull request #1434 from NCAR/ejh_docs_3 883f2d0 removed unused prototype 361d809 removed unused prototype ad1bac6 documentation imrprovements 60417c2 more documentation improvements 5756c8e more documentation fixes cb942bb documentation improvement bf1c58c Merge pull request #1433 from NCAR/ejh_docs_2 fdfeecd Merge branch 'master' into ejh_docs_2 b0483f2 Merge pull request #1432 from NCAR/ejh_docs 977095f more documentation d80d0d6 more documentation fixes 5db51a6 fixing documentation d22a00c more documentation and warning fixes 6fe3aed documentation fixes 5551321 documentation fixes a91e4f3 Merge pull request #1430 from NCAR/ejh_genf90_2 966279a cleanup 643234f now generating F90 files from .in files with genf90.pl 62b859f now generating F90 files from .in files with genf90.pl 81aedfa Merge pull request #1429 from NCAR/ejh_genf90 74d7c47 added genf90.pl 917827d now generate pionfatt_mod.F90 from pionfatt_mod.F90.in in autotools build 5653a48 now generate pionfatt_mod.F90 from pionfatt_mod.F90.in in autotools build 4fdfef2 now generate pionfatt_mod.F90 from pionfatt_mod.F90.in in autotools build b813b60 now generate pionfatt_mod.F90 from pionfatt_mod.F90.in in autotools build e7ea53f removed genf90.pl dea5c70 added scripts directory 37be328 Merge pull request #1428 from NCAR/ejh_perf_5 70bff1d changed size of data to fit memory 514988d make writes really async? 3cb4c6b merged master 2c5ef5a Merge pull request #1426 from NCAR/ejh_more_changes_from_PR a3495e7 combined check_mpi() and check_mpi2() dd4fbbb perf program changes af3cab2 Merge pull request #1419 from NCAR/ejh_max_name b1d38e3 changes as suggested by Jayesh 9e6115f changes as suggested by Jayesh 230fadd Merge pull request #1416 from NCAR/ejh_perf_4 7c58bf2 added development to version 7b05637 perf test development a75df83 perf test development a074378 perf test development fd16161 perf test development adf2b3e perf test development e70aed5 made data smaller 0c40d0b changed comment 4a57b6c Merge pull request #1415 from NCAR/ejh_perf_3 98ee55a more perf test development 618833c adding async perf test 624ca79 adding async perf test 229d05d adding async perf test 84634cd adding async perf test 36b0e33 adding async perf test f265ff8 adding async perf test ffad703 adding async perf test 3e333c9 adding async perf test 21229d9 Merge pull request #1414 from wkliao/fix_my_proc_list c84b201 Merge pull request #1412 from NCAR/ejh_lt_init 82f1b7e bug fix: allocate my_proc_list after checking component_count cb217dc changed AC_PROG_LIBTOOL to LT_INIT bd08dcc Merge pull request #1405 from NCAR/ejh_perf_2 29ff099 turned on test_async_manyproc f7cafe7 made pioperf run faster b15f88a more changes to test_perf2.c 991f34b changes to test_perf2 1ab5839 changes to test_perf2 4045cd5 changes to test_perf2 eb49aa9 changes to test_perf2 72ce726 Merge pull request #1404 from NCAR/ejh_docs1 e680dcb modified doxyfile to include all C source 6005e85 doc fixes, performance program fixes 70518f4 Merge pull request #1403 from NCAR/ejh_docs1 59b88bc fixed warning 0f9122e fixe codacity warning 080fe0a fixed codacy warnings cbf0a48 returned docs directory f395aa9 changed example 6d7a936 more doc fixes 5030bf3 more doc fixes 3f0112f updated README 4e1897e fixed docs 7d33589 fixed docs a4be8eb Merge pull request #1400 from NCAR/ejh_test 7d4f6eb updated docs for github pages af8adf0 change to trigger CI 1ff5c4e updating version info for new release 748255b update cdash builds to use master not develop cf1764e Merge pull request #1397 from NCAR/ejh_turn_off_tests 1640c98 allow tests to be built but not run a29460e Merge pull request #1395 from NCAR/ejh_perf_doc 8976ba8 cleaned up docs 0b2d445 more work on getting pioperformance working on theia 9b8bafb bumped version and also added more doc for pioperformance e207ef0 improved pioperf documentation ca6b558 automated test for pioperformance a8905ee more work on pioperformance cd22cf4 adding some documentation 94e2405 Merge pull request #1388 from jedwards4b/box_optimization 077be41 clean up 63717b2 Merge pull request #1393 from NCAR/ejh_pioperformance cce2306 fixing HAVE_PAPI automake conditional 08de2ed now getting pioperfornace to build! b5c31df more work on pioperformance 93d0298 more progress on pioperformance ba3e0d6 adding timing to autotools build 9cab9b2 fix spelling error in comment ed840ec Adding "inline" to idx_to_dim_list() and coord_to_lindex() 1228cb7 Optimizing box_rearrange_create on index conversion deb68f1 optimizing some code 44c8819 correct expected result ee2ed3e optimizing some code a936f8f Merge pull request #1391 from jedwards4b/msg_overwrite_fix db941b1 rephrase for clarity fe72532 need unique space for each message sender 3b570ff switch cmake build to use malloc not bget by default a5b9293 Merge pull request #1387 from NCAR/ejh_version 73a20fb Merge branch 'master' into ejh_version d250ef2 Merge pull request #1385 from NCAR/ejh_autotools_docs 162d119 changed version 496d343 Merge pull request #1386 from NCAR/ejh_perf 3f28eed changes 8ba35c2 changs to performance measuring program e723238 now build docs for autotools build 2402895 more work on performance program 3598cb5 changes in test_perf2 2882bb9 Merge pull request #1383 from NCAR/ejh_more_codacy 5f5ce5d Merge pull request #1382 from NCAR/ejh_next 9b2ffde fixed more codacy warnings cf96820 more codacy fixes 04c33a0 fixed more codacy warnings 9027cff fixed more codacy warnings 5ebede5 fixed some codacy warnings e6e14df fixed some codacy warnings 93b963d more codacy warnings 55165df fix for codacy warning 5a9c0ef Merge pull request #1379 from NCAR/ejh_next_fix_3 8a095f1 Merge pull request #1381 from NCAR/ejh_perf2 8cd99d9 moved memory use from stack to heap 4c67551 moved memory use from stack to heap 65202a2 working on performance test 437541a more codacy fixes c13e689 more codacy fixes 2c58077 more codacy warning fixes 0eff1f1 fixed codacy warnings 0f52ba4 fixed codacy warnings in test_decomp_frame.c 5c1fa0e Merge pull request #1378 from NCAR/ejh_fortran_build b0b28e8 Merge pull request #1377 from NCAR/ejh_fix_codacy 00212e5 fixed run_test scripts f7921f8 trying to fix codacy warning 249246f added tests/general *.in files to EXTRA_DIST e0501c3 fixed Makefile.am typo 0c22124 fixing missing pio_tutil.F90 file 5e1eef0 readded tests/general/util/Makefile.am e334e14 readded tests/general/util/Makefile.am 1c0464b now generating F90 files in tests/general 90130cb fixes for make distcheck build with --enable-fortran 7605f58 fixing use of tests/unit/input.nl with distcheck b77dad0 fixing use of tests/unit/input.nl with distcheck 0cf92fb fixing use of tests/unit/input.nl with distcheck ce7416e added FCFLAGS to travis 58fccb6 turning on --enable-fortran in DISTCHECK_CONFIGURE_FLAGS for travis 956f28f now move pio_tutil to tests/general dir during configure 5ed762b working on fortran tests 0d53ff7 working on fortran tests 729d7fa merged master a59ab5e fixed codacy warning in pioc_support.c 6f5ecda fixing codacy warning in test_rearr.c dd0e973 fixing codacy warning in test_rearr.c 0725be7 Merge pull request #1376 from NCAR/ejh_next_fix_2 feae14a Merge pull request #1375 from NCAR/ejh_next_fix 71d46ce working on fortran autotools build 3f65d1b turning off parallel build in test/general 654da51 turning off parallel build in test/unit b26d031 fixing fortran build in autotools d497232 added tests/general/util/Makefile.am f301384 added fortran to travis autotools build 9153947 fixing fortran tests in autotools build d6b257e more fortran tests e8b3350 more fortran tests in autotools build 654bcb7 working on fortran tests in autotools build dbaa196 getting fortran tests working 00524dc more work on fortran tests in autotools 112804c working on general fortran tests f6b85f6 getting fortran tests working b5054f6 getting fortran tests working d01847e merged master eed88a7 fixed memory leak on error warning from codacy ed7a0ee fixed memory leak on error warning from codacy b9259f3 fixed use of uninitialized variable in topology.c f0f128a fixed incorrect use of file before it was set in pio_msg.c b5b0ca6 changed error code 28185db working on memory warning in test_rearr.c 3422b55 working on memory warning in test_rearr.c c2c8d29 fixed memory leak warning in test_rearr.c 92ab215 fixed memory leak warning in test 42ec250 Merge pull request #1374 from NCAR/ejh_travis_asan 0140312 Merge pull request #1373 from NCAR/ejh_bug_fix2 7b9cc47 merged ejh_bug_fix2 31c64d0 turning on asan for cmake build in travis f70ce39 fixed remap memory leak e55de31 fixed memory problem in logging statement 75da528 fixed warning in test_darray_multivar3.c f7ac2b0 fixed warning in test_darray_multi.c 938680d fixed warning in test_perf2.c 8dd4fdc more fortran flags, plus fix warning b1cbbba adding set_flags.am 3a34128 added Makefile.am in tests/general which does noting f798cd2 merged master 5596b4d Merge pull request #1370 from NCAR/ejh_bug_fix 2e44db6 getting fortran tests working 5c139b0 starting to add fortran tests a13a100 initial fortran build working 4e37d6e merged ejh_bug_fix 64496c8 fixed warnings c45425d merged ejh_bug_fix branch 0d3556e for travis, only address sanitize autotools build 26ae9db travis with address sanitizer 7e799c7 turned on address sanitizer in travis 154dc95 fixed memory leaks cd1d9cf fixing leak on error a240cab fixing codacy warnings in test 27a8638 clean up of test_perf2.c 63abea0 change to trigger CI 3289961 Merge pull request #1363 from NCAR/ejh_minor 1a541d8 Merge pull request #1365 from NCAR/ejh_require_pnetcdf 13c1bc1 Merge pull request #1367 from NCAR/ejh_warnings 38e16a2 Merge pull request #1366 from NCAR/ejh_more_codacy 48a4923 fixed fscan warnings 79a0e58 removed redundant test_perf1.c fe1019e added some timing to test_perf2.c b996ca4 add --disable-pnetcdf configure option and require it if pnetcdf is not found 0869129 removed unused var cffcd55 fixed memory leak on error b58ac3f removed unused var in test 88c4201 fixed missing initializations in pio_msg.c 8b2952f fixed shell script warnings 544f6c7 Merge pull request #1357 from NCAR/ejh_fix_codacy_3 ef653a6 rolling back to most recent working travis build for reasons of mental health bcbcaae switched back to pnetcdf 1.11.0 524c5c9 working on fortran build 84f1284 getting fortran build working 9e9ea92 progress on fortran autotools build ebaf86e more fortran build badb9e2 starting to add fortran build dcc8bd4 starting to add fortran build to autotools 37eb88a removed cmake build in travis 2739c71 dorking around with cmake build in travis and cursing cmake b4e8d5f switched to pnetcdf 1.10 5ec13ea switched to pnetcdf 1.10 9b182c5 switched to HDF5 1.10.4 fdd9b6e Merge pull request #1358 from jedwards4b/type_size_fix 6a9a3ff minor bug fix in fortran interface 67f44d9 now build netcdf-4 from source in travis 11c1e92 cleaning up travis script 0b499b9 fixing over-sensitive error string test_pioc.c 01f1cb9 fixing over-sensitive error string test_pioc.c fa5a046 fixing over-sensitive error string test_pioc.c f99b500 trying to install shared library pnetcdf 52915d4 trying to install shared library pnetcdf 02b1346 trying to install pnetcdf 2c73319 trying to limit travis to pr build only 0c8d71d more work on travis build 2cf6a29 more work on travis build 10fa1ff more work on travis build 0923e21 more work on travis build 4a6b779 more travis work 849ed55 Merge pull request #1342 from jedwards4b/hashtables c9d014e trying cmake build in travis 65c08f6 revert this change 8e5dc56 trying cmake build in travis ed8b6e4 some mpis dont allow MPI_DATATYPE_NULL in MPI_Type_size a1f439a trying cmake build in travis 30ce045 trying cmake build in travis 733a15a trying cmake build in travis c1efe46 trying cmake build in travis 051ffbf trying cmake build in travis ebdfa77 trying cmake build in travis 0be3522 trying cmake build in travis f28f46f Merge pull request #1353 from NCAR/ejh_test_ci_3 0062a18 improve sorting scheme 72a0cf5 fixed codacy warning 0f7b828 update cheyenne modules f4884a7 add uthash.h to Makefile.am f56b569 no need to initialize here 2ed2e97 more cleanup e73bb95 cleanup 0ac12de move varlist to hash 23d71d3 replace linked list with hash lookup ebd44d3 Merge pull request #1349 from NetCDF-World-Domination-Council/ejh_travis1 c0e6b25 fixed warning f4a1480 fixed warning a0e3d04 fixed warning fcc89c4 fixed warning 0802b58 fixed warning 3988a50 fixed warning 50afb52 fixed warning 70e0e45 fixed warning 793a786 fixed warning f5365ab fixed warning 649ddc9 fixed warning f971884 changing travis file 7587cf6 change to trigger travis 19773d5 Merge pull request #1345 from NCAR/ejh_travis 6f08d49 added travis file 1a5f3ed Merge pull request #1343 from NCAR/ejh_benchmark cf8fecf making some changes suggested by codacy bfd150e fixed memory leak 74d5da5 fixed memory leak d85c2b7 fixed memory leak fc2fc45 converting to malloc instead of VLAs to move from stack to heap 163da37 starting to put map array allocations on heap with alloc instead of VLAs 933f426 starting to put map array allocations on heap with alloc instead of VLAs dc20149 starting to put map array allocations on heap with alloc instead of VLAs a6025c8 starting to put map array allocations on heap with alloc instead of VLAs 8f37cda starting to put map array allocations on heap with alloc instead of VLAs d4b6831 added to cmake but commented out 91b9b3b added another performance test f87b5e6 added logging 52998c2 benchmark development 1f9f218 benchmark development f4e962b benchmark development 7cccd5e benchmark development 0727181 remove tar files from repo e5c2b61 working on time output 34331ce moving for-loops out of test_perf1() function 85b9961 working with time 2c5acc9 fixed indents 91c3ae8 took out fill mode testing 6ba8a3c working with timing cc35519 working with timing 0c390bf Merge pull request #1335 from jedwards4b/support_type_conversion ff6c885 fix issue raised in codacy 72cf15a add new error type, change a test 9427840 removed 2d decomp 4ce3704 added some delay bff9aa8 added capability for multiple vars ec228ca further test development 702ac8e more perf test development da90671 got working with one var 9b42613 test development fdbcce5 now writing with 3D decomposition 299c256 more test work d198da1 more test work 824864d more test work fb5fb05 more test work cfabb5c more test work 9db86c1 took out tests of bad parameters 55887b8 fix the fillvalue in test e41d24f add some tests bffeeb9 remove restrictions to data conversion 8bf9c52 merged master 6e3be58 added mailing list to README fd5865a regenerated f39290b added more files b89700e 2.4.0 build of docs bd60aa9 added docs directory e090614 Merge pull request #1330 from NCAR/ejh_remove_use_only_mpi_scatter ddef8e9 Merge pull request #1333 from NCAR/ejh_fix_pio_version_number_cmake 080baff changed pio version to 2.4.0 in cmake 4978d60 removed mpi_scatter from only clause of use statement, which causes gfortran to error d77683e Merge pull request #1327 from NCAR/ejh_dumb_null_bug ee30e09 changed version in autotools to 2.4.0 04c6110 finally fixed NULL stride issues 254b32e fixed test 85637da fixed bug 630d32f modifying performance test c4be8d7 modifying performance test e5b74d1 fixed warnings in pioc.c a94caac changing name, adding timing 0488aed starting to add performance tests 130c564 Merge pull request #1321 from NCAR/add_pnetcdf_types 5724414 modify to address issue 1314 e062f76 fix issue in sorting and add test to catch it bb6137e increase MPI_TYPE_DEPTH bf6a987 modify test and update pgi test for cheyenne 317963f Merge pull request #1319 from NCAR/develop 56dcee4 Merge branch 'trytosort' into develop 2196994 add a test 205567f still working on it b4be30d update pgi test 415fcc1 try fixing the right file 9ee227c fix syntax 0ba25df fix syntax 4bc9b01 clean up ctest scripts fbd27d8 update sitename 3878280 update cheyenne gnu build e77b2cf remove debug print statements 6bbc245 working now I think 87e57b5 better but still has issues 8061b90a try to sort arrays - not working yet 96e562f Merge pull request #1311 from NESII/skip-pkgcomp-overload 29196d0 Do not overload user-defined PKGCOMPs 4091da5 Merge pull request #1308 from t-brown/master 66a498e Bugfix to the MPI_HAS_MPIIO check. 2f0fb4a Merge pull request #1306 from wkliao/vard_multi_var cad03a9 concatenate filetypes of multiple variables for vard API 7080803 skip creating an MPI derived datatype if a request is contiguous cfd66c6 Merge pull request #1300 from wkliao/patch-2 e8bd1b2 free an MPI communicator a018098 Merge pull request #1299 from NCAR/ejh_back_5 cb2cffd removed redeclaration of ret 8402f42 added documentation e9854d6 fixed problem with _FillValue 6d2fda3 changing fill value handling in write_darray 85e008b Merge pull request #1296 from NCAR/ejh_back2 3e80380 now run examples from autotools build as well efd9b10 Merge pull request #1294 from NCAR/ejh_back 8405ee0 Merge pull request #1293 from NCAR/ejh_docs 1ec8fea clean up c3b9d9d added documentation 5a9074a clean up 054da32 merged master 5de746f test 8b50911 test development 5395f97 test development cfc45a6 test development 2c3aa55 test development 4f08d2d test development 2c02644 test development 661ebcd test development e0ba296 test development 53450db test development e538c25 test development 65c34cd test development 50a2005 test development c42c550 test development 60e98ee test development 1642ce2 test development 435aff2 test development 1b18922 test development 5e38842 fixed iotype problem 77f73c6 Merge pull request #1292 from NCAR/ejh_logging e38c997 changed README 77b720f working on test f82e4e3 cleaned up logging statements 188b8df added some logging statements b23f6f1 added test 3fc7ce8 change to trigger build 377413b Merge pull request #1288 from jedwards4b/get_vard 70f0c64 work toward runtime vard switch c8cff06 fixes for vard and nag d513eac cleanup 38230b3 working now 3189787 test_darray works ea0f97c bug fixes aac1aa0 add for get_vard 576a1b4 comply with MPI standard in usage of MPI_IN_PLACE 4836393 Merge pull request #1285 from jedwards4b/add_pnetcdf_vard2 04b00aa replace changed parameter 6aa16c2 all tests pass with and without PIO_USE_PNETCDF_VARD 944315f fix issue with check_netcdf f8c9adc getting better d1d754b fix test 37b0975 getting closer 73f0dcf not working d5ba0b3 fix unit test dd18710 appears to work now 3a490e6 add support for pnetcdf vard function f28f2f3 Merge pull request #1284 from jedwards4b/fix_nc_error_handling d57c957 handle pnetcdf/netcdf4p errors better 7c92c48 Merge pull request #1278 from NCAR/ejh_test_4 fda1302 now assume frame=0 for darray read if frame was not set cc6a5fd fixed fill value problems in PIO 4e42e46 Merge pull request #1274 from NCAR/ejh_test_3 73d2197 merged ejh_test_3 419efdb removed varm functions bb5f72a Merge pull request #1272 from NCAR/ejh_test_2 856f951 Merge pull request #1273 from NCAR/ejh_fix_master e6b38f2 undo broken warning fix 77273d2 Merge pull request #1253 from NCAR/gnutocheyenne 01fa50a removed dead makefile.am code c9b16c0 fixed problem with test_intercomm2.c 3e04656 got make distcheck working b5342af properly cleaned up all files during clean d9170b8 Merge pull request #1261 from NCAR/ejh_warnings 496cc3a Merge pull request #1268 from NCAR/ejh_test_1 eee0cf3 added new line at end of .gitignore file ceed2f2 turned off verbose output in test 2158338 fixed run test script to correctly detect failure 5097578 added to gitignore 77c4219 updated version to 2.3.1 c7627bf fixed compiler warnings a976e18 modify script for use on cheyenne 8891fc1 Merge pull request #1252 from NCAR/cheyenne_cdash_update 5e4a1d4 reorder modules be2d445 Merge pull request #1250 from t-brown/master 365d729 Adding Cray Fortran specific flags. fbc22da Merge pull request #1247 from NCAR/maxblocksize_fix 39e4f11 more reasonable maxblock value git-subtree-dir: src/externals/pio2 git-subtree-split: 6f0afaa48bbc6eed4adff36b7442746981d8d86c

@ekluzek

* minor modification in directory structure * Update input locations on Theia * Update ESMF library on Stampede2 * Update esmf library on Theia * Check for correct restart file pointer when using NUOPC * fix for latent heat and net longwave radiation * Default PIO to version 1 on Stampede and turn off ESMF logs * fix for merging preciptiation with ice melt * Enable optional checkpointing of timing data during initialization Currently a timing checkpoint is saved at the end of the first simulation day, capturing both initialization cost and possibily anomalous first simulation day performance. However, when evaluating performance of initialization for high resolution cases, this may not be sufficiently fine grain, especially if the evaluation job runs out of time before completing the first simulation day. Here the env_run.xml TPROF_IN_INIT variable is introduced that enables saving timing checkpoints at two locations within the initialization. (This adds a new namelist variable, to seq_infodata_inparm in drv_in.) TPROF_IN_INIT is FALSE by default, in which case no additional checkpoint data is output. However, existing timer names associated with the writing out of performance data are modified slightly, to better attribute time associated with the new performance data writes. [BFB] - Bit-For-Bit [NML] - Namelist Changing * Unset OMP_NUM_THREADS in MPI-only runs * fix for edison * Change DATM_CLMNCEP_YR_ALIGN for present-day compsets The land group wants DATM_CLMNCEP_YR_ALIGN to match DATM_CLMNCEP_YR_START for present-day compsets. This will make the model year align with the forcing year. * Generalize DATM_CLMNCEP_YR_ALIGN for present-day compsets As noted in the previous commit: The land group wants DATM_CLMNCEP_YR_ALIGN to match DATM_CLMNCEP_YR_START for present-day compsets. This will make the model year align with the forcing year. This commit generalizes this rule and makes the setting less prone to maintenance errors: if someone changes the default DATM_CLMNCEP_YR_START for a given forcing dataset, they don't need to remember to also change DATM_CLMNCEP_YR_ALIGN. Similarly, if a user changes DATM_CLMNCEP_YR_START in their case, then they also do not need to remember to change DATM_CLMNCEP_YR_ALIGN. * better error reporting for refcase errors * minor fix in mediator code to merge it with FV3 branch * Change optional checkpoint of initialization to mandatory The addition of a namelist variable and env_run.xml support for enabling optional checkpointing of performance data during intialization in the previous commit is backed out here. Instead a new checkpoint timing file is now output right before the beginning of the run loop, with a name consistent with the other checkpoint timing files, i.e. including the simulation timestamp in the suffix. This is not optional. The internal reworking of the checkpoint write logic and tweaking of timer names in cime_comp_mod.F90 is preserved, and missing documentation for the TPROF_TOTAL env_run.xml variable is also added to config_component_e3sm.xml. [BFB] - Bit-For-Bit * replace tabs with spaces in buildnml * Update for cime5.6.15 * check existence of scalar fields before querying their value * Update Anvil to Slurm and SoftEnv built on CentOS6 * increase wallclock time for Vnuopc_Ln9.f19_g17.X test * Split NETCDF_PATH into C and Fortran paths * add netcdf fflags * Run in acme-centos6 partition on Anvil * change anvil nodename regex for centos6 nodes * Allow machine level customization of the run_exe * Add NLDAS2 datm forcing option This is a regional, 0.125 degree data set over the U.S., for use in forcing CTSM. This is only supported for present-day compsets. For others, I am setting the end year to earlier than the start year, so that preview_namelists will abort with an error like this: ERROR: Stream CLMNLDAS2.Solar starts at year 0, but ends at earlier year -1. I wanted to prevent users from trying to set up (say) a year-1850 or 20th century transient case with these forcing data. However, I didn't feel this was a likely enough event to warrant a lot of work putting in place a more meaningful error message. * Move custom run_exe into mpirun spec * COMPOSE: add COMPOSE options to namelist_*.xml; use COMPOSE in E3SM theta-l. Update E3SM namelist files with COMPOSE options. Make the theta-l E3SM target build with COMPOSE. * Remove lines referring to rcp compsets with nldas2 forcing @ekluzek says these will be removed imminently. * Also allow machine-mpirun level customization of the run_misc_suffix * Add more information in comment * C++/Kokkos: Refine a few build pieces. 1. Add KOKOS_CXXFLAGS to CXXFLAGS. 2. Add CPPDEFS to CXXFLAGS. 3. Do not add CFLAGS to CXXFLAGS. 4. For default build (i.e., no KOKKOS_OPTIONS provided), build Kokkos --with-openmp only if case.get_build_threaded(). [BFB] * Upate env_mach_specific schema and CIME docs * Fix incorrect var refference * Reset Anvil changes * Use RawConfigParser to load saved submit options * Missed a spot in wget that needed no-check-cert [BFB] * Progress on cam CMakeLists file * set stampede2 default PIO 2 and pnetcdf 1.11.1, change flux max iteration to 5 and fix grid of F tests * fixes for running f19_f19_mg17 * add izumi to testlist * Test with changing logic for ocn-glc coupling * dont require optional arguments * fix mpi-serial * fix archive dir for stampede * Minor cleanup to previous commit Including removing the addition of ocn_c2_glcshelf to seq_rest_read and seq_rest_write from a previous commit on this branch, now that ocn_c2_glcshelf is part of infodata. * fix stampede2 pnetcdf module version * Add FindPETSc * done with raw porting, now comes debugging * Fixes * Update CIME to ESMCI cime5.8.2-2 (#2908) Update CIME to ESMCI cime5.8.2-2 Squash merge of jgfouca/branch-for-to-acme-2019-05-06 Features * Nuopc update * nldas_forcing_v2: This is a regional, 0.125 degree data set over the U.S., for use in forcing CTSM. * Change DATM_CLMNCEP_YR_ALIGN for present-day compsets: Make DATM_CLMNCEP_YR_ALIGN match DATM_CLMNCEP_YR_START. This will make the model year align with the forcing year. For example, if RUN_STARTDATE is set to 2000-01-01, then the model will use year-2000 atmospheric forcing data in the first year, etc. non-BFB for any present-day compsets using datm (mostly I-cases and G-cases). Bug fix: * Fixes to NAG flags in scripts/Tools/Makefile [non-BFB] (datm) * send run two TestStatus.log to case1 log * Updates for pleiades modified: config/cesm/machines/config_compilers.xml modified: config/cesm/machines/config_machines.xml * Small upgrade to e3sm_cime_mgmt * changes to get mom cap working again * introduction of new aofluxes calculation in mediator * updates to get pop/ww3 caps working * fixes to get GECO compset running * add --xml-driver to create_test * changes to git dice working with Si_ifrac_01 * added new grid for pop forcing * changes to have nag working * updates for merge to latest nuopc-cmeps * fixed bug in coldair outbreak setting * changes for new calendar functionality * reverted back to original version for med_phases_aofluxes_mod.F90 due to requirement for cam to use shr_flux_mod.F90 in aqua-planet mode * removed shr_cal references * removal of use_string_mod * Start of changes to datm to point to new CO2 and presaero CMIP6 future scenarios SSP files, and remove old CMIP5 RCP's * set default for PIO_REARRANGER to box rearranger * Change CMIP5 RCP to CMIP6 SSP * Correct the SSP period portion in the compset names, and get the period to run over for SSP's correct * Tool for validating transition to CMake * Remove no longer-used cime_model variable It was added earlier in this branch but the usage of it was subsequently removed. * Cleanup formatting in compute_melt_fluxes() Whitespace has been adjusted in this routine to better match the rest of the module. Also, changed variable names nCells->gsize and iCell->n to be consistent with other loops in the module. * Change DATM_CLMNCEP_YR_ALIGN for present-day compsets (PR #3093), applied to maint-5.6 branch * Fix typo * Add in the SSP5-8.5 presaero file * Change FFLAGS_NOOPT to be an append * Correct the datasets add in the new SSP1-1.9 and SSP4-3.4 co2 files * Remove the presaero SSP files that aren't there put a null file in their place in an attempt to trigger that these files aren't there and you should abort * Update for cime5.6.16 tag * fix README * Update config_machines.xml update melvin to load cmake 3.10.3 instead of 2.8.12.2 * Add x2g_*_from_lnd lists for use in prep_glc LND routines In prep_glc_mod, there are two routines (prep_glc_calc_l2x_gx and prep_glc_merge_lnd_forcing) handling coupling from LND to GLC that operate on lists of coupling fields. Currently they operate on the lists seq_flds_x2g_states and seq_flds_x2g_fluxes. However, now with the addition of the OCN-GLC coupling, those lists include coupling fields that are not coming from LND, and therefore operating over the full lists leads to errors, inappropriate calculations, or unnecessary calculations. This commit introduces two new lists that can be used instead: seq_flds_x2g_states_from_lnd, seq_flds_x2g_fluxes_from_lnd These are restricted to the coupling fields only coming from LND and therefore maintain the existing behavior for these LND->GLC prep routines. One check was removed, because it was no longer meaningful: mct_aVect_nRattr(x2g_g) will no longer be equal num_flux_fields + num_state_fields when num_flux_fields and num_state_fields are restricted to fields from LND. * Progress changing cam/buildib to python * Remove Depends files for unsupported platforms * Port Depends to cmake * changes to define and use empty groups * else statement is removed to eliminate code duplication * Get cosp integration working * bld_diff can run with any python * Homme needs to use GMAKE_J and should do a VERBOSE build * fix memleak in med_phases_prep_ocn_mod * Provide sane default for the number of create_test parallel jobs E3SM's `e3sm_developer` test suite will launch a large number of parallel build on the login node unless explicitly passing create_test the number of parallel jobs (-j/--parallel-jobs) it should use (see #2923 ). This is because the current default is set by the MAX_MPITASKS_PER_NODE machine/env config variable, which for Cori-knl is 64. This commit: * sets the default number of parallel jobs to 3 * add a possible machine config (xml or env) variable, NTEST_PARALLEL_JOBS, which can be set to override the default number on a per machine basis The parallel jobs setting priority is now (highest to lowest): 1. -j/--parallel-jobs command line argument 2. NTEST_PARALLEL_JOBS config_machines.xml or environment variable 3. the default value * bld_diff should not fail so easily * The best way to deal with the circular deps between cosp and cam is to just put all the sources into cam * bless_test_results: Be able to handle build-only tests [BFB] * added new runseq directory and removed all nuopc_runseq files * bug fixes * Set default NTEST_PARALLEL_JOBS=MAX_MPITASKS_PER_NODE and limit E3SM machines This resets the default value of NTEST_PARALLEL_JOBS to MAX_MPITASKS_PER_NODE so as to not make any behavioral changes to CESM. Warning: This is not a safe value on machine with batch systems who's login nodes are more limited than the compute nodes and therefore NTEST_PARALLEL_JOBS should be set on these systems. @jgfouca found via E3SM testing that limiting to 4 parallel jobs was required for many of the testing machines with batch systems to prevent hammering login nodes. Therefore, we set that value for these E3SM machines: * cori-haswell * cori-knl * blues * anvil * bebop * theta * titan * summit Warning: Non test machines for E3SM that have a batch system may still oversubscribe parallel test jobs. * ChangeLog should be from master * Use truncated division operator in SEQ test for py2+3 When using python 3, the SEQ test will fail to set NTASKS_* because the XML set_value expects an integer, but a float is produced. This is because of the change from the `/` operator using truncated division in python 2 to using real division in python 3. Simply replacing `/` with the truncated division operator `//` fixes the issue (available since python 2.2). * Update cori's cmake version * fixed bugs in run sequence generation * fix pylint error * address pylint issues * fix py3 lint issue * get the name right * Update CIME to ESMCI cime5.8.2-3 (PR #2938) Update CIME to ESMCI cime5.8.2-3 Squash merge of jgfouca/branch-for-to-acme-2019-05-21 Features: * Allow custom run_exe and run_misc_suffix * send run two TestStatus.log to case1 log for 2-case tests Bugs: * Fix ConfigParser fails with some saved submit_options [BFB] * Update anvil cmake * Update Livermore Computing configs [BFB] - Bit-For-Bit See confluence for a more detailed description about these tags. * Fixes for anvil * Update theta cmake * remove cmeps from cime and make it external * update cheyenne intel compiler, add DOI * make it a link * update cime hash * Fix for bebop * addign the test * Add support for performance archiving on Compy Added logic for compy to provenance.py, specified the location of the performance archive in the compy entry in config_machines.xml (enabled for all projects) and added the job progress monitoring script syslog.compy. Also removed performance archiving support for edison, now that it has been decommissioned. [BFB] - Bit-For-Bit * Fix configure to work with cmake Depends files * Fix PNETCDF for some platforms * Another try for pnetcdf * Remove duped line * Fix bug in PET timestamp Need to use build as a library, not a subprocess. [BFB] * Import some fixes * Fix bug in generating baselines Need to use the base case id when parsing test opts. [BFB] * addition uf usermods documentation * Minor refactor of kokkos stuff in build.py * Better handling of kokkos * Progress * Adds cmake 3.11.4 module to Compy's machine files [BFB] - Bit-For-Bit * Fix cmake building of atm on anlworkstation [BFB] * Implement a more-advanced way of sharing builds within test suites Implements a concept of build groups within test_scheduler. [BFB] * Swtich build group output to debug * start over with tests * move Externals.cfg to ../Externals_cime.cfg (UFSCOMP) * Cleanup whitespace / indentation * make test optional * Move MAP xml variables into shared config_component.xml These are needed for some new drv namelist variables. When they were just in config_component_e3sm.xml, CESM tests failed with a message like this: ERROR: Namelist default for variable glc2ocn_fmapname refers to unknown XML variable GLC2OCN_FMAPNAME.' * fix indentation * revert change * moving thetasl test to shared execs set * Run_sub_or_cmd is not thread safe Need to use run_cmd. * Use idmap_ignore for optional mapping files These mapping files are only needed in certain configurations. We need to use idmap_ignore so that the driver's buildnml won't abort for configurations where these mapping files aren't provided and aren't needed. * Sandiatoss3 needs newer cmake * fix build issues for nuopc, add dir to .gitignore * updates for nuopc on stampede * rework nuopc build * fix nuopc K_TestCimeCase * fix py3 issue * Add logic to control activation of glcshelf_c2_ice Previously there was not an ability to disable the new glcshelf_c2_ice coupling direction if ice was active. This commit uses the recently added ocn_c2_glcshelf flag to control glcshelf_c2_ice (in addition to the glcshelf_c2_ocn direction it already controls). The thinking is that glc-ice coupling is never expected without an active ocean and glc-ocn coupling. More refined control could be added later as situations call for it. The important result is that glcshelf_c2_ice is default false unless the ocean model driver explicitly sets the ocn_c2_glcshelf flag to true. This commit also fixes logic for calling prep_ice_shelf_calc_g2x_ix, so that it's called based on glcshelf_c2_ice instead of glcshelf_c2_ocn. * do not move mediator build * fixes for nuopc scripts_regressions_tests to work * Update CIME to ESMCI cime5.8.2-3 (PR #2967) Update CIME to ESMCI cime5.8.2-3 Squash merge of jgfouca/branch-for-to-acme-2019-06-03 Features: * Provide default for the number of create_test parallel jobs * Nuopc cmeps removed (moved to separate repository) * RCP cmip5 scenarios - these have been removed and replaced in datm with the SSP scenarios of cmip6 Bug fix: * Use truncated division operator in SEQ SystemTest for py2+3 compatibility [BFB] * Update anvils cmake version [BFB] * fix nuopc build, update for stamepede esmf lib * update esmf nuopc build on cheyenne * change hires settings to lowres * moving tests to integration * Update for cime5.8.3 * Remove duped code * Revert "Merge pull request #3085 from ESMCI/azamat/threading/dont-set-threads-for-mpi-only-runs" This reverts commit 89fad14, reversing changes made to 5c43a15. * Fix pylint error * change test to allow for nuopc * Cmake macro no longer relies on environment So test drivers need to be updated to pass Cmake data as arguments. * Better fix for cmake macros * Typo fix * Another fix * Fix some occurances of FFLAGS_NOOPT that now need FFLAGS * move so that var is defined * require ids in namelist definition files to be lower case * Build groups need to be hashable for cesm Use tuple, not list. * if CIME_DRIVER=nuopc add pylint check for nuopc files * mods for Theia slurm job scheduler * remove comment * fix for Theia * Squashed 'src/externals/pio2/' changes from 0f241db..6f0afaa 6f0afaa Merge pull request #1496 from NCAR/ejh_next_version 67253c0 changed versions 7f1ae08 changed versions bc7091a changed versions 539b7ea Merge pull request #1495 from NCAR/ejh_release b323420 merged changes from master 12bee91 Merge pull request #1493 from NCAR/ejh_docs_fix 7942185 changed version numbers 7f16cf0 fixed fortran decomp docs ae8b174 Merge pull request #1491 from NCAR/ejh_logging 337d32a fix error handling b6522c4 now pio_init_logging() checks are returns error codes c2d8426 now pio_init_logging() checks are returns error codes a2897a0 now pio_init_logging() checks are returns error codes 2af631f Merge pull request #1489 from NCAR/ejh_mpe 9924038 whitespace cleanup bab1c80 added MPE to test_perf2.c 513190a Merge pull request #1486 from NCAR/ejh_isolate_gptl 0cc7164 no longer delete docs directory a8412c2 isolating GPTL calls 4f814ad Merge pull request #1481 from NCAR/ejh_cleanup_2 e0b1d8a fixing CDF5 issue 7b54b3e cleanup of comments in pio_types.F90 03a2580 more cleanup for pio_types.F90 826de45 more cleanup for pio_types.F90 e4cada7 starting to clean up pio_types.F90 0bf6599 Merge pull request #1479 from NCAR/ejh_cleanup 31a3ca0 whitespace cleanup de73965 fixed problem attempting to remove docs directory 96bc111 Merge pull request #1476 from NCAR/ejh_even_more_docs_2 e5190c8 Merge branch 'master' into ejh_even_more_docs_2 cf2c4a7 Merge pull request #1475 from NCAR/ejh_even_more_docs 6a239a4 Merge branch 'master' into ejh_even_more_docs f754949 Merge pull request #1472 from jedwards4b/jedwards/strnlen_fix c77ceac Merge branch 'master' into jedwards/strnlen_fix c370336 removed unneeded prototype for removed function 4b7a1fa putting vard functions in appropriate place in docs df1218b separated put functions into category by var/vara/var1/vars/vard for documentation 030e7d4 response to review 6de0e94 separated get functions into category by var/vara/var1/vars/vard for documentation 42a43de removed unused functions 2d3528b Merge pull request #1470 from NCAR/ejh_vard_functions 5aeae4e clean up daac77e redo cmake change e69191d fix warning in intel19 strnlen implicit 4819d30 adding tests for void * versions of vard functions e49c2b9 added rest of netcdf-4 atomic types b7aad13 adding more netcdf-4 atomic types to test f213355 adding netcdf-4 UBYTE type to test d83ca72 starting to add netcdf-4 atomic type tests f85ff96 test development 6618962 test development 341d753 moving iotype for loop f5b5d56 moving iotype for loop e98dff3 more tests, fixing char type bc03efa adding more testing, fixing some type stuff 44030a2 starting to add netcdf4 types 86f8a17 adding types 9f2a33a adding types 586b09c cleanup 8114b34 cleanup b6ea1d4 working on vard test 328afad working on vard test 2ec36c71 adding vard testing aa26496 disallow type conversion in vard reads (for now) b280e4a disallow type conversion in vard writes (for now) 9f84247 trying to fix cmake build f33f309 further work on vard functions c2a24fb more work on vard functions ee5c7ed starting to add vard functions f96b039 Merge pull request #1466 from NCAR/ejh_new_free_iosystem ac9612b Merge branch 'master' into ejh_new_free_iosystem 56cd15b Merge pull request #1468 from NCAR/ejh_memcheck_removal 3a4af14 removed home-rolled memory checking code d392ff9 changed examples to PIOc_free_iosystem() 9132d9f changed tests to PIOc_free_iosystem() f3840b4 documentation changes de57f08 moving function code for PIOc_free_iosystem() 5b652fb added PIOc_free_iosystem() ba3e18d Merge pull request #1465 from NCAR/ejh_doc_diagrams 8f79b6e fixed diagram in Makefile.am 76de3e1 more diagrams 6112687 adding diagrams, fixing diagrams 9b921fe more documentation improvements 09feb0e Merge pull request #1464 from NCAR/ejh_more_docs_6 9b12c1c gettng closer! e901b40 more documentation changes 866608a more documentation changes 7ba0816 Merge pull request #1462 from NCAR/ejh_more_docs_4 ce207c5 Merge branch 'master' into ejh_more_docs_4 bb52636 more doc work fe7b080 Merge pull request #1460 from NCAR/ejh_more_docs_3 f608641 moved more defgroups to beginning of file 9bccea5 moved defgroups to top of file 9f327b3 more documentation changes fe90e61 more docs work ad98a0b more docs work d282ec2 more docs work 1a1925d more docs work 54db8b2 more documentation work f9faae9 Merge pull request #1458 from NCAR/ejh_more_docs 5167124 more fortran doc changes f1b72e1 fortran documentation changes 8cc123f fortran documentation cleanup 7cffdfd Merge pull request #1454 from NCAR/ejh_even_more_docs 3765d09 more changes 81b60cc more documentation changes 0dc2f14 adding breif descriptions to defgroups 48702cd Merge pull request #1452 from NCAR/ejh_more_docs_2 9932f6e clean up error handling page f598b73 added iosystem.txt 1465335 Merge pull request #1451 from NCAR/ejh_more_docs 8b24763 adding users_guide.txt 37144d9 more documentation changes 11f4828 more documentation work 54c4530 documentation work e48b9f9 Merge pull request #1450 from NCAR/ejh_doc_images a7a576a added image 35561dd centralized COPYRIGHT notice b03bee5 adding images directory 281cf23 Merge pull request #1449 from NCAR/ejh_no_more_docs_folder 4fa0e85 removed docs cb379e9 Merge pull request #1448 from NCAR/ejh_check_developer_docs_in_travis 7e9209f changed --enable-docs to --enable-developer-docs 167d331 Merge pull request #1447 from NCAR/ejh_try_3 5188bc5 documentation fix for --enable-developer-docs abb1339 Merge pull request #1446 from NCAR/ejh_again ad5f1f1 added graphviz, working on fortranfree format thing 9be9905 moved more deprecated tags, working on fortranfree format thing 1949bb9 moved deprecated tag 4f9327e map f90 to FortranFree for doxygen cfc738d map f90 to FortranFree for doxygen 332199d added doxygen 4ee91b5 now building doc 61667d2 trying to find netcdf.inc 025e7aa trusty does not let me install libnetcdff-dev 66fa92d switched back to trusty 893b9f0 adding libnetcdff-dev to travis 473c69a turning off cmake build of examples/f03 3491e45 switched to xenial dist f833104 change to trigger CI 08d0dbc Merge pull request #1445 from NCAR/ejh_test 09f7a51 fixed Makefile.am in doc/source 548170d change to trigger CI 74153a0 finished separating C API from Fortran API d28b7aa more C API documentation 828cc91 more C API documentation 31ec493 C file operations df2524b starting separate manual for C/Fortran e2a58a2 change to trigger CI 04234a4 Merge pull request #1441 from NCAR/ejh_docs_8 fafbaea Merge branch 'master' into ejh_docs_8 56c19ba Merge pull request #1440 from NCAR/ejh_docs_7 bb15b50 cause make check to build documentation and check for warnings 22ebc9f fixed last of dixygen warnings, now documentation build fails if there are warnings 2103f65 Merge branch 'master' into ejh_docs_7 6b4dcc2 fixed documentation error c6a2a3e merged ejh_docs_7 561eb3d preprocessing F90 files for doxygen 615e4c8 more documentation fixes b5e97d5 more documentation fixes 29cac1e Merge pull request #1439 from NCAR/ejh_docs_6 cd4b080 Merge branch 'master' into ejh_docs_6 2c20802 Merge pull request #1438 from NCAR/ejh_docs_5 596ee10 more documentation fixes 6dd156c merged ejh_docs_5 298090c Merge pull request #1435 from NCAR/ejh_docs_4 d6acd33 more documentation fixes 05e3081 more documentation improvements 26b530f added --enable-developer-docs option to configure dc60db6 last of doxygen warnings for C library 527b999 documentation fixes 52ac338 Merge pull request #1434 from NCAR/ejh_docs_3 883f2d0 removed unused prototype 361d809 removed unused prototype ad1bac6 documentation imrprovements 60417c2 more documentation improvements 5756c8e more documentation fixes cb942bb documentation improvement bf1c58c Merge pull request #1433 from NCAR/ejh_docs_2 fdfeecd Merge branch 'master' into ejh_docs_2 b0483f2 Merge pull request #1432 from NCAR/ejh_docs 977095f more documentation d80d0d6 more documentation fixes 5db51a6 fixing documentation d22a00c more documentation and warning fixes 6fe3aed documentation fixes 5551321 documentation fixes a91e4f3 Merge pull request #1430 from NCAR/ejh_genf90_2 966279a cleanup 643234f now generating F90 files from .in files with genf90.pl 62b859f now generating F90 files from .in files with genf90.pl 81aedfa Merge pull request #1429 from NCAR/ejh_genf90 74d7c47 added genf90.pl 917827d now generate pionfatt_mod.F90 from pionfatt_mod.F90.in in autotools build 5653a48 now generate pionfatt_mod.F90 from pionfatt_mod.F90.in in autotools build 4fdfef2 now generate pionfatt_mod.F90 from pionfatt_mod.F90.in in autotools build b813b60 now generate pionfatt_mod.F90 from pionfatt_mod.F90.in in autotools build e7ea53f removed genf90.pl dea5c70 added scripts directory 37be328 Merge pull request #1428 from NCAR/ejh_perf_5 70bff1d changed size of data to fit memory 514988d make writes really async? 3cb4c6b merged master 2c5ef5a Merge pull request #1426 from NCAR/ejh_more_changes_from_PR a3495e7 combined check_mpi() and check_mpi2() dd4fbbb perf program changes af3cab2 Merge pull request #1419 from NCAR/ejh_max_name b1d38e3 changes as suggested by Jayesh 9e6115f changes as suggested by Jayesh 230fadd Merge pull request #1416 from NCAR/ejh_perf_4 7c58bf2 added development to version 7b05637 perf test development a75df83 perf test development a074378 perf test development fd16161 perf test development adf2b3e perf test development e70aed5 made data smaller 0c40d0b changed comment 4a57b6c Merge pull request #1415 from NCAR/ejh_perf_3 98ee55a more perf test development 618833c adding async perf test 624ca79 adding async perf test 229d05d adding async perf test 84634cd adding async perf test 36b0e33 adding async perf test f265ff8 adding async perf test ffad703 adding async perf test 3e333c9 adding async perf test 21229d9 Merge pull request #1414 from wkliao/fix_my_proc_list c84b201 Merge pull request #1412 from NCAR/ejh_lt_init 82f1b7e bug fix: allocate my_proc_list after checking component_count cb217dc changed AC_PROG_LIBTOOL to LT_INIT bd08dcc Merge pull request #1405 from NCAR/ejh_perf_2 29ff099 turned on test_async_manyproc f7cafe7 made pioperf run faster b15f88a more changes to test_perf2.c 991f34b changes to test_perf2 1ab5839 changes to test_perf2 4045cd5 changes to test_perf2 eb49aa9 changes to test_perf2 72ce726 Merge pull request #1404 from NCAR/ejh_docs1 e680dcb modified doxyfile to include all C source 6005e85 doc fixes, performance program fixes 70518f4 Merge pull request #1403 from NCAR/ejh_docs1 59b88bc fixed warning 0f9122e fixe codacity warning 080fe0a fixed codacy warnings cbf0a48 returned docs directory f395aa9 changed example 6d7a936 more doc fixes 5030bf3 more doc fixes 3f0112f updated README 4e1897e fixed docs 7d33589 fixed docs a4be8eb Merge pull request #1400 from NCAR/ejh_test 7d4f6eb updated docs for github pages af8adf0 change to trigger CI 1ff5c4e updating version info for new release 748255b update cdash builds to use master not develop cf1764e Merge pull request #1397 from NCAR/ejh_turn_off_tests 1640c98 allow tests to be built but not run a29460e Merge pull request #1395 from NCAR/ejh_perf_doc 8976ba8 cleaned up docs 0b2d445 more work on getting pioperformance working on theia 9b8bafb bumped version and also added more doc for pioperformance e207ef0 improved pioperf documentation ca6b558 automated test for pioperformance a8905ee more work on pioperformance cd22cf4 adding some documentation 94e2405 Merge pull request #1388 from jedwards4b/box_optimization 077be41 clean up 63717b2 Merge pull request #1393 from NCAR/ejh_pioperformance cce2306 fixing HAVE_PAPI automake conditional 08de2ed now getting pioperfornace to build! b5c31df more work on pioperformance 93d0298 more progress on pioperformance ba3e0d6 adding timing to autotools build 9cab9b2 fix spelling error in comment ed840ec Adding "inline" to idx_to_dim_list() and coord_to_lindex() 1228cb7 Optimizing box_rearrange_create on index conversion deb68f1 optimizing some code 44c8819 correct expected result ee2ed3e optimizing some code a936f8f Merge pull request #1391 from jedwards4b/msg_overwrite_fix db941b1 rephrase for clarity fe72532 need unique space for each message sender 3b570ff switch cmake build to use malloc not bget by default a5b9293 Merge pull request #1387 from NCAR/ejh_version 73a20fb Merge branch 'master' into ejh_version d250ef2 Merge pull request #1385 from NCAR/ejh_autotools_docs 162d119 changed version 496d343 Merge pull request #1386 from NCAR/ejh_perf 3f28eed changes 8ba35c2 changs to performance measuring program e723238 now build docs for autotools build 2402895 more work on performance program 3598cb5 changes in test_perf2 2882bb9 Merge pull request #1383 from NCAR/ejh_more_codacy 5f5ce5d Merge pull request #1382 from NCAR/ejh_next 9b2ffde fixed more codacy warnings cf96820 more codacy fixes 04c33a0 fixed more codacy warnings 9027cff fixed more codacy warnings 5ebede5 fixed some codacy warnings e6e14df fixed some codacy warnings 93b963d more codacy warnings 55165df fix for codacy warning 5a9c0ef Merge pull request #1379 from NCAR/ejh_next_fix_3 8a095f1 Merge pull request #1381 from NCAR/ejh_perf2 8cd99d9 moved memory use from stack to heap 4c67551 moved memory use from stack to heap 65202a2 working on performance test 437541a more codacy fixes c13e689 more codacy fixes 2c58077 more codacy warning fixes 0eff1f1 fixed codacy warnings 0f52ba4 fixed codacy warnings in test_decomp_frame.c 5c1fa0e Merge pull request #1378 from NCAR/ejh_fortran_build b0b28e8 Merge pull request #1377 from NCAR/ejh_fix_codacy 00212e5 fixed run_test scripts f7921f8 trying to fix codacy warning 249246f added tests/general *.in files to EXTRA_DIST e0501c3 fixed Makefile.am typo 0c22124 fixing missing pio_tutil.F90 file 5e1eef0 readded tests/general/util/Makefile.am e334e14 readded tests/general/util/Makefile.am 1c0464b now generating F90 files in tests/general 90130cb fixes for make distcheck build with --enable-fortran 7605f58 fixing use of tests/unit/input.nl with distcheck b77dad0 fixing use of tests/unit/input.nl with distcheck 0cf92fb fixing use of tests/unit/input.nl with distcheck ce7416e added FCFLAGS to travis 58fccb6 turning on --enable-fortran in DISTCHECK_CONFIGURE_FLAGS for travis 956f28f now move pio_tutil to tests/general dir during configure 5ed762b working on fortran tests 0d53ff7 working on fortran tests 729d7fa merged master a59ab5e fixed codacy warning in pioc_support.c 6f5ecda fixing codacy warning in test_rearr.c dd0e973 fixing codacy warning in test_rearr.c 0725be7 Merge pull request #1376 from NCAR/ejh_next_fix_2 feae14a Merge pull request #1375 from NCAR/ejh_next_fix 71d46ce working on fortran autotools build 3f65d1b turning off parallel build in test/general 654da51 turning off parallel build in test/unit b26d031 fixing fortran build in autotools d497232 added tests/general/util/Makefile.am f301384 added fortran to travis autotools build 9153947 fixing fortran tests in autotools build d6b257e more fortran tests e8b3350 more fortran tests in autotools build 654bcb7 working on fortran tests in autotools build dbaa196 getting fortran tests working 00524dc more work on fortran tests in autotools 112804c working on general fortran tests f6b85f6 getting fortran tests working b5054f6 getting fortran tests working d01847e merged master eed88a7 fixed memory leak on error warning from codacy ed7a0ee fixed memory leak on error warning from codacy b9259f3 fixed use of uninitialized variable in topology.c f0f128a fixed incorrect use of file before it was set in pio_msg.c b5b0ca6 changed error code 28185db working on memory warning in test_rearr.c 3422b55 working on memory warning in test_rearr.c c2c8d29 fixed memory leak warning in test_rearr.c 92ab215 fixed memory leak warning in test 42ec250 Merge pull request #1374 from NCAR/ejh_travis_asan 0140312 Merge pull request #1373 from NCAR/ejh_bug_fix2 7b9cc47 merged ejh_bug_fix2 31c64d0 turning on asan for cmake build in travis f70ce39 fixed remap memory leak e55de31 fixed memory problem in logging statement 75da528 fixed warning in test_darray_multivar3.c f7ac2b0 fixed warning in test_darray_multi.c 938680d fixed warning in test_perf2.c 8dd4fdc more fortran flags, plus fix warning b1cbbba adding set_flags.am 3a34128 added Makefile.am in tests/general which does noting f798cd2 merged master 5596b4d Merge pull request #1370 from NCAR/ejh_bug_fix 2e44db6 getting fortran tests working 5c139b0 starting to add fortran tests a13a100 initial fortran build working 4e37d6e merged ejh_bug_fix 64496c8 fixed warnings c45425d merged ejh_bug_fix branch 0d3556e for travis, only address sanitize autotools build 26ae9db travis with address sanitizer 7e799c7 turned on address sanitizer in travis 154dc95 fixed memory leaks cd1d9cf fixing leak on error a240cab fixing codacy warnings in test 27a8638 clean up of test_perf2.c 63abea0 change to trigger CI 3289961 Merge pull request #1363 from NCAR/ejh_minor 1a541d8 Merge pull request #1365 from NCAR/ejh_require_pnetcdf 13c1bc1 Merge pull request #1367 from NCAR/ejh_warnings 38e16a2 Merge pull request #1366 from NCAR/ejh_more_codacy 48a4923 fixed fscan warnings 79a0e58 removed redundant test_perf1.c fe1019e added some timing to test_perf2.c b996ca4 add --disable-pnetcdf configure option and require it if pnetcdf is not found 0869129 removed unused var cffcd55 fixed memory leak on error b58ac3f removed unused var in test 88c4201 fixed missing initializations in pio_msg.c 8b2952f fixed shell script warnings 544f6c7 Merge pull request #1357 from NCAR/ejh_fix_codacy_3 ef653a6 rolling back to most recent working travis build for reasons of mental health bcbcaae switched back to pnetcdf 1.11.0 524c5c9 working on fortran build 84f1284 getting fortran build working 9e9ea92 progress on fortran autotools build ebaf86e more fortran build badb9e2 starting to add fortran build dcc8bd4 starting to add fortran build to autotools 37eb88a removed cmake build in travis 2739c71 dorking around with cmake build in travis and cursing cmake b4e8d5f switched to pnetcdf 1.10 5ec13ea switched to pnetcdf 1.10 9b182c5 switched to HDF5 1.10.4 fdd9b6e Merge pull request #1358 from jedwards4b/type_size_fix 6a9a3ff minor bug fix in fortran interface 67f44d9 now build netcdf-4 from source in travis 11c1e92 cleaning up travis script 0b499b9 fixing over-sensitive error string test_pioc.c 01f1cb9 fixing over-sensitive error string test_pioc.c fa5a046 fixing over-sensitive error string test_pioc.c f99b500 trying to install shared library pnetcdf 52915d4 trying to install shared library pnetcdf 02b1346 trying to install pnetcdf 2c73319 trying to limit travis to pr build only 0c8d71d more work on travis build 2cf6a29 more work on travis build 10fa1ff more work on travis build 0923e21 more work on travis build 4a6b779 more travis work 849ed55 Merge pull request #1342 from jedwards4b/hashtables c9d014e trying cmake build in travis 65c08f6 revert this change 8e5dc56 trying cmake build in travis ed8b6e4 some mpis dont allow MPI_DATATYPE_NULL in MPI_Type_size a1f439a trying cmake build in travis 30ce045 trying cmake build in travis 733a15a trying cmake build in travis c1efe46 trying cmake build in travis 051ffbf trying cmake build in travis ebdfa77 trying cmake build in travis 0be3522 trying cmake build in travis f28f46f Merge pull request #1353 from NCAR/ejh_test_ci_3 0062a18 improve sorting scheme 72a0cf5 fixed codacy warning 0f7b828 update cheyenne modules f4884a7 add uthash.h to Makefile.am f56b569 no need to initialize here 2ed2e97 more cleanup e73bb95 cleanup 0ac12de move varlist to hash 23d71d3 replace linked list with hash lookup ebd44d3 Merge pull request #1349 from NetCDF-World-Domination-Council/ejh_travis1 c0e6b25 fixed warning f4a1480 fixed warning a0e3d04 fixed warning fcc89c4 fixed warning 0802b58 fixed warning 3988a50 fixed warning 50afb52 fixed warning 70e0e45 fixed warning 793a786 fixed warning f5365ab fixed warning 649ddc9 fixed warning f971884 changing travis file 7587cf6 change to trigger travis 19773d5 Merge pull request #1345 from NCAR/ejh_travis 6f08d49 added travis file 1a5f3ed Merge pull request #1343 from NCAR/ejh_benchmark cf8fecf making some changes suggested by codacy bfd150e fixed memory leak 74d5da5 fixed memory leak d85c2b7 fixed memory leak fc2fc45 converting to malloc instead of VLAs to move from stack to heap 163da37 starting to put map array allocations on heap with alloc instead of VLAs 933f426 starting to put map array allocations on heap with alloc instead of VLAs dc20149 starting to put map array allocations on heap with alloc instead of VLAs a6025c8 starting to put map array allocations on heap with alloc instead of VLAs 8f37cda starting to put map array allocations on heap with alloc instead of VLAs d4b6831 added to cmake but commented out 91b9b3b added another performance test f87b5e6 added logging 52998c2 benchmark development 1f9f218 benchmark development f4e962b benchmark development 7cccd5e benchmark development 0727181 remove tar files from repo e5c2b61 working on time output 34331ce moving for-loops out of test_perf1() function 85b9961 working with time 2c5acc9 fixed indents 91c3ae8 took out fill mode testing 6ba8a3c working with timing cc35519 working with timing 0c390bf Merge pull request #1335 from jedwards4b/support_type_conversion ff6c885 fix issue raised in codacy 72cf15a add new error type, change a test 9427840 removed 2d decomp 4ce3704 added some delay bff9aa8 added capability for multiple vars ec228ca further test development 702ac8e more perf test development da90671 got working with one var 9b42613 test development fdbcce5 now writing with 3D decomposition 299c256 more test work d198da1 more test work 824864d more test work fb5fb05 more test work cfabb5c more test work 9db86c1 took out tests of bad parameters 55887b8 fix the fillvalue in test e41d24f add some tests bffeeb9 remove restrictions to data conversion 8bf9c52 merged master 6e3be58 added mailing list to README fd5865a regenerated f39290b added more files b89700e 2.4.0 build of docs bd60aa9 added docs directory e090614 Merge pull request #1330 from NCAR/ejh_remove_use_only_mpi_scatter ddef8e9 Merge pull request #1333 from NCAR/ejh_fix_pio_version_number_cmake 080baff changed pio version to 2.4.0 in cmake 4978d60 removed mpi_scatter from only clause of use statement, which causes gfortran to error d77683e Merge pull request #1327 from NCAR/ejh_dumb_null_bug ee30e09 changed version in autotools to 2.4.0 04c6110 finally fixed NULL stride issues 254b32e fixed test 85637da fixed bug 630d32f modifying performance test c4be8d7 modifying performance test e5b74d1 fixed warnings in pioc.c a94caac changing name, adding timing 0488aed starting to add performance tests 130c564 Merge pull request #1321 from NCAR/add_pnetcdf_types 5724414 modify to address issue 1314 e062f76 fix issue in sorting and add test to catch it bb6137e increase MPI_TYPE_DEPTH bf6a987 modify test and update pgi test for cheyenne 317963f Merge pull request #1319 from NCAR/develop 56dcee4 Merge branch 'trytosort' into develop 2196994 add a test 205567f still working on it b4be30d update pgi test 415fcc1 try fixing the right file 9ee227c fix syntax 0ba25df fix syntax 4bc9b01 clean up ctest scripts fbd27d8 update sitename 3878280 update cheyenne gnu build e77b2cf remove debug print statements 6bbc245 working now I think 87e57b5 better but still has issues 8061b90a try to sort arrays - not working yet 96e562f Merge pull request #1311 from NESII/skip-pkgcomp-overload 29196d0 Do not overload user-defined PKGCOMPs 4091da5 Merge pull request #1308 from t-brown/master 66a498e Bugfix to the MPI_HAS_MPIIO check. 2f0fb4a Merge pull request #1306 from wkliao/vard_multi_var cad03a9 concatenate filetypes of multiple variables for vard API 7080803 skip creating an MPI derived datatype if a request is contiguous cfd66c6 Merge pull request #1300 from wkliao/patch-2 e8bd1b2 free an MPI communicator a018098 Merge pull request #1299 from NCAR/ejh_back_5 cb2cffd removed redeclaration of ret 8402f42 added documentation e9854d6 fixed problem with _FillValue 6d2fda3 changing fill value handling in write_darray 85e008b Merge pull request #1296 from NCAR/ejh_back2 3e80380 now run examples from autotools build as well efd9b10 Merge pull request #1294 from NCAR/ejh_back 8405ee0 Merge pull request #1293 from NCAR/ejh_docs 1ec8fea clean up c3b9d9d added documentation 5a9074a clean up 054da32 merged master 5de746f test 8b50911 test development 5395f97 test development cfc45a6 test development 2c3aa55 test development 4f08d2d test development 2c02644 test development 661ebcd test development e0ba296 test development 53450db test development e538c25 test development 65c34cd test development 50a2005 test development c42c550 test development 60e98ee test development 1642ce2 test development 435aff2 test development 1b18922 test development 5e38842 fixed iotype problem 77f73c6 Merge pull request #1292 from NCAR/ejh_logging e38c997 changed README 77b720f working on test f82e4e3 cleaned up logging statements 188b8df added some logging statements b23f6f1 added test 3fc7ce8 change to trigger build 377413b Merge pull request #1288 from jedwards4b/get_vard 70f0c64 work toward runtime vard switch c8cff06 fixes for vard and nag d513eac cleanup 38230b3 working now 3189787 test_darray works ea0f97c bug fixes aac1aa0 add for get_vard 576a1b4 comply with MPI standard in usage of MPI_IN_PLACE 4836393 Merge pull request #1285 from jedwards4b/add_pnetcdf_vard2 04b00aa replace changed parameter 6aa16c2 all tests pass with and without PIO_USE_PNETCDF_VARD 944315f fix issue with check_netcdf f8c9adc getting better d1d754b fix test 37b0975 getting closer 73f0dcf not working d5ba0b3 fix unit test dd18710 appears to work now 3a490e6 add support for pnetcdf vard function f28f2f3 Merge pull request #1284 from jedwards4b/fix_nc_error_handling d57c957 handle pnetcdf/netcdf4p errors better 7c92c48 Merge pull request #1278 from NCAR/ejh_test_4 fda1302 now assume frame=0 for darray read if frame was not set cc6a5fd fixed fill value problems in PIO 4e42e46 Merge pull request #1274 from NCAR/ejh_test_3 73d2197 merged ejh_test_3 419efdb removed varm functions bb5f72a Merge pull request #1272 from NCAR/ejh_test_2 856f951 Merge pull request #1273 from NCAR/ejh_fix_master e6b38f2 undo broken warning fix 77273d2 Merge pull request #1253 from NCAR/gnutocheyenne 01fa50a removed dead makefile.am code c9b16c0 fixed problem with test_intercomm2.c 3e04656 got make distcheck working b5342af properly cleaned up all files during clean d9170b8 Merge pull request #1261 from NCAR/ejh_warnings 496cc3a Merge pull request #1268 from NCAR/ejh_test_1 eee0cf3 added new line at end of .gitignore file ceed2f2 turned off verbose output in test 2158338 fixed run test script to correctly detect failure 5097578 added to gitignore 77c4219 updated version to 2.3.1 c7627bf fixed compiler warnings a976e18 modify script for use on cheyenne 8891fc1 Merge pull request #1252 from NCAR/cheyenne_cdash_update 5e4a1d4 reorder modules be2d445 Merge pull request #1250 from t-brown/master 365d729 Adding Cray Fortran specific flags. fbc22da Merge pull request #1247 from NCAR/maxblocksize_fix 39e4f11 more reasonable maxblock value git-subtree-dir: src/externals/pio2 git-subtree-split: 6f0afaa48bbc6eed4adff36b7442746981d8d86c * fix more conflicts * Makefile cleanup for mpi-serial build * reset default pio_version to 1 * fix linker error

rljacob and others added 22 commits March 6, 2017 18:29

Restore ACME orbit calculation

5268915

ACME is still using the older algorithm in shr_orb_cosz so restore that.

Trying to get acme_developer to work

f289396

Minor change to clm buildnml

2078026

Fix MPAS compset names in ACME test suites

1f48509

Conflicts: cime/utils/python/update_acme_tests.py

More fixes to 5.2

f50ed3c

More fixes to get SMS_Ly3.1x1_smallvilleIA.ICLM45CNCROP.melvin_gnu.fo…

f826b37

…rce_netcdf_pio working

Need uppercase boolean strings

adf8bf2

Fix a couple places that were using the outdated 'CCSM_COMPSET' entry

fa11925

Progress getting MPAS to work with 5.2

41140ff

Change ROF2OCN_RMAPNAME to LIQ and ICE RMAPNAME

845b851

Change all instances of ROF2OCN_RMAPNAME to pairs of ROF2OCN_ICE_RMAPNAME and ROF2OCN_LIQ_RMAPNAME. The same mapfile is used for both.

Get HOMME test working again

0582420

Get HOMME test working again

Fix whitespace error in ACME Makefile

5daf9e5

Disable sharing of sharedlib in ACME

b4a4594

Apparently too much of our build infrastructure cannot handle it.

Fix for clm buildnml script

fc06ce2

Update configs after conflict resolution

ddf5e9d

Update config files with the results of resolving conlicts after a merge of rljacob/uptocime5.2 to next. modified: ../config_grids.xml modified: config_batch.xml modified: config_machines.xml

Add ARCHIVE_SPEC_FILE entry

37fccd5

Add ARCHIVE_SPEC_FILE entry to config_files.xml. Needed for the new splitting of the archive configs.

Ensure CCSM_CO2_PPMV comes in as a floating point

d96a9cc

Otherwise, the appended e-6 later will result in an invalid number.

Restore OCN_NCPL for A cases

250e990

Make sure OCN_NCPL is still 1 for A cases which now have SLND instead of DLND%NULL. Keeps BFB compared to 5.1 A cases.

Update main config_archive

8f883bc

Update acme's main config_archive.xml to version 2.0 remove data model entries. replace dart with esp.

rljacob added the CIME label Mar 7, 2017

rljacob assigned jgfouca Mar 7, 2017

rljacob mentioned this pull request Mar 7, 2017

Update CIME to 5.2 #1261

Closed

rljacob added the BFB PR leaves answers BFB label Mar 7, 2017

Add more SLND-based settings for A-cases.

6c42c2f

The A case was slightly redefined to use SLND instead of DLND. That by itself won't change answers but config settings that were keying "DLND" need to now use "SLND". This commit should allow A-cases to be BFB with 5.1 baselines.

rljacob added a commit that referenced this pull request Mar 8, 2017

Merge branch 'rljacob/cime/uptocime5.2.0' into next (PR #1300)

24c8d6e

Second merge of this branch to add a fix for A-cases

jgfouca added 4 commits March 8, 2017 18:13

Get HOMME working again

84aea1b

Fix typo in clm buildnml

a9a41eb

ACME must do a namelist-gen at case.setup

8bbdd3e

Revert "Fix typo in clm buildnml"

6bb00ea

This reverts commit a9a41eb. Perl syntax looks like typos

rljacob merged commit 6bb00ea into master Mar 15, 2017

rljacob added the bug fix PR label Mar 15, 2017

agsalin pushed a commit that referenced this pull request Apr 13, 2017

Merge pull request #1300 from gold2718/esmfLog

3d76b10

Set a default value for esmf_logging

rljacob mentioned this pull request May 17, 2017

Update to cime5.3-alpha10 #1490

Merged

jgfouca deleted the rljacob/cime/uptocime5.2.0 branch June 7, 2017 14:28

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Update CIME to 5.2.0 #1300

Update CIME to 5.2.0 #1300

rljacob commented Mar 7, 2017 •

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rljacob commented Mar 8, 2017

rljacob commented Mar 8, 2017

Update CIME to 5.2.0 #1300

Update CIME to 5.2.0 #1300

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rljacob commented Mar 7, 2017 • edited Loading

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rljacob commented Mar 8, 2017

rljacob commented Mar 7, 2017 •

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