Update CIME to ESMCI cime5.8.8 #3155
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Default libs might be sufficient. These are backup in case we run into missing library issues.
…9-06-10 Jgfouca/branch for acme split 2019 06 10 Changes: * Fix bug in PET timestamp (need to use build as a library, not a subprocess) (#2949) * Fix bug in generating baselines (Need to use the base case id when parsing test opts.) (#2950) * Change FFLAGS_NOPT to be an append to the normal set of flags. This reduces duplication with FFLAGS (#2922) * Add ability to ask for CMake args (get_standard_cmake_args) (#2922) * CMake macros should NOT be looking at environment, just CMake vars (#2922) * case_setup will make both macro types (Make and CMake) (#2922) * Import a FindPetsc CMake module (#2922) * Implement a more-advanced way of sharing builds within test suites (Implements a concept of build groups within test_scheduler.) (#2961) Test suite: scripts_regression_tests Test baseline: Test namelist changes: Test status: [bit for bit, roundoff, climate changing] Fixes [CIME Github issue #] User interface changes?: Update gh-pages html (Y/N)?: Code review:
move so that var is defined Move an Include statement in the Makefile so that it is defined before use. Test suite: scripts_regression_tests.py, SMS_D_Ld5.f10_f10_musgs.I2000Clm50BgcCropRtm.izumi_nag.rtm-default Test baseline: Test namelist changes: Test status: bit for bit Fixes #3142 User interface changes?: Update gh-pages html (Y/N)?: Code review:
Update Spectrum MPI module for PGI, XL and GNU.
Update XL version which has compatible parallel-netcdf install.
Update parallel-netcdf module.
More updates:
Add basic CXX settings to enable PIO2 builds. Fixes #2988
Backup config for home dir based builds in comments.
** Add options for HOME directory based builds in case performance issues are encountered with network file system. This is not enabled by default as space may not be sufficient
Upgrade PGI to 19.4
** Fixes #2980 slow compilation of CAM with PGI on Summit.
Move the batch_jobs portion of config_batch.xml to config_workflow.xml Test suite: scripts_regression_tests.py Test baseline: Test namelist changes: Test status: bit for bit Fixes [CIME Github issue #] User interface changes?: Adds a --workflow-case option to create_newcase Update gh-pages html (Y/N)?: Code review:
Use tuple, not list.
Build groups need to be hashable for cesm Use tuple, not list. Test suite: code_checker Test baseline: Test namelist changes: Test status: bit for bit Fixes [CIME Github issue #] User interface changes?: Update gh-pages html (Y/N)?: Code review: @jedwards4b
require ids in namelist definition files to be lower case. Due to issue #3144 inforce that namelist definition entries be lower case. Test suite: scripts_regression_tests.py Test baseline: Test namelist changes: Test status: bit for bit Fixes [CIME Github issue #] User interface changes?: Update gh-pages html (Y/N)?: Code review:
if CIME_DRIVER=nuopc add pylint check for nuopc files. Add the external files in the nuopc directory to code_checker if the CIME_DRIVER=nuopc Test suite: CIME_DRIVER=nuopc scripts_regression_tests.py Test baseline: Test namelist changes: Test status: bit for bit Fixes [CIME Github issue #] User interface changes?: Update gh-pages html (Y/N)?: Code review:
An earlier commit changed the job error and output from slurm.err and slurm.out to <Case Name>.run.<Job id>. This change requires a corresponding change in the compy support in provenance.py . [BFB]
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
Pio2 update Update to the latest pio2 development version 2.4.4, set pio2 as default (thought I had already done this) Test suite: scripts_regression_tests.py Test baseline: Test namelist changes: Test status: bit for bit Fixes User interface changes?: Update gh-pages html (Y/N)?: Code review:
porting Theia to slurm ... This PR aims to update Theia job scheduler to Slurm Test suite: Tested by hand on The, no other machine is affected Test baseline: N/A Test namelist changes: Test status: [bit for bit, roundoff, climate changing] Fixes [CIME Github issue #] User interface changes?: Update gh-pages html (Y/N)?: Code review:jedwards
This test was added to the e3sm_atm_integration suite modified: cime/config/e3sm/tests.py
modified: cime/config/e3sm/tests.py
There are two approaches to implement: 1: use following conditional compiling when calling erf: ifndef HAVE_ERF_INTRINSICS use shr_spfn_mod, only: erf => shr_spfn_erf endif The advantage is that developers know exactly which erf to use, also I only need to change codes for atm 2. change shr_spfn_mod.F90 to define erf interface instead of shr_spfn_erf (as suggested by Phil Jones). Tha advantage is that which erf to use can be totally controlled by shr_spfn_mod. But I need to change erf appearance in all source codes instead of cam only. Currently using approach 1. NON-BFB
Previous domain files were erroneously created using an ocean mask from the coarse oQU240 grid. This updates the ne30pg2 configuration to use new domain files generated using the gx1v6 grid file for the ocean mask. This clears up issues along coastlines and inland bodies of water, such as the Caspian and Black seas. domain files for the oECv3 grid were also generated and put on the inputdata server, so those have been included as well. [non-BFB] for ne30pg2, BFB otherwise.
* esmci_remote_for_split/master: (1867 commits) Added check to trap invalid compset names update ncpl and cpl_seq_option for mom6 overindented line fixed improve the config_compilers.xml schema async interface not working Squashed 'src/externals/pio2/' changes from 6f0afaa48..20457f902 make sure output_root path is abspath Use correct mask for ne16pg3 resolution Created test for bad compset bug, 3189 Point to new mapping files for r05 <-> f10 mapping Fix some test fails Fixes for broken stuff on master fix an issue with shr_assert_mod in mkDepends Update for cime5.8.7 revert whitespace change all stubs is not supported in nuopc Remove a file that was accidently added. Fixes for ne120 gx1v7 masks Fixes for ne120 and se CONUS grid masks resolve conflicts ... # Conflicts: # src/drivers/nuopc/cime_config/config_component.xml
…tests Because, when the command fails, it hangs forever on the python debugger.
…9-08-20 Jgfouca/branch for acme split 2019 08 20 Features: * Add new ne30 grids with active MALI * Improve accuracy of the SCM "Replay" mode * Update climate reproducibility tests (MVK, PGN, TSC) Bug Fixes: * bless_test_results: hot fix to handle empty bless logs * Fix batch submission command for summit * preview_run: Fix case where mpirun cmd uses env vars Test suite: scripts_regression_tests Test baseline: Test namelist changes: Test status: [bit for bit, roundoff, climate changing] Fixes [CIME Github issue #] User interface changes?: Update gh-pages html (Y/N)?: Code review: @jedwards4b
CISL changed the names of cheyenne login nodes. This was causing the regex matches to fail when doing a create_newcase. The regex was updated to provide better matches, and will also work if the login names are restored to the original names. Test suite: ./create_newcase --compset A --res f19_g17 --case TEST Test baseline: Test namelist changes: Test status: bit for bit Fixes [CIME Github issue #] User interface changes?: Update gh-pages html (Y/N)?: Code review:
After the cori OS update, the cori-haswell and cori-knl modules needed to be updated. PAPI was removed for cori-haswell. Test suite: scripts_regression_tests on cori-haswell, SMS.f19_g17.A.cori-knl_intel Test baseline: Test namelist changes: Test status: bit for bit Fixes [CIME Github issue #] User interface changes?: Update gh-pages html (Y/N)?: Code review:
This fixes failing nag debug builds on Izumi. Test suite: scripts_regressions_tests on izumi, SMS_D_Ld3.f45_g37_rx1.A.hobart_nag Test baseline: Test namelist changes: Test status: bit for bit Fixes [CIME Github issue #] User interface changes?: Update gh-pages html (Y/N)?: Code review:
Add support for ne120pg3 grid using tx01.v3 mask. Test suite: scripts_regressions_tests, SMS_Ln9.ne120pg3_ne120pg3_mt13.F2000climo.cheyenne_intel Test baseline: Test namelist changes: Test status: bit for bit Fixes [CIME Github issue #] User interface changes?: Update gh-pages html (Y/N)?: Code review:
…branch-for-to-acme-2019-08-26 * commit 'a9c9289f147ccce071d207fcb594152c2fb9fe89': (3265 commits) Update regex to match changed cheyenne login names We NEVER want to pass --debug to cime commands in scripts_regression_tests Update for cori modules File should not have been added back Fix nag on izumi add tx0.1v3 mask for ne120np4.pg3 Update config_machines.xml to add default test suite preview_run: Fix case where mpirun cmd uses env vars Update CIME to ESMCI cime5.8.7-2 (PR #3126) Add MVK test to e3sm_atm_nbfb test suite Refactor climate reproducibility ests for e3sm_simple env and EVV release Fix batch submission command for summit Apparently still need the PERL Switch alternative as it's still not on Cori login nodes. Added check to trap invalid compset names Unload the hugepages module (craype-hugepages2M) that is now default loaded after Cori upgrade as it causes issues with GNU-built executables. In the past, the hugepages module had no impact on our performance. Update for cime5.6.21 Update config_machines to update pgi support on cheyenne bless_test_results: hot fix to handle empty bless logs if filename is abspath use for filepath update ncpl and cpl_seq_option for mom6 ...
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Update CIME to ESMCI cime5.8.7-3 Squash merge of jgfouca/branch-for-to-acme-2019-08-26 Features: * Fix bad compset: Added a check for an invalid compset name. Bug fixes: * nml fix: If a stream filename (such as DOCN_AQP_FILENAME) is an absolute path then use it to set the filepath argument, otherwise use domain_filepath. * avoid undefined variable error when checking input files [BFB]
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jgfouca
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Host climate reproducibility tests at machine specific locations This adds the ability to specify an CIME_HTML_ROOT and CIME_URL_ROOT in config_machines.xml so that output websites produced by the climate reproducibility tests (MVK, PGN, TSC) can be copied into a location that is hosted, and the URL reported in TestStatus.log so it appears on CDASH Both CIME_HTML_ROOT and CIME_URL_ROOT can be following this hierarchy: * Environment variable * File $HOME/.cime/config * config_machines.xml CIME_HTML_ROOT and CIME_URL_ROOT are currently only specified for cori-knl and cori-haswell [BFB] * jhkennedy/jhkennedy/cime/test-http-out: Host climate reproducibility tests at machine specific locations Update CIME to ESMCI cime5.8.7-3 (PR #3155)
jgfouca
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Aug 30, 2019
Host climate reproducibility tests at machine specific locations This adds the ability to specify an CIME_HTML_ROOT and CIME_URL_ROOT in config_machines.xml so that output websites produced by the climate reproducibility tests (MVK, PGN, TSC) can be copied into a location that is hosted, and the URL reported in TestStatus.log so it appears on CDASH Both CIME_HTML_ROOT and CIME_URL_ROOT can be following this hierarchy: * Environment variable * File $HOME/.cime/config * config_machines.xml CIME_HTML_ROOT and CIME_URL_ROOT are currently only specified for cori-knl and cori-haswell [BFB] * jhkennedy/jhkennedy/cime/test-http-out: Host climate reproducibility tests at machine specific locations Update CIME to ESMCI cime5.8.7-3 (PR #3155)
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Oct 4, 2019
Update CIME to ESMCI cime5.8.7-3 Squash merge of jgfouca/branch-for-to-acme-2019-08-26 Features: * Fix bad compset: Added a check for an invalid compset name. (Fixes #3152) Bug fixes: * nml fix: If a stream filename (such as DOCN_AQP_FILENAME) is an absolute path then use it to set the filepath argument, otherwise use domain_filepath. * avoid undefined variable error when checking input files [BFB]
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Update CIME to ESMCI cime5.8.8
Squash merge of jgfouca/branch-for-to-acme-2019-08-26
Features:
Bug fixes:
[BFB]