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CIME5 user_nl scripts do not recognize array elements #1311

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jonbob opened this issue Mar 15, 2017 · 2 comments
Closed

CIME5 user_nl scripts do not recognize array elements #1311

jonbob opened this issue Mar 15, 2017 · 2 comments
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@jgfouca
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bug CIME Fixed in ESMCI Scripts

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@jonbob
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jonbob commented Mar 15, 2017

In CIME2, we could enter array elements in user_nl and have those changes picked up by the scripts. In CIME5, that no longer works. As an example, we change one array element in user_nl_datm:
tintalgo(3) = ‘coszen’
That has always worked, but in CIME5 we get the following error:
ERROR: Error in parsing namelist: 'tintalgo(3)' is not a valid variable name at line 5, column 11
It does work if we set the entire array, i.e.:
tintalgo = "linear", "linear", "coszen", "linear", "linear", "linear", "linear", "linear", "linear", "linear", "linear", “linear"
but this seems like an unnecessary loss of functionality.
@rljacob rljacob assigned rljacob and jgfouca and unassigned rljacob Mar 15, 2017
@rljacob
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rljacob commented Mar 15, 2017

Can you also enter this on ESCMI CIME issues?

@jonbob jonbob mentioned this issue Mar 15, 2017
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@jonbob
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jonbob commented Mar 15, 2017

Also tracking as ESMCI #1248

agsalin pushed a commit that referenced this issue Apr 13, 2017
@jedwards4b
Merge pull request #1311 from ESMCI/jgfouca/better_name_for_answer
7370b02 
Change flag for answer to create_newcase
@agsalin agsalin mentioned this issue Apr 16, 2017
Merged
jgfouca added a commit that referenced this issue Apr 19, 2017
@jgfouca
Merge branch 'agsalin/update-to-cime5.3' (PR #1413)
46f6a17 
Update CIME to cime5.3

Update ACME to use CIME 5.3.x up to ESMCI hash 6156e0a from Thursday 4/13.

scripts_regression_tests and acme_developer tests pass on penn workstation.

This CIME change involves a large cosmetic change in CIME. Several directories have been renamed.

    The main interface to CIME, the scripts dir remains unchanged.
    cime/cime_config is renamed to cime/config
    The Fortran source code has been consolidated in src directory: externals, components, share, and drivers
    The driver_cpl directory has been moved to src/drivers/mct to prepare for multiple coupler options
    The share/csm_share/share directory has been renamed src/share/util.
    The cime script infrastructure source, utils/python/CIME, has moved to scripts/lib/CIME.

@singhbalwinder : please make sure PNNL cluster merge look correct
@mfdeakin-sandia : please look at cprnc/CMakeLists.txt and also confirm no run_acme changes.

Fixes #1311
Fixes #1380
Fixes #1382
Fixes #1383
Fixes #1396
Fixes #1402
Fixes #1416

[BFB]

* agsalin/update-to-cime5.3: (5649 commits)
  Fix titan problem
  Reset invalid pio_numiotasks
  Fix merge mistake
  Re-add eca testmod, was somehow lost in big merge
  Restore ACME version of shr_orb_cosz
  Fixed whitespace errors in Makefile killing COSP
  HOMME test typo fix
  Fixes to get tests to pass.
  Update ACME for new CIME directory structure
  More renaming.
  Rename ACME/cime directories in prep for CIME merge
  HOMME Improvement
  More edits to README
  Suggest a more portable usage of mktemp
  Tweak a comment
  Add comment on acme side
  Fix case for new unit_testing attribute to get_mpirun
  Allow run_tests.py to auto-determine the machine name
  fix an error
  make user-compset a seperate test
  ...
jgfouca added a commit that referenced this issue Jun 2, 2017
@jgfouca
Merge branch 'agsalin/update-to-cime5.3' (PR #1413)
ab892b9 
Update CIME to cime5.3

Update ACME to use CIME 5.3.x up to ESMCI hash 6156e0a from Thursday 4/13.

scripts_regression_tests and acme_developer tests pass on penn workstation.

This CIME change involves a large cosmetic change in CIME. Several directories have been renamed.

    The main interface to CIME, the scripts dir remains unchanged.
    cime/cime_config is renamed to cime/config
    The Fortran source code has been consolidated in src directory: externals, components, share, and drivers
    The driver_cpl directory has been moved to src/drivers/mct to prepare for multiple coupler options
    The share/csm_share/share directory has been renamed src/share/util.
    The cime script infrastructure source, utils/python/CIME, has moved to scripts/lib/CIME.

@singhbalwinder : please make sure PNNL cluster merge look correct
@mfdeakin-sandia : please look at cprnc/CMakeLists.txt and also confirm no run_acme changes.

Fixes #1311
Fixes #1380
Fixes #1382
Fixes #1383
Fixes #1396
Fixes #1402
Fixes #1416

[BFB]

* agsalin/update-to-cime5.3: (5649 commits)
  Fix titan problem
  Reset invalid pio_numiotasks
  Fix merge mistake
  Re-add eca testmod, was somehow lost in big merge
  Restore ACME version of shr_orb_cosz
  Fixed whitespace errors in Makefile killing COSP
  HOMME test typo fix
  Fixes to get tests to pass.
  Update ACME for new CIME directory structure
  More renaming.
  Rename ACME/cime directories in prep for CIME merge
  HOMME Improvement
  More edits to README
  Suggest a more portable usage of mktemp
  Tweak a comment
  Add comment on acme side
  Fix case for new unit_testing attribute to get_mpirun
  Allow run_tests.py to auto-determine the machine name
  fix an error
  make user-compset a seperate test
  ...
jgfouca added a commit that referenced this issue Feb 27, 2018
@jgfouca
Merge branch 'agsalin/update-to-cime5.3' (PR #1413)
f93f0cc 
Update CIME to cime5.3

Update ACME to use CIME 5.3.x up to ESMCI hash 6156e0a from Thursday 4/13.

scripts_regression_tests and acme_developer tests pass on penn workstation.

This CIME change involves a large cosmetic change in CIME. Several directories have been renamed.

    The main interface to CIME, the scripts dir remains unchanged.
    cime/cime_config is renamed to cime/config
    The Fortran source code has been consolidated in src directory: externals, components, share, and drivers
    The driver_cpl directory has been moved to src/drivers/mct to prepare for multiple coupler options
    The share/csm_share/share directory has been renamed src/share/util.
    The cime script infrastructure source, utils/python/CIME, has moved to scripts/lib/CIME.

@singhbalwinder : please make sure PNNL cluster merge look correct
@mfdeakin-sandia : please look at cprnc/CMakeLists.txt and also confirm no run_acme changes.

Fixes #1311
Fixes #1380
Fixes #1382
Fixes #1383
Fixes #1396
Fixes #1402
Fixes #1416

[BFB]

* agsalin/update-to-cime5.3: (5649 commits)
  Fix titan problem
  Reset invalid pio_numiotasks
  Fix merge mistake
  Re-add eca testmod, was somehow lost in big merge
  Restore ACME version of shr_orb_cosz
  Fixed whitespace errors in Makefile killing COSP
  HOMME test typo fix
  Fixes to get tests to pass.
  Update ACME for new CIME directory structure
  More renaming.
  Rename ACME/cime directories in prep for CIME merge
  HOMME Improvement
  More edits to README
  Suggest a more portable usage of mktemp
  Tweak a comment
  Add comment on acme side
  Fix case for new unit_testing attribute to get_mpirun
  Allow run_tests.py to auto-determine the machine name
  fix an error
  make user-compset a seperate test
  ...
jgfouca added a commit that referenced this issue Mar 14, 2018
@jgfouca
Merge branch 'agsalin/update-to-cime5.3' (PR #1413)
3bc293f 
Update CIME to cime5.3

Update ACME to use CIME 5.3.x up to ESMCI hash 6156e0a from Thursday 4/13.

scripts_regression_tests and acme_developer tests pass on penn workstation.

This CIME change involves a large cosmetic change in CIME. Several directories have been renamed.

    The main interface to CIME, the scripts dir remains unchanged.
    cime/cime_config is renamed to cime/config
    The Fortran source code has been consolidated in src directory: externals, components, share, and drivers
    The driver_cpl directory has been moved to src/drivers/mct to prepare for multiple coupler options
    The share/csm_share/share directory has been renamed src/share/util.
    The cime script infrastructure source, utils/python/CIME, has moved to scripts/lib/CIME.

@singhbalwinder : please make sure PNNL cluster merge look correct
@mfdeakin-sandia : please look at cprnc/CMakeLists.txt and also confirm no run_acme changes.

Fixes #1311
Fixes #1380
Fixes #1382
Fixes #1383
Fixes #1396
Fixes #1402
Fixes #1416

[BFB]

* agsalin/update-to-cime5.3: (5649 commits)
  Fix titan problem
  Reset invalid pio_numiotasks
  Fix merge mistake
  Re-add eca testmod, was somehow lost in big merge
  Restore ACME version of shr_orb_cosz
  Fixed whitespace errors in Makefile killing COSP
  HOMME test typo fix
  Fixes to get tests to pass.
  Update ACME for new CIME directory structure
  More renaming.
  Rename ACME/cime directories in prep for CIME merge
  HOMME Improvement
  More edits to README
  Suggest a more portable usage of mktemp
  Tweak a comment
  Add comment on acme side
  Fix case for new unit_testing attribute to get_mpirun
  Allow run_tests.py to auto-determine the machine name
  fix an error
  make user-compset a seperate test
  ...
jgfouca pushed a commit that referenced this issue Jun 25, 2019
@jedwards4b
Squashed 'src/externals/pio2/' changes from 0f241db..6f0afaa
41c0649 
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
jgfouca added a commit that referenced this issue Jun 25, 2019
@jgfouca
Update CIME to ESMCI cime5.8.3 (#3010)
204b570 
* 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 pushed a commit that referenced this issue Apr 16, 2021
@jgfouca
Merge branch 'agsalin/update-to-cime5.3' (PR #1413)
18ae9cc 
Update CIME to cime5.3

Update ACME to use CIME 5.3.x up to ESMCI hash 6156e0a from Thursday 4/13.

scripts_regression_tests and acme_developer tests pass on penn workstation.

This CIME change involves a large cosmetic change in CIME. Several directories have been renamed.

    The main interface to CIME, the scripts dir remains unchanged.
    cime/cime_config is renamed to cime/config
    The Fortran source code has been consolidated in src directory: externals, components, share, and drivers
    The driver_cpl directory has been moved to src/drivers/mct to prepare for multiple coupler options
    The share/csm_share/share directory has been renamed src/share/util.
    The cime script infrastructure source, utils/python/CIME, has moved to scripts/lib/CIME.

@singhbalwinder : please make sure PNNL cluster merge look correct
@mfdeakin-sandia : please look at cprnc/CMakeLists.txt and also confirm no run_acme changes.

Fixes #1311
Fixes #1380
Fixes #1382
Fixes #1383
Fixes #1396
Fixes #1402
Fixes #1416

[BFB]

* agsalin/update-to-cime5.3: (5649 commits)
  Fix titan problem
  Reset invalid pio_numiotasks
  Fix merge mistake
  Re-add eca testmod, was somehow lost in big merge
  Restore ACME version of shr_orb_cosz
  Fixed whitespace errors in Makefile killing COSP
  HOMME test typo fix
  Fixes to get tests to pass.
  Update ACME for new CIME directory structure
  More renaming.
  Rename ACME/cime directories in prep for CIME merge
  HOMME Improvement
  More edits to README
  Suggest a more portable usage of mktemp
  Tweak a comment
  Add comment on acme side
  Fix case for new unit_testing attribute to get_mpirun
  Allow run_tests.py to auto-determine the machine name
  fix an error
  make user-compset a seperate test
  ...
rljacob pushed a commit that referenced this issue Apr 16, 2021
@jgfouca
Merge branch 'agsalin/update-to-cime5.3' (PR #1413)
996a9c5 
Update CIME to cime5.3

Update ACME to use CIME 5.3.x up to ESMCI hash 6156e0a from Thursday 4/13.

scripts_regression_tests and acme_developer tests pass on penn workstation.

This CIME change involves a large cosmetic change in CIME. Several directories have been renamed.

    The main interface to CIME, the scripts dir remains unchanged.
    cime/cime_config is renamed to cime/config
    The Fortran source code has been consolidated in src directory: externals, components, share, and drivers
    The driver_cpl directory has been moved to src/drivers/mct to prepare for multiple coupler options
    The share/csm_share/share directory has been renamed src/share/util.
    The cime script infrastructure source, utils/python/CIME, has moved to scripts/lib/CIME.

@singhbalwinder : please make sure PNNL cluster merge look correct
@mfdeakin-sandia : please look at cprnc/CMakeLists.txt and also confirm no run_acme changes.

Fixes #1311
Fixes #1380
Fixes #1382
Fixes #1383
Fixes #1396
Fixes #1402
Fixes #1416

[BFB]

* agsalin/update-to-cime5.3: (5649 commits)
  Fix titan problem
  Reset invalid pio_numiotasks
  Fix merge mistake
  Re-add eca testmod, was somehow lost in big merge
  Restore ACME version of shr_orb_cosz
  Fixed whitespace errors in Makefile killing COSP
  HOMME test typo fix
  Fixes to get tests to pass.
  Update ACME for new CIME directory structure
  More renaming.
  Rename ACME/cime directories in prep for CIME merge
  HOMME Improvement
  More edits to README
  Suggest a more portable usage of mktemp
  Tweak a comment
  Add comment on acme side
  Fix case for new unit_testing attribute to get_mpirun
  Allow run_tests.py to auto-determine the machine name
  fix an error
  make user-compset a seperate test
  ...
rljacob pushed a commit that referenced this issue May 6, 2021
@jgfouca
Merge branch 'agsalin/update-to-cime5.3' (PR #1413)
282b381 
Update CIME to cime5.3

Update ACME to use CIME 5.3.x up to ESMCI hash 9802d59 from Thursday 4/13.

scripts_regression_tests and acme_developer tests pass on penn workstation.

This CIME change involves a large cosmetic change in CIME. Several directories have been renamed.

    The main interface to CIME, the scripts dir remains unchanged.
    cime/cime_config is renamed to cime/config
    The Fortran source code has been consolidated in src directory: externals, components, share, and drivers
    The driver_cpl directory has been moved to src/drivers/mct to prepare for multiple coupler options
    The share/csm_share/share directory has been renamed src/share/util.
    The cime script infrastructure source, utils/python/CIME, has moved to scripts/lib/CIME.

@singhbalwinder : please make sure PNNL cluster merge look correct
@mfdeakin-sandia : please look at cprnc/CMakeLists.txt and also confirm no run_acme changes.

Fixes #1311
Fixes #1380
Fixes #1382
Fixes #1383
Fixes #1396
Fixes #1402
Fixes #1416

[BFB]

* agsalin/update-to-cime5.3: (5649 commits)
  Fix titan problem
  Reset invalid pio_numiotasks
  Fix merge mistake
  Re-add eca testmod, was somehow lost in big merge
  Restore ACME version of shr_orb_cosz
  Fixed whitespace errors in Makefile killing COSP
  HOMME test typo fix
  Fixes to get tests to pass.
  Update ACME for new CIME directory structure
  More renaming.
  Rename ACME/cime directories in prep for CIME merge
  HOMME Improvement
  More edits to README
  Suggest a more portable usage of mktemp
  Tweak a comment
  Add comment on acme side
  Fix case for new unit_testing attribute to get_mpirun
  Allow run_tests.py to auto-determine the machine name
  fix an error
  make user-compset a seperate test
  ...
rljacob pushed a commit that referenced this issue May 6, 2021
@jgfouca
Merge branch 'agsalin/update-to-cime5.3' (PR #1413)
0e7dd3b 
Update CIME to cime5.3

Update ACME to use CIME 5.3.x up to ESMCI hash 9802d59 from Thursday 4/13.

scripts_regression_tests and acme_developer tests pass on penn workstation.

This CIME change involves a large cosmetic change in CIME. Several directories have been renamed.

    The main interface to CIME, the scripts dir remains unchanged.
    cime/cime_config is renamed to cime/config
    The Fortran source code has been consolidated in src directory: externals, components, share, and drivers
    The driver_cpl directory has been moved to src/drivers/mct to prepare for multiple coupler options
    The share/csm_share/share directory has been renamed src/share/util.
    The cime script infrastructure source, utils/python/CIME, has moved to scripts/lib/CIME.

@singhbalwinder : please make sure PNNL cluster merge look correct
@mfdeakin-sandia : please look at cprnc/CMakeLists.txt and also confirm no run_acme changes.

Fixes #1311
Fixes #1380
Fixes #1382
Fixes #1383
Fixes #1396
Fixes #1402
Fixes #1416

[BFB]

* agsalin/update-to-cime5.3: (5649 commits)
  Fix titan problem
  Reset invalid pio_numiotasks
  Fix merge mistake
  Re-add eca testmod, was somehow lost in big merge
  Restore ACME version of shr_orb_cosz
  Fixed whitespace errors in Makefile killing COSP
  HOMME test typo fix
  Fixes to get tests to pass.
  Update ACME for new CIME directory structure
  More renaming.
  Rename ACME/cime directories in prep for CIME merge
  HOMME Improvement
  More edits to README
  Suggest a more portable usage of mktemp
  Tweak a comment
  Add comment on acme side
  Fix case for new unit_testing attribute to get_mpirun
  Allow run_tests.py to auto-determine the machine name
  fix an error
  make user-compset a seperate test
  ...
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