Update mpas source #2918

mark-petersen · 2019-05-11T02:37:42Z

Includes:

LIGHT update (MPAS-Ocean Lagrangian particles): Adds LIGHT modes and capabilities (passive floats, improved sampling) MPAS-Dev/MPAS-Model#56
clean up ice shelf melt flag: Update sub-ice-shelf melt to remove coupled flag MPAS-Dev/MPAS-Model#164
merge coastal branch: Adds wetting and drying capabilities to RK4 with dam break MPAS-Dev/MPAS-Model#54
CONUS mesh update: CONUS mesh update MPAS-Dev/MPAS-Model#201
Major COMPASS upgrade to python 3: Update COMPASS ocean API for python 3 and using conda packages MPAS-Dev/MPAS-Model#229
Eliminate outdated -DUNDERSCORE flag: Eliminate need for -DUNDERSCORE by using F2003's ISO_C_BINDING MPAS-Dev/MPAS-Model#156
PIO Version Compatibility Check - PGI Compiler Bug Fix: PIO Version Compatibility Check - PGI Compiler Bug Fix MPAS-Dev/MPAS-Model#212

These changes do not alter E3SM standard cases or testing on next. COMPASS is the MPAS testing infrastructure. LIGHT and coastal changes are protected by flags and not used in normal E3SM tests.

[NML]
[BFB]

mark-petersen · 2019-05-11T02:41:47Z

Passes MPAS-Ocean nightly regression suite with gnu and intel/debug, and is bfb on both with previous head. In E3SM, tested with:

PASS SMS_D_Ln9.T62_oQU120_ais20.MPAS_LISIO_TEST.cori-knl_gnu RUN time=129
PASS SMS_D_Ln9.T62_oQU120_ais20.MPAS_LISIO_TEST.cori-knl_intel RUN time=380
PASS PEM_Ln9.ne30_oECv3wLI.A_WCYCL1850-DIB-ISMF_CMIP6.cori-knl_gnu COMPARE_base_modpes
PASS PET_Ln3.T62_oEC60to30v3wLI.GMPAS-DIB-IAF-ISMF.cori-knl_gnu COMPARE_base_single_thread

mark-petersen · 2019-05-20T20:05:21Z

Rebased and tested again, passes same tests as above.

mark-petersen · 2019-05-20T20:58:12Z

Because this changes a large number of files, I wanted to filter out files that have no bearing on E3SM:

cd components/mpas-source/

git diff 0ca29df --numstat  | \
grep -v core_atmosphere  | \              filter out changes to atmospheric core 
grep -v core_init_atmosphere | \          filter out changes to atmospheric init core 
grep -v 'testing_and_setup/compass' | \   COMPASS only, not used by E3SM 
grep -v 'src/core_ocean/mode_init' # ocean init mode, not used by E3SM

git diff 0ca29df --numstat  | grep -v core_atmosphere|grep -v core_init_atmosphere | grep -v 'testing_and_setup/compass' | grep -v 'src/core_ocean/mode_init'
20	20	Makefile
1	1	README.md
0	6	src/Makefile.in.E3SM
1	1	src/core_landice/Registry.xml
70	1	src/core_ocean/Registry.xml
88	1	src/core_ocean/analysis_members/Registry_lagrangian_particle_tracking.xml
1203	85	src/core_ocean/analysis_members/mpas_ocn_lagrangian_particle_tracking.F
2	2	src/core_ocean/analysis_members/mpas_ocn_okubo_weiss.F
23	10	src/core_ocean/analysis_members/mpas_ocn_okubo_weiss_eigenvalues.c
11	11	src/core_ocean/analysis_members/mpas_ocn_particle_list.F
11	0	src/core_ocean/driver/mpas_ocn_core_interface.F
5	0	src/core_ocean/mode_forward/mpas_ocn_forward_mode.F
60	3	src/core_ocean/mode_forward/mpas_ocn_time_integration_rk4.F
1	1	src/core_ocean/mode_forward/mpas_ocn_time_integration_split.F
8	2	src/core_ocean/shared/Makefile
44	12	src/core_ocean/shared/mpas_ocn_diagnostics.F
6	30	src/core_ocean/shared/mpas_ocn_surface_land_ice_fluxes.F
25	1	src/core_ocean/shared/mpas_ocn_tendency.F
309	0	src/core_ocean/shared/mpas_ocn_tidal_forcing.F
461	0	src/core_ocean/shared/mpas_ocn_wetting_drying.F
1	1	src/core_seaice/Registry.xml
1	1	src/core_sw/Registry.xml
1	1	src/core_test/Registry.xml
29	4	src/framework/mpas_pool_routines.F
22	4	src/framework/mpas_stream_manager.F
14	10	src/framework/pool_hash.c
20	11	src/framework/random_id.c

of these, the following are simply version number updates from 6.2 to 6.3:

1	1	src/core_landice/Registry.xml
1	1	src/core_seaice/Registry.xml
1	1	src/core_sw/Registry.xml
1	1	src/core_test/Registry.xml

These only involve Lagrangian particles or Okubo-Weiss diagnostics that are default off:

88	1	src/core_ocean/analysis_members/Registry_lagrangian_particle_tracking.xml
1203	85	src/core_ocean/analysis_members/mpas_ocn_lagrangian_particle_tracking.F
2	2	src/core_ocean/analysis_members/mpas_ocn_okubo_weiss.F
23	10	src/core_ocean/analysis_members/mpas_ocn_okubo_weiss_eigenvalues.c
11	11	src/core_ocean/analysis_members/mpas_ocn_particle_list.F

These involve wetting and drying in RK4 or surface forcing in stand-alone, which are not used by E3SM (but still compiled by E3SM):

60	3	src/core_ocean/mode_forward/mpas_ocn_time_integration_rk4.F
44	12	src/core_ocean/shared/mpas_ocn_diagnostics.F
309	0	src/core_ocean/shared/mpas_ocn_tidal_forcing.F
461	0	src/core_ocean/shared/mpas_ocn_wetting_drying.F

The remainder can be explained by looking at the MPAS pull requests at the top of the page, or by browsing the individual changes.

rljacob · 2019-05-21T15:33:40Z

Does this replace #2852?

mark-petersen · 2019-05-21T16:40:33Z

No, this will go first (hopefully merged to next today) and then #2852 will be after that. #2852 is not bfb and we didn't have time to run longer simulations last week, so I put this one first. All the commits on this PR are already merged onto MPAS repo, and the MPAS PRs for #2852 will be merged after this.

jonbob

OK by visual inspection

jonbob · 2019-05-21T20:02:27Z

@mark-petersen - because this PR touches one of our MPAS Registry files, it will have namelist diffs. Plus I will have to go through the process of regenerating the bld and namelist scripts -- so it may not get done today

jonbob · 2019-05-21T21:29:14Z

@mark-petersen - there's an issue with file mode_init/Registry_tidal_boundary.xml. It has missing quotes in this line:
description="Depth of the bottom of the ocean in northern-most end.
that cause the autogeneration scripts to fail

jonbob · 2019-05-21T21:31:23Z

@mark-petersen - has this code been run through the delinter?

mark-petersen · 2019-05-21T22:01:02Z

Thanks. Checking now.

Includes: 1. LIGHT update (MPAS-Ocean Lagrangian particles): MPAS-Dev/MPAS-Model#56 2. clean up ice shelf melt flag: MPAS-Dev/MPAS-Model#164 3. merge coastal branch: MPAS-Dev/MPAS-Model#54 4. CONUS mesh update: MPAS-Dev/MPAS-Model#201 5. Major COMPASS upgrade to python 3: MPAS-Dev/MPAS-Model#229 6. Eliminate outdated -DUNDERSCORE flag: MPAS-Dev/MPAS-Model#156 7. PIO Version Compatibility Check - PGI Compiler Bug Fix: MPAS-Dev/MPAS-Model#212 These changes do not alter E3SM standard cases or testing on next. COMPASS is the MPAS testing infrastructure. LIGHT and coastal changes are protected by flags and not used in normal E3SM tests.

mark-petersen · 2019-05-22T13:39:25Z

@jonbob, I de-linted and added those two quotes. Thanks for running the namelist scripts.

Update mpas source This PR update the mpas-source git submodule but only includes changes that will not impact E3SM. These changes include: * LIGHT update (MPAS-Ocean Lagrangian particles): MPAS-Dev/MPAS-Model#56 * clean up ice shelf melt flag: MPAS-Dev/MPAS-Model#164 * merge coastal branch: MPAS-Dev/MPAS-Model#54 * CONUS mesh update: MPAS-Dev/MPAS-Model#201 * Major COMPASS upgrade to python 3: MPAS-Dev/MPAS-Model#229 * Eliminate outdated -DUNDERSCORE flag: MPAS-Dev/MPAS-Model#156 * PIO Version Compatibility Check - PGI Compiler Bug Fix: MPAS-Dev/MPAS-Model#212 These changes do not alter E3SM standard cases or tested configurations. COMPASS is the MPAS testing infrastructure. LIGHT and coastal changes are protected by flags and not used in normal E3SM tests. [NML] [BFB]

jonbob · 2019-05-22T20:25:56Z

merged to next

Update mpas source This PR update the mpas-source git submodule but only includes changes that will not impact E3SM. These changes include: * LIGHT update (MPAS-Ocean Lagrangian particles): MPAS-Dev/MPAS-Model#56 * clean up ice shelf melt flag: MPAS-Dev/MPAS-Model#164 * merge coastal branch: MPAS-Dev/MPAS-Model#54 * CONUS mesh update: MPAS-Dev/MPAS-Model#201 * Major COMPASS upgrade to python 3: MPAS-Dev/MPAS-Model#229 * Eliminate outdated -DUNDERSCORE flag: MPAS-Dev/MPAS-Model#156 * PIO Version Compatibility Check - PGI Compiler Bug Fix: MPAS-Dev/MPAS-Model#212 These changes do not alter E3SM standard cases or tested configurations. COMPASS is the MPAS testing infrastructure. LIGHT and coastal changes are protected by flags and not used in normal E3SM tests. [NML] [BFB]

jonbob · 2019-05-23T16:42:22Z

merged to master

mark-petersen added mpas-ocean BFB PR leaves answers BFB labels May 11, 2019

mark-petersen requested a review from jonbob May 11, 2019 02:41

rljacob assigned jonbob May 12, 2019

mark-petersen force-pushed the mark-petersen/update_mpas_bfb branch from cab5373 to b7ad821 Compare May 20, 2019 18:59

jonbob approved these changes May 21, 2019

View reviewed changes

jonbob added the NML label May 21, 2019

mark-petersen force-pushed the mark-petersen/update_mpas_bfb branch from b7ad821 to 36763e1 Compare May 22, 2019 13:38

Update namelist scripts to reflect changes in mpas-ocean Registry files

fd97485

jonbob merged commit fd97485 into master May 23, 2019

jonbob deleted the mark-petersen/update_mpas_bfb branch May 23, 2019 16:57

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Update mpas source #2918

Update mpas source #2918

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Update mpas source #2918

Update mpas source #2918

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