Fixes to COMPASS to support conda MPI by xylar · Pull Request #480 · MPAS-Dev/MPAS-Model

xylar · 2020-03-20T21:43:51Z

This merge converts several script calls to function calls, which seems to work more reliably with conda MPI:

The paraview extractor can now be called as a function rather than a script, and this is done during base-mesh generation and culling
SCRIP files are now created with a function call

With these changes, calls to python scripts that use NetCDF in the parallel conda enviornment will now work as long as they are called with mpirun -np 1

This merge also adds support for a conda_mpi attribute to step tags in COMPASS XML files.
If this is set to true or false, the step will have mpirun -np 1 prepended to the executable in conda environments with MPI support. If no conda_mpi attribute is specified, mpirun -np 1 is prepended only to python scripts (calls starting with python or ending with .py).

This is needed to support compass conda environments with MPI. Python scripts and modules that use the netcdf4 package with mpich support will work property if they are called with mpirun.

Changes are made to setup_testcase.py in b1a2b3b, so this commit should be merged to develop in a separate PR.

xylar · 2020-03-20T21:44:33Z

This PR is based off #468 so it should be merged with (or after) that PR.

xylar · 2020-03-20T22:01:02Z

Testing

I successfully ran all steps of the QU240wISC test case on Anvil with these changes and with the compass and mpas_tools packages from MPAS-Dev/MPAS-Tools#303 (not yet released).

xylar · 2020-04-06T14:30:33Z

I got this working on my laptop and on Grizzly today. This required modifications to the approach, but these changes mean COMPASS users will not have to do anything other than load a compass conda environment, and setup_testcase.py will figure out whether MPI is available in the conda environment or not and what to do from there.

So far, it is not necessary to specify the conda_mpi attribute on the step tag anywhere I've tested. setup_testcase.py automatically determines that it should not be used to call run.py scripts from the driver script but that it should be used elsewhere. However, the attribute is there if we discover we need it.

xylar · 2020-04-06T14:31:47Z

I will try to run all the test cases I can once #506, #507, #508, #510 and #511 are merged, and I can run cleaner tests.

This merge moves soma/4km/32to4km and soma/8km/32to8km test cases into a new subdirectory called "broken" since these test cases are not working and won't be fixed anytime soon. With this change, `./list_testcases.py` and `./setup_testcases.py` won't pick up these tests because their driver config files aren't at the expected directory level.

The Maine, QU60 and SOQU60to15 test cases now have the links to the python script for defining their vertical grids that they need to be set up successfully.

We no longer define a path to metis in the config file, so the version from the conda environment needs to be used instead.

Add support for a "conda_mpi" attribute to "step" tags. If this attribute is set to "true" and MPI is present in the conda environment, that command will be called with `mpirun` from the conda envrionment. This is needed to support compass conda enviornments with mpich. Python scripts and modules that use the netcdf4 package with mpich support don't work properly on many compute nodes (e.g. Grizzly at LANL and Anvil at ANL) unless they are prefixed with `mpirun -np 1`

The paraview extractor can now be called as a function rather than a script, and this is done during base-mesh generation and culling. SCRIP files can now also be created with a function, so a script call is replaced with a function here as well. With these changes, calls to python scripts that use NetCDF in the parallel conda enviornment will now work as long as they are called with `mpirun -np 1`

Also rename the load script for convenience.

This will make sure the compatible version of MPI gets used.

Since we can't detect automatically that this is a python script, (and that it needs to support compass mpi) we need to say so explicitly

xylar · 2020-04-09T08:38:36Z

Testing of all ocean test cases on grizzly:

Successful tests

Tests checked here were successful, those unchecked have not run yet:

Tests that fail

All these tests failed for reasons unrelated to the PR

These tests need to copy define_base_mesh.py, not link to . (the "old" way) because of a change to build_mesh.py in #495:

40: -o ocean -c Gaussian_hump -r USDEQU120cr10rr2 -t build_mesh
49: -o ocean -c coastal -r Maine -t init
50: -o ocean -c coastal -r USDEQU120cr10rr2 -t build_mesh
85: -o ocean -c hurricane -r USDEQU120at30cr10rr2 -t build_mesh
87: -o ocean -c hurricane -r USDEQU60at15cr5rr1 -t build_mesh

These tests are missing local links to a python script called ./comparison.py:

53: -o ocean -c drying_slope -r hybrid -t 1km
54: -o ocean -c drying_slope -r hybrid -t 250m
57: -o ocean -c drying_slope -r sigma -t 1km
58: -o ocean -c drying_slope -r sigma -t 250m
59: -o ocean -c drying_slope -r zstar -t 1km
60: -o ocean -c drying_slope -r zstar -t 250m
131: -o ocean -c surface_waves -r direct -t 1km
132: -o ocean -c surface_waves -r thickness_source -t 1km

All the above test cases should be fixed in #514

This test case is missing a local link to a file called ./check_particle_sampling.py :

`116: -o ocean -c soma -r 32km -t default

This test case crashes during forward run on 4 nodes (144 cores) with insufficient memory and
should be configured to indicate how many cores are actually needed:

134: -o ocean -c ziso -r 2.5km -t default

Tests that were skipped

Some have prerequisites that are broken, others are too big to test:

41: -o ocean -c Gaussian_hump -r USDEQU120cr10rr2 -t delaware: needs 40 (broken)
64: -o ocean -c global_ocean -r CUSP12 -t spin_up: too involved, too many nodes
66: -o ocean -c global_ocean -r CUSP8 -t spin_up: same as above
86: -o ocean -c hurricane -r USDEQU120at30cr10rr2 -t sandy: needs 85 (broken)
88: -o ocean -c hurricane -r USDEQU60at15cr5rr1 -t sandy: needs 87 (broken)

Ran only partly (because it takes too long):

47: -o ocean -c baroclinic_channel -r 1km -t rpe_test

xylar · 2020-04-10T12:08:19Z

@mark-petersen, this has been thoroughly tested on Grizzly and is now ready to test and merge. To test, please make sure you use the environment compass_0.1.3_mpich:

source /usr/projects/climate/SHARED_CLIMATE/anaconda_envs/base/etc/profile.d/conda.sh
conda activate compass_0.1.3_mpich

Important: you need to use this environment both to set up the test cases and to run them. If you don't use this conda environment during setup, links to the wrong mpirun will be hard-coded into run.py scripts in your work directory (or mpirun from the conda environment won't be detected, and ./setup_testcase.py won't do its magic in determining which scripts need to be called with it). If you run with a different conda environment, you risk not having libraries (such as libnetcdf) that are compatible with the version of mpirun that is being called.

…evelop Optionally add links to load_compass_env.sh in test cases #492 This is specified either in the config file or at the command line. Like #480, this involves changes to common COMPASS infrastructure and we should consider making a separate PR to develop instead of merging those changes to ocean/develop. closes #490

xylar · 2020-04-11T12:44:51Z

@mark-petersen, I'm not sure what is different in compass_0.1.3_mpich vs compass_test_mpich (or perhaps something else in my testing) but I am now seeing errors when I run analysis_mapping, no matter how many MPI tasks I use (I tried 1 or 2). I'm seeing errors when I run with 1 task on my laptop as well, but it works there when I run with 2.

So it seems like there's still something to sort out here and maybe the MPICH environment still isn't ready for general use.

pwolfram · 2020-05-14T14:03:26Z

@xylar, check_particle_sampling.py is at https://github.com/MPAS-Dev/MPAS-Model/blob/ocean/coastal/testing_and_setup/compass/ocean/soma/analysis/check_particle_sampling.py

pwolfram · 2020-05-14T14:04:46Z

comparison.py file is at https://github.com/MPAS-Dev/MPAS-Model/blob/ocean/coastal/testing_and_setup/compass/ocean/drying_slope/analysis/comparison.py

pwolfram · 2020-05-14T14:06:29Z

Can you please be more specific about what "broken link" means? Also, what is best way you propose to remediate the issue now that the file location is identified?

xylar · 2020-05-14T15:00:19Z

@pwolfram, I suggest you try setting up the test case with --work_dir and see that it fails. And debug that. I don't feel like I have the time to maintain every test case, which is why I had asked if the number of test cases could be reduced. You said, no, so I will keep reporting problems.

mark-petersen · 2020-05-18T22:18:37Z

So it seems like there's still something to sort out here and maybe the MPICH environment still isn't ready for general use.

@xylar I confirmed on LANL IC that mapping_analysis fails using compass_0.1.5, trying to run either with python or mpirun commands.

error message

(compass_0.1.5) gr1361:e3sm_coupling$ /usr/projects/climate/SHARED_CLIMATE/anaconda_envs/base/envs/compass_0.1.5/bin/mpirun -np 1 python create_E3SM_coupling_files.py
****** Creating E3SM coupling files ******
- ice_shelf_cavities set to False
- author's name autodetected from git config: Mark Petersen
- author's email autodetected from git config: mpetersen@lanl.gov
- date string autodetected from today's date: 200518
- creation date autodetected from today's date: 05/18/2020 15:08:50
- maximum ocean depth autodetected mesh file: 3000.0
- number of vertical levels in the ocean autodetected mesh file: 16
- mesh long name specified in config file: QU240kmL16E3SMv2r01
- mesh short name specified in config file: QU240E2r01

****** initial_condition_ocean ******
Disabled in .ini file

****** graph_partition_ocean ******
Disabled in .ini file

****** initial_condition_seaice ******
Disabled in .ini file

****** scrip ******
Disabled in .ini file

****** transects_and_regions ******
Disabled in .ini file

****** mapping_analysis ******
running: /usr/projects/climate/SHARED_CLIMATE/anaconda_envs/base/envs/compass_0.1.5/bin/ESMF_RegridWeightGen --source ./src_mesh.nc --destination ./dst_mesh.nc --weight map_QU240kmL16E3SMv2r01_to_0.5x0.5degree_bilinear.nc --method bilinear --netcdf4 --no_log --src_regional --ignore_unmapped
[cli_0]: write_line error; fd=5 buf=:cmd=init pmi_version=1 pmi_subversion=1
:
system msg for write_line failure : Bad file descriptor
[cli_0]: Unable to write to PMI_fd
[cli_0]: write_line error; fd=5 buf=:cmd=get_appnum
:
system msg for write_line failure : Bad file descriptor
Fatal error in PMPI_Init: Other MPI error, error stack:
MPIR_Init_thread(586):
MPID_Init(175).......: channel initialization failed
MPID_Init(463).......: PMI_Get_appnum returned -1
[cli_0]: write_line error; fd=5 buf=:cmd=abort exitcode=1093647
:
system msg for write_line failure : Bad file descriptor
!!! FAILURE !!!
Traceback (most recent call last):
  File "create_E3SM_coupling_files.py", line 127, in main
    function(config)
  File "create_E3SM_coupling_files.py", line 321, in mapping_analysis
    make_analysis_lat_lon_map(config, mesh_name)
  File "create_E3SM_coupling_files.py", line 1022, in make_analysis_lat_lon_map
    tempdir='.')
  File "/usr/projects/climate/SHARED_CLIMATE/anaconda_envs/base/envs/compass_0.1.5/lib/python3.7/site-packages/pyremap/remapper.py", line 214, in build_mapping_file
    subprocess.check_call(args, stdout=DEVNULL)
  File "/usr/projects/climate/SHARED_CLIMATE/anaconda_envs/base/envs/compass_0.1.5/lib/python3.7/subprocess.py", line 363, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/usr/projects/climate/SHARED_CLIMATE/anaconda_envs/base/envs/compass_0.1.5/bin/ESMF_RegridWeightGen', '--source', './src_mesh.nc', '--destination', './dst_mesh.nc', '--weight', 'map_QU240kmL16E3SMv2r01_to_0.5x0.5degree_bilinear.nc', '--method', 'bilinear', '--netcdf4', '--no_log', '--src_regional', '--ignore_unmapped']' returned non-zero exit status 15.

python create_E3SM_coupling_files.py
--> same error message

I can get mapping_analysis to work with conda activate compass_0.1.4:

details

python create_E3SM_coupling_files.py
WARNING:root:Setting cartopy.config["pre_existing_data_dir"] to /usr/projects/climate/SHARED_CLIMATE/anaconda_envs/base/envs/compass_0.1.4/share/cartopy. Don't worry, this is probably intended behaviour to avoid failing downloads of geological data behind a firewall.
****** Creating E3SM coupling files ******
- ice_shelf_cavities set to False
- author's name autodetected from git config: Mark Petersen
- author's email autodetected from git config: mpetersen@lanl.gov
- date string autodetected from today's date: 200518
- creation date autodetected from today's date: 05/18/2020 15:58:36
- maximum ocean depth autodetected mesh file: 3000.0
- number of vertical levels in the ocean autodetected mesh file: 16
- mesh long name specified in config file: QU240kmL16E3SMv2r01
- mesh short name specified in config file: QU240E2r01

****** initial_condition_ocean ******
Disabled in .ini file

****** graph_partition_ocean ******
Disabled in .ini file

****** initial_condition_seaice ******
Disabled in .ini file

****** scrip ******
Disabled in .ini file

****** transects_and_regions ******
Disabled in .ini file

****** mapping_analysis ******
running: /usr/projects/climate/SHARED_CLIMATE/anaconda_envs/base/envs/compass_0.1.4/bin/ESMF_RegridWeightGen --source ./src_mesh.nc --destination ./dst_mesh.nc --weight map_QU240kmL16E3SMv2r01_to_0.5x0.5degree_bilinear.nc --method bilinear --netcdf4 --no_log --src_regional --ignore_unmapped
running: /usr/projects/climate/SHARED_CLIMATE/anaconda_envs/base/envs/compass_0.1.4/bin/ESMF_RegridWeightGen --source ./src_mesh.nc --destination ./dst_mesh.nc --weight map_QU240kmL16E3SMv2r01_to_6000.0x6000.0km_10.0km_Antarctic_stereo_bilinear.nc --method bilinear --netcdf4 --no_log --src_regional --dst_regional --ignore_unmapped
running: /usr/projects/climate/SHARED_CLIMATE/anaconda_envs/base/envs/compass_0.1.4/bin/ESMF_RegridWeightGen --source ./src_mesh.nc --destination ./dst_mesh.nc --weight map_QU240kmL16E3SMv2r01_to_6000.0x6000.0km_10.0km_Arctic_stereo_bilinear.nc --method bilinear --netcdf4 --no_log --src_regional --dst_regional --ignore_unmapped
SUCCESS

This may be a clue: the mpirun command from the compass_0.1.5 directory is successful after conda activate compass_0.1.4.

details

(compass_0.1.4) gr0235:e3sm_coupling$/usr/projects/climate/SHARED_CLIMATE/anaconda_envs/base/envs/compass_0.1.5/bin/mpirun -np 1 python create_E3SM_coupling_files.py
WARNING:root:Setting cartopy.config["pre_existing_data_dir"] to /usr/projects/climate/SHARED_CLIMATE/anaconda_envs/base/envs/compass_0.1.4/share/cartopy. Don't worry, this is probably intended behaviour to avoid failing downloads of geological data behind a firewall.
****** Creating E3SM coupling files ******
- ice_shelf_cavities set to False
- author's name autodetected from git config: Mark Petersen
- author's email autodetected from git config: mpetersen@lanl.gov
- date string autodetected from today's date: 200518
- creation date autodetected from today's date: 05/18/2020 16:03:11
- maximum ocean depth autodetected mesh file: 3000.0
- number of vertical levels in the ocean autodetected mesh file: 16
- mesh long name specified in config file: QU240kmL16E3SMv2r01
- mesh short name specified in config file: QU240E2r01

****** initial_condition_ocean ******
Disabled in .ini file

****** graph_partition_ocean ******
Disabled in .ini file

****** initial_condition_seaice ******
Disabled in .ini file

****** scrip ******
Disabled in .ini file

****** transects_and_regions ******
Disabled in .ini file

****** mapping_analysis ******
running: /usr/projects/climate/SHARED_CLIMATE/anaconda_envs/base/envs/compass_0.1.4/bin/ESMF_RegridWeightGen --source ./src_mesh.nc --destination ./dst_mesh.nc --weight map_QU240kmL16E3SMv2r01_to_0.5x0.5degree_bilinear.nc --method bilinear --netcdf4 --no_log --src_regional --ignore_unmapped
running: /usr/projects/climate/SHARED_CLIMATE/anaconda_envs/base/envs/compass_0.1.4/bin/ESMF_RegridWeightGen --source ./src_mesh.nc --destination ./dst_mesh.nc --weight map_QU240kmL16E3SMv2r01_to_6000.0x6000.0km_10.0km_Antarctic_stereo_bilinear.nc --method bilinear --netcdf4 --no_log --src_regional --dst_regional --ignore_unmapped
running: /usr/projects/climate/SHARED_CLIMATE/anaconda_envs/base/envs/compass_0.1.4/bin/ESMF_RegridWeightGen --source ./src_mesh.nc --destination ./dst_mesh.nc --weight map_QU240kmL16E3SMv2r01_to_6000.0x6000.0km_10.0km_Arctic_stereo_bilinear.nc --method bilinear --netcdf4 --no_log --src_regional --dst_regional --ignore_unmapped
SUCCESS

So we don't need to revert this commit, we could temporarily point load_latest_compass.sh to 1.4.0 and everything still works.

One side note, it seems to be hanging on something for a long time IC. With all steps disabled, the create_E3SM_coupling_files.py script takes 41 seconds. Based on the output, it looks like the header section.

… ocean/develop Optionally add links to load_compass_env.sh in test cases MPAS-Dev#492 This is specified either in the config file or at the command line. Like MPAS-Dev#480, this involves changes to common COMPASS infrastructure and we should consider making a separate PR to develop instead of merging those changes to ocean/develop. closes MPAS-Dev#490

xylar added Ocean COMPASS in progress labels Mar 20, 2020

xylar requested a review from mark-petersen March 20, 2020 21:43

xylar assigned mark-petersen Mar 20, 2020

xylar mentioned this pull request Mar 20, 2020

Update conda package and compass to better support MPI MPAS-Dev/MPAS-Tools#303

Merged

xylar added this to the Bathymetry, mesh, IC for E3SM V2 milestone Mar 23, 2020

xylar mentioned this pull request Mar 24, 2020

Add COMPASS step for remapping prescribed ISMF #469

Merged

mark-petersen removed this from the Bathymetry, mesh, IC for E3SM V2 milestone Mar 24, 2020

xylar force-pushed the add_compass_mpi_support branch from e28457c to 9126dab Compare March 25, 2020 10:51

xylar mentioned this pull request Mar 26, 2020

Optionally add links to load_compass_env.sh in test cases #492

Merged

xylar force-pushed the add_compass_mpi_support branch from d1ee55b to ace9375 Compare March 29, 2020 12:54

xylar force-pushed the add_compass_mpi_support branch from ace9375 to 8f5b2d1 Compare April 6, 2020 12:46

xylar force-pushed the add_compass_mpi_support branch 3 times, most recently from 5e93015 to cd7ae92 Compare April 7, 2020 10:35

xylar added 8 commits April 8, 2020 09:08

Add missing define_vertical_trid.py links

925da04

The Maine, QU60 and SOQU60to15 test cases now have the links to the python script for defining their vertical grids that they need to be set up successfully.

Use conda env gpmetis for surface_waves/thickness_source/1km

933ec42

We no longer define a path to metis in the config file, so the version from the conda environment needs to be used instead.

Update compass environment version

9f0bb70

Also rename the load script for convenience.

Add full mpirun path to ESMF_RegridWeightGen calls

566390a

This will make sure the compatible version of MPI gets used.

Add mpi_conda to planar_hex calls

190338d

Since we can't detect automatically that this is a python script, (and that it needs to support compass mpi) we need to say so explicitly

xylar force-pushed the add_compass_mpi_support branch from cd7ae92 to 190338d Compare April 9, 2020 08:12

xylar removed the in progress label Apr 10, 2020

mark-petersen merged commit 190338d into MPAS-Dev:ocean/develop Apr 10, 2020

xylar deleted the add_compass_mpi_support branch April 10, 2020 18:40

xylar mentioned this pull request May 14, 2020

Add prerequisite tags to all necessary test cases #560

Closed

xylar mentioned this pull request May 19, 2020

e3sm_coupling failing with load_latest_compass.sh on LANL IC #564

Closed

matthewhoffman added COMPASS Ocean labels Mar 17, 2021

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Fixes to COMPASS to support conda MPI#480

Fixes to COMPASS to support conda MPI#480
mark-petersen merged 8 commits intoMPAS-Dev:ocean/developfrom
xylar:add_compass_mpi_support

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Testing of all ocean test cases on grizzly:

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