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GCHP run directory fixes and improvements #2326

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merged 6 commits into from
Jun 26, 2024

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lizziel
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@lizziel lizziel commented Jun 13, 2024

Name and Institution (Required)

Name: Lizzie Lundgren
Institution: Harvard University

Describe the update

This update applies minor bug fixes and improvements to GCHP run directories.

  • Fixed ExtData.rc entry for lightning climatology files (off by default unless using GEOS-IT so does not impact benchmark).
  • Removed enabling O-server in GCHP for high core counts. Using the O-server only works for some combinations of file system and MPI stacks. Updates in docs/dev better document this.
  • Added clarifying comments in GCHP configuration files for several settings, particularly related to domain decomposition, mass fluxes, and stretched grid
  • Added pre-run GCHP configuration checks to setCommonRunSettings.sh related to domain decomposition, mass fluxes, and stretched grid. The run script will exit with an error prior to executing GCHP if there are problems detected that would cause an issue in MAPL.
  • Changed search criteria for GCHP auto-update of met-field refresh frequency to not rely on presence of MetDir symlink in ExtData.rc file path. Users no longer must have MetDir in path which is useful when testing new met inventories.

Expected changes

This is a zero diff update for benchmarks. Differences are expected only when using lightning climatology which is off by default in benchmarks.

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None

Related Github Issue

None

@lizziel lizziel added this to the 14.4.1 milestone Jun 13, 2024
@lizziel lizziel added topic: GCHP Related to GCHP only topic: Run Directories Related to run directory issues and run directory creation labels Jun 13, 2024
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
…ation

Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
- Clarifying comments
- Moved allow species in restart option to frequently changed settings
- Changed criteria for dynamics field entries in ExtData.rc to update
  based on timestep. Now searches for whitespace+name+whitespace rather
  than whitespace+name and MetDir. Start of line is still required.
- Added end of script message that run is complete
- Added check that grid resolution is even
- Added checks for runs using mass fluxes*
    1. check that stretched grid is off
    2. check that input and grid resolutions are evenly divisible
    3. check that grid/run resolutions evenly divisible by  NX and NY/6

*Checks assume either GEOS-FP or GEOS-IT source for mass fluxes and
that C180x180x6 appears in GEOS-IT filename.
@lizziel lizziel changed the base branch from main to dev/no-diff-to-benchmark June 17, 2024 14:24
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
@lizziel lizziel marked this pull request as ready for review June 17, 2024 19:11
@lizziel lizziel requested a review from yantosca June 17, 2024 19:12
@yantosca yantosca self-assigned this Jun 25, 2024
@yantosca yantosca added the category: Feature Request New feature or request label Jun 25, 2024
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Thanks @lizziel! I'll start bringing this in for 14.4.1.

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All GEOS-Chem Classic integration tests passed:

==============================================================================
GEOS-Chem Classic: Execution Test Results

GCClassic #4f71c4a GEOS-Chem submod update: Merge PR #2348 (14.4.0 in CESM updates)
GEOS-Chem #e0e6e2fb0 Merge PR #2326 (GCHP run directory fixes and improvements)
HEMCO     #55d27e2 Merge PR #280 (Now use comma-separated list in stale.yml )

Using 24 OpenMP threads
Number of execution tests: 28

Submitted as SLURM job: 37515708
==============================================================================

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Furthermore, all tests were zero-diff w/r/t PR #2348 except for:

  • TOMAS (parallelization error?)

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All GCHP integration tests passed:

==============================================================================
GCHP: Execution Test Results

GCHP      #212f21a GEOS-Chem submod update: Merge PR #2348 (14.4.0 in CESM updates)
GEOS-Chem #e0e6e2fb0 Merge PR #2326 (GCHP run directory fixes and improvements)
HEMCO     #

Number of execution tests: 11

Submitted as SLURM job: 37515920
==============================================================================
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Furthermore, all tests were zero-diff w/r/t PR #2348.

@yantosca yantosca merged commit e0e6e2f into dev/no-diff-to-benchmark Jun 26, 2024
@yantosca yantosca deleted the dev/gchp_improvements branch June 26, 2024 13:52
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