Remove FMS from UFS MPAS Atmosphere

[dustinswales]

Commit Queue Requirements:

• This PR addresses a relevant WM issue (if not, create an issue).
• All subcomponent pull requests (if any) have been reviewed by their code managers.
• Run the full Intel+GNU RT suite (compared to current baselines), preferably on Ursa (Derecho or Hercules are acceptable alternatives). Exceptions: documentation-only PRs, CI-only PRs, etc.
  • Commit log file w/full results from RT suite run (if applicable).
  • Verify that test_changes.list indicates which tests, if any, are changed by this PR. Commit test_changes.list, even if it is empty.
• Fill out all sections of this template.

Description

This PR removes all FMS dependencies in the MPAS enabled UFS.

For logging and error handling, we now use the MPAS native logging functionality.

ESMF has replaced FMS for clock management. Most of the FMS functionality is included with ESMF, so this was straightforward.

With the FMS removal, we had to create some new infrastructure to provide MPAS configurability. This was necessary since we relied on FMS for runtime configurability.
A new routine, ufs_mpas_read_stream_lists, allows for runtime control over which fields are included in the various MPAS output streams (e.g., output, restart, diag, etc...). This provides the same functionality of standalone MPAS.

Initial tracer/constituent handling. This replaces the FMS tracer_tables. This may be revamped in the future to handle constituents differently.

New, non-FMS, handling of the atmospheric namelist.

Other things (non-FMS related) included here:

Added new interval to write restart files at different interval than output files. These are controlled by the UFS model_configure file.

Adopted/modified shared UFS tool to control restart, and output, file frequency, shr_is_restart_fh_mod. This is used by other UFS components NUOPC caps. Thanks @NickSzapiro-NOAA

Output/restart file format now matches with standalone MPAS-A. Timestamp in file name was HH:MM:SS, changed to HH.MM.SS. This addresses #3209

Commit Message:

* UFSWM - Remove FMS dependency from MPAS Atmosphere
  * UFSATM - Remove FMS dependency from MPAS Atmosphere

Priority:

• Critical Bugfix: Reason
• High: MPAS in the UFS is a high-priority and we have a backlog of PRs we need to get in.
• [] Normal

Git Tracking

UFSWM:

• Closes Remove FMS dependency in UFSATM/mpas #3181 MPAS RTs on NCARs Derecho #3209

Sub component Pull Requests:

• UFSATM: Remove FMS from UFS MPAS Atmosphere + More MPAS infrastructure in UFS NOAA-EMC/ufsatm#1100

UFSWM Blocking Dependencies:

N/A

Documentation:

N/A

Changes

Regression Test Changes (Please commit test_changes.list):

• PR Adds New Tests/Baselines.
• PR Updates/Changes Baselines. MPAS RTs fail due to a change in file format (Now matches standalone MPAS)
• No Baseline Changes.

Input data Changes:

• None.
• PR adds input data. New stream_lists and tracer file needs to be added to staged IC directories.
• PR changes existing input data.

Library Changes/Upgrades:

• No Updates

Testing Log:

• RDHPCS
  • Orion
  • Hercules
  • GaeaC6
  • Derecho
  • Ursa
• WCOSS2
  • Dogwood/Cactus
  • Acorn
• CI
• opnReqTest (complete task if unnecessary)

Several tests increased by 1 remark# 10448, which is the ifort deprecation remark. This will resolve with the move to spack-stack v2.1.x.

[FernandoAndrade-NOAA]

It looks like history.2023-03-10_15.00.00.nc is not being generated, resulting in failures for both tests during creation.

baseline dir = /scratch4/NAGAPE/epic/role-epic/UFS-WM_RT/NEMSfv3gfs/develop-20260515/control_gfs_mpas_gnu
working dir  = /scratch3/NAGAPE/epic/Fernando.Andrade-maldonado/stmp/RT_RUNDIRS/Fernando.Andrade-maldonado/FV3_RT/rt_4183664/control_gfs_mpas_gnu
Checking test control_gfs_mpas_gnu results ....
Moving baseline control_gfs_mpas_gnu files ....
 Moving history.2023-03-10_15.00.00.nc .........NOT OK. Missing /scratch3/NAGAPE/epic/Fernando.Andrade-maldonado/stmp/RT_RUNDIRS/Fernando.Andrade-maldonado/FV3_RT/rt_4183664/control_gfs_mpas_gnu/history.2023-03-10_15.00.00.nc
 Moving history.2023-03-10_18.00.00.nc .........OK
 Moving history.2023-03-10_21.00.00.nc .........OK
 Moving history.2023-03-11_00.00.00.nc .........OK
 Moving history.2023-03-11_03.00.00.nc .........OK

please refer to the following on Ursa
/scratch3/NAGAPE/epic/Fernando.Andrade-maldonado/stmp/RT_RUNDIRS/Fernando.Andrade-maldonado/FV3_RT/rt_4183664

[dustinswales]

It looks like history.2023-03-10_15.00.00.nc is not being generated, resulting in failures for both tests during creation.

baseline dir = /scratch4/NAGAPE/epic/role-epic/UFS-WM_RT/NEMSfv3gfs/develop-20260515/control_gfs_mpas_gnu
working dir  = /scratch3/NAGAPE/epic/Fernando.Andrade-maldonado/stmp/RT_RUNDIRS/Fernando.Andrade-maldonado/FV3_RT/rt_4183664/control_gfs_mpas_gnu
Checking test control_gfs_mpas_gnu results ....
Moving baseline control_gfs_mpas_gnu files ....
 Moving history.2023-03-10_15.00.00.nc .........NOT OK. Missing /scratch3/NAGAPE/epic/Fernando.Andrade-maldonado/stmp/RT_RUNDIRS/Fernando.Andrade-maldonado/FV3_RT/rt_4183664/control_gfs_mpas_gnu/history.2023-03-10_15.00.00.nc
 Moving history.2023-03-10_18.00.00.nc .........OK
 Moving history.2023-03-10_21.00.00.nc .........OK
 Moving history.2023-03-11_00.00.00.nc .........OK
 Moving history.2023-03-11_03.00.00.nc .........OK

please refer to the following on Ursa /scratch3/NAGAPE/epic/Fernando.Andrade-maldonado/stmp/RT_RUNDIRS/Fernando.Andrade-maldonado/FV3_RT/rt_4183664

@FernandoAndrade-NOAA Sorry. There is no output at the initial time step. I updated the test files.

[gspetro-NOAA]

Several tests increased by 1 remark# 10448, which is the ifort deprecation remark. This will resolve with the move to spack-stack v2.1.x, so the PR can proceed despite the failing CI test.