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Add S2SA nems.configure template #1593

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WalterKolczynski-NOAA
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@WalterKolczynski-NOAA WalterKolczynski-NOAA commented May 10, 2023

Description
Most of the configuration was setup to allow S2SA, but there was no appropriate nems.configure template. A new one was created by starting with the S2SWA template and removing the wave portions. This functionality will support coupled DA development.

The experiment setup documentation for cycled mode had not been updated as coupled capability was added, so that has now been updated. Also added notes to both the cycled and forecast-only section that ATMW is currently not working.

Also added two UFSDA scripts that were missing from the git ignore list.

Fixes #1592

Type of change

  • New feature (non-breaking change which adds functionality)
  • This change requires a documentation update

How Has This Been Tested?

- [ ] S2SA cycled test on Orion

  • S2SA forecast-only

Checklist

  • My code follows the style guidelines of this project
  • I have performed a self-review of my own code
  • I have commented my code, particularly in hard-to-understand areas
  • My changes need updates to the documentation. I have made corresponding changes to the documentation
  • My changes generate no new warnings
  • New and existing tests pass with my changes
  • Any dependent changes have been merged and published

@WalterKolczynski-NOAA
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Testing is waiting on an unrelated IC issue to be resolved.

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@aerorahul aerorahul left a comment

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makes sense to me.

@aerorahul
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@junwang-noaa would you please comment on the nems.configure template for the S2SA use case?

@WalterKolczynski-NOAA
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With the gocart emissions updated, having an issue with the forecast during (seemingly) the first GOCART loop:

0: PASS: fcstRUN phase 1, n_atmsteps =                0 time is        17.056236
 0: UFS Aerosols: Advancing from 2021-03-23T12:00:00 to 2021-03-23T12:20:00
 4: pe=00004 FAIL at line=00827    SU2G_GridCompMod.F90                     <status=29>
 4: pe=00004 FAIL at line=00685    SU2G_GridCompMod.F90                     <status=29>
 4: pe=00004 FAIL at line=01806    MAPL_Generic.F90                         <status=29>
 4: pe=00004 FAIL at line=00167    BaseProfiler.F90                         <Timer <GOCART2G> does not match start timer <SU>>
 4: pe=00004 FAIL at line=01824    MAPL_Generic.F90                         <status=1>
 4: pe=00004 FAIL at line=00161    Aerosol_GridComp.F90                     <Failed to run child component>
 4: pe=00004 FAIL at line=01806    MAPL_Generic.F90                         <status=1>
 4: pe=00004 FAIL at line=01192    MAPL_CapGridComp.F90                     <status=1>
 4: pe=00004 FAIL at line=01144    MAPL_CapGridComp.F90                     <status=1>
 4: pe=00004 FAIL at line=00812    MAPL_CapGridComp.F90                     <status=1>
 4: pe=00004 FAIL at line=00952    MAPL_CapGridComp.F90                     <status=1>

The PET logs also have this error message:

20230601 162253.786 ERROR            PET00 Aerosol_Cap.F90:464 Invalid object  - Passing error in return code
20230601 162253.787 ERROR            PET00 CHM:src/addon/NUOPC/src/NUOPC_ModelBase.F90:2226 Invalid object  - Passing error in return code
20230601 162253.787 ERROR            PET00 UFS Driver Grid Comp:src/addon/NUOPC/src/NUOPC_Driver.F90:3340 Invalid object  - Phase 'RunPhase1' Run for modelComp 3 did not return ESMF_SUCCESS
20230601 162253.787 ERROR            PET00 UFS Driver Grid Comp:src/addon/NUOPC/src/NUOPC_Driver.F90:3625 Invalid object  - Passing error in return code
20230601 162253.787 ERROR            PET00 UFS Driver Grid Comp:src/addon/NUOPC/src/NUOPC_Driver.F90:3255 Invalid object  - Passing error in return code
20230601 162253.787 ERROR            PET00 UFS.F90:403 Invalid object  - Aborting UFS

Seems like something that should be a straightforward error, but I'm not sure what. Error in my new nems.configure? Issue with the ICs? This is a warm-start from ICs. @bbakernoaa @lipan-NOAA @junwang-noaa

Working directory: /work2/noaa/stmp/wkolczyn/RUNDIRS/S2SA_cyc/fcst.376447
Log: /work2/noaa/global/wkolczyn/noscrub/global-workflow/S2SA_cyc/logs/2021032312/gdasfcst.log

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bbakernoaa commented Jun 2, 2023

@WalterKolczynski-NOAA This is due to the volcanic emission dataset. Sorry I missed this. They are there for future years but in a different directory.

If you modify the SU2G_instance_SU.rc file: Line 11

before

volcano_srcfilen: ExtData/volcanic/so2_volcanic_emissions_Carns.%y4%m2%d2.rc

after

volcano_srcfilen: ExtData/nexus/VOLCANO/v2021-09/%y4/so2_volcanic_emissions_Carns.%y4%m2%d2.rc 

I'll take blame for this one

@WalterKolczynski-NOAA
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@bbakernoaa Even after making that change, I get the same error

Working directory: /work2/noaa/stmp/wkolczyn/RUNDIRS/S2SA_cyc/fcst.430195

@bbakernoaa
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@WalterKolczynski-NOAA I can't open up the latest log file

/work2/noaa/global/wkolczyn/noscrub/global-workflow/S2SA_cyc/logs/2021032312/gdasfcst.log: Permission denied

@WalterKolczynski-NOAA
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@WalterKolczynski-NOAA I can't open up the latest log file

/work2/noaa/global/wkolczyn/noscrub/global-workflow/S2SA_cyc/logs/2021032312/gdasfcst.log: Permission denied

Not sure why that one was any different, but should be fixed now.

@bbakernoaa
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@WalterKolczynski-NOAA found the error in my suggestion

it should include the month in the path... my fault.... sorry

volcano_srcfilen: ExtData/nexus/VOLCANO/v2021-09/%y4/%m2/so2_volcanic_emissions_Carns.%y4%m2%d2.rc

@WalterKolczynski-NOAA
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@bbakernoaa That worked, thanks.

Most of the configuration was setup to allow S2SA, but there was no
appropriate nems.configure template. A new one was created by
starting with the S2SWA template and removing the wave portions.

Also added two UFSDA scripts that were missing from the git ignore
list.

Fixes NOAA-EMC#1592
The experiment setup documentation for cycled mode had not been
updated as coupled capability was added. Also added notes to both
the cycled and forecast-only section that ATMW is currently not
working.
setup_expt would only detect two of the possible S2S options when
staging cycled ICs.

Refs: NOAA-EMC#1592
The volcanic aerosol data was moved to a new location within the
GOCART emissions directory.

Refs: NOAA-EMC#1592
The enkf versions of coupled settings (DO_OCN, etc.) do not work
properly because some settings have already been determined by that
point based on the non-enkf versions of the settings. The enkf
versions are now disabled until there is a solution (see NOAA-EMC#1692).

Refs: NOAA-EMC#1593
Refs: NOAA-EMC#1692
The task list for the free-forecast was checking against a list of
apps that did not include S2SA to determine whether ocnpost is
included. That check is now changed to check on do_ocean rather than
looking at the app directly.

Refs: NOAA-EMC#1593
@WalterKolczynski-NOAA
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While waiting for IC staging to be updated for cycled, tested using forecast-only mode instead.

@WalterKolczynski-NOAA WalterKolczynski-NOAA marked this pull request as ready for review June 27, 2023 21:39
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Looks good. Assume the nems.configure.cpld_aero.IN gets tested in an S2SA app run.
Just 2 comments on non-existent files that are being ignored.

.gitignore Outdated Show resolved Hide resolved
.gitignore Outdated Show resolved Hide resolved
workflow/setup_expt.py Show resolved Hide resolved
A couple of scripts that had been added to the git ignore list during
the course of this update have since been removed and no longer need
to be ignored.
@WalterKolczynski-NOAA WalterKolczynski-NOAA added the CI-Hera-Ready **CM use only** PR is ready for CI testing on Hera label Jun 28, 2023
@WalterKolczynski-NOAA WalterKolczynski-NOAA added the CI-Orion-Ready **CM use only** PR is ready for CI testing on Orion label Jun 28, 2023
@emcbot emcbot added CI-Orion-Building **Bot use only** CI testing is cloning/building on Orion CI-Hera-Building **Bot use only** CI testing is cloning/building on Hera CI-Hera-Running **Bot use only** CI testing on Hera for this PR is in-progress and removed CI-Orion-Ready **CM use only** PR is ready for CI testing on Orion CI-Hera-Ready **CM use only** PR is ready for CI testing on Hera CI-Hera-Building **Bot use only** CI testing is cloning/building on Hera labels Jun 28, 2023
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Automated global-workflow Testing Results:

Machine: Hera
Start: Wed Jun 28 02:48:26 UTC 2023 on hfe05
---------------------------------------------------
Checkout:                      *SUCCESS*
Checkout: Completed at Wed Jun 28 02:52:24 UTC 2023
Build:                         *SUCCESS*
Build: Completed at Wed Jun 28 04:03:05 UTC 2023
Created experiment:            *SUCCESS*
Case setup: Completed at Wed Jun 28 04:03:08 UTC 2023 for experiment C48_S2S
Created experiment:            *SUCCESS*
Case setup: Completed at Wed Jun 28 04:03:11 UTC 2023 for experiment C96C48_hybatmDA
Created experiment:            *SUCCESS*
Case setup: Completed at Wed Jun 28 04:03:14 UTC 2023 for experiment C96_atm3DVar

@emcbot emcbot added CI-Orion-Running **Bot use only** CI testing on Orion for this PR is in-progress and removed CI-Orion-Building **Bot use only** CI testing is cloning/building on Orion labels Jun 28, 2023
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Automated global-workflow Testing Results:

Machine: Orion
Start: Tue Jun 27 21:48:16 CDT 2023 on Orion-login-1.HPC.MsState.Edu
---------------------------------------------------
Checkout:                      *SUCCESS*
Checkout: Completed at Tue Jun 27 21:50:01 CDT 2023
Build:                         *SUCCESS*
Build: Completed at Tue Jun 27 23:06:00 CDT 2023
Created experiment:            *SUCCESS*
Case setup: Completed at Tue Jun 27 23:06:10 CDT 2023 for experiment C48_S2S
Created experiment:            *SUCCESS*
Case setup: Completed at Tue Jun 27 23:06:14 CDT 2023 for experiment C96_atm3DVar
Created experiment:            *SUCCESS*
Case setup: Completed at Tue Jun 27 23:06:18 CDT 2023 for experiment C96C48_hybatmDA

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emcbot commented Jun 28, 2023

Automated global-workflow Testing Results:

Machine: Orion
Start: Tue Jun 27 21:48:16 CDT 2023 on Orion-login-1.HPC.MsState.Edu
---------------------------------------------------
Checkout:                      *SUCCESS*
Checkout: Completed at Tue Jun 27 21:50:01 CDT 2023
Build:                         *SUCCESS*
Build: Completed at Tue Jun 27 23:06:00 CDT 2023
Created experiment:            *SUCCESS*
Case setup: Completed at Tue Jun 27 23:06:10 CDT 2023 for experiment C48_S2S
Created experiment:            *SUCCESS*
Case setup: Completed at Tue Jun 27 23:06:14 CDT 2023 for experiment C96_atm3DVar
Created experiment:            *SUCCESS*
Case setup: Completed at Tue Jun 27 23:06:18 CDT 2023 for experiment C96C48_hybatmDA
Experiment C48_S2S completed: *SUCCESS*
Experiment C48_S2S Completed at Tue Jun 27 23:39:07 CDT 2023
with 18 successfully completed jobs

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emcbot commented Jun 28, 2023

Automated global-workflow Testing Results:

Machine: Hera
Start: Wed Jun 28 02:48:26 UTC 2023 on hfe05
---------------------------------------------------
Checkout:                      *SUCCESS*
Checkout: Completed at Wed Jun 28 02:52:24 UTC 2023
Build:                         *SUCCESS*
Build: Completed at Wed Jun 28 04:03:05 UTC 2023
Created experiment:            *SUCCESS*
Case setup: Completed at Wed Jun 28 04:03:08 UTC 2023 for experiment C48_S2S
Created experiment:            *SUCCESS*
Case setup: Completed at Wed Jun 28 04:03:11 UTC 2023 for experiment C96C48_hybatmDA
Created experiment:            *SUCCESS*
Case setup: Completed at Wed Jun 28 04:03:14 UTC 2023 for experiment C96_atm3DVar
Experiment C48_S2S completed: *SUCCESS*
Experiment C48_S2S Completed at Wed Jun 28 04:48:10 UTC 2023
with 18 successfully completed jobs

@emcbot
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emcbot commented Jun 28, 2023

Automated global-workflow Testing Results:

Machine: Hera
Start: Wed Jun 28 02:48:26 UTC 2023 on hfe05
---------------------------------------------------
Checkout:                      *SUCCESS*
Checkout: Completed at Wed Jun 28 02:52:24 UTC 2023
Build:                         *SUCCESS*
Build: Completed at Wed Jun 28 04:03:05 UTC 2023
Created experiment:            *SUCCESS*
Case setup: Completed at Wed Jun 28 04:03:08 UTC 2023 for experiment C48_S2S
Created experiment:            *SUCCESS*
Case setup: Completed at Wed Jun 28 04:03:11 UTC 2023 for experiment C96C48_hybatmDA
Created experiment:            *SUCCESS*
Case setup: Completed at Wed Jun 28 04:03:14 UTC 2023 for experiment C96_atm3DVar
Experiment C48_S2S completed: *SUCCESS*
Experiment C48_S2S Completed at Wed Jun 28 04:48:10 UTC 2023
with 18 successfully completed jobs
Experiment C96C48_hybatmDA completed: *SUCCESS*
Experiment C96C48_hybatmDA Completed at Wed Jun 28 06:36:17 UTC 2023
with 148 successfully completed jobs

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emcbot commented Jun 28, 2023

Automated global-workflow Testing Results:

Machine: Hera
Start: Wed Jun 28 02:48:26 UTC 2023 on hfe05
---------------------------------------------------
Checkout:                      *SUCCESS*
Checkout: Completed at Wed Jun 28 02:52:24 UTC 2023
Build:                         *SUCCESS*
Build: Completed at Wed Jun 28 04:03:05 UTC 2023
Created experiment:            *SUCCESS*
Case setup: Completed at Wed Jun 28 04:03:08 UTC 2023 for experiment C48_S2S
Created experiment:            *SUCCESS*
Case setup: Completed at Wed Jun 28 04:03:11 UTC 2023 for experiment C96C48_hybatmDA
Created experiment:            *SUCCESS*
Case setup: Completed at Wed Jun 28 04:03:14 UTC 2023 for experiment C96_atm3DVar
Experiment C48_S2S completed: *SUCCESS*
Experiment C48_S2S Completed at Wed Jun 28 04:48:10 UTC 2023
with 18 successfully completed jobs
Experiment C96C48_hybatmDA completed: *SUCCESS*
Experiment C96C48_hybatmDA Completed at Wed Jun 28 06:36:17 UTC 2023
with 148 successfully completed jobs
Experiment C96_atm3DVar completed: *SUCCESS*
Experiment C96_atm3DVar Completed at Wed Jun 28 07:06:07 UTC 2023
with 86 successfully completed jobs

@emcbot emcbot added CI-Hera-Passed **Bot use only** CI testing on Hera for this PR has completed successfully and removed CI-Hera-Running **Bot use only** CI testing on Hera for this PR is in-progress labels Jun 28, 2023
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emcbot commented Jun 28, 2023

Automated global-workflow Testing Results:

Machine: Hera
Start: Wed Jun 28 02:48:26 UTC 2023 on hfe05
---------------------------------------------------
Checkout:                      *SUCCESS*
Checkout: Completed at Wed Jun 28 02:52:24 UTC 2023
Build:                         *SUCCESS*
Build: Completed at Wed Jun 28 04:03:05 UTC 2023
Created experiment:            *SUCCESS*
Case setup: Completed at Wed Jun 28 04:03:08 UTC 2023 for experiment C48_S2S
Created experiment:            *SUCCESS*
Case setup: Completed at Wed Jun 28 04:03:11 UTC 2023 for experiment C96C48_hybatmDA
Created experiment:            *SUCCESS*
Case setup: Completed at Wed Jun 28 04:03:14 UTC 2023 for experiment C96_atm3DVar
Experiment C48_S2S completed: *SUCCESS*
Experiment C48_S2S Completed at Wed Jun 28 04:48:10 UTC 2023
with 18 successfully completed jobs
Experiment C96C48_hybatmDA completed: *SUCCESS*
Experiment C96C48_hybatmDA Completed at Wed Jun 28 06:36:17 UTC 2023
with 148 successfully completed jobs
Experiment C96_atm3DVar completed: *SUCCESS*
Experiment C96_atm3DVar Completed at Wed Jun 28 07:06:07 UTC 2023
with 86 successfully completed jobs

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emcbot commented Jun 28, 2023

Automated global-workflow Testing Results:

Machine: Orion
Start: Tue Jun 27 21:48:16 CDT 2023 on Orion-login-1.HPC.MsState.Edu
---------------------------------------------------
Checkout:                      *SUCCESS*
Checkout: Completed at Tue Jun 27 21:50:01 CDT 2023
Build:                         *SUCCESS*
Build: Completed at Tue Jun 27 23:06:00 CDT 2023
Created experiment:            *SUCCESS*
Case setup: Completed at Tue Jun 27 23:06:10 CDT 2023 for experiment C48_S2S
Created experiment:            *SUCCESS*
Case setup: Completed at Tue Jun 27 23:06:14 CDT 2023 for experiment C96_atm3DVar
Created experiment:            *SUCCESS*
Case setup: Completed at Tue Jun 27 23:06:18 CDT 2023 for experiment C96C48_hybatmDA
Experiment C48_S2S completed: *SUCCESS*
Experiment C48_S2S Completed at Tue Jun 27 23:39:07 CDT 2023
with 18 successfully completed jobs
Experiment C96_atm3DVar completed: *SUCCESS*
Experiment C96_atm3DVar completed: *SUCCESS*
Experiment C96_atm3DVar Completed at Wed Jun 28 17:06:09 CDT 2023
Experiment C96_atm3DVar Completed at Wed Jun 28 17:06:09 CDT 2023
with 86 successfully completed jobs
with 86 successfully completed jobs

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emcbot commented Jun 28, 2023

Automated global-workflow Testing Results:

Machine: Orion
Start: Tue Jun 27 21:48:16 CDT 2023 on Orion-login-1.HPC.MsState.Edu
---------------------------------------------------
Checkout:                      *SUCCESS*
Checkout: Completed at Tue Jun 27 21:50:01 CDT 2023
Build:                         *SUCCESS*
Build: Completed at Tue Jun 27 23:06:00 CDT 2023
Created experiment:            *SUCCESS*
Case setup: Completed at Tue Jun 27 23:06:10 CDT 2023 for experiment C48_S2S
Created experiment:            *SUCCESS*
Case setup: Completed at Tue Jun 27 23:06:14 CDT 2023 for experiment C96_atm3DVar
Created experiment:            *SUCCESS*
Case setup: Completed at Tue Jun 27 23:06:18 CDT 2023 for experiment C96C48_hybatmDA
Experiment C48_S2S completed: *SUCCESS*
Experiment C48_S2S Completed at Tue Jun 27 23:39:07 CDT 2023
with 18 successfully completed jobs
Experiment C96_atm3DVar completed: *SUCCESS*
Experiment C96_atm3DVar completed: *SUCCESS*
Experiment C96_atm3DVar Completed at Wed Jun 28 17:06:09 CDT 2023
Experiment C96_atm3DVar Completed at Wed Jun 28 17:06:09 CDT 2023
with 86 successfully completed jobs
with 86 successfully completed jobs

@emcbot
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emcbot commented Jun 28, 2023

Automated global-workflow Testing Results:

Machine: Orion
Start: Tue Jun 27 21:48:16 CDT 2023 on Orion-login-1.HPC.MsState.Edu
---------------------------------------------------
Checkout:                      *SUCCESS*
Checkout: Completed at Tue Jun 27 21:50:01 CDT 2023
Build:                         *SUCCESS*
Build: Completed at Tue Jun 27 23:06:00 CDT 2023
Created experiment:            *SUCCESS*
Case setup: Completed at Tue Jun 27 23:06:10 CDT 2023 for experiment C48_S2S
Created experiment:            *SUCCESS*
Case setup: Completed at Tue Jun 27 23:06:14 CDT 2023 for experiment C96_atm3DVar
Created experiment:            *SUCCESS*
Case setup: Completed at Tue Jun 27 23:06:18 CDT 2023 for experiment C96C48_hybatmDA
Experiment C48_S2S completed: *SUCCESS*
Experiment C48_S2S Completed at Tue Jun 27 23:39:07 CDT 2023
with 18 successfully completed jobs
Experiment C96_atm3DVar completed: *SUCCESS*
Experiment C96_atm3DVar completed: *SUCCESS*
Experiment C96_atm3DVar Completed at Wed Jun 28 17:06:09 CDT 2023
Experiment C96_atm3DVar Completed at Wed Jun 28 17:06:09 CDT 2023
with 86 successfully completed jobs
with 86 successfully completed jobs
Experiment C96C48_hybatmDA completed: *SUCCESS*
Experiment C96C48_hybatmDA Completed at Wed Jun 28 17:06:17 CDT 2023
with 148 successfully completed jobs

@emcbot emcbot added CI-Orion-Passed **Bot use only** CI testing on Orion for this PR has completed successfully and removed CI-Orion-Running **Bot use only** CI testing on Orion for this PR is in-progress labels Jun 28, 2023
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emcbot commented Jun 28, 2023

Automated global-workflow Testing Results:

Machine: Orion
Start: Tue Jun 27 21:48:16 CDT 2023 on Orion-login-1.HPC.MsState.Edu
---------------------------------------------------
Checkout:                      *SUCCESS*
Checkout: Completed at Tue Jun 27 21:50:01 CDT 2023
Build:                         *SUCCESS*
Build: Completed at Tue Jun 27 23:06:00 CDT 2023
Created experiment:            *SUCCESS*
Case setup: Completed at Tue Jun 27 23:06:10 CDT 2023 for experiment C48_S2S
Created experiment:            *SUCCESS*
Case setup: Completed at Tue Jun 27 23:06:14 CDT 2023 for experiment C96_atm3DVar
Created experiment:            *SUCCESS*
Case setup: Completed at Tue Jun 27 23:06:18 CDT 2023 for experiment C96C48_hybatmDA
Experiment C48_S2S completed: *SUCCESS*
Experiment C48_S2S Completed at Tue Jun 27 23:39:07 CDT 2023
with 18 successfully completed jobs
Experiment C96_atm3DVar completed: *SUCCESS*
Experiment C96_atm3DVar completed: *SUCCESS*
Experiment C96_atm3DVar Completed at Wed Jun 28 17:06:09 CDT 2023
Experiment C96_atm3DVar Completed at Wed Jun 28 17:06:09 CDT 2023
with 86 successfully completed jobs
with 86 successfully completed jobs
Experiment C96C48_hybatmDA completed: *SUCCESS*
Experiment C96C48_hybatmDA Completed at Wed Jun 28 17:06:17 CDT 2023
with 148 successfully completed jobs

ATM_omp_num_threads: @[atm_omp_num_threads]
ATM_attributes::
Verbosity = 0
DumpFields = @[DumpFields]
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Do we need this variable in GW? This might only be used for debug purpose. I think it can be set to false.

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@junwang-noaa I think we are just being consistent w/ the other nems.configure templates. It is default set to .false. I think. If not, we can address in a later PR.

OCN_omp_num_threads: @[ocn_omp_num_threads]
OCN_attributes::
Verbosity = 0
DumpFields = @[DumpFields]
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Same here.

ICE_omp_num_threads: @[ice_omp_num_threads]
ICE_attributes::
Verbosity = 0
DumpFields = @[DumpFields]
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and here

@aerorahul aerorahul merged commit 2d31847 into NOAA-EMC:develop Jun 30, 2023
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Add S2SA nems.configure template
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