Add run time information and update fv3 to use unified missing value

[junwang-noaa]

Description

This PR will add run time information in FV3ATM, CICE6 and MOM6 component and update fv3atm to use unified missing value

Input data additions/changes

• No changes are expected to input data.
• Changes are expected to input data:
  • New input data.
  • Updated input data.

Anticipated changes to regression tests:

• No changes are expected to any regression test.
• Changes are expected to the following tests: All the RT tests with atmf history output files will change results.

Subcomponents involved:

• AQM
• CDEPS
• CICE
• CMEPS
• CMakeModules
• FV3
• GOCART
• HYCOM
• MOM6
• NOAHMP
• WW3
• stochastic_physics
• none

Library Updates/Changes

• Not Needed
• Create separate issue in JCSDA/spack-stack asking for update to library. Include library name, library version.
• Add issue link from JCSDA/spack-stack following this item

Combined with PR's (If Applicable):

Commit Queue Checklist:

• Link PR's from all sub-components involved in section below
• Confirm reviews completed in ALL sub-component PR's
• Add all appropriate labels to this PR.
• Run full RT suite on either Hera/Cheyenne AND attach log to a PR comment.
• Add list of any failed regression tests to "Anticipated changes to regression tests" section.

Linked PR's and Issues:

Dependent PRs:

• Depends on Add run time info and upp NOAA-EMC/fv3atm#678
• Depends on Update CICE from Consortium/main, add run-time and history-write logging NOAA-EMC/CICE#65
• Depends on add run time info NOAA-EMC/MOM6#114
• Closes Adding run time information for fv3 grid component NOAA-EMC/fv3atm#677
• Closes Timing information for the coupled runs #1782
• Closes Update CICE to latest Consortium/main NOAA-EMC/CICE#64
• Closes File to indicate output file is fully written NOAA-EMC/CICE#57

Testing Day Checklist:

• This PR is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR.
• Move new/updated input data on RDHPCS Hera and propagate input data changes to all supported systems.

Testing Log (for CM's):

• RDHPCS
  • Hera
  • Orion
  • Jet
  • Gaea
  • Cheyenne
• WCOSS2
  • Dogwood/Cactus
  • Acorn
• CI
  • Completed
• opnReqTest
  • N/A
  • Log attached to comment

[junwang-noaa]

The full RT passed on hera, the log file is at:

/scratch1/NCEPDEV/nems/Jun.Wang/nems/vlab/20230705/ufs-weather-model/tests/logs/RegressionTests_gaea.log_20230828

[BrianCurtis-NOAA]

The full RT passed on hera, the log file is at:

/scratch1/NCEPDEV/nems/Jun.Wang/nems/vlab/20230705/ufs-weather-model/tests/logs/RegressionTests_gaea.log_20230828

Did you mean to link to the Gaea log?

[junwang-noaa]

Good catch! I copied the wrong log file to this temporary file, now I lost my hera log file. I will run full RT again..

[junwang-noaa]

The hera RT log file is at:
/scratch1/NCEPDEV/nems/Jun.Wang/nems/vlab/20230705/ufs-weather-model/tests/logs/RegressionTests_hera.log_20230830

[BrianCurtis-NOAA]

@jkbk2004 who is assigned to this PR?

[FernandoAndrade-NOAA]

It looks like Acorn will be skipped for this PR, @junwang-noaa please go ahead and resolve/mark resolved conversations in the sub PRs as well as in this PR.

[junwang-noaa]

@FernandoAndrade-NOAA Done

[DeniseWorthen]

@FernandoAndrade-NOAA Are we ready for subcomponent PR merges?

[FernandoAndrade-NOAA]

@DeniseWorthen yes everything looks good to go, please continue with the merge process

[DeniseWorthen]

CICE is ready, hash is 2ed3c05

[jiandewang]

MOM6 merged, hash # is be40a4136

[jkbk2004]

FV3 merged as well, new hash NOAA-EMC/fv3atm@a9fa26e

[junwang-noaa]

I will update my UWM branch

[junwang-noaa]

Updated.