update MOM6 to its main repository 20231218 commit (disable FPEs) + Add stochastic physics pattern update frequency options within SPP and LNDP ('sppint' and 'lndpint') #2077 + Updates to ufs.configure for use in global applications #2074 + Doc Updates #2030

[jiandewang]

Commit Queue Requirements:

• Fill out all sections of this template.
• All sub component pull requests have been reviewed by their code managers.
• Run the full RT suite (compared to current baselines) on either Hera/Derecho/Hercules AND have committed the log to my PR branch.
• Add list of all failed regression tests in "Regression Tests" section.

PR Information

Description

• MOM6 main repository was updated on 20231218 to fix its CI test issue. See detail at Disable FPEs in MacOS testing mom-ocean/MOM6#1617. The change has no impact on UFSWM S2S results.
• updates several templates ufs.configure.*.IN used in the global applications so that they can be shared between the ufs-weather-model regression testing framework and the global applications.
• moves the templates by adding _esmf for ESMF-managed threading and _fast where the wave coupling is in the fast loop (as opposed to _slow where it was in the slow loop)
• updates the files under tests/ to use the appropriately renamed template.
• option for users to apply a stochastic physics pattern update frequency which will keep the pattern fixed for 'sppint' or 'lndpint' seconds for SPP and LNDP stochastic physics, respectively.
• Updated links and test information in Configurations.rst to correspond with the new arrangement of RRFS/regional tests
• Modified information on the LND & CDEPS Input files required for land configurations
• Updated nems.configure references to ufs.configure
• Added crosslinks in various sections so that other UFS documentation projects can take advantage of intersphinx mapping to link to the WM docs.

Commit Message

• Update MOM6 to its main repository 20231218 updating (disable FPEs)
• Updates ufs.configure templates for use in global-applications.
• Adds the stochastic pattern interval (sppint) option to SPP and (lndpint) to the land perturbations (LNDP)
• Doc update for LND & CDEPS Input files required for land configurations

UFSWM issue #2079, MOM6 issue NOAA-EMC/MOM6#123 and MOM6 PR NOAA-EMC/MOM6#124

Priority

• Critical Bugfix (This PR contains a critical bug fix and should be prioritized.)
• High (This PR contains a feature or fix needed for a time-sensitive project (eg, retrospectives, implementations))
• Normal

Blocking Dependencies

Git Issues and PRs fixed/closed By This PR

• close UFSWM update MOM6 to its main repository 20231218 (disable FPEs) commit #2079, close MOM6 isseu update MOM6 to its main repo. 20231218 commit (disable FPEs in MacOS testing) NOAA-EMC/MOM6#123
• Updates to ufs.configure for use in global applications #2074 and part of add component defaults, rename templates to .in, rename ufs.configure for application, cleanup tests #2010
• Add stochastic physics pattern update frequency options within SPP and LNDP ('sppint' and 'lndpint') #2077 and Add 'sppint' and 'lndpint' stochastic physics variables and related namelist options #2071
• WM Documentation Updates #2030 and Update WM Documentation #2029

Changes

Subcomponent (with links)

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

Input data

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

Regression Tests:

• No changes are expected to any regression test.
• Changes are expected to the following tests:

FAILED REGRESSION TESTS

Libraries

• Not Needed
• 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

Testing Log:

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

[jiandewang]

@jkbk2004 could you add this to commit queue ? this is a very simple PR without BL change so it can be combined with others.

[jiandewang]

full rt.sh successful on HERA and log file being committed to PR branch, it can also be seen at
https://www.emc.ncep.noaa.gov/gc_wmb/wd20xw/JD/RegressionTests_hera.log

[jkbk2004]

@jiandewang I was checking develop branch. Looks like running ok on hera : /scratch1/NCEPDEV/stmp2/Jong.Kim/FV3_RT/rt_79405/cpld_control_p8_mixedmode_intel. Can you double check?

[DeniseWorthen]

@jiandewang Looks like you need to update FV3 also.

[jiandewang]

@DeniseWorthen this is the steps I just did:
(1) checkout my PR branch, .... submodule update --init --recursive
(2) git remote add upstream https://github.com/ufs-community/ufs-weather-model
(3) git fetch upstream
(4) git merge upstream/develop
(5) git checkout --ours tests/logs/RegressionTests_hera.log
(6) git status, ...... here I saw RegressionTests_hera.log anf fv3 have been changed, but don't understand why fv3 is involved
(7) git add tests/logs/RegressionTests_hera.log fv3
(8) git commit -m 'xxxxxx'
(9) git push origin mybranch

now I saw there is one file in fv3 that has been changed in my PR which shouldn't, see
https://github.com/ufs-community/ufs-weather-model/pull/2080/files

what's wrong in my doing above ?
the requirement to commit run log to users PR branch is something new and I think we need to have someone put a standard step on wiki page as I am sure I am not the only one who is not familiar with this.

[DeniseWorthen]

@jiandewang The commit you merged in (spack-stack) included an update to FV3. So it should have shown as updated. You needed to commit that update to your branch.

We used to always have folks commit the logs, then we tried having them attach the logs, but most people continued to commit the log. So I think people are used to committing. Once you commit the log showing you've run the full RT, then you should just keep merging to the top of develop and not worry about your log being different.

[jiandewang]

@DeniseWorthen is my step (7) doing the fv3 updating ? I must mess up one step but can't figure out which one.
also when you say "keep merging to the top of develop and not worry about your log being different", do you mean I do "checkout --ours" each time I do the sync ?

[jkbk2004]

@BrianCurtis-NOAA The PR ran ok on hera.

[jkbk2004]

Alright! all tests are done. we start merging process.

[jiandewang]

just merged MOM6, hash # 60c397b