Add CICE end of run restart file capability+Update submodule FV3/atmos_cubed_sphere to fix a typo when printing out the nest grid corner locations #2323+Bump urllib3 from 2.2.1 to 2.2.2 in /doc/UsersGuide #2329 + Orion changes for switch to new OS - Rocky-9 #2336

[dpsarmie]

The CICE hash includes changed that will add the ability to write a restart file at the end of the run via the CMEPS configuration. This is in conjunction with a similar PR for the MOM6 model.

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 Intel+GNU RT suite (compared to current baselines) on either Hera/Derecho/Hercules
• Commit 'test_changes.list' from previous step

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Description:

This PR adds changes to the CICE submodule that allows for the creation of restart files at the end of the model run. This option is controlled in CMEPS via the write_restart_at_endofrun config option. This should allow for files to be written when the interval write time does not sync up with the total run time (ex. 27h forecast with 12h restart write intervals). This change was also done in another PR for MOM6.

Commit Message:

  * CICE - Adds restart write capability at the end of a run for CICE
  * FV3 - 
    * atmos_cubed_sphere - Update submodule FV3/atmos_cubed_sphere to fix a typo when printing out the nest grid corner locations
    * doc/UsersGuide/requirements.txt: Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.2.1 to 2.2.2.
    * Orion Spack stack modulefile update: Rocky-9
    * update detect_machine.sh: hercules

Priority:

• Normal

Git Tracking

• Closes Ensure restart-at-end functionality is working in CMEPS #2236 and CMEPS issue 118
• Closes allow cice, cmeps and mom6 to write restarts at end of run  #1207

Sub component Pull Requests:

• UFS-WM: Orion changes for switch to new OS - Rocky-9 #2336
• CICE: Add end of run functionality to CICE NOAA-EMC/CICE#77
• FV3ATM: (Update submodule atmos_cubed_sphere to fix a typo/bug when printing out the nest grid corner locations NOAA-EMC/fv3atm#847) PR-2323
• atmos_cubed_sphere: (Correct the jc index when print out the nest grid corner locations NOAA-GFDL/GFDL_atmos_cubed_sphere#341) PR-2323

UFSWM Blocking Dependencies:

• None

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Changes

Regression Test Changes (Please commit test_changes.list):

• No Baseline Changes.

Input data Changes:

• None.

Library Changes/Upgrades:

• No Updates

---

Testing Log:

• RDHPCS
  • Hera
  • Orion
  • Hercules
  • Jet
  • Gaea
  • Derecho
• WCOSS2
  • Dogwood/Cactus
  • Acorn
• CI
• opnReqTest (complete task if unnecessary)

[DeniseWorthen]

@dpsarmie Since at this point we'd have the capability to turn this for CMEPS, CICE and MOM6, we'd want to add a configurable setting to the various ufs.configure files. We can set that false by default, but that will allow the G-W to set it optionally .true.

[dpsarmie]

@dpsarmie Since at this point we'd have the capability to turn this for CMEPS, CICE and MOM6, we'd want to add a configurable setting to the various ufs.configure files. We can set that false by default, but that will allow the G-W to set it optionally .true.

@DeniseWorthen That makes sense. The change will be rolled into this PR. The ufs.configure files have been changed and retested everything for completeness.

[DeniseWorthen]

@dpsarmie We need this as a configurable variable, so that users can set it true if they need to but we can use false in the RT.

[DeniseWorthen]

@dpsarmie Thanks for making those changes. I think this is ready.

[dpsarmie]

@DeniseWorthen Ok great! The RTs just finished on Hercules using the latest version of the branch and it was good to go on my end.

[jkbk2004]

@dpsarmie can you sync up branches? We like to start working on this pr. Can you combine in #2323 to this pr? Just need to points to @BinLiu-NOAA 's fv3 feature branch: NOAA-EMC/fv3atm#847

[dpsarmie]

@jkbk2004 I just want ahead and edited the gitmodules file to point to Bin's branch and brought the PR up to date. Let me know if you need anything else.

[FernandoAndrade-NOAA]

@dpsarmie I'm not seeing Bin's latest commit in your FV3, only the latest fv3 develop commit of 07c26d1 which does not look like it contains Bin's newer a6fdff7 for atmos cubed sphere. Could you double check your hashes for fv3/atmos cubed sphere?

4fd5f0e for FV3 and a6fdff7 for atmos cubed sphere should be present

[dpsarmie]

@FernandoAndrade-NOAA Sorry, I had it in 1561588 but then overwrote it back with the e5b9eed commit. Looks like Jong made the update to the hash. Thanks Jong!

[jkbk2004]

@dpsarmie it looks reverted. Let me fix one more time. I will update urllib3 version as well: #2329

[jkbk2004]

All looks good. @FernandoAndrade-NOAA This PR is ready for testing. @zach1221 I will check if I can run on Orion. @BrianCurtis-NOAA FYI

[zach1221]

@zach1221 I'd like to copy over one of your other debug test rundirs. Where are they located?

Apologies for the delay. Please see rundir below for failed case.
/glade/derecho/scratch/zshrader/FV3_RT/rt_96451/cpld_debug_gfsv17_intel

[DeniseWorthen]

@zach1221 I think you misunderstood. You said that you could confirm that the other debug tests ran OK on derecho. Where are those rundirs located?

[zach1221]

@zach1221 I think you misunderstood. You said that you could confirm that the other debug tests ran OK on derecho. Where are those rundirs located?

Sure, location is here.
/glade/derecho/scratch/zshrader/FV3_RT/rt_10335

[BrianCurtis-NOAA]

@jkbk2004 We are OK disabling that test on Derecho and moving forward. Please create an issue with all we've learned about the problem so we can follow up on fixing it.

[jkbk2004]

@dpsarmie @zach1221 can we create git issue to follow on derecho cpld_debug_gfsv17_intel failure ? We can turn off the case on derecho and go for merging. @BrianCurtis-NOAA @DeniseWorthen would it be ok?

[jkbk2004]

@BrianCurtis-NOAA Thanks!

[jkbk2004]

#2338

[jkbk2004]

Sorry for the delay. But we can move on for merging process with cpld_debug_gfsv17_intel disabled on derecho.

[DeniseWorthen]

@jkbk2004 We don't have a derecho log yet.

[FernandoAndrade-NOAA]

Ok I think we're set to continue, the failed test in the Derecho log has already been disabled in a previous commit.

[DeniseWorthen]

CICE has been merged hash 9452de8