Make assorted updates to waves

[JessicaMeixner-NOAA]

Description

This PR adds the following:

• converting from inp -> nml (@sbanihash)
• turning on PIO for waves for restarts (@sbanihash)
• enabling cycling for WW3 which required some updates to wave prep jobs + changing what restarts are being saved/etc
• changed the way CEMPS, MOM6, CICE and WW3 write restarts to be in sync with FV3 for IAU, which required moving the ufs-weather-model forward one hash to use the new flexible restart feature. (UFS PR Flexible restart write times (restart_fh) for med, ocn, ice, wav ufs-community/ufs-weather-model#2419)
• adds uglo_15km - the targeted new wave grid.
• Update to use new esmf_threading ufs.configure files which changes the toggle between how you use esmf threading versus traditional threading (UFS PR Sync with ESCOMP/CDEPS (2024-12-16) + Add support for traditional threading (#2533) ufs-community/ufs-weather-model#2538)

Notes on ufs-weather-model updates:

Commit date	Commit hash/ PR	Notes for g-w changes	Baseline Changes
Dec 11, 2024	ufs-community/ufs-weather-model@409bc85 ufs-community/ufs-weather-model#2419	Enables flexible restart writes - changes included in g-w PR	none
Dec 16, 2024	ufs-community/ufs-weather-model@6ec6b45 ufs-community/ufs-weather-model#2528 ufs-community/ufs-weather-model#2469	n/a	HAFs test changes, no global changes
Dec 18, 2024	ufs-community/ufs-weather-model@e119370 ufs-community/ufs-weather-model#2448	Adds Gaea C6 support (changes in other g-w PRs, not here)	none
Dec 23, 2024	ufs-community/ufs-weather-model@2950089 ufs-community/ufs-weather-model#2533 ufs-community/ufs-weather-model#2538	changes for ESMF vs traditional threading	none
Dec 30, 2024	ufs-community/ufs-weather-model@241dd8e ufs-community/ufs-weather-model#2485	n/a	changes in conus13km, no global changes
Jan 3, 2025	ufs-community/ufs-weather-model@76471dc ufs-community/ufs-weather-model#2530	n/a	changes in regional tests, no global changes

Note this PR requires the following:

• update to fix files to add uglo_15km
• staging ICs for high resolution test case for uglo_15km

Co-author: @sbanihash

Related Issues:

• Fixes updates from RTs for wave restart name and nml files #1457
• Fixes Update to use new WW3 grid, targeted for GFSv17 #3154
• Fixes Cycled waves for GFSv17 #1795
• related to Enable IAU across components in the coupled model #1776

Type of change

• Bug fix (fixes something broken)
• New feature (adds functionality)

Change characteristics

• Is this a breaking change (a change in existing functionality)? NO
• Does this change require a documentation update? YES/NO
• Does this change require an update to any of the following submodules? YES (If YES, please add a link to any PRs that are pending.)
  • EMC verif-global
  • GDAS
  • GFS-utils
  • GSI
  • GSI-monitor
  • GSI-utils
  • UFS-utils
  • UFS-weather-model Flexible restart write times (restart_fh) for med, ocn, ice, wav ufs-community/ufs-weather-model#2419 (Already merged)
  • wxflow

How has this been tested?

Tests were done by adding waves to C48mx500 3DVar tests for cycling.
High resolution tests cases were also added.

This likely needs a new round of testing before CI and after staged ICs & new fix files are added.

Checklist

• Any dependent changes have been merged and published
• 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
• I have documented my code, including function, input, and output descriptions
• My changes generate no new warnings
• New and existing tests pass with my changes
• This change is covered by an existing CI test or a new one has been added
• Any new scripts have been added to the .github/CODEOWNERS file with owners
• I have made corresponding changes to the system documentation if necessary

[JessicaMeixner-NOAA]

I just merged in the latest change from develop - i'm not sure if that'll take care of the issues here or not.

I wouldn't expect it to.

@WalterKolczynski-NOAA - cannot confirm the fix yet, but I suspect i've pushed the fix now.

[JessicaMeixner-NOAA]

@WalterKolczynski-NOAA - My test has gotten past the previous failure: /work2/noaa/marine/jmeixner/hercules/PR3190wcdatest/wcda1/COMROOT/wcda1/logs/2021032418/gdas_fcst_seg0.log

[emcbot]

CI Passed on Hera in Build# 4
Built and ran in directory /scratch1/NCEPDEV/global/CI/3190

Experiment C96_S2SWA_gefs_replay_ics_8fde3150 Completed 1 Cycles: *SUCCESS* at Thu Jan 16 22:53:33 UTC 2025
Experiment C48mx500_3DVarAOWCDA_8fde3150 Completed 2 Cycles: *SUCCESS* at Thu Jan 16 23:00:42 UTC 2025
Experiment C48_ATM_8fde3150 Completed 2 Cycles: *SUCCESS* at Thu Jan 16 23:06:53 UTC 2025
Experiment C48mx500_hybAOWCDA_8fde3150 Completed 2 Cycles: *SUCCESS* at Thu Jan 16 23:06:56 UTC 2025
Experiment C96C48_hybatmaerosnowDA_8fde3150 Completed 3 Cycles: *SUCCESS* at Fri Jan 17 00:20:43 UTC 2025
Experiment C96_atm3DVar_8fde3150 Completed 3 Cycles: *SUCCESS* at Fri Jan 17 00:27:05 UTC 2025
Experiment C96C48_hybatmDA_8fde3150 Completed 3 Cycles: *SUCCESS* at Fri Jan 17 00:27:36 UTC 2025
Experiment C48_S2SWA_gefs_8fde3150 Completed 1 Cycles: *SUCCESS* at Fri Jan 17 00:39:52 UTC 2025
Experiment C48_S2SW_8fde3150 Completed 2 Cycles: *SUCCESS* at Fri Jan 17 00:52:09 UTC 2025
Experiment C96C48_ufs_hybatmDA_8fde3150 Completed 3 Cycles: *SUCCESS* at Fri Jan 17 00:58:15 UTC 2025

[emcbot]

CI Passed on Hercules in Build# 5
Built and ran in directory /work2/noaa/global/CI/HERCULES/3190

Experiment C48_ATM_8fde3150 Completed 2 Cycles: *SUCCESS* at Thu Jan 16 21:41:48 CST 2025
Experiment C48mx500_3DVarAOWCDA_8fde3150 Completed 2 Cycles: *SUCCESS* at Thu Jan 16 21:47:49 CST 2025
Experiment C48mx500_hybAOWCDA_8fde3150 Completed 2 Cycles: *SUCCESS* at Thu Jan 16 22:00:00 CST 2025
Experiment C96_S2SWA_gefs_replay_ics_8fde3150 Completed 1 Cycles: *SUCCESS* at Thu Jan 16 22:06:11 CST 2025
Experiment C96_atm3DVar_8fde3150 Completed 3 Cycles: *SUCCESS* at Thu Jan 16 23:00:27 CST 2025
Experiment C48_S2SW_8fde3150 Completed 2 Cycles: *SUCCESS* at Thu Jan 16 23:00:30 CST 2025
Experiment C96C48_hybatmDA_8fde3150 Completed 3 Cycles: *SUCCESS* at Thu Jan 16 23:00:34 CST 2025
Experiment C48_S2SWA_gefs_8fde3150 Completed 1 Cycles: *SUCCESS* at Thu Jan 16 23:19:06 CST 2025