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Add more ocean variables for post-processing in GEFS #2995

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EricSinsky-NOAA
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@EricSinsky-NOAA EricSinsky-NOAA commented Oct 9, 2024

Description

This PR adds an ocean variable tob (Sea Water Potential Temperature at Sea Floor) for post-processing in GEFS, which is a variable that has been requested for GEFSv13 and the reforecast.

Also, this PR moves the atmos variable PEVPR from the "b" group to the "a" group of pgrb products in GEFS. This was requested by a reforecast stakeholder.

Resolves #2993

Type of change

  • Bug fix (fixes something broken)
  • New feature (adds functionality)
  • Maintenance (code refactor, clean-up, new CI test, etc.)

Change characteristics

  • Is this a breaking change (a change in existing functionality)? NO
  • Does this change require a documentation update? NO
  • Does this change require an update to any of the following submodules? YES

How has this been tested?

These changes have been tested on WCOSS2. This PR will be left as a draft until the necessary gfs-utils PR is merged.

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
  • I have made corresponding changes to the system documentation if necessary

@EricSinsky-NOAA
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After testing this branch with the latest gfs_utils hash, the new ocean variable tob is successfully being post-processed in the ocean_prod task. Also, PEVPR is being successfully written to the "a" atmos pgrb file group. Marking this PR as ready for review.

@EricSinsky-NOAA EricSinsky-NOAA marked this pull request as ready for review October 10, 2024 19:46
@WalterKolczynski-NOAA WalterKolczynski-NOAA added the CI-Hercules-Ready **CM use only** PR is ready for CI testing on Hercules label Oct 10, 2024
@emcbot emcbot added CI-Hercules-Building **Bot use only** CI testing is cloning/building on Hercules CI-Hercules-Running **Bot use only** CI testing on Hercules for this PR is in-progress CI-Hercules-Failed **Bot use only** CI testing on Hercules for this PR has failed and removed CI-Hercules-Ready **CM use only** PR is ready for CI testing on Hercules CI-Hercules-Building **Bot use only** CI testing is cloning/building on Hercules CI-Hercules-Running **Bot use only** CI testing on Hercules for this PR is in-progress labels Oct 10, 2024
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emcbot commented Oct 10, 2024

Experiment C96_S2SWA_gefs_replay_ics FAILED on Hercules in Build# 1 in
/work2/noaa/stmp/CI/HERCULES/2995/RUNTESTS/EXPDIR/C96_S2SWA_gefs_replay_ics_172223cd

@EricSinsky-NOAA
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A change needed to be made to the name of one of the extractvars dependencies due to the changes made in PR #2981. This change has been committed in d7a10a9.

@emcbot emcbot added CI-Hercules-Failed **Bot use only** CI testing on Hercules for this PR has failed and removed CI-Hercules-Failed **Bot use only** CI testing on Hercules for this PR has failed labels Oct 11, 2024
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CI Failed on Hercules in Build# 1
Built and ran in directory /work2/noaa/stmp/CI/HERCULES/2995


Experiment C48_ATM_172223cd Completed 1 Cycles: *SUCCESS* at Thu Oct 10 17:10:58 CDT 2024
Experiment C96_S2SWA_gefs_replay_ics_172223cd Terminated with 0 tasks failed and 0 dead at Thu Oct 10 17:17:06 CDT 2024
Experiment C96_S2SWA_gefs_replay_ics_172223cd Terminated: *STALLED*
Experiment C96_atm3DVar_172223cd Completed 3 Cycles: *SUCCESS* at Thu Oct 10 18:11:56 CDT 2024
Experiment C96C48_hybatmDA_172223cd Completed 3 Cycles: *SUCCESS* at Thu Oct 10 18:30:24 CDT 2024
Experiment C48_S2SW_172223cd Completed 1 Cycles: *SUCCESS* at Thu Oct 10 19:24:18 CDT 2024
Experiment C48_S2SWA_gefs_172223cd Completed 1 Cycles: *SUCCESS* at Thu Oct 10 19:31:16 CDT 2024

@WalterKolczynski-NOAA WalterKolczynski-NOAA added CI-Hercules-Ready **CM use only** PR is ready for CI testing on Hercules and removed CI-Hercules-Failed **Bot use only** CI testing on Hercules for this PR has failed labels Oct 15, 2024
@emcbot emcbot added CI-Hercules-Building **Bot use only** CI testing is cloning/building on Hercules and removed CI-Hercules-Ready **CM use only** PR is ready for CI testing on Hercules labels Oct 15, 2024
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TerrenceMcGuinness-NOAA commented Oct 15, 2024

@WalterKolczynski-NOAA Build fail with gfs_utils, seems to cause a Jenkins failure, not sure how the two are related:

guild_gfs_utils.log

@TerrenceMcGuinness-NOAA TerrenceMcGuinness-NOAA added CI-Hercules-Failed **Bot use only** CI testing on Hercules for this PR has failed and removed CI-Hercules-Building **Bot use only** CI testing is cloning/building on Hercules labels Oct 15, 2024
EricSinsky-NOAA added a commit that referenced this pull request Oct 28, 2024
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# Description
<!-- This description will become the commit message for the PR. -->
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Describe your changes. Focus on the *what* and *why*. The *how* will be
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This PR brings recent changes from the develop branch to the GEFS
reforecast branch. This PR updates the GEFS reforecast branch to develop
hash ac3cde5 (10/11/2024). This version
of global-workflow uses the ufs-weather-model hash
[6a4e09e](https://github.com/ufs-community/ufs-weather-model/tree/6a4e09e94773ffa39ce7ab6a54a885efada91f21)
(9/9/2024).

Furthermore, this PR ensures the following adjustments for the
reforecast:

- [x] Speed up rocoto by grouping post job
- [x] Optimize PE configuration
- [x]  Remove duplicate OCNSPPT and EPBL settings
- [x] Set restart_interval to fhmax
- [x] Turn off SHUM in config.efcs
- [x] Set FHMIN_WAV to 3 in config.base 
- [x] Turn off ATM history file output
- [x] Change  HMS=${cyc}0000 to HMS=030000 in Wavepostpnt script (#2788)
- [x] Include YYYYMMDDHH (PDY) in job name
- [x] Change CA seed based on case and cyc for control member and
perturbed members
- [x] Fix post ensemble info
- [x] Add tob to ocean products (#2995 )
- [x] Move PEVPR from b group to a group for atmos products (#2995)
- [x] Add option to download initial condition from HPSS
- [x] Add ability to download and stage replay analysis from AWS, which
is needed for the repair_replay task
- [x] Add capability to run forecasts in 7-day intervals  (#2928)
- [x] Update defaults.yaml so that many of the reforecast-specific
settings can be used by default

<!-- For more on writing good commit messages, see
https://cbea.ms/git-commit/ -->

# Type of change
- [ ] Bug fix (fixes something broken)
- [ ] New feature (adds functionality)
- [x] Maintenance (code refactor, clean-up, new CI test, etc.)

# Change characteristics
<!-- Choose YES or NO from each of the following and delete the other
-->
- Is this a breaking change (a change in existing functionality)? NO
- Does this change require a documentation update? NO
- Does this change require an update to any of the following submodules?
NO
  - [ ] EMC verif-global <!-- NOAA-EMC/EMC_verif-global#1234 -->
  - [ ] GDAS <!-- NOAA-EMC/GDASApp#1234 -->
  - [ ] GFS-utils <!-- NOAA-EMC/gfs-utils#1234 -->
  - [ ] GSI <!-- NOAA-EMC/GSI#1234 -->
  - [ ] GSI-monitor <!-- NOAA-EMC/GSI-Monitor#1234 -->
  - [ ] GSI-utils <!-- NOAA-EMC/GSI-Utils#1234 -->
  - [ ] UFS-utils <!-- ufs-community/UFS_UTILS#1234 -->
  - [ ] UFS-weather-model <!-- ufs-community/ufs-weather-model#1234 -->
  - [ ] wxflow <!-- NOAA-EMC/wxflow#1234 -->

# How has this been tested?
<!-- Please list any test you conducted, including the machine.

Example:
- Clone and build on WCOSS
- Cycled test on Orion
- Forecast-only on Hera
-->

This branch is being tested on WCOSS2. When testing has succeeded, this
PR will be marked as ready for review.

# 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
- [ ] I have made corresponding changes to the system documentation if
necessary

---------

Co-authored-by: Wei Huang <wei.huang@noaa.gov>
Co-authored-by: Kate Friedman <kate.friedman@noaa.gov>
Co-authored-by: Cory Martin <cory.r.martin@noaa.gov>
Co-authored-by: Andrew.Tangborn <Andrew.Tangborn@noaa.gov>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Co-authored-by: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Co-authored-by: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com>
Co-authored-by: AnningCheng-NOAA <48297505+AnningCheng-NOAA@users.noreply.github.com>
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: AntonMFernando-NOAA <167725623+AntonMFernando-NOAA@users.noreply.github.com>
Co-authored-by: BoCui-NOAA <53531984+BoCui-NOAA@users.noreply.github.com>
Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>
Co-authored-by: Jeffrey Whitaker <jeffrey.s.whitaker@noaa.gov>
Co-authored-by: mingshichen-noaa <48537176+mingshichen-noaa@users.noreply.github.com>
Co-authored-by: Jiarui Dong <Jiarui.Dong@noaa.gov>
Co-authored-by: David Huber <david.huber@noaa.gov>
Co-authored-by: Guillaume Vernieres <guillaume.vernieres@gmail.com>
Co-authored-by: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Co-authored-by: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com>
Co-authored-by: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com>
@WalterKolczynski-NOAA WalterKolczynski-NOAA added CI-Hera-Ready **CM use only** PR is ready for CI testing on Hera CI-Hercules-Ready **CM use only** PR is ready for CI testing on Hercules and removed CI-Hercules-Failed **Bot use only** CI testing on Hercules for this PR has failed CI-Hera-Ready **CM use only** PR is ready for CI testing on Hera CI-Hercules-Ready **CM use only** PR is ready for CI testing on Hercules labels Oct 30, 2024
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CI Passed on Hercules in Build# 1
Built and ran in directory /work2/noaa/global/CI/HERCULES/2995


Experiment C48_ATM_3d331677 Completed 2 Cycles: *SUCCESS* at Thu Oct 31 13:01:20 CDT 2024
Experiment C96_S2SWA_gefs_replay_ics_3d331677 Completed 1 Cycles: *SUCCESS* at Thu Oct 31 13:31:37 CDT 2024
Experiment C96_atm3DVar_3d331677 Completed 3 Cycles: *SUCCESS* at Thu Oct 31 14:26:47 CDT 2024
Experiment C96C48_hybatmDA_3d331677 Completed 3 Cycles: *SUCCESS* at Thu Oct 31 14:44:52 CDT 2024
Experiment C48_S2SW_3d331677 Completed 2 Cycles: *SUCCESS* at Thu Oct 31 14:56:57 CDT 2024
Experiment C48_S2SWA_gefs_3d331677 Completed 1 Cycles: *SUCCESS* at Thu Oct 31 15:33:33 CDT 2024

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CI Passed on Hera in Build# 2
Built and ran in directory /scratch1/NCEPDEV/global/CI/2995


Experiment C96_S2SWA_gefs_replay_ics_3d331677 Completed 1 Cycles: *SUCCESS* at Thu Oct 31 19:53:04 UTC 2024
Experiment C48_ATM_3d331677 Completed 2 Cycles: *SUCCESS* at Thu Oct 31 19:59:01 UTC 2024
Experiment C48mx500_3DVarAOWCDA_3d331677 Completed 2 Cycles: *SUCCESS* at Thu Oct 31 20:35:59 UTC 2024
Experiment C48_S2SWA_gefs_3d331677 Completed 1 Cycles: *SUCCESS* at Thu Oct 31 23:12:49 UTC 2024
Experiment C48_S2SW_3d331677 Completed 2 Cycles: *SUCCESS* at Thu Oct 31 23:40:03 UTC 2024
Experiment C96_atm3DVar_3d331677 Completed 3 Cycles: *SUCCESS* at Thu Oct 31 23:58:27 UTC 2024
Experiment C96C48_hybatmaerosnowDA_3d331677 Completed 3 Cycles: *SUCCESS* at Fri Nov  1 00:04:58 UTC 2024
Experiment C96C48_hybatmDA_3d331677 Completed 3 Cycles: *SUCCESS* at Fri Nov  1 03:26:58 UTC 2024
Experiment C96C48_ufs_hybatmDA_3d331677 Completed 3 Cycles: *SUCCESS* at Fri Nov  1 05:05:00 UTC 2024

@WalterKolczynski-NOAA WalterKolczynski-NOAA merged commit d95630a into NOAA-EMC:develop Nov 1, 2024
10 of 11 checks passed
@EricSinsky-NOAA EricSinsky-NOAA deleted the feature/addmoreprods branch November 8, 2024 15:43
danholdaway added a commit to danholdaway/global-workflow that referenced this pull request Jan 27, 2025
* develop:
  Remove WAFS files and references from `develop` (NOAA-EMC#3263)
  fix intel stack version number on c5 (NOAA-EMC#3258)
  Update gsi_monitor and ufs_utils hashes to recent hashes for C5/C6 build and run (NOAA-EMC#3252)
  Enable DA cycling on gaea C5/C6 (NOAA-EMC#3255)
  Copy post-processed sea ice increment for diagnostics (NOAA-EMC#3235)
  Only run METplus in the 3Dvar tests (NOAA-EMC#3245)
  Clone, build, and run C48_ATM and C48_S2SW on Gaea C5 and C6 (NOAA-EMC#3106)
  Add echgres as a dependency only for RUN=enkfgdas, not enkfgfs (NOAA-EMC#3246)
  Add domain level to wave gridded COM path (NOAA-EMC#3137)
  CI JJOB Tests using CMake (NOAA-EMC#3214)
  Make assorted updates to waves (NOAA-EMC#3190)
  Move WCOSS2 LD_LIBRARY_PATH patches to load_ufsda_modules.sh (NOAA-EMC#3236)
  Adding a gefs_arch task to GEFS workflow (NOAA-EMC#3211)
  Add additional GEFS variables needed for AI/ML applications  (NOAA-EMC#3221)
  Add bmat task dependency to marine LETKF task (NOAA-EMC#3224)
  Resolve bug with LMOD_TMOD_FIND_FIRST setting affecting build on WCOSS2 (NOAA-EMC#3229)
  Reinstate product groups (NOAA-EMC#3208)
  Additional fixes for downstream jobs (NOAA-EMC#3187)
  Turn IAU off during staging job for cold start experiments (NOAA-EMC#3215)
  Update the gdas.cd hash and enable GDASApp to run on WCOSS2 (NOAA-EMC#3220)
  Update upload-artifact to v4 (NOAA-EMC#3216)
  Prevent duplicate case generation in generate_workflows.sh (NOAA-EMC#3217)
  Update g-w to cycle with C1152 ATM (NOAA-EMC#3206)
  Separate use of initial increment/perturbation file from REPLAY/+03 ICs  (NOAA-EMC#3119)
  Update gsi_enkf hash and gsi_ver (NOAA-EMC#3207)
  Remove cpus-per-task from APRUN_OCNANALECEN on WCOSS2 (NOAA-EMC#3212)
  Remove 5WAVH from AWIPS GRIB2 parm files (NOAA-EMC#3146)
  Remove multi-grid wave support (NOAA-EMC#3188)
  Add echgres as a dependency for earc (NOAA-EMC#3202)
  Ensure OCNRES and ICERES have 3 digits in the archive script (NOAA-EMC#3199)
  Set runtime shell requirements within Jenkins Pipeline (NOAA-EMC#3171)
  Add efcs and epos to ufs_hybatm xml (NOAA-EMC#3192) (NOAA-EMC#3193)
  Fix GEFS and SFS compile flags in build_all.sh (NOAA-EMC#3197)
  Remove early-cycle EnKF forecast (NOAA-EMC#3185)
  Fix mod_icec bug in atmos_prod (NOAA-EMC#3167)
  Create compute build option (NOAA-EMC#3186)
  Support global-workflow using Rocky 8 on CSPs (NOAA-EMC#2998)
  Change orog gravity wave drag scheme for grid sizes less than 10km (NOAA-EMC#3175)
  Switch snow DA to use 2DVar for deterministic and ensemble mean (NOAA-EMC#3163)
  Update compression options for GEFS history files (NOAA-EMC#3184)
  Update compression options for high res history files (NOAA-EMC#3178)
  Turn DO_TEST_MODE off (NOAA-EMC#3177)
  Hotfix for gdas_arch div/0 (NOAA-EMC#3169)
  Allow building of the ufs-weather-model, WW3 pre/post execs for GFS, GEFS, SFS in the same clone of global-workflow (NOAA-EMC#3098)
  Switch Aerosol DA to use JCB and Jedi class (NOAA-EMC#3125)
  Update ufs-weather-model to 2024-12-06 commit  (NOAA-EMC#3145)
  Enable traditional threading as an option (NOAA-EMC#3149)
  Update HPC_ACCOUNT on Hercules to fv3-cpu (NOAA-EMC#3164)
  Turn C96C48_ufs_hybatmDA and C48mx500_3DVarAOWCDA into a regression test (NOAA-EMC#3120)
  Update GSI analysis jobs to use COMIN/COMOUT (NOAA-EMC#3092)
  Update HPC Tier Definitions (NOAA-EMC#3138)
  Add marine hybrid envar (NOAA-EMC#3041)
  Archive the experiment directory along with git status/diff output (NOAA-EMC#3105)
  Use stochastic restart patterns on rerun (NOAA-EMC#3077)
  Point Jenkinsfile back to CI/ (NOAA-EMC#3139)
  Fix wave restart for cold start and add ic version file (NOAA-EMC#3112)
  Allow users to override the default account at setup time (NOAA-EMC#3127)
  Refactor gridded wave post (NOAA-EMC#3014)
  Update docs related to NOAA CSPs (NOAA-EMC#3043)
  Allow APP to differ between RUNs (NOAA-EMC#2943)
  Run one executable for soca2cice (instead of two) (NOAA-EMC#3118)
  Speed up GSI analysis jobs in CI testing (NOAA-EMC#3115)
  Make aerosol output frequency variable (NOAA-EMC#2982)
  Add new stations to GFS BUFR sounding products (NOAA-EMC#3107)
  JCB-based obs+bias staging, Jedi class updates, and marine B-matrix refactoring (NOAA-EMC#2992)
  Enable tapering of atm ens perts at the model top (NOAA-EMC#3097)
  Update JGDAS ENKF POST  job  (NOAA-EMC#3090)
  SFS Runs at C96mx100  (NOAA-EMC#2960)
  Move machine-based options from config.base to host files (NOAA-EMC#3053)
  Remove RUNDIRS before running CI cases to cover re-run events (NOAA-EMC#3076)
  CI GitHub pipeline (hotfix) update for fetching repo name (NOAA-EMC#3084)
  Update JGDAS ENKF ECEN job  (NOAA-EMC#3050)
  Update snow obs processing job (NOAA-EMC#3055)
  Update to action workflow pipeline in default repo for development  (NOAA-EMC#3062)
  Update to action workflow pipeline in default repo for development (NOAA-EMC#3061)
  Update workflow pipeline (NOAA-EMC#3060)
  PW CI pipeline update5 ready for review so it can be merged and tested (NOAA-EMC#3059)
  Revert "GitHub CI Pipeline update for debugging forked PR support" (NOAA-EMC#3057)
  GitHub CI Pipeline update for debugging forked PR support (NOAA-EMC#3056)
  Add more ocean variables for post-processing in GEFS (NOAA-EMC#2995)
  Auto provisioning of PW clusters from GitHub CI added (NOAA-EMC#3051)
  Fix the name of the TC tracker filenames in archive.py (NOAA-EMC#3030)
  Make wxflow links static instead of from link_workflow (NOAA-EMC#3008)
  Update global jdas enkf diag job with COMIN/COMOUT for COM prefix (NOAA-EMC#2959)
  Add run and finalize methods to marine LETKF task (NOAA-EMC#2944)
  Fix wave restarts and GEFS FHOUT/FHMAX (NOAA-EMC#3009)
  Disabling hyper-threading (NOAA-EMC#2965)
  GitHub Actions Pipeline Updates for Self-Hosted Runners on PW (NOAA-EMC#3018)
  CI jekninsfile update hotfix (NOAA-EMC#3038)
  Update gdas.cd (NOAA-EMC#2978)
  Add ability to add tag to pslots with generate_workflows (NOAA-EMC#3036)
  CI update to shell environment with HOMEgfs to HOME_GFS for systems that need the path (NOAA-EMC#3013)
  Quick updated to Jenkins (health check) launch script (NOAA-EMC#3033)
  Document the generate_workflows.sh script (NOAA-EMC#3028)
  Replace gfs_cyc with an interval (NOAA-EMC#2928)
  Hotfix: Fix generate_workflows.sh optional build flags (NOAA-EMC#3024)
  Add a tool to run multiple YAML cases locally (NOAA-EMC#3004)
  Hotfix: Correctly set overwrite option when specified (NOAA-EMC#3021)
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Add more ocean variables for ocean post-processing in GEFS
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