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WW3 feature: Langmuir turbulence parameterization #2195

Merged
merged 21 commits into from
Mar 29, 2024
Merged

WW3 feature: Langmuir turbulence parameterization #2195

merged 21 commits into from
Mar 29, 2024

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MatthewMasarik-NOAA
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@MatthewMasarik-NOAA MatthewMasarik-NOAA commented Mar 15, 2024 •
edited by zach1221
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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

Description:

Adds Langmuir turbulence parameterization developed by ESCOMP to allow computing Stokes drift diagnostics within the WW3 sub-component.

Commit Message:

Add Langmuir turbulence parameterization for computing Stokes drift diagnostics. Authors: @qingli411, @alperaltuntas

  * WW3 - Langmuir turbulence parameterization

Priority:

  • Normal.

Git Tracking

UFSWM:

Sub component Pull Requests:

UFSWM Blocking Dependencies:

  • None

Changes

Regression Test Changes (Please commit test_changes.list):

  • No Baseline Changes.

2024-03-13.RegressionTests_hera.log.txt, test_changes.list commited: 517e05d

Input data Changes:

  • Updated input data.

New mod_def's for all RTs are the updates to the input data. Directory location containing new mod_defs: /scratch1/NCEPDEV/climate/Matthew.Masarik/waves/share/ufs/moddefs/WW3_input_data_20240214.

Library Changes/Upgrades:

  • No Updates

Testing Log:

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

@MatthewMasarik-NOAA MatthewMasarik-NOAA mentioned this pull request Mar 15, 2024
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14 tasks
@MatthewMasarik-NOAA MatthewMasarik-NOAA marked this pull request as ready for review March 21, 2024 12:53
@DeniseWorthen DeniseWorthen added the New Input Data Req'd This PR requires new data to be sync across platforms label Mar 26, 2024
@jkbk2004
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@MatthewMasarik-NOAA can you sync up branch?

@MatthewMasarik-NOAA
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Hi @jkbk2004, looks like theres a merge conflict. Let me look into it

@MatthewMasarik-NOAA
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Hi @jkbk2004, the conflict is just in rt.sh. The difference is INPUTDATA_ROOT_WW3 which I set to the directory with the updated mod_defs. @JessicaMeixner-NOAA had advised this. Should I resolve this by committing my version of rt.sh, or revert it to the normal state?

@jkbk2004
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@MatthewMasarik-NOAA I rsynced up to WW3_input_data_20220624 on hera. Do you like to have WW3_input_data_20240214 in baseline input directory? I backed up WW3_input_data_20220624. So no problem to go with WW3_input_data_20240214.

@MatthewMasarik-NOAA
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@jkbk2004, yes that sounds great. please add WW3_input_data_20240214 to the baseline input directory.

So for my side, I should set INPUTDATA_ROOT_WW3=${INPUTDATA_ROOT}/WW3_input_data_20240214 in rt.sh to resolve the conflict, is that correct?

@DeniseWorthen
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@jkbk2004 Do not over-write the existing WW3_input_data_20220624. You need to create a new dated WW3_input_data inside of input-data for the new mod_def files.

@jkbk2004
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@jkbk2004, yes that sounds great. please add WW3_input_data_20240214 to the baseline input directory.

So for my side, I should set INPUTDATA_ROOT_WW3=${INPUTDATA_ROOT}/WW3_input_data_20240214 in rt.sh to resolve the conflict, is that correct?

@MatthewMasarik-NOAA /scratch2/NAGAPE/epic/UFS-WM_RT/NEMSfv3gfs/input-data-20221101/WW3_input_data_20240214 is there now. Go ahead to set as INPUTDATA_ROOT_WW3=${INPUTDATA_ROOT}/WW3_input_data_20240214. @BrianCurtis-NOAA @zach1221 @FernandoAndrade-NOAA FYI

@jkbk2004
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WW3_input_data_20220624

WW3_input_data_20220624 is intact on hera.

@DeniseWorthen
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Please make sure that the original WW3_input_data_20220624/ is in place. If I look on Hera, those files have the current day's timestamp.

@MatthewMasarik-NOAA
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@MatthewMasarik-NOAA /scratch2/NAGAPE/epic/UFS-WM_RT/NEMSfv3gfs/input-data-20221101/WW3_input_data_20240214 is there now. Go ahead to set as INPUTDATA_ROOT_WW3=${INPUTDATA_ROOT}/WW3_input_data_20240214.

@jkbk2004, I'll go ahead with that

@MatthewMasarik-NOAA
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@jkbk2004, I just resolved the conflict and updated my branch. I'm not completely sure if the FV3,MOM6 updates come in OK. please let me know if not

@jkbk2004
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@jkbk2004, I just resolved the conflict and updated my branch. I'm not completely sure if the FV3,MOM6 updates come in OK. please let me know if not

looks good now.

@jkbk2004 jkbk2004 added Ready for Commit Queue The PR is ready for the Commit Queue. All checkboxes in PR template have been checked. No Baseline Change No Baseline Change labels Mar 28, 2024
@jkbk2004
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hera is slow today. But I submitted jobs. @zach1221 @FernandoAndrade-NOAA please, pick up other machines. @BrianCurtis-NOAA FYI: this pr is ready.

@jkbk2004
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@FernandoAndrade-NOAA can you reflect to this pr for the STMP/PTMP gaea line update needed to cover #2198 ? We need to update the ecflow version number for hera as well.

@jkbk2004
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looks like we need to resolve conflicts on rt.sh in this pr. @MatthewMasarik-NOAA we don't need to update rt.sh except https://github.com/MatthewMasarik-NOAA/ufs-weather-model/blob/feature/langmuir-parameterization/tests/rt.sh#L938, right?

@FernandoAndrade-NOAA
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looks like we need to resolve conflicts on rt.sh in this pr. @MatthewMasarik-NOAA we don't need to update rt.sh except https://github.com/MatthewMasarik-NOAA/ufs-weather-model/blob/feature/langmuir-parameterization/tests/rt.sh#L938, right?

the conditionals and load for rocoto and ecflow were removed with this PRs rt.sh changes as well

@FernandoAndrade-NOAA
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looks like we need to resolve conflicts on rt.sh in this pr. @MatthewMasarik-NOAA we don't need to update rt.sh except https://github.com/MatthewMasarik-NOAA/ufs-weather-model/blob/feature/langmuir-parameterization/tests/rt.sh#L938, right?

I restored rt.sh, updated the WW3 input date and added the Gaea paths update for stmp and ptmp for users outside of the epic group.

@MatthewMasarik-NOAA
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looks like we need to resolve conflicts on rt.sh in this pr. @MatthewMasarik-NOAA we don't need to update rt.sh except https://github.com/MatthewMasarik-NOAA/ufs-weather-model/blob/feature/langmuir-parameterization/tests/rt.sh#L938, right?

@jkbk2004
this was the only line I thought needed to be updated: https://github.com/MatthewMasarik-NOAA/ufs-weather-model/blob/055b13ffbe0e49abbcf8d4e503ee617a8e78e5be/tests/rt.sh#L990

@FernandoAndrade-NOAA FernandoAndrade-NOAA linked an issue Mar 28, 2024 that may be closed by this pull request
rt.sh crashes with 'Permission denied' error while creating run directory on Gaea #2198
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@MatthewMasarik-NOAA
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Regarding rt.sh, test_changes.list, and whitespace --
please let me know if I should make these updates to the branch, or if these comments are for CMs

@FernandoAndrade-NOAA
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looks like we need to resolve conflicts on rt.sh in this pr. @MatthewMasarik-NOAA we don't need to update rt.sh except https://github.com/MatthewMasarik-NOAA/ufs-weather-model/blob/feature/langmuir-parameterization/tests/rt.sh#L938, right?

@jkbk2004 this was the only line I thought needed to be updated: https://github.com/MatthewMasarik-NOAA/ufs-weather-model/blob/055b13ffbe0e49abbcf8d4e503ee617a8e78e5be/tests/rt.sh#L990

That's the line he was pointing to before I restored and resynced rt.sh, sorry about that confusion.

@zach1221
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Ok let's start the merge process.

@zach1221 zach1221 mentioned this pull request Mar 29, 2024
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@JessicaMeixner-NOAA
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JessicaMeixner-NOAA commented Mar 29, 2024 •
edited by zach1221
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WW3 is merged: NOAA-EMC/WW3@d9b3172
@MatthewMasarik-NOAA

@zach1221 zach1221 merged commit 87c27b9 into ufs-community:develop Mar 29, 2024
zhanglikate added a commit to zhanglikate/ufs-weather-model that referenced this pull request May 3, 2024
@zhanglikate
Squashed commit of the following:
2ce5436 
commit f234a3e
Author: Ufuk Turunçoğlu <[email protected]>
Date:   Tue Apr 30 11:35:25 2024 -0600

    Fix for land component model (ufs-community#2191)

    * UFSWM - fix fully coupled land component configuration
      * NOAHMP - get fixed information from surface file

commit 04bbc15
Author: jiandewang <[email protected]>
Date:   Thu Apr 25 14:52:00 2024 -0400

    update MOM6 to its main repo. 20240401 commit (ufs-community#2241)

    * UFSWM -
      * MOM6 - update MOM6 to its main repo. 20240401 commit (NCAR-candidate-20240319)

commit b6c576d
Author: Daniel Sarmiento <[email protected]>
Date:   Tue Apr 23 12:24:22 2024 -0400

    Merged global namelist (ufs-community#2173)

    * UFSWM - global_control.nml_IN has been added as the new regression test namelist template for all global regression tests. The namelist now uses pointers (i.e. @[abc]) for variables and default values have been added to the default_vars.sh script. A new section in default_vars.sh has been added (export_tiled) to account for tiled RTs that pulls the correct parameter files using the ATMRES variable.
    Regression tests have been modified to account for these changes. Tests that were not compatible with the GFSv17_p8 core have been disabled for now. They will be turned on as they are updated from GFSv16 to GFSv17.

commit 5d2ca19
Author: WenMeng-NOAA <[email protected]>
Date:   Fri Apr 19 13:59:12 2024 -0400

    Update upp submodule (ufs-community#2213)

    * UFSWM - Update inline post
      * FV3 - Update upp submodule for inline post

commit 47c0099
Author: Brian Curtis <[email protected]>
Date:   Wed Apr 17 15:59:48 2024 -0400

    Add bash linting to CI. Cleanup .sh scripts a bit. Address .sh bugs. Adds -v Verbose option. (ufs-community#2218)  Remove nowarn Intel compiler flag (ufs-community#2225)

    * UFSWM
    - Add bash linting to CI:
      - uses superlinter to check for consistent bash code writing
    - Cleans up .sh scripts to comply with superlinter
    - Cleans up .sh scripts to be more consistent, easier to read.
    - Add's -v verbose option if debugging outputs needed, otherwise simplifies rt.sh run echo's.
    - Addresses smaller bugs
      - quota/timeout search logic adjusted.
      - check for dirs existing (DISKNM, STMP, PTMP) before starting.
      - adjustments/cleanup to ecflow/rocoto sections
      - rt.sh will attempt to start ecflow, and only stop ecflow if it started from rt.sh.
      - fix for issue where run_dir will not delete properly.
    * FV3: Address compiler warnings
      * atmos_cubed_sphere: Address compiler warnings.

commit 4f32a4b
Author: Rick Grubin <[email protected]>
Date:   Mon Apr 15 07:21:08 2024 -0600

    Document ATMW / ATMAERO / HAFS WM configurations (ufs-community#2160)

    * UFSWM
      * doc/Userguide
        * source
          * conf.py
          * Configurations.rst
          * FAQ.rst
          * InputsOutputs.rst
          * Introduction.rst

commit ac4445d
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Apr 15 08:59:42 2024 -0400

    Bump idna from 3.6 to 3.7 in /doc/UsersGuide (ufs-community#2234)

    *doc/UserGuide
       *requirements.txt - updates inda version from 3.6 to 3.7

commit 281b32f
Author: Samuel Trahan (NOAA contractor) <[email protected]>
Date:   Mon Apr 15 08:38:01 2024 -0400

    bug fixes: kchunk3d ignored, hailwat uninitialized in dycore, tile_num wrong for nests (ufs-community#2201)

    * UFSWM - None.
      * FV3 - Write component will use kchunk3d. Model init sends the right tile number to CCPP.
        * atmos_cubed_sphere - Initialize the hailwat variable. Pass global_tile index to model.

commit 8a5f711
Author: Denise Worthen <[email protected]>
Date:   Thu Apr 11 13:32:26 2024 -0400

    Add PIO namelist control for CICE (ufs-community#2145)

    Update to CICE-Consortium/CICE aca8357. Adds implementation of namelist PIO options for CICE

commit 45c8b2a
Author: JONG KIM <[email protected]>
Date:   Thu Apr 4 19:49:13 2024 -0400

    Hotfix/cubed sphere hash fix: HAILCAST diagnostic code (units issue) (ufs-community#2223)

    cubed_sphere hash update: f060e85 for a bug- fix in the HAILCAST diagnostic code (units issue)

commit 26e6db6
Author: Denise Worthen <[email protected]>
Date:   Wed Apr 3 19:57:08 2024 -0400

    Enable cpl_scalars export from ATM and NoahMP for use by CMEPS (ufs-community#2175)

      * CMEPS - allow additional dimension in cpl_scalars for CSG and regional ATM domains for use in mediator history files
      * CMEPS - fix mapping mask for lnd->atm
      * FV3 - add export of cpl_scalars
      * NOAHMP - add export of cpl_scalars

commit 1411b90
Author: Dusan Jovic <[email protected]>
Date:   Mon Apr 1 18:04:44 2024 -0400

    Update module_write_netcdf to avoid hangs in RRFS runs (ufs-community#2193)

    * UFSWM - Update module_write_netcdf to avoid hangs in RRFS runs
      * FV3 - Update module_write_netcdf to avoid hangs in RRFS runs

commit 87c27b9
Author: Matthew Masarik <[email protected]>
Date:   Fri Mar 29 15:23:42 2024 -0400

    WW3 feature:  Langmuir turbulence parameterization (ufs-community#2195)

      * WW3 - Langmuir turbulence parameterization

commit c54e986
Author: Samuel Trahan (NOAA contractor) <[email protected]>
Date:   Wed Mar 27 16:11:03 2024 -0400

    regression test system bug fixes, eliminate MOM6 warnings (ufs-community#2197), add xr_cnvcld flag to FV3 (ufs-community#2185) (ufs-community#2202)

    * UFSWM - atparse.bash: correctly handle input that doesn't end with an end-of-line character. Fix some bugs in Rocoto support and clean up rt.sh.
      * FV3 - namelist flag xr_cnvcld to control if suspended grid-mean convective cloud condensate should be included in cloud fraction and optical depth calculation in radiation in the GFS suite
        * ccpp - physics-level changes to implement new namelist variable
      * MOM6 - update MOM6 code to eliminate all compiler warnings
@grantfirl grantfirl mentioned this pull request May 23, 2024
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@DeniseWorthen DeniseWorthen DeniseWorthen left review comments

@BrianCurtis-NOAA BrianCurtis-NOAA BrianCurtis-NOAA approved these changes

@jkbk2004 jkbk2004 jkbk2004 approved these changes

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@MatthewMasarik-NOAA @jkbk2004 @DeniseWorthen @FernandoAndrade-NOAA @zach1221 @JessicaMeixner-NOAA @BrianCurtis-NOAA