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Add flexibility for ocean/ice output time-steps #1629

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JessicaMeixner-NOAA opened this issue May 18, 2023 · 14 comments
Closed

Add flexibility for ocean/ice output time-steps #1629

JessicaMeixner-NOAA opened this issue May 18, 2023 · 14 comments
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feature New feature or request

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@JessicaMeixner-NOAA
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JessicaMeixner-NOAA commented May 18, 2023

Description
Currently it's hard-coded in the diag_table that ocean output is 6 hourly: https://github.com/NOAA-EMC/global-workflow/blob/develop/parm/parm_fv3diag/diag_table#L3

However, @jiandewang found that there are currently constraints in that the ocean/ice (which must be consistent because of the currently combined grib output), must also be the same as the forecast model due to these lines in the scripts:
ush/forecast_postdet.sh:

   fhrlst=$OUTPUT_FH

    for fhr in $fhrlst; do
      if [ $fhr = 'anl' ]; then  # Looking at OUTPUT_FH, this is never true. TODO: remove this block
        continue
      fi
      VDATE=$($NDATE $fhr $IDATE)
      YYYY=$(echo $VDATE | cut -c1-4)
      MM=$(echo $VDATE | cut -c5-6)
      DD=$(echo $VDATE | cut -c7-8)
      HH=$(echo $VDATE | cut -c9-10)
      SS=$((10#$HH*3600))

Requirements
Ideally we can run without hard-coding the 6-> (atm time step) and have the ocean/ice model have different time steps.

Acceptance Criteria (Definition of Done)
Be able to run with 3 hourly atm time-steps and 6 hourly ocean or 3 hourly atm and ocn/ice and not have to change anything other than a config file.

@JessicaMeixner-NOAA JessicaMeixner-NOAA added the feature New feature or request label May 18, 2023
@JessicaMeixner-NOAA JessicaMeixner-NOAA added this to the HR2 milestone May 18, 2023
@aerorahul
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@JessicaMeixner-NOAA
The lines referred to in the description are pointing to an aerosol section. Can you please update the issue? Thanks!

@jiandewang
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see https://github.com/NOAA-EMC/global-workflow/blob/develop/ush/forecast_postdet.sh#L773-L787
here Vdate relies on Idate, but Idate is defined on fv3 side

@aerorahul
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actually, IDATE=CDATE on

export IDATE=${CDATE}
.
CDATE is defined at the top as the current cycle and does not change.

@aerorahul
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@jiandewang
I don't understand the issue here.
The output frequency is controlled via the diag_table. It is currently set to 6 hourly. In addition, it seems like these are 6 hour averages, not instantaneous.
For this reason, the model outputs the data in a file with the datetime that is the midpoint.

This file with midpoint date is then linked to COM with a valid datetime and midpoint datetime. I don't see why that is necessary and we will simplify this section in coming PRs.

If the issue is to have a different averaging time for ocean, I think we can update the diag_table and ensure that it is consistent with the script through a configuration variable. Note however, this will not be accomplished in time for v17.

@JessicaMeixner-NOAA
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The frequency of the ocean output in GFSv17 is currently undecided, my understanding of the issue was found when we were trying to use 3 hourly atm output and 6 hourly ocean output, however, since
https://github.com/NOAA-EMC/global-workflow/blob/develop/ush/forecast_postdet.sh#L760: fhrlst=${OUTPUT_FH}
we get a list of forecast hours based on a variable set by the atm forecast hour, not the ocean forecast output time which as you mentioned is set/hard-coded to 6 hourly in the diag_table.

@jiandewang
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@aerorahul
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@JessicaMeixner-NOAA
These are structural changes and we would like to know what we are working with as soon as possible. There is a lot of hard-wired information that was put in place for prototype experiments. We won't be doing that for the GFS. Please plan accordingly.

@WalterKolczynski-NOAA WalterKolczynski-NOAA removed this from the HR2 milestone Sep 12, 2023
@WalterKolczynski-NOAA WalterKolczynski-NOAA self-assigned this Sep 20, 2023
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Sep 22, 2023
Changes the output frequency from 3 to 6. While we may leave this
setting as the default for development, it is required right now
because the ocean frequency is hard-coded to 6 but links are created
based on `$FHOUT_GFS`. Resolving NOAA-EMC#1629 should correct this limitation.

Refs NOAA-EMC#1606
Refs NOAA-EMC#1629
WalterKolczynski-NOAA added a commit that referenced this issue Sep 29, 2023
When the prototype S2S was first added, we placed some settings in
a `config.defaults.s2sw` file to avoid interference with existing
settings. Now that we are moving towards v17 and run S2S regularly,
it is time to merge these settings back into the other config files.

The wave output frequency settings are updated to the coarser fre-
quency as that is more suitable for development. The prior (ops)
settings are noted as comments.

There are a couple of settings that control ice fields within FV3.
These are placed in `config.ice`, so when the ice model is on those
settings are still used.

Changes the output frequency from 3 to 6. While we may leave this
setting as the default for development, it is required right now
because the ocean frequency is hard-coded to 6 but links are created
based on `$FHOUT_GFS`. Resolving #1629 should correct this limitation.

"Gaussian" archive is updated to the former override values.

Resolves #1606
Refs #1629
@JessicaMeixner-NOAA
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From @NeilBarton-NOAA -- we control the ice output frequency by the FHOUT variable here:
https://github.com/NOAA-EMC/global-workflow/blob/develop/ush/parsing_namelists_CICE.sh#L84-L85 :

 histfreq       = 'm','d','h','x','x'
   histfreq_n     =  0 , 0 , ${FHOUT} , 1 , 1

Note that the first lines "h" for hour corresponds to the "FHOUT" variable.

jkhender added a commit to jkhender/global-workflow that referenced this issue Jan 13, 2024
  global-workflow:  02Jan24, 9d901db
  UFS:              21Dec23, 991d652
  UPP:              07Nov23, 78f369b

Squashed commit of the following:

commit 4e4e50803d95566e1c7967cf4cfa575391d77f25
Author: Judy.K.Henderson <[email protected]>
Date:   Fri Jan 12 00:44:59 2024 +0000

     Change default HPSS_PROJECT to fim

     Change restart_interval_gfs to -1 so no files are written ro RERUN_RESTART directory

commit 791d7a27c6b12f07d9c12ce491338e3da59eb1d8
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 11 23:34:36 2024 +0000

     Add namelist parameter, nord_tr, for GSL suites

commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 11 23:31:22 2024 +0000

     Add changes for running v17p8_mynn

     - new field table, field_table_thompson_aero_tke_progsigma
     - updated namelist parameters in config.fcst

commit 982a1f02e3b880be43f4ae8a3f0ffbb34c056aea
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 02:26:22 2024 +0000

     Add experiment setup script for p8_ugwpv1

commit c5a3697d22fdbb02bb80ddffee2629dddc10c702
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 02:19:13 2024 +0000

     Add memory report to srun command in env/HERA.env

commit ece7e516ca65ec0240899e7d84321310a6887595
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 02:13:42 2024 +0000

     Updated GSL-specific files under ufs_utils.fd_gsl

commit 1b153fc95b93a16eb40b791be7322100fde4a3d4
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 01:52:56 2024 +0000

     Create new branch, gsl_ufs_dev, from dev_02jan24_9d901db

     Add initial GSL modifications
      - changes to workflow files
        * GSL paths, projects, entities
      - new FV3_GFS_v17_p8_ugwpv1_mynn suite definition file (SDF)
      - updated namelist parameters in ush/parsing_namelists_FV3.sh
      - create new GSL directories: ufs_model.fd_gsl and ufs_utils.fd_gsl
        * new SDFs, add instantaneous flux variables to grib2 configuration files
        * add Thompson tracers to initial conditions
      - new sync script: rsync_gsl.sh
      - new job files:  getic.sh, makeinit_link.sh
      - modify build_ufs.sh to include MYNN SDF

commit 9d901dbbff4d41586580316bdc094d24760119e6
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Jan 2 10:30:33 2024 -0700

    Stop Gempak pgrb2 spec from modifying $DATA (#2147)

    This PR addresses issue #1224. The following is accomplished:

    - Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time;
    - Shell linter exceptions are addressed accordingly;
    - The respective GEMPAK tasks is added to the Rocoto mesh.

    Resolves #1224

commit 31ad23527802f7d07171132cc620f7135c4d8cba
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Jan 2 10:27:30 2024 -0700

    Reorganize NPOESS scripts (#2166)

    This PR addresses issue #1226. The following is accomplished:

    - Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure
    of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated;
    - Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh`
    are moved accordingly; this specifically applies to the environment variable `FHOUR`,
    `SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`;
    - The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level
    (if necessary);
    - Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however,
    this may not be necessary (see `TODO` note within draft PR.

    Resolves #1226

commit 22bd82fa93b49e5ce98eb3f69123956dd5018049
Author: Kate Friedman <[email protected]>
Date:   Tue Jan 2 11:55:03 2024 -0500

    Orog fix file reorg and fix directory variable standardization (#2181)

    This PR makes updates to use the newly reorganized `orog/20231027`
    fix file version and standardizes the fix file directory variables.

    Changes:

    1. Update UFS_UTILS hash to ce385ce
    2. Update fix file version file to use new orog timestamp: `orog_ver=20231027`
    3. Add ".mx$(OCNRES)" to `oro_data` filenames in scripts
    4. Remove ".mx$(ocn_res)_frac" from the directory names for atmosphere
    resolutions under the `/orog` folder
    5. Adds fix file directory variables to `config.base`, many of which are pulled
    up out of lower scripts; introduce `FIXcpl`
    6. Renamed/replaced the following fix file directory variables:

    - `FV3JEDI_FIX` --> `FIXgdas`
    - `FIXfv3`, `FIX_orog` and `OROFIX` --> `FIXorog`
    - `FIX_ugwd` and `OROFIX_ugwd` --> `FIXugwd`
    - `FIX_am`, `FIXgsm`, `FIXSYND` --> `FIXam`
    - `FIX_lut` --> `FIXlut`
    - `FIX_aer` --> `FIXaer`
    - `FIX_SFC` --> `FIXsfc`
    - `FIX_DIR` --> `FIXgfs`
    - `RTMFIX` and `FIXCRTM` --> `CRTM_FIX` (is `CRTM_FIX` in crtm module,
    so not using `FIXcrtm`)

    7. Correct the defaults for `FIXwave` in wave JJOB scripts
    8. Update variable names in `*fixed_files.yaml` files, as well as update naming
    convention for `oro_data` files

    Resolves #1984
    Resolves #1981
    Resolves #2175

commit 03d03bf53b43914a55c384cb33eb06f6a9a443a6
Author: Andrew Collard <[email protected]>
Date:   Tue Jan 2 11:53:44 2024 -0500

    Remove HIRS from GSI processing (#2183)

    With the update to CRTM 2.4.0.1, an issue with versioning of CRTM HIRS
    files has been exposed. This is documented in JCSDA/crtm#42.

    As HIRS radiances are no longer used in the GSI, these data should be removed
    from processing until a suitable update to CRTM is available.

    Resolves #2182

commit a3c50998d35525a39a66d5592fbf327ab3569e8b
Author: Jessica Meixner <[email protected]>
Date:   Fri Dec 22 18:07:48 2023 -0500

    Update ufs-weather-model version  (#2186)

    * update model to latest version which includes needed bugfixes for HR3

commit 774c7302e618370ef578bec3ccabc70486d6da1b
Author: David Huber <[email protected]>
Date:   Fri Dec 22 11:34:53 2023 -0500

    Fix analysis post processing's handling of 0-padded negative integers (#2187)

    This screens for the analysis 'forecast' hour (-001) and handles the '-' and circumvents octal issues.

commit d1251360325faf75af9df0608557fcd10202a883
Author: Barry Baker <[email protected]>
Date:   Thu Dec 21 11:23:48 2023 -0500

    Fix for restoring cycling aerosols in fo-mode post COM refactor (#2179)

    - Update to COM reorg aerosol initialization job
    - Address bug in joining paths for data dependency in this job

    ---------

    Co-authored-by: Rahul Mahajan <[email protected]>

commit e55a05980709288d902ad1bd894164bfa5a18a65
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Dec 20 22:14:01 2023 -0500

    Stop calling ufs-utils link script (#2172)

    The `link_workflow.sh` script was calling the ufs_utils version of the
    same. That step is only necessary if a user is going to run one of the
    stand-alone ufs-utils, which is rare.

commit ef3e5ad7c63be1644c82333c95853c3caf2d8995
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Dec 19 22:02:55 2023 -0500

    Fix handling of excluded hosts list (#2170)

    This PR fixes the issue with `create_experment.py` so that the yaml configuration
    file can have a string of list of strings when specifying the host name to exclude
    from the CI tests.

commit ea74a5719efc8f0fe631c5ff93426a4299a614f3
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Tue Dec 19 16:21:41 2023 -0500

    Add COMOUT_OBS to marine obs prep (#2173)

    Adds `COMOUT_OBS` (defined from `COM_OBS_TMPL`) to marine obs prep task to properly handle marine obs prep files. Used to keep obs after IODA conversion, QC, and other prep.

    Towards resolving NOAA-EMC/GDASApp#815

commit c2500feace0bb7c04ce67a90dd3182120ee67b2e
Author: David Huber <[email protected]>
Date:   Tue Dec 19 14:55:20 2023 -0500

    Return failed status if a build fails. (#2171)

    If any of the builds fail, this makes build_all.sh return the sum of the error codes encountered.

    Fixes #2168

commit 76fdd81cd84ed812181996a102379d8d964ba27a
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 19 13:24:34 2023 -0500

    Update index.rst for new GFSv16.3.12 in ops (#2169)

    Refs #2096

commit a81da33e8fe7541a36f68e7a4f14a384cadd36c8
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 19 10:22:21 2023 -0500

    Set place=shared for shared jobs on WCOSS2 (develop) (#2156)

    Set job as shared when not exclusive on WCOSS2

    WCOSS2 defaults to exclusive when it is not specified as
    either exclusive (place=exclhost) or shared (place=shared).
    Now set shared when job should be shared.

    Refs #2135

commit 89aea972f7964dac3f515e8070d7c534812c5fb4
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Dec 15 16:31:06 2023 -0500

    Update gfs-utils version for Hercules (#2163)

    An update of gfs-utils was misssing from the previous PR that added
    initial Hercules support (#2128).

    Also includes gfs-utils update for new marine post.

commit 9505cb4abc6ca2643a8ab254d14ca2000747fa44
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Dec 14 16:15:31 2023 -0500

    CI Updates to support Hercules (#2155)

    If merged, this PR will update the CI scripts so they will run on Hercules for forecast only
    NOTE: This is a stop gap to issue #2131 until its block on #1588 is removed.

    Resolves #2154

commit c5ca82f04a2efae78389dec1c46b94ef4fb5bbe5
Author: Rahul Mahajan <[email protected]>
Date:   Thu Dec 14 16:05:33 2023 -0500

    Correct fbwind (#2161)

commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a
Author: Kate Friedman <[email protected]>
Date:   Thu Dec 14 12:06:23 2023 -0500

    Add MOS jobs to rocoto mesh (#2148)

    Create separate jobs for GFS MOS - extracted from now-retired vrfy job

    Refs #2068

commit bb6151aa50c27253cb9b8f0a6601ddd58526b8b3
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Dec 14 05:38:29 2023 -0500

    Replace checkout script with submodules (#2142)

    Replaces the checkout script with git submodules. This change brings workflow in
    line with other repos and git standards.

    Due to these changes, the build system is updated slightly. First, the options that
    were formerly used with `checkout.sh` to reduce unneeded builds (`-g` for GSI
    and `-u` for UFSDA) are moved to `build_all.sh` instead. This is needed since build
    all will not be able to key off directories existing or not to determine which com-
    ponents to build. Second, the partial build system is removed. It was rarely, if ever,
    used, and parts of it were already ignored with the previous changes to base builds
    off whether directories exist. The manage externals file is also removed since that is
    also not being used.

    Following these changes, clones/checkout will need to either be recursive, or
    `git submodule update` will need to be called separately to make sure components
    are properly checked out (non-exhaustive list):

    ```
    ## Checkout develop (method 1)
    git clone --recursive https://github.com/NOAA-EMC/global-workflow destination

    ## Checkout develop (method 2)
    git clone  --jobs 8 https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git submodule update --init --recursive --jobs 8

    ## Checkout existing branch some_branch (method 1)
    git clone --recursive  --jobs 8 -b some_branch https://github.com/NOAA-EMC/global-workflow destination

    ## Checkout existing branch some_branch (method 2)
    git clone https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git checkout --recurse-submodules some_branch

    ## Checkout existing branch some_branch (method 3)
    git clone https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git checkout some_branch
    git submodule update --init --recursive  --jobs 8

    ## Checkout new branch new_branch
    git clone https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git checkout -b new_branch
    git submodule update --init --recursive  --jobs 8
    ```

    The git ignore list had to be updated to use explicit paths as the wildcard paths pick
    up the ones that are now submodules.

    UFS creates files during the build process that are not in its ignore list, so that sub-
    module ignores the "dirty" state to avoid confusing users running `git status`.

    CI and documentation are also updated to reflect the changes.

    Resolves #2141

commit 1332188ce2409e012ec127d44880e49732f7f379
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Dec 13 09:32:57 2023 -0500

    Enable radar reflectivity output (#2143)

    Turns on radar reflectivity output from FV3. This eliminates missing values appearing in the grib2 files.

commit 24d898ec0ec0c7fcbda6966988f9a986f528ed14
Author: David Huber <[email protected]>
Date:   Wed Dec 13 09:32:24 2023 -0500

    Fix Hercules hostname (#2150)

    * Allow lower or upper hostname on hercules.
    * Add Hercules to issue template.

commit 2896bb8787698be28ad20f2298589e6e95eaf9fb
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 12 09:13:06 2023 -0500

    Fix module load typo (#2145)

    Fix typo with loading the crtm module in the UPP hack for WCOSS2

    Refs #2144

commit 29d34172a67d976f910e78158ff0337e1ef099ca
Author: Cory Martin <[email protected]>
Date:   Thu Dec 7 15:12:05 2023 -0500

    Update GDAS hash to most recent stable versions (#2138)

commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Dec 7 10:41:05 2023 -0700

    Corrected typo in a gempak job gempakncdcupapgif . (#2137)

commit 3483f550db1ae35a680de49f7485ce5a11902dd9
Author: Cory Martin <[email protected]>
Date:   Thu Dec 7 12:34:56 2023 -0500

    Add support for FGAT and IAU for aerosol DA (#1940)

commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9
Author: David Huber <[email protected]>
Date:   Thu Dec 7 12:33:46 2023 -0500

    Enable forecast-only experiments on Hercules (#2128)

    This add forecast-only support for Hercules to the global workflow. Partially satisfies #1588.
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

commit a29f751aed05312da3d80d396159bb5a906d6ce4
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Dec 6 13:45:56 2023 -0700

    Adds GEMPAK and related jobs to rocoto task mesh (#2127)

commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082
Author: Rahul Mahajan <[email protected]>
Date:   Tue Dec 5 15:47:52 2023 -0500

    Separate offline UPP from interpolated grib2 product generation (#2110)

    This PR:
    - Replaces the use of  `JGLOBAL_ATMOS_POST` with `JGLOBAL_ATMOS_UPP`
    and `JGLOBAL_ATMOS_PRODUCTS`.
    - Introduces `JGLOBAL_ATMOS_PRODUCTS` that is responsible for creating
    grib2 products from the master file produced by UPP (inline from the model,
    or offline by running `JGLOBAL_ATMOS_UPP`).  Rocoto job `atmos_products.sh`,
    ex-script `exglobal_atmos_products.sh` are also added along with a
    `config.atmos_products`. Updates are made to the relevant `env` files as well as
    `config.resources` to reflect the addition of this job.
    - reduces the number of cores needed appropriately for forecast products when
    there is no offline UPP necessary.
    - renames older `fv3gfs_dwn_nems.sh` to `interp_atmos_master.sh` and
    `inter_flux.sh` to `interp_atmos_sflux.sh`
    - removes `fv3gfs_downstream_nems.sh` as it is absorbed into
    `exglobal_atmos_products.sh`
    - removes no longer used scripts for `gfs_post.sh`, `gfs_transfer.sh` (DBN alerts
    are absorbed into `exglobal_atmos_products.sh`), `post.sh`,
    `JGLOBAL_ATMOS_POST`, `ex${RUN}_atmos_post.sh` scripts.
    - Rocoto workflow related scripts are updated to add `atmos_products` as a job.
    When `WRITE_DOPOST` is `.false.`, `upp.sh` job to run the UPP offline is also
    added.  Dependencies have been appropriately applied.
    - removes `PGB1F` option that creates 1-degree grib1 products that are no longer
    needed in GFSv17.

    The hacks from (now deleted) `post.sh` had to be reinstated in `upp.sh` to load the
    modules from UPP instead of `load_fv3gfs_modules.sh`.

commit 44186f594aaf5f8feea0eadd4c5c3b59de3a825e
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 5 12:28:08 2023 -0500

    Update index.rst for new GFSv16.3.11 version (#2121)

    Refs #1356

commit e62a3a73cd22701962b7bf210fdfee37f37a5474
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Dec 5 09:08:12 2023 -0700

    Splits AWIPS jobs into seperate tasks (#2094)

    This PR addresses issue #1228. The following is accomplished:

    - Separate rocoto jobs have been created beneath `jobs/rocoto/`
    -- `awips_20sh` and `awips_g2sh`; these jobs replace `awips.sh` which was
    calling multiple J-jobs within the respective `awips.sh` scripts;
    - New tasks has been added to `workflow/rocoto/tasks.py` for the new
    AWIPS scripts;
    - The `gfs_cycled` and `gfs_forecast_only` modules beneath
    `workflow/rocoto` have been updated accordingly.

      Resolves #1228

commit 04d97e9aa7ab84b9754ab670074cfb19d543aa26
Author: Kate Friedman <[email protected]>
Date:   Mon Dec 4 13:38:30 2023 -0500

    Consolidate VMINMON and cleanup monitor scripts (#2088)

    This PR combines the GDAS and GFS versions of the VMINMON JJOB
    and ex-driver scripts into single GLOBAL/global versions. Additionally:

    * some further cleanup of the GSI-Monitor scripts is done; variable
    settings in ex-driver scripts are moved up to the JJOB level
    * the fix symlinks are consolidated into a new `fix/mon` subfolder (formerly
    `fix/gdas`) and copies of the gfs monitor fix files under `fix/products` are
    removed

    Resolves #1925

commit a286a11fdcbc31c8bc6d944890bc56294bc8caf6
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Dec 4 17:48:44 2023 +0000

    Robust CI Restarts (#2093)

    Improved CI robustness for reverting back to **CI-Ready** from any
    given state

    New Features:

    - Improved `scancel` routine (refactored into bash "subroutine")
    - Improved messaging (see below) when ever a user changes state
    - Any and all previous build scripts and running experiments are killed as
    a result of reset to **Ready**

    Resolves #2060

commit 73621e9b20b20f85e8b21e4c1e09ed1d80ecd46f
Author: David Huber <[email protected]>
Date:   Sun Dec 3 11:19:19 2023 -0500

    Upgrade to spack-stack/1.5.1 and Intel 2022 on non-production machines (#2084)

    Update module files to spack-stack/1.5.1 and compilers to Intel 2022+ on all non-production machines.

commit 6d548b250688861eb20a7e0dc852a0e4ba9e64f4
Author: jiandewang <[email protected]>
Date:   Thu Nov 30 12:00:21 2023 -0500

    Add variable tob in diag_table for ocean model output(#2105)

commit c19810cce252fcdb25fd9960c05b08b5f8d8b1ad
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Wed Nov 29 15:17:36 2023 -0500

    Added variables to config.prepoceanobs (#2101)

commit c2d78a61a224678fb804eed19f39d1f07408ae5f
Author: Kate Friedman <[email protected]>
Date:   Wed Nov 29 12:39:08 2023 -0500

    Add missing cut to VDATE setting in JGFS_ATMOS_VERIFICATION (#2098)

    Refs #2097

commit c1c025f91ddac73aea595cc9fa4dd0bea80575fc
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Nov 29 17:15:10 2023 +0000

    Add wave init to GEFS (#2089)

    Adds the wave init job to GEFS. Since the output would be the same for
    every member, the job is only run once for the control, then links are
    created in each of the member directories pointing to that copy.

    New ww3_multi and ww3_shell templates for GEFS are copied from the
    GFS versions.

    The GEFS restart frequency is changed to not be zero, and the comment
    about not setting it to zero is copied from the gfs config.base. The restart
    interval for the GEFS perturbed members is changed to equal that of the
    control.

    Also fixes a bug where `RUNwave` was not defined for ensemble forecasts,
    and another bug in the GEFS stage_ic dependency.

    Resolves #2017

commit 64a2470ce29b7d8d5cb85ebcb4048ff82958f64e
Author: Kate Friedman <[email protected]>
Date:   Wed Nov 29 11:26:34 2023 -0500

    Adjust permissions for jobs/JGFS_ATMOS_VERIFICATION (#2095)

    Add execute permissions (755)

commit 964b77bc6de67291973c2c70598a1f8cb72501c5
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Nov 28 18:45:51 2023 +0000

    Make proper j-job for MET+ (#2090)

    Creates a proper j-job for the metp job, moving much of the material
    from the `jobs/rocoto` script there (some of it within `jjob_header`).

    Also updates the old `COMIN` variable for the COM refactor (although
    it does not appear used in the verify scripts currently).

    This is a partial step towards restoring/improving metp functionality
    and remains untested.

    Refs #1575

commit 8c11eeb8556619e8db4e0efb6394ce5a2c1aae0f
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Nov 23 10:31:32 2023 -0700

    Adds FBWINDS support to global-workflow (#2082)

    This PR addresses issue #1221. The following was accomplished:

    - A new Rocoto job is added; `jobs/rocoto/fbwinds.sh`;
    - `workflow/applications/gfs_cycled.py` is updated to include the `fbwinds` task;
    - `workflow/applications/gfs_forecast_only.py` is updated to include the `fbwinds` task;
    -  A new function is added to `workflow/rocoto/gfs_tasks.py`, `fbwinds` is added as new GFS (only) task;
    - `workflow/rocoto/tasks.py` is updated to include the `fbwinds` task.

    Resolves #1221

commit 513db190d21f9ede0724a2cd5606372b1d7605de
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Nov 21 22:52:58 2023 -0700

    Adds NPOESS support to global-workflow (#2083)

    This PR addresses issue #1225. The following was accomplished:

    - A new Rocoto job is added; `jobs/rocoto/npoess.sh`;
    - `workflow/applications/gfs_cycled.py` is updated to include the `npoess`
    task;
    - `workflow/applications/gfs_forecast_only.py` is updated to include the
    `npoess` task;
    -  A new function is added to `workflow/rocoto/gfs_tasks.py`, `npoess` is
    added as new GFS (only) task;
    - `workflow/rocoto/tasks.py` is updated to include the `npoess` task.

    Resolves #1225

commit 62d8e99e77ffe44784f4c61c3f2296c6d1a72413
Author: Kate Friedman <[email protected]>
Date:   Fri Nov 17 20:25:50 2023 -0500

    Retire vrfy job (#2080)

    Retires the `vrfy` job from the global-workflow system. All associated
    scripts, configs, and references to the job are removed.

    Additionally, the switches listed in RTD were updated to reflect new
    ones added in other PRs for issue #235.

    Resolves #2069
    Refs #235

commit ea386abf11ecbacef407388e8d57e71b30148a35
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Nov 17 23:59:46 2023 +0000

    Enable different coupled settings for ensemble (#2030)

    Adds the ability to turn off some coupled components for the ensemble.

    To enable this, many settings are moved out of `config.fcst` and into `config.ufs`
    so they are calculated after any overrides of `DO_*` have been made. Some
    settings also had to be moved out of `config.base` for the same reason. A
    switch to turn on gocart is added to `config.ufs`, but unlike the other switches
    this one takes no arguments.

    The name of the ufs configure template used is converted from a partial file
    name to the full file name.

    Resolves #1692

commit fe792c0c9a1c46908cbd18c7e71eb836974cf1de
Author: Kate Friedman <[email protected]>
Date:   Fri Nov 17 17:19:16 2023 -0500

    Add --cpus-per-task to srun commands for Hera and Orion (#2077)

    This PR adds the `--cpus-per-task` flag to non-CFP `APRUN`/srun commands
    in the env files for Orion and Hera. This is needed as a result of an upgrade
    to SLURM on Orion that no longer exported the thread value to the
    environment. Issue #1996 was a hotfix to add this flag for the analysis job
    that was suddenly running slowly after the SLURM upgrade. A similar SLURM
    upgrade was done on Hera but the sysadmins there implemented a
    workaround so this issue did not appear there.

    This PR adds the `--cpus-per-task` flag for both machines...needed on Orion
    and as a safety measure on Hera.

    Also included in this PR is a fix to indentations in the
    `scripts/exglobal_diag.sh` script that was noticed during work for this PR.

    Timing differences were not observed for other jobs after adding this srun
    flag. Job timings were of a similar variation between control and test runs.
    Any potential additional speedup was not observed. The test runs also
    reproduced the control runs with `develop`.

    Resolves #2044

commit 42c943be305c297a56b104bb50727938c1ba688f
Author: Kate Friedman <[email protected]>
Date:   Fri Nov 17 15:41:34 2023 -0500

    Adjust modules in post.sh for WCOSS2 (#2079)

    On WCOSS2 the grib_util module is named a bit different and
    needs the libjpeg module loaded beforehand.

commit cd4e6a1987e7fd71dff06766f540b5d32c8b648d
Author: Jessica Meixner <[email protected]>
Date:   Fri Nov 17 11:49:32 2023 -0500

    Update ufs-weather-model and remove upp hack (#2071)

    Updates the model to the most recent commit of ufs-weather-model.  This
    should allow for the removal of the UPP hack that was added in PR #2042

    This required changing nems.configure -> ufs.configure.

    Resolves #1942

commit 5a2d97e142aa4999b122fd5a130c63e59ea9f8e2
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Nov 16 22:15:53 2023 +0000

    Fix check for existence of preamble functions (#2066)

    A few of the setup scripts were checking for the existence of
    functions set by the preamble before calling them so they could
    also be used stand-alone. However, the `type` command returns `1`
    if the function name does not exist, which will cause the script
    to die is `set -e` is on. Now the `type` command fails over to an
    empty string.

commit ed2ee7c2b1457b71b271a2c40f0dfa356e0f52f8
Author: WenMeng-NOAA <[email protected]>
Date:   Thu Nov 16 16:38:11 2023 -0500

    Update UPP products for GFS v17 (#1973)

    Updates of generating GFS V17 UPP products to support HR3:

    - Update g2tmpl to 1.0.12
    - Add changes to launch cfp on WCOSS2 to generate pgrb2/pgrb2b files
    - Changes for generating new products (MERRA2, six winter weather variables,
    1km HLCY, SDEN) in pgrb2 files

    Resolves #1965
    Resolves #1994

commit 635c4719e603538ce7cccf9ea6b31f3f84f20849
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Nov 16 20:35:30 2023 +0000

    Fix some rocoto dependencies (#2074)

    A few small errors/cleanup in the dependencies, mostly in fcst:

    A few small errors/cleanup have crept into the dependencies with recent changes,
    mostly in fcst:

    - Fixed the offset, as it would yield a string rocoto doesn't recognize when the
    interval was 24+ hrs
    - Removed the duplicate wave dependency. When `waveprep` is included, it
    depends on `waveinit` so there is no need to add a `waveinit` dependency.
    - Converted an interval in the archive job that was missed in #2039

    Resolves #2075

commit d4c7508260975c6b94fc92fd085f39d4faf3f027
Author: Rahul Mahajan <[email protected]>
Date:   Wed Nov 15 16:44:03 2023 -0500

    Fix missing _PREV in ocean restart file location (#2070)

commit 255616d37505c785bdddd5d3e39e8399110b626e
Author: mdtoyNOAA <[email protected]>
Date:   Wed Nov 15 12:02:09 2023 -0700

    Update functionality for Prototype HR3 UGWP (#1987)

    This PR adds/modifies namelist options and activates new 'ccpp' suite definition
    files for the updated Unified Gravity Wave Physics (UGWP) in the ufs-weather-
    model recently updated for HR3.  The changes to UGWP are the use of the GSL
    drag suite for orographic gravity wave drag (GWD) and blocking, as well as the
    new UGWP Version 1 non-stationary GWD.  See
    ufs-community/ufs-weather-model#1923 for details.

    Resolves #1986

commit be9085e62aae147e3c74602e2f82a99b374fc783
Author: Guillaume Vernieres <[email protected]>
Date:   Wed Nov 15 13:48:58 2023 -0500

    Save the required CICE history for the sea-ice DA (#2062)

    The hist_avg setting of CICE was changed to be an array.

commit 85f1f5131ffd70061231304ea477bde0559eb67b
Author: Guoqing Ge <[email protected]>
Date:   Wed Nov 15 11:47:21 2023 -0700

    Use assim_freq to configure "offset" in dependencies (#2039)

    Use the assim_freq from config.base to configure "offset" in dependencies
    instead of hard-coding them.

    Resolves #2038

commit 4e3d82ba3a1fa7cdd4443bcd4cf83b2f8835137c
Author: Kate Friedman <[email protected]>
Date:   Wed Nov 15 13:39:14 2023 -0500

    Resolve ENKF archive script bugs (#2065)

    Fix two bugs in the exgdas_enkf_earc.sh script:

    1) Replace ARCH_LIST with DATA to match changes done in PR #2000
    and update path to generated archive list files.
    2) Add status check and exit after script attempts to make tarball on HPSS.

    Refs #2064

commit 42d7f2f0c48fab898b764e09cfbbd7a9fabbae08
Author: Kate Friedman <[email protected]>
Date:   Tue Nov 14 17:54:29 2023 -0500

    Separate tracker and genesis jobs from vrfy job (#2058)

    This PR creates new individual jobs for the tracker and genesis jobs that are being
    pulled out of the `vrfy` job (issue #235). The `tracker` and `genesis` jobs will be on
    by default while the `genesis_fsu` job will be off by default. This mimics the current
    settings in the `vrfy` job.

    No enhancements or upgrades are made to the jobs themselves in this PR, only to
    separate them from the `vrfy` job. However, one change compared to how they
    currently run in the `vrfy` job is to no longer run the `tracker` in the gdas suite. This
    mimics how the `ens_tracker` package is run in operations (gfs only).

    Changes in this PR:

    1. Create rocoto job scripts for tracker/genesis jobs.
    2. Create configs for tracker/genesis jobs, as well as `config.tropcy` for shared
    settings.
    3. Add tracker/genesis jobs to `config.resources`; use resources from the ecf scripts
    for `ens_tracker` jobs in operations
    4. Add tracker/genesis jobs to rocoto setup for both cycled and forecast-only
    modes.
    5. Update arguments for `jjob_header.sh` script in tracker/genesis JJOB scripts to use
    specific job names and configs instead of vrfy.
    6. Rename `tracker_ver` to `ens_tracker_ver` in version files to mimic variable within
    tracker package.
    7. Rename and move tracker/genesis switches to `config.base`.
    8. Remove tracker/genesis jobs from `vrfy` job (`jobs/rocoto/vrfy` and `config.vrfy`).
    9. Reduce vrfy job resources to accommodate tasks having been removed.

    Refs #235
    Resolves #1988
    Resolves #2048

commit 0a0d6984e094d2a551d5d8331102142e7db13fc2
Author: Rahul Mahajan <[email protected]>
Date:   Tue Nov 14 14:08:26 2023 -0500

    Enable warm starting of the model for forecast-only mode (#2031)

    This PR:
    - adds an option to warm|cold start the ufs-weather-model when setting up an experiment for GFS/GEFS
    - adds the capability to stage FV3 restarts when the atmosphere is warm started from FV3 restarts. This would be used in the GEFS free-forecast for part of the reforecast capability.
    - If a coupled model is warm started for the atmosphere, also check if mediator restarts are present. If so, stage mediator restarts to allow restarting the coupled model.

    Fixes #2016

commit 2cd6a589305a9ac9d3a9a0d2136e66e42f09d3bf
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Nov 14 12:05:20 2023 -0700

    Moves UFS WM configuration files to `COM_CONF` (#2054)

    The UFS weather-model (WM) files are place in the COM_CONF path rather than the respective component model COM history paths.
    Resolves #2015

commit 6f1693081662f241fafc930b1afc88125f7f5aff
Author: Kate Friedman <[email protected]>
Date:   Tue Nov 14 11:15:02 2023 -0500

    Refine fit2obs job in rocoto mesh (#2047)

    This PR adjusts the `fit2obs` job in the rocoto mesh to better define when it exists
    and how the archive job dependencies accommodate it not being in the first half
    cycle.

    Changes in PR:

    1. Remove the `fit2obs` job from the first half cycle `cycledef`.
    2. Adjust the archive job dependencies to now include the `fit2obs` job in the new
    logic check added in PR #1983. The `gdasarch` job in the first half cycle will check if
    `gdasfit2obs` is complete OR no prior cycle exists. Also cleaned up this new logic
    check block some to make it a tad simpler.
    3. Also, fix the addition of the `fit2obs` config to the config list in setup scripts. Now
    tied to whether `fit2obs` job is on instead of always adding the config to the list.

    Resolves #2043

commit 5730a71fa5d311e49d9bb11528b500f27f33d69d
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Nov 14 09:13:11 2023 -0700

    Add `waveinit` and `waveprep` to half-cycle. (#2037)

    This PR addresses issue #1444. The `waveinit` and `waveprep` tasks have been added to
    the GDAS have cycle. The downstream dependencies for the respective GFS and GDAS
    forecast tasks have been removed.

    Resolves #1444

commit 28d2e93c3857de95b0309a089cd7dac736ccaded
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Nov 14 16:11:47 2023 +0000

    Update wave IC source for C384 (#2055)

    The default wave grid for C384 has changed since P8, so a single wave
    IC on the new grid is available under a different IC name.

commit 81dd2d9855091315611106a5afbdaeaa15e6e4ae
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Nov 9 17:19:57 2023 +0000

    Fix analysis and post on Orion (#2046)

    Fixes a couple things to get workflow to work on Orion again:

    First, while #2042 allowed post to be built, the `upp.x` executable would fail due
    to a missing library. Now post jobs (temporarily) uses the UPP modules (plus
    others needed for runtime) instead of the normal workflow runtime module. This
    should actually fix #2041. This hack can likely be removed once we move to
    spack-stack.

    Second, the launcher command for the analysis jobs on Orion are updated to
    specify the number of CPUs per task. This was necessary as a recent slurm update
    on Orion discontinued reading that value from the scheduler. Other jobs will be
    handled later (see #2044).

    Additionally, a change is made to `module-setup.sh` that will eliminate the
    annoyance of `gw_setup.sh` breaking tab completion because undefined variable
    checking was turned on for the script but not back off.

    Resolves #1996
    Resolves #2041
    Refs #2044

commit 13d06ded4155cba2d08ef2a2cd553024c5abe29d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Nov 8 18:25:47 2023 +0000

    Hack UPP version (#2042)

    The stack UPP was using on Orion was recently deleted, leaving us
    unable to build the UFS verison of UPP there. UPP has an updated
    version using spack-stack that works, so the checkout script is
    modified to check out that version of UPP after UFS has been
    checked out.

    This temporary hack can be removed once we move to a UFS version
    that advances the UPP version to or beyond 78f369b.

    Resolves #2041

commit 20f6eceb8ff58f84174a27eb849c1d74566a3e03
Author: jiandewang <[email protected]>
Date:   Wed Nov 8 11:14:55 2023 -0500

    Add basic C1152 settings (#2020)

    Adding C1152 setting in host.yaml, config.base and config.stage_ic so that can run C1152 S2SW.

    Resolves #2019

commit 5183c43bbbd07285869feacb49d8680afe85929a
Author: Barry Baker <[email protected]>
Date:   Tue Nov 7 01:14:40 2023 -0500

    Update UFS for dust fix and remove nitrates by default  (#1989)

    This PR updates the `ufs-weather-model` to the latest hash that included the dust fix (PR #1922).
    Along with this I removed the nitrates by default in support of the GEFSv13 EP4 and EP5
    experiments. Removed unneeded inputs that should help with speed improvements.

commit 34a73cf2ed5afefc776d9cc73b6ebf439122a1bb
Author: David Huber <[email protected]>
Date:   Mon Nov 6 14:00:51 2023 -0500

    Reduce gdas builds to 8 #2029 (#2036)

    Reduce the default number of build jobs for the GDASApp to 8 from 16.

    This is needed for Orion as the build crashes during a linking step.  Though not verified, it
    appears this may be caused by using too much memory with 16 builds.  The issue disappears
    when using 8 build jobs.

    Resolves #2029

commit 75269e4bb9764b81589efc7d703825b80e74c8f5
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Nov 6 17:34:47 2023 +0000

    Streamline CI reporting to PRs (#2026)

    Cleaned up the logs for CI PRs sent to the GitHub Messages:

    - Eliminates redundant accumulative reporting
    - Reports on all created or skipped experiment instantiations in a single message
    - Gives one line report once  for each experiment completion
    - Single final report completion of CI

    See some examples in forked [PR 195](https://github.com/TerrenceMcGuinness-NOAA/global-workflow/pull/195)

    Resolves #2007

commit 8d55126bb0b27c79c8bee7f72b014abd34950ff9
Author: Guillaume Vernieres <[email protected]>
Date:   Fri Nov 3 17:06:09 2023 -0400

    Implement IAU Cycling Type with Marine Data Assimilation Enabled (#1944)

    Allows cycling in IAU mode with the S2S UFS model, soca and the GSI.

    Most of the work related to making IAU work was done by @JessicaMeixner-NOAA . Thanks @JessicaMeixner-NOAA !

    Resolves #1943
    Refs #1776

commit 2563806821d4ae3b57120bc61aa0575139a708f0
Author: jiandewang <[email protected]>
Date:   Fri Nov 3 11:49:37 2023 -0400

    Add two ucx modules in load_ufswm_modules.sh to solve C768 and C1152 S2SW job hanging issue on WCOSS2 (#2021)

commit cbdc09711a83493f363a737d1e3e46c48a09719d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Nov 3 04:09:33 2023 +0000

    Fix staging of MOM data (#2028)

    During the update to stage_ic, the copying of the additional res_N files for
    0p25 was omitted. These are now properly copied.

    Resolves #2027

commit bd4c56d99c23c5c41f0bd5f8a980ef99ee160888
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Thu Nov 2 16:09:59 2023 -0400

    changed optional script name vars for ocean analysis (#2025)

commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6
Author: Kate Friedman <[email protected]>
Date:   Thu Nov 2 16:01:18 2023 -0400

    Create separate GSI monitor jobs and remove from vrfy job (#1983)

    This PR will move the GSI monitor tasks from the `vrfy` job into their own separate jobs in
    the rocoto mesh. This takes care of part of issue #235.

    Changes in this PR:

    1. Create new individual GSI monitor jobs in the rocoto mesh to match how it is done in
    operations. The new jobs are: `gdasverfozn`, `gdasverfrad`, `gdasvminmon`, and `gfsvminmon`.
    The names correspond to the names in operations and the ecf script names. The jobs are only
    added to cycled mode, none of the jobs are run in forecast-only mode.
    2. Updates to GSI monitor scripts:
      * Update `ush/jjob_header.sh` arguments in JJOB scripts to call new individual job names and
    configs.
      * Introduce `COM_*` variables and use of the `generate_com` utility. This results in the outputs
    landing in `COM` subfolders, like occurs in operations, instead of landing in the online archive.
      * Some variable cleanup in JJOB and ush scripts, includes cleaning up usage of `DATA` variable
    and its removal at the end of the jobs.
      * Add missing exit statements to `JGFS_ATMOS_VMINMON` and `JGDAS_ATMOS_VERFRAD`.
    3. Create new rocoto job scripts for the new individual GSI monitor jobs.
    4. Create new configs for the new individual GSI monitor jobs.
    5. Add new individual GSI monitor jobs to resource configuration, using the same resources as
    in operations.
    6. Move and rename GSI monitor job switches from `config.vrfy` to `config.base`. Also add
    switches to setup system. New switches to control each job being added to the rocoto mesh
    are: `DO_VERFOZN`, `DO_VERFRAD`, `DO_VMINMON`
    7. Add GSI monitor job output to archival job and into resulting HPSS tarballs or local tarballs.
    This now matches what is done in operations.
    8. Remove the GSI monitor tasks from the rocoto `vrfy` job and associated `config.vrfy`.

    Example output locations and files (not showing contents of oznmon/horiz or oznmon/time for
    brevity, see archival script for full list of output files):
    ```
    kate.friedman@dlogin09:/lfs/h2/emc/ptmp/kate.friedman/comrot/testmonitor2> ll gdas.20211221/00/products/atmos/*mon
    gdas.20211221/00/products/atmos/minmon:
    total 112
    -rw-r--r-- 1 kate.friedman emc 14030 Oct 25 15:00 2021122100.costs.txt
    -rw-r--r-- 1 kate.friedman emc 84932 Oct 25 15:00 2021122100.cost_terms.txt
    -rw-r--r-- 1 kate.friedman emc   808 Oct 25 15:00 2021122100.gnorms.ieee_d
    -rw-r--r-- 1 kate.friedman emc   808 Oct 25 15:00 2021122100.reduction.ieee_d
    -rw-r--r-- 1 kate.friedman emc    80 Oct 25 15:00 gnorm_data.txt

    gdas.20211221/00/products/atmos/oznmon:
    total 8
    drwxr-sr-x 2 kate.friedman emc 4096 Oct 25 15:05 horiz
    drwxr-sr-x 2 kate.friedman emc 4096 Oct 25 15:05 time

    gdas.20211221/00/products/atmos/radmon:
    total 21036
    -rw-r--r-- 1 kate.friedman emc      231 Oct 25 15:12 bad_diag.2021122100
    -rw-r--r-- 1 kate.friedman emc     9035 Oct 25 15:12 bad_pen.2021122100
    -rw-r--r-- 1 kate.friedman emc     1449 Oct 25 15:12 low_count.2021122100
    -rw-r--r-- 1 kate.friedman emc 20523403 Oct 25 15:07 radmon_angle.tar.gz
    -rw-r--r-- 1 kate.friedman emc   217272 Oct 25 15:08 radmon_bcoef.tar.gz
    -rw-r--r-- 1 kate.friedman emc   502151 Oct 25 15:10 radmon_bcor.tar.gz
    -rw-r--r-- 1 kate.friedman emc   264480 Oct 25 15:12 radmon_time.tar.gz
    -rw-r--r-- 1 kate.friedman emc      684 Oct 25 15:12 warning.2021122100
    kate.friedman@dlogin09:/lfs/h2/emc/ptmp/kate.friedman/comrot/testmonitor2> ll gfs.20211221/00/products/atmos/minmon/
    total 88
    -rw-r--r-- 1 kate.friedman emc 10530 Oct 25 14:55 2021122100.costs.txt
    -rw-r--r-- 1 kate.friedman emc 63882 Oct 25 14:55 2021122100.cost_terms.txt
    -rw-r--r-- 1 kate.friedman emc   808 Oct 25 14:55 2021122100.gnorms.ieee_d
    -rw-r--r-- 1 kate.friedman emc   608 Oct 25 14:55 2021122100.reduction.ieee_d
    -rw-r--r-- 1 kate.friedman emc    80 Oct 25 14:55 gnorm_data.txt
    ```

    Lingering work and considerations:

    1. Issue #1925
    2. Consider not hardcoding the list of types in archival and perhaps tie it to something reliable or
    configurable (maybe into `config.verfozn`?):
    `subtyplist="gome_metop-b omi_aura ompslp_npp ompsnp_n20 ompsnp_npp ompstc8_n20 ompstc8_npp sbuv2_n19"`

    Resolves #1908

commit 31b05a99b77d0f6eaa8b116485a41a43867d20e1
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Nov 2 12:23:32 2023 -0600

    Move analysis post to new stand-alone task (#1979)

    This PR addresses issue #1130. A new task `postanl.sh` has been added such that the
    `anl` post-processing is not it's own task within the Rocoto workflow. This change
    prevents the GDAS experiment from breaking due to failures caused by the `anl` not
    being available for the first cycle.

    Resolves #1130

commit 247cdf8c7e10e6c98f782799fc51c069b6474e70
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Nov 2 11:18:53 2023 -0600

    Corrects missing local variable reference (#2023)

    Fixes missing `$` in variable reference in archive job.

    Resolves #2022

commit 241742b246da1794646b68e41c3d6fe00b95dd07
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Wed Nov 1 14:19:55 2023 -0400

    Updates to prep ocean obs task (#1870)

commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Nov 1 12:09:33 2023 -0600

    No longer write archive lists COM (#2000)

    Changes the respective `.txt` files used for the HPSS archive to the `DATA` path. Each
    defined text file has been updated to explicitly write to `DATA` rather than `COM` such
    that the files are deleted rather than being archived.

    Resolves #760

commit 517b92f9c20c9e44abba3183325e35a95a7334a5
Author: David Huber <[email protected]>
Date:   Tue Oct 31 16:33:11 2023 -0400

    Parallelize the build scripts (#1998)

    Optimized/parallelized build scripts.

    A few notes:

    1) The default number of build jobs is 20, but one could argue for using 40.  When researching
    this, I looked up what the SRW is compiling with.  That system uses 40 cores, which seems a
    little excessive, but on testing the global workflow, the actual number of cores being used at
    any given time rarely exceeds 16 when running with 40 cores.  This is because the builds tend to
    use multiple threads in the beginning when compiling low-level modules while the higher-level
    modules are more or less serial AND because the GDASApp takes several minutes to initialize
    all of its subrepositories by which time the smaller builds are complete.

    2) I also updated checkout.sh so that all checkouts are simultaneous.  The CPU load for
    `git submodule` is quite low, so running 16 instead of 8 jobs at once is not much more expensive.

    3) To make this work, I had to add `-j` options to most of the build scripts.  The only exception is
    build_upp, for which the build script within the UPP is hard coded to use 6 cores.

    4) I fixed a few small bugs in the build scripts along the way.

    5) Lastly, this reduce the total build time from ~2.5 hours for the entire system (including GDAS
    and GSI in the same build) to ~40 minutes when running with `-j 40`.

    Resolves #1978

commit 67c050c201f92e855d09211e41a5f51ee1cb5230
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Oct 31 19:00:47 2023 +0000

    Add missing export for rCDUMP in stage_ic (#2009)

    rCDUMP is needed by the exscript but was never exported by the jjob.

commit 872068cb5ea78b311f7a77e97ee1428ae027cb61
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Oct 31 14:37:55 2023 +0000

    Add output error log to user for create_experiment.py on fail in CI (#1974)

    Small changes to driver CI bash scripts to recapture error log from `create_experment.py` logger
    Fixes #1939

commit b2e4a2e9d269842acbb1b37dd563ee5dee2adf0f
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Oct 31 13:57:02 2023 +0000

    Allow CI case to exclude running on certain platforms (#2001)

commit 7cc137116f1619bf1e5a12eaacb98d17da97c223
Author: Jeff Whitaker <[email protected]>
Date:   Tue Oct 31 07:54:24 2023 -0600

    Add initial C96/1 deg coupled model support (#1991)

commit 7086ddc4bece6fb2a8c1c2e6090800d4293e410e
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Mon Oct 30 19:58:43 2023 -0400

    Add ocean analysis files to HPSS archiving task (#1985)

    This PR adds the files under `analysis/ocean` (except those in `bump` and `vrfy`) to the
    HPSS archiving job, in `gdasocean_analysis.tar`, which were previously not archived.

    Resolves NOAA-EMC/GDASApp/issues/693

commit eabc82ad30c118645c0e6e216162d823882a8139
Author: Guillaume Vernieres <[email protected]>
Date:   Mon Oct 30 10:31:27 2023 -0400

    Make the early cycle work with the coupled UFS configured as S2S  (#1954)

commit aff6ca7ae559e424dae128d6cfd5da4a4e3049e7
Author: Anil Kumar <[email protected]>
Date:   Fri Oct 27 14:11:55 2023 -0400

    GEFS Staging in exglobal_stage_ic  (#1892)

    Adjusts source paths for forecast-only ICs in support of extension to ensembles.
    New paths omit the resolution (that is captured by the IC id name) and allow for
    a member level.

    Directories with the reorganized ICs have been added to the three tier-1 machines
    under glopara space.

    Building on this, also adds capability to stage GEFS ICs.

    Resolves #911

commit 77c1ff2bfa26b341b01f41e50ee0ecb31cc4f661
Author: RussTreadon-NOAA <[email protected]>
Date:   Thu Oct 26 23:44:27 2023 -0400

    Update GDASApp hash (#1975)

    Update GDASApp hash to bring recent UFSDA development into g-w.

    Resolves #1972

commit 962368884991670d3a1ee1c5a065d5bce4b7561a
Author: David Huber <[email protected]>
Date:   Thu Oct 26 16:10:23 2023 -0400

    Test tarballs for rstprod before calling chgrp (#1967)

    Certain tarballs may or may not contain `rstprod` data.  For instance, the first half cycle
    gdas and enkfgdas tarballs will not contain `rstprod`, while future cycles likely will.  Also,
    some systems do not have `rstprod` on them.  This will test the contents of the tarballs
    first before attempting to change the group to rstprod.

    Resolves #1460

commit c02e118c0ac5485109c9bd33472ff42db309cd9b
Author: Jessica Meixner <[email protected]>
Date:   Thu Oct 26 15:05:05 2023 -0400

    Update ufs model to version from 10-12-23 (#1933)

    This updates the ufs-weather-model to the commit hash from 10-12-23 from the HR2 tag.
    The diffs can be seen here: https://github.com/ufs-community/ufs-weather-model/compare/GFSv17.HR2...68050e58589a82ab509aaefaafdc2a6b90f34e48

    Resolves #1811

commit 8556541daa79b0180fde48a58a8dcfb2f8c56ea5
Author: Rahul Mahajan <[email protected]>
Date:   Wed Oct 25 16:15:28 2023 -0400

    Fix incorrect usage of CFP on WCOSS2 (#1977)

commit 0b5cf9b67a8146d9d4815ea6545f7f2524120d83
Author: Kate Friedman <[email protected]>
Date:   Wed Oct 25 13:17:28 2023 -0400

    Update GFS version in index.rst to v16.3.10 (#1976)

    Update the "State of operations" GFS version number to new v16.3.10 (Annual CO2 fix file update in operations).

    Refs #1924

commit e817f5dd38c26a88f76d90eb71124f1acbfc5a8f
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Oct 25 02:03:14 2023 +0000

    Fix path for marine products (#1966)

    When PR #1823 was merged, the name of the marine product template
    was not updated in ocnpost, leading the products to be placed in
    the wrong location and missed by the archive job.

    Resolves #1902

commit 7cdfad4eaa7abe0769ff13396c54e6d93afebf8f
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Oct 24 22:19:46 2023 +0000

    Build GDASapp for CI tests (#1964)

    * added -u to global checkout so CI test builds tests for GDASapps

    * Update check_ci.sh

    needed more quotes

    ---------

    Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>

commit c58deae0cf078d1ee093529064d74f60482aa3f4
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Oct 24 16:19:04 2023 -0600

    Updates for NOAA CSP AWS global-workflow related file paths. (#1970)

    Co-authored-by: henrywinterbottom-wxdev <[email protected]>

commit 1b00224e18842cd873eb1779be08f96687e49e1f
Author: Kate Friedman <[email protected]>
Date:   Tue Oct 24 14:48:24 2023 -0400

    Set SENDCOM=YES for tracker/genesis tasks (#1971)

    Set SENDCOM to YES in config.vrfy to get outputs copied back to COM.

    Will reevaluate the need for SENDCOM when moving the tracker/genesis jobs out of the vrfy job with issue #235 work.

    Refs #1947

commit e2c624d8904cd988394c73d0edb22fa593229d3f
Author: RussTreadon-NOAA <[email protected]>
Date:   Tue Oct 24 13:32:52 2023 -0400

    Refactor UFSDA ATM var and ens layout (#1945)

commit 8940adddfe9d21189740e71487603fb2acee2336
Author: David Huber <[email protected]>
Date:   Tue Oct 24 11:02:29 2023 -0400

    Optimize the checkout script (#1956)

    * Multithread the checkout script #1953

commit 4b5cd0bc435fc158258ca38c3d5f44add6b60469
Author: Rahul Mahajan <[email protected]>
Date:   Mon Oct 23 12:04:26 2023 -0400

    Fix nth_eupd in gfs/config.resources.  remove sections of jobs not run as part of gefs from gefs/config.resources (#1952)

commit 08ce4f8d3ed8e07b4d488a80b5054c6206b04404
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Oct 20 16:14:53 2023 +0000

    Fix enkfgfs cleanup dependency (#1941)

    When #1906 was merged, the dependency for enkf cycles was hard-coded
    to use the enkfgdas archive instead of depending on the `RUN`.

commit 1a5d0b51642eb70f71e693355e86212d3607b7b3
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Oct 20 15:54:33 2023 +0000

    Split clean-up into separate job (#1906)

    Moves the clean-up that was previously done in the archive jobs into
    their own separate job. The clean-up is also streamlined considerably
    by using only `COM_TOP` instead of going through every template.
    There is also additional streamlining/corrections in the function that
    does the actual removing.

    Some settings used by both jobs were elevated to `config.base`.
    Others only needed for cleanup were moved to the new config for
    that job.

    Also corrects a small error encountered when attempting to rerun an
    ensemble forecast.

    Resolves #583
    Resolves #1872

commit 3de102c28daf9eb50ce65e0afe911f5a416ce861
Author: Rahul Mahajan <[email protected]>
Date:   Tue Oct 17 09:30:18 2023 -0400

    Updates to CI to clarify HOMEgfs (#1931)

    * replace HOMEgfs_PR with HOMEgfs, and HOMEgfs with ROOT_DIR. ROOT_DIR is the location where the ci scripts live
    * update type to system in case yamls
    * move create_experiment.py to workflow/
    * detect HOMEgfs in create_experiment.py based on location.  update to use jinja templates in the cases
    * remove export of HOMEgfs from driver.sh

commit bfea2594207a477ea00e3b7fef95c2d7befd492b
Author: Henry R. Winterbottom <[email protected]>
Date:   Sun Oct 15 23:27:47 2023 -0600

    Remove SENDCOM (#1929)

    This PR addresses issue #1501. All instances of `SENDCOM` gates have been
    removed. The workflow was inconsistent in its use of `SENDCOM` to gate
    movement of files to `COM` and have been removed based on NCO guidelines.

    Resolves #1501.

commit 9a8911a0b30f0367d061facfb3b835480728081d
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri Oct 13 14:21:01 2023 +0000

    update nth_eupd to 8 for Orion because of out of memmory errors (#1927)

    Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>

commit ea4dfa5800b5cb529478cc64d329f567393fa37d
Author: Guillaume Vernieres <[email protected]>
Date:   Thu Oct 12 21:29:19 2023 -0400

    Marine DA configuration updates (#1922)

    Minor updates the configuration related to running the marine DA and the coupled UFS.
    What's proposed in this PR:
    - Memory increased for the marine DA analysis step
    - The coupled UFS is (was?) running out of memory without the changes in `config.ufs`.
    - Updates to the IAU section of MOM_input to allow for a current increment.

commit c2d112b40a926c9f33a653cfbb832cb811a60352
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Oct 12 23:52:43 2023 +0000

    Fix missing pipe in check_ci (#1926)

    Bugfix:  left out pipe to word count` | wc -l` after updating:

    `num_platforms=$(ls ../platforms/config.* | wc -l)` to
    `num_platforms=$(find ../platforms -type f -name "config.*")`

    when it was flagged by the BASH linter.

commit 51d93e15eb30382017aaf72813d34f7010f47948
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Oct 10 19:09:26 2023 +0000

    Updated cron bash ci script to remove weekly CI test PR on success (#1915)

    This PR updates the check CI bash script in cron to remove the PR that is created by
    the weekly CI test driver when all the tests has passed on all the platforms.

    This is done by the script checking if all other labels for all the platforms for the PR
    that has currently been flagged to have run to a successful completion by the check
    ci bash script.

commit 2d64b74a0b0407d01d6f657efa6af9637a131448
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Wed Oct 4 22:33:25 2023 +0000

    CI driver_weekly bugfix deleting new branch if is already on repo (#1899)

    Bugfix and updates to weekly CI test that deletes the new modified branch
    if it is already on the repo but now also makes sure that the intermediary
    branch that creates the PR is coming from emcbot.

commit e4a6c35ae020253f07921ca34a17f19e928b0b6c
Author: Rahul Mahajan <[email protected]>
Date:   Wed Oct 4 09:42:12 2023 -0400

    Fix typo in cice history filename

commit d50938bc4f6705b722338bbea03f925614f953ed
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Oct 3 23:37:39 2023 -0400

    Change metp dependency (#1900)

    MET+ jobs rely on files already having been placed in the local
    archive directory, but the job only depended on post, resulting
    in the job prematurely firing. The dependency is now updated to
    be on the archive job instead.

    Resolves #1756

commit 836642bb201cd2e5e205eda2ae4a28993623355d
Author: Rahul Mahajan <[email protected]>
Date:   Tue Oct 3 14:45:57 2023 -0400

    Use deterministic marine resolutions for ensemble (#1894)

    This PR determines the ensemble resolution for ocean, ice and waves based on the
    deterministic configuration as there is no dual-resolution capability requested for
    these model components.

    For cycled DA, if the deterministic uses a coupled model, the ensemble will also be
    a coupled model.  This can be turned off manually via adding `DO_AERO_ENKF`,
    `DO_OCN_ENKF`, `DO_ICE_ENKF` and `DO_WAVE_ENKF` flags set in `config.base` or
    `config.efcs`.  This is currently handled manually and will be automated when a
    requirement arises for this flexibility.

    Fixes #1730

commit 48ba775909870f0d27275128bd07ec134b92c356
Author: Kate Friedman <[email protected]>
Date:   Mon Oct 2 13:34:02 2023 -0400

    Update vrfy.sh to only run MINMON in cycled mode (#1901)

    Update MINMON if-block in jobs/rocoto/vrfy.sh to only invoke this section when MODE is cycled.

    Refs #1076

commit e65162f3083c34b639854e3216e2355ff6fccc0b
Author: RussTreadon-NOAA <[email protected]>
Date:   Fri Sep 29 19:18:07 2023 -0400

    Update module loads to intel/2022 for jobs running gsi.x and enkf.x (#1882)

    This PR changes the module loads in g-w jobs `anal.sh`, `eobs.sh`, and `eupd.sh`
    to use machine specific modulefiles from `sorc/gsi_enkf.fd/modulefiles`.  This is
    necessary because [NOAA-EMC/GSI#571](https://github.com/NOAA-EMC/GSI/pull/571)
    updated `gsi.x` and `enkf.x` builds to intel/2022 on NOAA RDHPCS machines.

    Resolves #1863

commit cd439d0bf2ae5fb57139fcb9983aa2755fdc9b2c
Author: Rahul Mahajan <[email protected]>
Date:   Fri Sep 29 15:35:54 2023 -0400

    Add coupled forecast-only tests for S2S and S2SW (#1895)

    This PR:
    - replaces the PR C48 S2S forecast-only test with a S2SW configuration
    - adds a weekly C384 S2SWA forecast-only test.

    The C384 S2SWA is a weekly test and will not be triggered/tested in this PR, but will
    be tested on Friday.  See notes on Orion below in the testing section.

    @JessicaMeixner-NOAA kindly provided the details in
    https://github.com/NOAA-EMC/global-workflow/issues/1794#issuecomment-1740768751

commit 02787fe9ba9e5a6881e5ccf9a9e352545eeadb9d
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri Sep 29 18:03:23 2023 +0000

    Ci rename platform scripts (#1896)

    Simply renaming the platform config files in ${HOMEgfs}/ci/platforms to
    config.${MACHINE} so wxflow can read them too in support of up and
    coming functional testing.

commit bb5a58541d6514d16901dca240dfbbc810bd31c8
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Sep 29 13:28:39 2023 -0400

    Merge S2S defaults config back into other configs (#1876)

    When the prototype S2S was first added, we placed some settings in
    a `config.defaults.s2sw` file to avoid interference with existing
    settings. Now that we are moving towards v17 and run S2S regularly,
    it is time to merge these settings back into the other config files.

    The wave output frequency settings are updated to the coarser fre-
    quency as that is more suitable for development. The prior (ops)
    settings are noted as comments.

    There are a couple of settings that control ice fields within FV3.
    These are placed in `config.ice`, so when the ice model is on those
    settings are still used.

    Changes the output frequency from 3 to 6. While we may leave this
    setting as the default for development, it is required right now
    because the ocean frequency is hard-coded to 6 but links are created
    based on `$FHOUT_GFS`. Resolving #1629 should correct this limitation.

    "Gaussian" archive is updated to the former override values.

    Resolves #1606
    Refs #1629

commit 49dc315c1ef6c5f4952a06b0ba70c36e771f128e
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Sep 29 13:25:58 2023 -0400

    Move product functions to separate script (#1891)

    PR #1822 converted some formerly stand-alone scripts and moved them
    inside one of the standard product scripts. However, `trim_rh.sh`
    is also used by gempak and AWIPS, so this change caused those jobs
    to start failing (they are not yet tested by CI).

    Those functions have now been moved into a separate product functions
    script that can be sourced by all the scripts that need the functions.
    A third similar script was also eliminated and converted into a
    function.

    Additionally fixes a base bug in AWIPS and updates some scripts to
    satisfy (or at least mostly satisfy) the linter.

    **AWIPS still failing when creating GRIB1 products.** That will be addressed
    in a future PR (and may need a subject-matter expert).

    Resolves #1890

commit 3e750d10be577106fb269a78e18765b8d2b8030d
Author: Rahul Mahajan <[email protected]>
Date:   Thu Sep 28 16:21:52 2023 -0400

    Fix a few bugs reported by devs (#1893)

    This PR fixes a few bugs that were reported by developers:
    - a namelist section is unclosed in `parsing_namelists_FV3.sh`
    - resolution is not being properly cut from `CASE`
    - date should be in UTC to properly go back and forth around DST dates.

    Resolves #1796

commit e886e8aef633389d65e23cc42456827e1db2a771
Author: Kate Friedman <[email protected]>
Date:   Tue Sep 26 13:01:17 2023 -0400

    Fix wavepostbndpntbll data dependency (#1888)

    Update the data dependency path for the wavepostbndpntbll
    job to use the ATMOS/atmos subfolder instead of WAVE/wave
    for the atm.logf file it needs to fire off.

    Refs #1887

commit bb1e561c6a519b9b1cf3fb3ac724e2d240bc3b5b
Author: Andy Tangborn <[email protected]>
Date:   Tue Sep 26 11:08:49 2023 -0400

    Update aero analysis for new bump files and archive aero diags (#1886)

    This PR updates the global workflow so that it can handle the latest version of the JEDI
    aero staticb, and also archives the aerosol diagnostic files.

commit 3d2b72ecd395585f650b2801b2ec3471bd938d63
Author: David Huber <[email protected]>
Date:   Tue …
jkhender added a commit to jkhender/global-workflow that referenced this issue Jan 29, 2024
Squashed commit of the following:

commit 3c0c126a376af31866a93aef4cdd0b4145150c58
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 16 17:32:25 2024 +0000

     Add script for remapping 1/4 degree grib2 grids to other domains

commit f217d4ed9a500e9a1bdcc17548729d972a1763ac
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 16 16:46:25 2024 +0000

     Update link script for ufs_utils.fd

commit 5b21b31900955013b4e8106d3ae906b9da93b361
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 16 16:45:25 2024 +0000

     Add GSL archive scripts for initial conditions

commit abb88baf9dd536a3b2ea1e24eaa99cbfe85af799
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 16 16:42:17 2024 +0000

     Move configuration files for getic and init from jobs/rocoto to parm/config/gfs

commit 45b235180719ab79d2514f0317207fbebfb8aedd
Author: Judy.K.Henderson <[email protected]>
Date:   Sun Jan 14 03:21:15 2024 +0000

     Add suite definition file for v17p8_ugwpv1_c3 to sorc/ufs_model.fd_gsl

commit 147b1fce99254dcb602c333cc559feaa9a396e81
Author: Judy.K.Henderson <[email protected]>
Date:   Sun Jan 14 01:57:22 2024 +0000

     Add getic and init tasks to workflow to create initial conditions in realtime

commit 4e4e50803d95566e1c7967cf4cfa575391d77f25
Author: Judy.K.Henderson <[email protected]>
Date:   Fri Jan 12 00:44:59 2024 +0000

     Change default HPSS_PROJECT to fim

     Change restart_interval_gfs to -1 so no files are written ro RERUN_RESTART directory

commit 791d7a27c6b12f07d9c12ce491338e3da59eb1d8
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 11 23:34:36 2024 +0000

     Add namelist parameter, nord_tr, for GSL suites

commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 11 23:31:22 2024 +0000

     Add changes for running v17p8_mynn

     - new field table, field_table_thompson_aero_tke_progsigma
     - updated namelist parameters in config.fcst

commit 982a1f02e3b880be43f4ae8a3f0ffbb34c056aea
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 02:26:22 2024 +0000

     Add experiment setup script for p8_ugwpv1

commit c5a3697d22fdbb02bb80ddffee2629dddc10c702
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 02:19:13 2024 +0000

     Add memory report to srun command in env/HERA.env

commit ece7e516ca65ec0240899e7d84321310a6887595
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 02:13:42 2024 +0000

     Updated GSL-specific files under ufs_utils.fd_gsl

commit 1b153fc95b93a16eb40b791be7322100fde4a3d4
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 01:52:56 2024 +0000

     Create new branch, gsl_ufs_dev, from dev_02jan24_9d901db

     Add initial GSL modifications
      - changes to workflow files
        * GSL paths, projects, entities
      - new FV3_GFS_v17_p8_ugwpv1_mynn suite definition file (SDF)
      - updated namelist parameters in ush/parsing_namelists_FV3.sh
      - create new GSL directories: ufs_model.fd_gsl and ufs_utils.fd_gsl
        * new SDFs, add instantaneous flux variables to grib2 configuration files
        * add Thompson tracers to initial conditions
      - new sync script: rsync_gsl.sh
      - new job files:  getic.sh, makeinit_link.sh
      - modify build_ufs.sh to include MYNN SDF

commit 9d901dbbff4d41586580316bdc094d24760119e6
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Jan 2 10:30:33 2024 -0700

    Stop Gempak pgrb2 spec from modifying $DATA (#2147)

    This PR addresses issue #1224. The following is accomplished:

    - Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time;
    - Shell linter exceptions are addressed accordingly;
    - The respective GEMPAK tasks is added to the Rocoto mesh.

    Resolves #1224

commit 31ad23527802f7d07171132cc620f7135c4d8cba
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Jan 2 10:27:30 2024 -0700

    Reorganize NPOESS scripts (#2166)

    This PR addresses issue #1226. The following is accomplished:

    - Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure
    of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated;
    - Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh`
    are moved accordingly; this specifically applies to the environment variable `FHOUR`,
    `SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`;
    - The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level
    (if necessary);
    - Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however,
    this may not be necessary (see `TODO` note within draft PR.

    Resolves #1226

commit 22bd82fa93b49e5ce98eb3f69123956dd5018049
Author: Kate Friedman <[email protected]>
Date:   Tue Jan 2 11:55:03 2024 -0500

    Orog fix file reorg and fix directory variable standardization (#2181)

    This PR makes updates to use the newly reorganized `orog/20231027`
    fix file version and standardizes the fix file directory variables.

    Changes:

    1. Update UFS_UTILS hash to ce385ce
    2. Update fix file version file to use new orog timestamp: `orog_ver=20231027`
    3. Add ".mx$(OCNRES)" to `oro_data` filenames in scripts
    4. Remove ".mx$(ocn_res)_frac" from the directory names for atmosphere
    resolutions under the `/orog` folder
    5. Adds fix file directory variables to `config.base`, many of which are pulled
    up out of lower scripts; introduce `FIXcpl`
    6. Renamed/replaced the following fix file directory variables:

    - `FV3JEDI_FIX` --> `FIXgdas`
    - `FIXfv3`, `FIX_orog` and `OROFIX` --> `FIXorog`
    - `FIX_ugwd` and `OROFIX_ugwd` --> `FIXugwd`
    - `FIX_am`, `FIXgsm`, `FIXSYND` --> `FIXam`
    - `FIX_lut` --> `FIXlut`
    - `FIX_aer` --> `FIXaer`
    - `FIX_SFC` --> `FIXsfc`
    - `FIX_DIR` --> `FIXgfs`
    - `RTMFIX` and `FIXCRTM` --> `CRTM_FIX` (is `CRTM_FIX` in crtm module,
    so not using `FIXcrtm`)

    7. Correct the defaults for `FIXwave` in wave JJOB scripts
    8. Update variable names in `*fixed_files.yaml` files, as well as update naming
    convention for `oro_data` files

    Resolves #1984
    Resolves #1981
    Resolves #2175

commit 03d03bf53b43914a55c384cb33eb06f6a9a443a6
Author: Andrew Collard <[email protected]>
Date:   Tue Jan 2 11:53:44 2024 -0500

    Remove HIRS from GSI processing (#2183)

    With the update to CRTM 2.4.0.1, an issue with versioning of CRTM HIRS
    files has been exposed. This is documented in JCSDA/crtm#42.

    As HIRS radiances are no longer used in the GSI, these data should be removed
    from processing until a suitable update to CRTM is available.

    Resolves #2182

commit a3c50998d35525a39a66d5592fbf327ab3569e8b
Author: Jessica Meixner <[email protected]>
Date:   Fri Dec 22 18:07:48 2023 -0500

    Update ufs-weather-model version  (#2186)

    * update model to latest version which includes needed bugfixes for HR3

commit 774c7302e618370ef578bec3ccabc70486d6da1b
Author: David Huber <[email protected]>
Date:   Fri Dec 22 11:34:53 2023 -0500

    Fix analysis post processing's handling of 0-padded negative integers (#2187)

    This screens for the analysis 'forecast' hour (-001) and handles the '-' and circumvents octal issues.

commit d1251360325faf75af9df0608557fcd10202a883
Author: Barry Baker <[email protected]>
Date:   Thu Dec 21 11:23:48 2023 -0500

    Fix for restoring cycling aerosols in fo-mode post COM refactor (#2179)

    - Update to COM reorg aerosol initialization job
    - Address bug in joining paths for data dependency in this job

    ---------

    Co-authored-by: Rahul Mahajan <[email protected]>

commit e55a05980709288d902ad1bd894164bfa5a18a65
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Dec 20 22:14:01 2023 -0500

    Stop calling ufs-utils link script (#2172)

    The `link_workflow.sh` script was calling the ufs_utils version of the
    same. That step is only necessary if a user is going to run one of the
    stand-alone ufs-utils, which is rare.

commit ef3e5ad7c63be1644c82333c95853c3caf2d8995
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Dec 19 22:02:55 2023 -0500

    Fix handling of excluded hosts list (#2170)

    This PR fixes the issue with `create_experment.py` so that the yaml configuration
    file can have a string of list of strings when specifying the host name to exclude
    from the CI tests.

commit ea74a5719efc8f0fe631c5ff93426a4299a614f3
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Tue Dec 19 16:21:41 2023 -0500

    Add COMOUT_OBS to marine obs prep (#2173)

    Adds `COMOUT_OBS` (defined from `COM_OBS_TMPL`) to marine obs prep task to properly handle marine obs prep files. Used to keep obs after IODA conversion, QC, and other prep.

    Towards resolving NOAA-EMC/GDASApp#815

commit c2500feace0bb7c04ce67a90dd3182120ee67b2e
Author: David Huber <[email protected]>
Date:   Tue Dec 19 14:55:20 2023 -0500

    Return failed status if a build fails. (#2171)

    If any of the builds fail, this makes build_all.sh return the sum of the error codes encountered.

    Fixes #2168

commit 76fdd81cd84ed812181996a102379d8d964ba27a
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 19 13:24:34 2023 -0500

    Update index.rst for new GFSv16.3.12 in ops (#2169)

    Refs #2096

commit a81da33e8fe7541a36f68e7a4f14a384cadd36c8
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 19 10:22:21 2023 -0500

    Set place=shared for shared jobs on WCOSS2 (develop) (#2156)

    Set job as shared when not exclusive on WCOSS2

    WCOSS2 defaults to exclusive when it is not specified as
    either exclusive (place=exclhost) or shared (place=shared).
    Now set shared when job should be shared.

    Refs #2135

commit 89aea972f7964dac3f515e8070d7c534812c5fb4
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Dec 15 16:31:06 2023 -0500

    Update gfs-utils version for Hercules (#2163)

    An update of gfs-utils was misssing from the previous PR that added
    initial Hercules support (#2128).

    Also includes gfs-utils update for new marine post.

commit 9505cb4abc6ca2643a8ab254d14ca2000747fa44
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Dec 14 16:15:31 2023 -0500

    CI Updates to support Hercules (#2155)

    If merged, this PR will update the CI scripts so they will run on Hercules for forecast only
    NOTE: This is a stop gap to issue #2131 until its block on #1588 is removed.

    Resolves #2154

commit c5ca82f04a2efae78389dec1c46b94ef4fb5bbe5
Author: Rahul Mahajan <[email protected]>
Date:   Thu Dec 14 16:05:33 2023 -0500

    Correct fbwind (#2161)

commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a
Author: Kate Friedman <[email protected]>
Date:   Thu Dec 14 12:06:23 2023 -0500

    Add MOS jobs to rocoto mesh (#2148)

    Create separate jobs for GFS MOS - extracted from now-retired vrfy job

    Refs #2068

commit bb6151aa50c27253cb9b8f0a6601ddd58526b8b3
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Dec 14 05:38:29 2023 -0500

    Replace checkout script with submodules (#2142)

    Replaces the checkout script with git submodules. This change brings workflow in
    line with other repos and git standards.

    Due to these changes, the build system is updated slightly. First, the options that
    were formerly used with `checkout.sh` to reduce unneeded builds (`-g` for GSI
    and `-u` for UFSDA) are moved to `build_all.sh` instead. This is needed since build
    all will not be able to key off directories existing or not to determine which com-
    ponents to build. Second, the partial build system is removed. It was rarely, if ever,
    used, and parts of it were already ignored with the previous changes to base builds
    off whether directories exist. The manage externals file is also removed since that is
    also not being used.

    Following these changes, clones/checkout will need to either be recursive, or
    `git submodule update` will need to be called separately to make sure components
    are properly checked out (non-exhaustive list):

    ```
    ## Checkout develop (method 1)
    git clone --recursive https://github.com/NOAA-EMC/global-workflow destination

    ## Checkout develop (method 2)
    git clone  --jobs 8 https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git submodule update --init --recursive --jobs 8

    ## Checkout existing branch some_branch (method 1)
    git clone --recursive  --jobs 8 -b some_branch https://github.com/NOAA-EMC/global-workflow destination

    ## Checkout existing branch some_branch (method 2)
    git clone https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git checkout --recurse-submodules some_branch

    ## Checkout existing branch some_branch (method 3)
    git clone https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git checkout some_branch
    git submodule update --init --recursive  --jobs 8

    ## Checkout new branch new_branch
    git clone https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git checkout -b new_branch
    git submodule update --init --recursive  --jobs 8
    ```

    The git ignore list had to be updated to use explicit paths as the wildcard paths pick
    up the ones that are now submodules.

    UFS creates files during the build process that are not in its ignore list, so that sub-
    module ignores the "dirty" state to avoid confusing users running `git status`.

    CI and documentation are also updated to reflect the changes.

    Resolves #2141

commit 1332188ce2409e012ec127d44880e49732f7f379
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Dec 13 09:32:57 2023 -0500

    Enable radar reflectivity output (#2143)

    Turns on radar reflectivity output from FV3. This eliminates missing values appearing in the grib2 files.

commit 24d898ec0ec0c7fcbda6966988f9a986f528ed14
Author: David Huber <[email protected]>
Date:   Wed Dec 13 09:32:24 2023 -0500

    Fix Hercules hostname (#2150)

    * Allow lower or upper hostname on hercules.
    * Add Hercules to issue template.

commit 2896bb8787698be28ad20f2298589e6e95eaf9fb
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 12 09:13:06 2023 -0500

    Fix module load typo (#2145)

    Fix typo with loading the crtm module in the UPP hack for WCOSS2

    Refs #2144

commit 29d34172a67d976f910e78158ff0337e1ef099ca
Author: Cory Martin <[email protected]>
Date:   Thu Dec 7 15:12:05 2023 -0500

    Update GDAS hash to most recent stable versions (#2138)

commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Dec 7 10:41:05 2023 -0700

    Corrected typo in a gempak job gempakncdcupapgif . (#2137)

commit 3483f550db1ae35a680de49f7485ce5a11902dd9
Author: Cory Martin <[email protected]>
Date:   Thu Dec 7 12:34:56 2023 -0500

    Add support for FGAT and IAU for aerosol DA (#1940)

commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9
Author: David Huber <[email protected]>
Date:   Thu Dec 7 12:33:46 2023 -0500

    Enable forecast-only experiments on Hercules (#2128)

    This add forecast-only support for Hercules to the global workflow. Partially satisfies #1588.
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

commit a29f751aed05312da3d80d396159bb5a906d6ce4
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Dec 6 13:45:56 2023 -0700

    Adds GEMPAK and related jobs to rocoto task mesh (#2127)

commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082
Author: Rahul Mahajan <[email protected]>
Date:   Tue Dec 5 15:47:52 2023 -0500

    Separate offline UPP from interpolated grib2 product generation (#2110)

    This PR:
    - Replaces the use of  `JGLOBAL_ATMOS_POST` with `JGLOBAL_ATMOS_UPP`
    and `JGLOBAL_ATMOS_PRODUCTS`.
    - Introduces `JGLOBAL_ATMOS_PRODUCTS` that is responsible for creating
    grib2 products from the master file produced by UPP (inline from the model,
    or offline by running `JGLOBAL_ATMOS_UPP`).  Rocoto job `atmos_products.sh`,
    ex-script `exglobal_atmos_products.sh` are also added along with a
    `config.atmos_products`. Updates are made to the relevant `env` files as well as
    `config.resources` to reflect the addition of this job.
    - reduces the number of cores needed appropriately for forecast products when
    there is no offline UPP necessary.
    - renames older `fv3gfs_dwn_nems.sh` to `interp_atmos_master.sh` and
    `inter_flux.sh` to `interp_atmos_sflux.sh`
    - removes `fv3gfs_downstream_nems.sh` as it is absorbed into
    `exglobal_atmos_products.sh`
    - removes no longer used scripts for `gfs_post.sh`, `gfs_transfer.sh` (DBN alerts
    are absorbed into `exglobal_atmos_products.sh`), `post.sh`,
    `JGLOBAL_ATMOS_POST`, `ex${RUN}_atmos_post.sh` scripts.
    - Rocoto workflow related scripts are updated to add `atmos_products` as a job.
    When `WRITE_DOPOST` is `.false.`, `upp.sh` job to run the UPP offline is also
    added.  Dependencies have been appropriately applied.
    - removes `PGB1F` option that creates 1-degree grib1 products that are no longer
    needed in GFSv17.

    The hacks from (now deleted) `post.sh` had to be reinstated in `upp.sh` to load the
    modules from UPP instead of `load_fv3gfs_modules.sh`.

commit 44186f594aaf5f8feea0eadd4c5c3b59de3a825e
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 5 12:28:08 2023 -0500

    Update index.rst for new GFSv16.3.11 version (#2121)

    Refs #1356

commit e62a3a73cd22701962b7bf210fdfee37f37a5474
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Dec 5 09:08:12 2023 -0700

    Splits AWIPS jobs into seperate tasks (#2094)

    This PR addresses issue #1228. The following is accomplished:

    - Separate rocoto jobs have been created beneath `jobs/rocoto/`
    -- `awips_20sh` and `awips_g2sh`; these jobs replace `awips.sh` which was
    calling multiple J-jobs within the respective `awips.sh` scripts;
    - New tasks has been added to `workflow/rocoto/tasks.py` for the new
    AWIPS scripts;
    - The `gfs_cycled` and `gfs_forecast_only` modules beneath
    `workflow/rocoto` have been updated accordingly.

      Resolves #1228

commit 04d97e9aa7ab84b9754ab670074cfb19d543aa26
Author: Kate Friedman <[email protected]>
Date:   Mon Dec 4 13:38:30 2023 -0500

    Consolidate VMINMON and cleanup monitor scripts (#2088)

    This PR combines the GDAS and GFS versions of the VMINMON JJOB
    and ex-driver scripts into single GLOBAL/global versions. Additionally:

    * some further cleanup of the GSI-Monitor scripts is done; variable
    settings in ex-driver scripts are moved up to the JJOB level
    * the fix symlinks are consolidated into a new `fix/mon` subfolder (formerly
    `fix/gdas`) and copies of the gfs monitor fix files under `fix/products` are
    removed

    Resolves #1925

commit a286a11fdcbc31c8bc6d944890bc56294bc8caf6
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Dec 4 17:48:44 2023 +0000

    Robust CI Restarts (#2093)

    Improved CI robustness for reverting back to **CI-Ready** from any
    given state

    New Features:

    - Improved `scancel` routine (refactored into bash "subroutine")
    - Improved messaging (see below) when ever a user changes state
    - Any and all previous build scripts and running experiments are killed as
    a result of reset to **Ready**

    Resolves #2060

commit 73621e9b20b20f85e8b21e4c1e09ed1d80ecd46f
Author: David Huber <[email protected]>
Date:   Sun Dec 3 11:19:19 2023 -0500

    Upgrade to spack-stack/1.5.1 and Intel 2022 on non-production machines (#2084)

    Update module files to spack-stack/1.5.1 and compilers to Intel 2022+ on all non-production machines.

commit 6d548b250688861eb20a7e0dc852a0e4ba9e64f4
Author: jiandewang <[email protected]>
Date:   Thu Nov 30 12:00:21 2023 -0500

    Add variable tob in diag_table for ocean model output(#2105)

commit c19810cce252fcdb25fd9960c05b08b5f8d8b1ad
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Wed Nov 29 15:17:36 2023 -0500

    Added variables to config.prepoceanobs (#2101)

commit c2d78a61a224678fb804eed19f39d1f07408ae5f
Author: Kate Friedman <[email protected]>
Date:   Wed Nov 29 12:39:08 2023 -0500

    Add missing cut to VDATE setting in JGFS_ATMOS_VERIFICATION (#2098)

    Refs #2097

commit c1c025f91ddac73aea595cc9fa4dd0bea80575fc
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Nov 29 17:15:10 2023 +0000

    Add wave init to GEFS (#2089)

    Adds the wave init job to GEFS. Since the output would be the same for
    every member, the job is only run once for the control, then links are
    created in each of the member directories pointing to that copy.

    New ww3_multi and ww3_shell templates for GEFS are copied from the
    GFS versions.

    The GEFS restart frequency is changed to not be zero, and the comment
    about not setting it to zero is copied from the gfs config.base. The restart
    interval for the GEFS perturbed members is changed to equal that of the
    control.

    Also fixes a bug where `RUNwave` was not defined for ensemble forecasts,
    and another bug in the GEFS stage_ic dependency.

    Resolves #2017

commit 64a2470ce29b7d8d5cb85ebcb4048ff82958f64e
Author: Kate Friedman <[email protected]>
Date:   Wed Nov 29 11:26:34 2023 -0500

    Adjust permissions for jobs/JGFS_ATMOS_VERIFICATION (#2095)

    Add execute permissions (755)

commit 964b77bc6de67291973c2c70598a1f8cb72501c5
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Nov 28 18:45:51 2023 +0000

    Make proper j-job for MET+ (#2090)

    Creates a proper j-job for the metp job, moving much of the material
    from the `jobs/rocoto` script there (some of it within `jjob_header`).

    Also updates the old `COMIN` variable for the COM refactor (although
    it does not appear used in the verify scripts currently).

    This is a partial step towards restoring/improving metp functionality
    and remains untested.

    Refs #1575

commit 8c11eeb8556619e8db4e0efb6394ce5a2c1aae0f
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Nov 23 10:31:32 2023 -0700

    Adds FBWINDS support to global-workflow (#2082)

    This PR addresses issue #1221. The following was accomplished:

    - A new Rocoto job is added; `jobs/rocoto/fbwinds.sh`;
    - `workflow/applications/gfs_cycled.py` is updated to include the `fbwinds` task;
    - `workflow/applications/gfs_forecast_only.py` is updated to include the `fbwinds` task;
    -  A new function is added to `workflow/rocoto/gfs_tasks.py`, `fbwinds` is added as new GFS (only) task;
    - `workflow/rocoto/tasks.py` is updated to include the `fbwinds` task.

    Resolves #1221

commit 513db190d21f9ede0724a2cd5606372b1d7605de
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Nov 21 22:52:58 2023 -0700

    Adds NPOESS support to global-workflow (#2083)

    This PR addresses issue #1225. The following was accomplished:

    - A new Rocoto job is added; `jobs/rocoto/npoess.sh`;
    - `workflow/applications/gfs_cycled.py` is updated to include the `npoess`
    task;
    - `workflow/applications/gfs_forecast_only.py` is updated to include the
    `npoess` task;
    -  A new function is added to `workflow/rocoto/gfs_tasks.py`, `npoess` is
    added as new GFS (only) task;
    - `workflow/rocoto/tasks.py` is updated to include the `npoess` task.

    Resolves #1225

commit 62d8e99e77ffe44784f4c61c3f2296c6d1a72413
Author: Kate Friedman <[email protected]>
Date:   Fri Nov 17 20:25:50 2023 -0500

    Retire vrfy job (#2080)

    Retires the `vrfy` job from the global-workflow system. All associated
    scripts, configs, and references to the job are removed.

    Additionally, the switches listed in RTD were updated to reflect new
    ones added in other PRs for issue #235.

    Resolves #2069
    Refs #235

commit ea386abf11ecbacef407388e8d57e71b30148a35
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Nov 17 23:59:46 2023 +0000

    Enable different coupled settings for ensemble (#2030)

    Adds the ability to turn off some coupled components for the ensemble.

    To enable this, many settings are moved out of `config.fcst` and into `config.ufs`
    so they are calculated after any overrides of `DO_*` have been made. Some
    settings also had to be moved out of `config.base` for the same reason. A
    switch to turn on gocart is added to `config.ufs`, but unlike the other switches
    this one takes no arguments.

    The name of the ufs configure template used is converted from a partial file
    name to the full file name.

    Resolves #1692

commit fe792c0c9a1c46908cbd18c7e71eb836974cf1de
Author: Kate Friedman <[email protected]>
Date:   Fri Nov 17 17:19:16 2023 -0500

    Add --cpus-per-task to srun commands for Hera and Orion (#2077)

    This PR adds the `--cpus-per-task` flag to non-CFP `APRUN`/srun commands
    in the env files for Orion and Hera. This is needed as a result of an upgrade
    to SLURM on Orion that no longer exported the thread value to the
    environment. Issue #1996 was a hotfix to add this flag for the analysis job
    that was suddenly running slowly after the SLURM upgrade. A similar SLURM
    upgrade was done on Hera but the sysadmins there implemented a
    workaround so this issue did not appear there.

    This PR adds the `--cpus-per-task` flag for both machines...needed on Orion
    and as a safety measure on Hera.

    Also included in this PR is a fix to indentations in the
    `scripts/exglobal_diag.sh` script that was noticed during work for this PR.

    Timing differences were not observed for other jobs after adding this srun
    flag. Job timings were of a similar variation between control and test runs.
    Any potential additional speedup was not observed. The test runs also
    reproduced the control runs with `develop`.

    Resolves #2044

commit 42c943be305c297a56b104bb50727938c1ba688f
Author: Kate Friedman <[email protected]>
Date:   Fri Nov 17 15:41:34 2023 -0500

    Adjust modules in post.sh for WCOSS2 (#2079)

    On WCOSS2 the grib_util module is named a bit different and
    needs the libjpeg module loaded beforehand.

commit cd4e6a1987e7fd71dff06766f540b5d32c8b648d
Author: Jessica Meixner <[email protected]>
Date:   Fri Nov 17 11:49:32 2023 -0500

    Update ufs-weather-model and remove upp hack (#2071)

    Updates the model to the most recent commit of ufs-weather-model.  This
    should allow for the removal of the UPP hack that was added in PR #2042

    This required changing nems.configure -> ufs.configure.

    Resolves #1942

commit 5a2d97e142aa4999b122fd5a130c63e59ea9f8e2
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Nov 16 22:15:53 2023 +0000

    Fix check for existence of preamble functions (#2066)

    A few of the setup scripts were checking for the existence of
    functions set by the preamble before calling them so they could
    also be used stand-alone. However, the `type` command returns `1`
    if the function name does not exist, which will cause the script
    to die is `set -e` is on. Now the `type` command fails over to an
    empty string.

commit ed2ee7c2b1457b71b271a2c40f0dfa356e0f52f8
Author: WenMeng-NOAA <[email protected]>
Date:   Thu Nov 16 16:38:11 2023 -0500

    Update UPP products for GFS v17 (#1973)

    Updates of generating GFS V17 UPP products to support HR3:

    - Update g2tmpl to 1.0.12
    - Add changes to launch cfp on WCOSS2 to generate pgrb2/pgrb2b files
    - Changes for generating new products (MERRA2, six winter weather variables,
    1km HLCY, SDEN) in pgrb2 files

    Resolves #1965
    Resolves #1994

commit 635c4719e603538ce7cccf9ea6b31f3f84f20849
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Nov 16 20:35:30 2023 +0000

    Fix some rocoto dependencies (#2074)

    A few small errors/cleanup in the dependencies, mostly in fcst:

    A few small errors/cleanup have crept into the dependencies with recent changes,
    mostly in fcst:

    - Fixed the offset, as it would yield a string rocoto doesn't recognize when the
    interval was 24+ hrs
    - Removed the duplicate wave dependency. When `waveprep` is included, it
    depends on `waveinit` so there is no need to add a `waveinit` dependency.
    - Converted an interval in the archive job that was missed in #2039

    Resolves #2075

commit d4c7508260975c6b94fc92fd085f39d4faf3f027
Author: Rahul Mahajan <[email protected]>
Date:   Wed Nov 15 16:44:03 2023 -0500

    Fix missing _PREV in ocean restart file location (#2070)

commit 255616d37505c785bdddd5d3e39e8399110b626e
Author: mdtoyNOAA <[email protected]>
Date:   Wed Nov 15 12:02:09 2023 -0700

    Update functionality for Prototype HR3 UGWP (#1987)

    This PR adds/modifies namelist options and activates new 'ccpp' suite definition
    files for the updated Unified Gravity Wave Physics (UGWP) in the ufs-weather-
    model recently updated for HR3.  The changes to UGWP are the use of the GSL
    drag suite for orographic gravity wave drag (GWD) and blocking, as well as the
    new UGWP Version 1 non-stationary GWD.  See
    ufs-community/ufs-weather-model#1923 for details.

    Resolves #1986

commit be9085e62aae147e3c74602e2f82a99b374fc783
Author: Guillaume Vernieres <[email protected]>
Date:   Wed Nov 15 13:48:58 2023 -0500

    Save the required CICE history for the sea-ice DA (#2062)

    The hist_avg setting of CICE was changed to be an array.

commit 85f1f5131ffd70061231304ea477bde0559eb67b
Author: Guoqing Ge <[email protected]>
Date:   Wed Nov 15 11:47:21 2023 -0700

    Use assim_freq to configure "offset" in dependencies (#2039)

    Use the assim_freq from config.base to configure "offset" in dependencies
    instead of hard-coding them.

    Resolves #2038

commit 4e3d82ba3a1fa7cdd4443bcd4cf83b2f8835137c
Author: Kate Friedman <[email protected]>
Date:   Wed Nov 15 13:39:14 2023 -0500

    Resolve ENKF archive script bugs (#2065)

    Fix two bugs in the exgdas_enkf_earc.sh script:

    1) Replace ARCH_LIST with DATA to match changes done in PR #2000
    and update path to generated archive list files.
    2) Add status check and exit after script attempts to make tarball on HPSS.

    Refs #2064

commit 42d7f2f0c48fab898b764e09cfbbd7a9fabbae08
Author: Kate Friedman <[email protected]>
Date:   Tue Nov 14 17:54:29 2023 -0500

    Separate tracker and genesis jobs from vrfy job (#2058)

    This PR creates new individual jobs for the tracker and genesis jobs that are being
    pulled out of the `vrfy` job (issue #235). The `tracker` and `genesis` jobs will be on
    by default while the `genesis_fsu` job will be off by default. This mimics the current
    settings in the `vrfy` job.

    No enhancements or upgrades are made to the jobs themselves in this PR, only to
    separate them from the `vrfy` job. However, one change compared to how they
    currently run in the `vrfy` job is to no longer run the `tracker` in the gdas suite. This
    mimics how the `ens_tracker` package is run in operations (gfs only).

    Changes in this PR:

    1. Create rocoto job scripts for tracker/genesis jobs.
    2. Create configs for tracker/genesis jobs, as well as `config.tropcy` for shared
    settings.
    3. Add tracker/genesis jobs to `config.resources`; use resources from the ecf scripts
    for `ens_tracker` jobs in operations
    4. Add tracker/genesis jobs to rocoto setup for both cycled and forecast-only
    modes.
    5. Update arguments for `jjob_header.sh` script in tracker/genesis JJOB scripts to use
    specific job names and configs instead of vrfy.
    6. Rename `tracker_ver` to `ens_tracker_ver` in version files to mimic variable within
    tracker package.
    7. Rename and move tracker/genesis switches to `config.base`.
    8. Remove tracker/genesis jobs from `vrfy` job (`jobs/rocoto/vrfy` and `config.vrfy`).
    9. Reduce vrfy job resources to accommodate tasks having been removed.

    Refs #235
    Resolves #1988
    Resolves #2048

commit 0a0d6984e094d2a551d5d8331102142e7db13fc2
Author: Rahul Mahajan <[email protected]>
Date:   Tue Nov 14 14:08:26 2023 -0500

    Enable warm starting of the model for forecast-only mode (#2031)

    This PR:
    - adds an option to warm|cold start the ufs-weather-model when setting up an experiment for GFS/GEFS
    - adds the capability to stage FV3 restarts when the atmosphere is warm started from FV3 restarts. This would be used in the GEFS free-forecast for part of the reforecast capability.
    - If a coupled model is warm started for the atmosphere, also check if mediator restarts are present. If so, stage mediator restarts to allow restarting the coupled model.

    Fixes #2016

commit 2cd6a589305a9ac9d3a9a0d2136e66e42f09d3bf
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Nov 14 12:05:20 2023 -0700

    Moves UFS WM configuration files to `COM_CONF` (#2054)

    The UFS weather-model (WM) files are place in the COM_CONF path rather than the respective component model COM history paths.
    Resolves #2015

commit 6f1693081662f241fafc930b1afc88125f7f5aff
Author: Kate Friedman <[email protected]>
Date:   Tue Nov 14 11:15:02 2023 -0500

    Refine fit2obs job in rocoto mesh (#2047)

    This PR adjusts the `fit2obs` job in the rocoto mesh to better define when it exists
    and how the archive job dependencies accommodate it not being in the first half
    cycle.

    Changes in PR:

    1. Remove the `fit2obs` job from the first half cycle `cycledef`.
    2. Adjust the archive job dependencies to now include the `fit2obs` job in the new
    logic check added in PR #1983. The `gdasarch` job in the first half cycle will check if
    `gdasfit2obs` is complete OR no prior cycle exists. Also cleaned up this new logic
    check block some to make it a tad simpler.
    3. Also, fix the addition of the `fit2obs` config to the config list in setup scripts. Now
    tied to whether `fit2obs` job is on instead of always adding the config to the list.

    Resolves #2043

commit 5730a71fa5d311e49d9bb11528b500f27f33d69d
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Nov 14 09:13:11 2023 -0700

    Add `waveinit` and `waveprep` to half-cycle. (#2037)

    This PR addresses issue #1444. The `waveinit` and `waveprep` tasks have been added to
    the GDAS have cycle. The downstream dependencies for the respective GFS and GDAS
    forecast tasks have been removed.

    Resolves #1444

commit 28d2e93c3857de95b0309a089cd7dac736ccaded
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Nov 14 16:11:47 2023 +0000

    Update wave IC source for C384 (#2055)

    The default wave grid for C384 has changed since P8, so a single wave
    IC on the new grid is available under a different IC name.

commit 81dd2d9855091315611106a5afbdaeaa15e6e4ae
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Nov 9 17:19:57 2023 +0000

    Fix analysis and post on Orion (#2046)

    Fixes a couple things to get workflow to work on Orion again:

    First, while #2042 allowed post to be built, the `upp.x` executable would fail due
    to a missing library. Now post jobs (temporarily) uses the UPP modules (plus
    others needed for runtime) instead of the normal workflow runtime module. This
    should actually fix #2041. This hack can likely be removed once we move to
    spack-stack.

    Second, the launcher command for the analysis jobs on Orion are updated to
    specify the number of CPUs per task. This was necessary as a recent slurm update
    on Orion discontinued reading that value from the scheduler. Other jobs will be
    handled later (see #2044).

    Additionally, a change is made to `module-setup.sh` that will eliminate the
    annoyance of `gw_setup.sh` breaking tab completion because undefined variable
    checking was turned on for the script but not back off.

    Resolves #1996
    Resolves #2041
    Refs #2044

commit 13d06ded4155cba2d08ef2a2cd553024c5abe29d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Nov 8 18:25:47 2023 +0000

    Hack UPP version (#2042)

    The stack UPP was using on Orion was recently deleted, leaving us
    unable to build the UFS verison of UPP there. UPP has an updated
    version using spack-stack that works, so the checkout script is
    modified to check out that version of UPP after UFS has been
    checked out.

    This temporary hack can be removed once we move to a UFS version
    that advances the UPP version to or beyond 78f369b.

    Resolves #2041

commit 20f6eceb8ff58f84174a27eb849c1d74566a3e03
Author: jiandewang <[email protected]>
Date:   Wed Nov 8 11:14:55 2023 -0500

    Add basic C1152 settings (#2020)

    Adding C1152 setting in host.yaml, config.base and config.stage_ic so that can run C1152 S2SW.

    Resolves #2019

commit 5183c43bbbd07285869feacb49d8680afe85929a
Author: Barry Baker <[email protected]>
Date:   Tue Nov 7 01:14:40 2023 -0500

    Update UFS for dust fix and remove nitrates by default  (#1989)

    This PR updates the `ufs-weather-model` to the latest hash that included the dust fix (PR #1922).
    Along with this I removed the nitrates by default in support of the GEFSv13 EP4 and EP5
    experiments. Removed unneeded inputs that should help with speed improvements.

commit 34a73cf2ed5afefc776d9cc73b6ebf439122a1bb
Author: David Huber <[email protected]>
Date:   Mon Nov 6 14:00:51 2023 -0500

    Reduce gdas builds to 8 #2029 (#2036)

    Reduce the default number of build jobs for the GDASApp to 8 from 16.

    This is needed for Orion as the build crashes during a linking step.  Though not verified, it
    appears this may be caused by using too much memory with 16 builds.  The issue disappears
    when using 8 build jobs.

    Resolves #2029

commit 75269e4bb9764b81589efc7d703825b80e74c8f5
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Nov 6 17:34:47 2023 +0000

    Streamline CI reporting to PRs (#2026)

    Cleaned up the logs for CI PRs sent to the GitHub Messages:

    - Eliminates redundant accumulative reporting
    - Reports on all created or skipped experiment instantiations in a single message
    - Gives one line report once  for each experiment completion
    - Single final report completion of CI

    See some examples in forked [PR 195](https://github.com/TerrenceMcGuinness-NOAA/global-workflow/pull/195)

    Resolves #2007

commit 8d55126bb0b27c79c8bee7f72b014abd34950ff9
Author: Guillaume Vernieres <[email protected]>
Date:   Fri Nov 3 17:06:09 2023 -0400

    Implement IAU Cycling Type with Marine Data Assimilation Enabled (#1944)

    Allows cycling in IAU mode with the S2S UFS model, soca and the GSI.

    Most of the work related to making IAU work was done by @JessicaMeixner-NOAA . Thanks @JessicaMeixner-NOAA !

    Resolves #1943
    Refs #1776

commit 2563806821d4ae3b57120bc61aa0575139a708f0
Author: jiandewang <[email protected]>
Date:   Fri Nov 3 11:49:37 2023 -0400

    Add two ucx modules in load_ufswm_modules.sh to solve C768 and C1152 S2SW job hanging issue on WCOSS2 (#2021)

commit cbdc09711a83493f363a737d1e3e46c48a09719d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Nov 3 04:09:33 2023 +0000

    Fix staging of MOM data (#2028)

    During the update to stage_ic, the copying of the additional res_N files for
    0p25 was omitted. These are now properly copied.

    Resolves #2027

commit bd4c56d99c23c5c41f0bd5f8a980ef99ee160888
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Thu Nov 2 16:09:59 2023 -0400

    changed optional script name vars for ocean analysis (#2025)

commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6
Author: Kate Friedman <[email protected]>
Date:   Thu Nov 2 16:01:18 2023 -0400

    Create separate GSI monitor jobs and remove from vrfy job (#1983)

    This PR will move the GSI monitor tasks from the `vrfy` job into their own separate jobs in
    the rocoto mesh. This takes care of part of issue #235.

    Changes in this PR:

    1. Create new individual GSI monitor jobs in the rocoto mesh to match how it is done in
    operations. The new jobs are: `gdasverfozn`, `gdasverfrad`, `gdasvminmon`, and `gfsvminmon`.
    The names correspond to the names in operations and the ecf script names. The jobs are only
    added to cycled mode, none of the jobs are run in forecast-only mode.
    2. Updates to GSI monitor scripts:
      * Update `ush/jjob_header.sh` arguments in JJOB scripts to call new individual job names and
    configs.
      * Introduce `COM_*` variables and use of the `generate_com` utility. This results in the outputs
    landing in `COM` subfolders, like occurs in operations, instead of landing in the online archive.
      * Some variable cleanup in JJOB and ush scripts, includes cleaning up usage of `DATA` variable
    and its removal at the end of the jobs.
      * Add missing exit statements to `JGFS_ATMOS_VMINMON` and `JGDAS_ATMOS_VERFRAD`.
    3. Create new rocoto job scripts for the new individual GSI monitor jobs.
    4. Create new configs for the new individual GSI monitor jobs.
    5. Add new individual GSI monitor jobs to resource configuration, using the same resources as
    in operations.
    6. Move and rename GSI monitor job switches from `config.vrfy` to `config.base`. Also add
    switches to setup system. New switches to control each job being added to the rocoto mesh
    are: `DO_VERFOZN`, `DO_VERFRAD`, `DO_VMINMON`
    7. Add GSI monitor job output to archival job and into resulting HPSS tarballs or local tarballs.
    This now matches what is done in operations.
    8. Remove the GSI monitor tasks from the rocoto `vrfy` job and associated `config.vrfy`.

    Example output locations and files (not showing contents of oznmon/horiz or oznmon/time for
    brevity, see archival script for full list of output files):
    ```
    kate.friedman@dlogin09:/lfs/h2/emc/ptmp/kate.friedman/comrot/testmonitor2> ll gdas.20211221/00/products/atmos/*mon
    gdas.20211221/00/products/atmos/minmon:
    total 112
    -rw-r--r-- 1 kate.friedman emc 14030 Oct 25 15:00 2021122100.costs.txt
    -rw-r--r-- 1 kate.friedman emc 84932 Oct 25 15:00 2021122100.cost_terms.txt
    -rw-r--r-- 1 kate.friedman emc   808 Oct 25 15:00 2021122100.gnorms.ieee_d
    -rw-r--r-- 1 kate.friedman emc   808 Oct 25 15:00 2021122100.reduction.ieee_d
    -rw-r--r-- 1 kate.friedman emc    80 Oct 25 15:00 gnorm_data.txt

    gdas.20211221/00/products/atmos/oznmon:
    total 8
    drwxr-sr-x 2 kate.friedman emc 4096 Oct 25 15:05 horiz
    drwxr-sr-x 2 kate.friedman emc 4096 Oct 25 15:05 time

    gdas.20211221/00/products/atmos/radmon:
    total 21036
    -rw-r--r-- 1 kate.friedman emc      231 Oct 25 15:12 bad_diag.2021122100
    -rw-r--r-- 1 kate.friedman emc     9035 Oct 25 15:12 bad_pen.2021122100
    -rw-r--r-- 1 kate.friedman emc     1449 Oct 25 15:12 low_count.2021122100
    -rw-r--r-- 1 kate.friedman emc 20523403 Oct 25 15:07 radmon_angle.tar.gz
    -rw-r--r-- 1 kate.friedman emc   217272 Oct 25 15:08 radmon_bcoef.tar.gz
    -rw-r--r-- 1 kate.friedman emc   502151 Oct 25 15:10 radmon_bcor.tar.gz
    -rw-r--r-- 1 kate.friedman emc   264480 Oct 25 15:12 radmon_time.tar.gz
    -rw-r--r-- 1 kate.friedman emc      684 Oct 25 15:12 warning.2021122100
    kate.friedman@dlogin09:/lfs/h2/emc/ptmp/kate.friedman/comrot/testmonitor2> ll gfs.20211221/00/products/atmos/minmon/
    total 88
    -rw-r--r-- 1 kate.friedman emc 10530 Oct 25 14:55 2021122100.costs.txt
    -rw-r--r-- 1 kate.friedman emc 63882 Oct 25 14:55 2021122100.cost_terms.txt
    -rw-r--r-- 1 kate.friedman emc   808 Oct 25 14:55 2021122100.gnorms.ieee_d
    -rw-r--r-- 1 kate.friedman emc   608 Oct 25 14:55 2021122100.reduction.ieee_d
    -rw-r--r-- 1 kate.friedman emc    80 Oct 25 14:55 gnorm_data.txt
    ```

    Lingering work and considerations:

    1. Issue #1925
    2. Consider not hardcoding the list of types in archival and perhaps tie it to something reliable or
    configurable (maybe into `config.verfozn`?):
    `subtyplist="gome_metop-b omi_aura ompslp_npp ompsnp_n20 ompsnp_npp ompstc8_n20 ompstc8_npp sbuv2_n19"`

    Resolves #1908

commit 31b05a99b77d0f6eaa8b116485a41a43867d20e1
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Nov 2 12:23:32 2023 -0600

    Move analysis post to new stand-alone task (#1979)

    This PR addresses issue #1130. A new task `postanl.sh` has been added such that the
    `anl` post-processing is not it's own task within the Rocoto workflow. This change
    prevents the GDAS experiment from breaking due to failures caused by the `anl` not
    being available for the first cycle.

    Resolves #1130

commit 247cdf8c7e10e6c98f782799fc51c069b6474e70
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Nov 2 11:18:53 2023 -0600

    Corrects missing local variable reference (#2023)

    Fixes missing `$` in variable reference in archive job.

    Resolves #2022

commit 241742b246da1794646b68e41c3d6fe00b95dd07
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Wed Nov 1 14:19:55 2023 -0400

    Updates to prep ocean obs task (#1870)

commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Nov 1 12:09:33 2023 -0600

    No longer write archive lists COM (#2000)

    Changes the respective `.txt` files used for the HPSS archive to the `DATA` path. Each
    defined text file has been updated to explicitly write to `DATA` rather than `COM` such
    that the files are deleted rather than being archived.

    Resolves #760

commit 517b92f9c20c9e44abba3183325e35a95a7334a5
Author: David Huber <[email protected]>
Date:   Tue Oct 31 16:33:11 2023 -0400

    Parallelize the build scripts (#1998)

    Optimized/parallelized build scripts.

    A few notes:

    1) The default number of build jobs is 20, but one could argue for using 40.  When researching
    this, I looked up what the SRW is compiling with.  That system uses 40 cores, which seems a
    little excessive, but on testing the global workflow, the actual number of cores being used at
    any given time rarely exceeds 16 when running with 40 cores.  This is because the builds tend to
    use multiple threads in the beginning when compiling low-level modules while the higher-level
    modules are more or less serial AND because the GDASApp takes several minutes to initialize
    all of its subrepositories by which time the smaller builds are complete.

    2) I also updated checkout.sh so that all checkouts are simultaneous.  The CPU load for
    `git submodule` is quite low, so running 16 instead of 8 jobs at once is not much more expensive.

    3) To make this work, I had to add `-j` options to most of the build scripts.  The only exception is
    build_upp, for which the build script within the UPP is hard coded to use 6 cores.

    4) I fixed a few small bugs in the build scripts along the way.

    5) Lastly, this reduce the total build time from ~2.5 hours for the entire system (including GDAS
    and GSI in the same build) to ~40 minutes when running with `-j 40`.

    Resolves #1978

commit 67c050c201f92e855d09211e41a5f51ee1cb5230
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Oct 31 19:00:47 2023 +0000

    Add missing export for rCDUMP in stage_ic (#2009)

    rCDUMP is needed by the exscript but was never exported by the jjob.

commit 872068cb5ea78b311f7a77e97ee1428ae027cb61
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Oct 31 14:37:55 2023 +0000

    Add output error log to user for create_experiment.py on fail in CI (#1974)

    Small changes to driver CI bash scripts to recapture error log from `create_experment.py` logger
    Fixes #1939

commit b2e4a2e9d269842acbb1b37dd563ee5dee2adf0f
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Oct 31 13:57:02 2023 +0000

    Allow CI case to exclude running on certain platforms (#2001)

commit 7cc137116f1619bf1e5a12eaacb98d17da97c223
Author: Jeff Whitaker <[email protected]>
Date:   Tue Oct 31 07:54:24 2023 -0600

    Add initial C96/1 deg coupled model support (#1991)

commit 7086ddc4bece6fb2a8c1c2e6090800d4293e410e
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Mon Oct 30 19:58:43 2023 -0400

    Add ocean analysis files to HPSS archiving task (#1985)

    This PR adds the files under `analysis/ocean` (except those in `bump` and `vrfy`) to the
    HPSS archiving job, in `gdasocean_analysis.tar`, which were previously not archived.

    Resolves NOAA-EMC/GDASApp/issues/693

commit eabc82ad30c118645c0e6e216162d823882a8139
Author: Guillaume Vernieres <[email protected]>
Date:   Mon Oct 30 10:31:27 2023 -0400

    Make the early cycle work with the coupled UFS configured as S2S  (#1954)

commit aff6ca7ae559e424dae128d6cfd5da4a4e3049e7
Author: Anil Kumar <[email protected]>
Date:   Fri Oct 27 14:11:55 2023 -0400

    GEFS Staging in exglobal_stage_ic  (#1892)

    Adjusts source paths for forecast-only ICs in support of extension to ensembles.
    New paths omit the resolution (that is captured by the IC id name) and allow for
    a member level.

    Directories with the reorganized ICs have been added to the three tier-1 machines
    under glopara space.

    Building on this, also adds capability to stage GEFS ICs.

    Resolves #911

commit 77c1ff2bfa26b341b01f41e50ee0ecb31cc4f661
Author: RussTreadon-NOAA <[email protected]>
Date:   Thu Oct 26 23:44:27 2023 -0400

    Update GDASApp hash (#1975)

    Update GDASApp hash to bring recent UFSDA development into g-w.

    Resolves #1972

commit 962368884991670d3a1ee1c5a065d5bce4b7561a
Author: David Huber <[email protected]>
Date:   Thu Oct 26 16:10:23 2023 -0400

    Test tarballs for rstprod before calling chgrp (#1967)

    Certain tarballs may or may not contain `rstprod` data.  For instance, the first half cycle
    gdas and enkfgdas tarballs will not contain `rstprod`, while future cycles likely will.  Also,
    some systems do not have `rstprod` on them.  This will test the contents of the tarballs
    first before attempting to change the group to rstprod.

    Resolves #1460

commit c02e118c0ac5485109c9bd33472ff42db309cd9b
Author: Jessica Meixner <[email protected]>
Date:   Thu Oct 26 15:05:05 2023 -0400

    Update ufs model to version from 10-12-23 (#1933)

    This updates the ufs-weather-model to the commit hash from 10-12-23 from the HR2 tag.
    The diffs can be seen here: https://github.com/ufs-community/ufs-weather-model/compare/GFSv17.HR2...68050e58589a82ab509aaefaafdc2a6b90f34e48

    Resolves #1811

commit 8556541daa79b0180fde48a58a8dcfb2f8c56ea5
Author: Rahul Mahajan <[email protected]>
Date:   Wed Oct 25 16:15:28 2023 -0400

    Fix incorrect usage of CFP on WCOSS2 (#1977)

commit 0b5cf9b67a8146d9d4815ea6545f7f2524120d83
Author: Kate Friedman <[email protected]>
Date:   Wed Oct 25 13:17:28 2023 -0400

    Update GFS version in index.rst to v16.3.10 (#1976)

    Update the "State of operations" GFS version number to new v16.3.10 (Annual CO2 fix file update in operations).

    Refs #1924

commit e817f5dd38c26a88f76d90eb71124f1acbfc5a8f
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Oct 25 02:03:14 2023 +0000

    Fix path for marine products (#1966)

    When PR #1823 was merged, the name of the marine product template
    was not updated in ocnpost, leading the products to be placed in
    the wrong location and missed by the archive job.

    Resolves #1902

commit 7cdfad4eaa7abe0769ff13396c54e6d93afebf8f
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Oct 24 22:19:46 2023 +0000

    Build GDASapp for CI tests (#1964)

    * added -u to global checkout so CI test builds tests for GDASapps

    * Update check_ci.sh

    needed more quotes

    ---------

    Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>

commit c58deae0cf078d1ee093529064d74f60482aa3f4
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Oct 24 16:19:04 2023 -0600

    Updates for NOAA CSP AWS global-workflow related file paths. (#1970)

    Co-authored-by: henrywinterbottom-wxdev <[email protected]>

commit 1b00224e18842cd873eb1779be08f96687e49e1f
Author: Kate Friedman <[email protected]>
Date:   Tue Oct 24 14:48:24 2023 -0400

    Set SENDCOM=YES for tracker/genesis tasks (#1971)

    Set SENDCOM to YES in config.vrfy to get outputs copied back to COM.

    Will reevaluate the need for SENDCOM when moving the tracker/genesis jobs out of the vrfy job with issue #235 work.

    Refs #1947

commit e2c624d8904cd988394c73d0edb22fa593229d3f
Author: RussTreadon-NOAA <[email protected]>
Date:   Tue Oct 24 13:32:52 2023 -0400

    Refactor UFSDA ATM var and ens layout (#1945)

commit 8940adddfe9d21189740e71487603fb2acee2336
Author: David Huber <[email protected]>
Date:   Tue Oct 24 11:02:29 2023 -0400

    Optimize the checkout script (#1956)

    * Multithread the checkout script #1953

commit 4b5cd0bc435fc158258ca38c3d5f44add6b60469
Author: Rahul Mahajan <[email protected]>
Date:   Mon Oct 23 12:04:26 2023 -0400

    Fix nth_eupd in gfs/config.resources.  remove sections of jobs not run as part of gefs from gefs/config.resources (#1952)

commit 08ce4f8d3ed8e07b4d488a80b5054c6206b04404
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Oct 20 16:14:53 2023 +0000

    Fix enkfgfs cleanup dependency (#1941)

    When #1906 was merged, the dependency for enkf cycles was hard-coded
    to use the enkfgdas archive instead of depending on the `RUN`.

commit 1a5d0b51642eb70f71e693355e86212d3607b7b3
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Oct 20 15:54:33 2023 +0000

    Split clean-up into separate job (#1906)

    Moves the clean-up that was previously done in the archive jobs into
    their own separate job. The clean-up is also streamlined considerably
    by using only `COM_TOP` instead of going through every template.
    There is also additional streamlining/corrections in the function that
    does the actual removing.

    Some settings used by both jobs were elevated to `config.base`.
    Others only needed for cleanup were moved to the new config for
    that job.

    Also corrects a small error encountered when attempting to rerun an
    ensemble forecast.

    Resolves #583
    Resolves #1872

commit 3de102c28daf9eb50ce65e0afe911f5a416ce861
Author: Rahul Mahajan <[email protected]>
Date:   Tue Oct 17 09:30:18 2023 -0400

    Updates to CI to clarify HOMEgfs (#1931)

    * replace HOMEgfs_PR with HOMEgfs, and HOMEgfs with ROOT_DIR. ROOT_DIR is the location where the ci scripts live
    * update type to system in case yamls
    * move create_experiment.py to workflow/
    * detect HOMEgfs in create_experiment.py based on location.  update to use jinja templates in the cases
    * remove export of HOMEgfs from driver.sh

commit bfea2594207a477ea00e3b7fef95c2d7befd492b
Author: Henry R. Winterbottom <[email protected]>
Date:   Sun Oct 15 23:27:47 2023 -0600

    Remove SENDCOM (#1929)

    This PR addresses issue #1501. All instances of `SENDCOM` gates have been
    removed. The workflow was inconsistent in its use of `SENDCOM` to gate
    movement of files to `COM` and have been removed based on NCO guidelines.

    Resolves #1501.

commit 9a8911a0b30f0367d061facfb3b835480728081d
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri Oct 13 14:21:01 2023 +0000

    update nth_eupd to 8 for Orion because of out of memmory errors (#1927)

    Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>

commit ea4dfa5800b5cb529478cc64d329f567393fa37d
Author: Guillaume Vernieres <[email protected]>
Date:   Thu Oct 12 21:29:19 2023 -0400

    Marine DA configuration updates (#1922)

    Minor updates the configuration related to running the marine DA and the coupled UFS.
    What's proposed in this PR:
    - Memory increased for the marine DA analysis step
    - The coupled UFS is (was?) running out of memory without the changes in `config.ufs`.
    - Updates to the IAU section of MOM_input to allow for a current increment.

commit c2d112b40a926c9f33a653cfbb832cb811a60352
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Oct 12 23:52:43 2023 +0000

    Fix missing pipe in check_ci (#1926)

    Bugfix:  left out pipe to word count` | wc -l` after updating:

    `num_platforms=$(ls ../platforms/config.* | wc -l)` to
    `num_platforms=$(find ../platforms -type f -name "config.*")`

    when it was flagged by the BASH linter.

commit 51d93e15eb30382017aaf72813d34f7010f47948
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Oct 10 19:09:26 2023 +0000

    Updated cron bash ci script to remove weekly CI test PR on success (#1915)

    This PR updates the check CI bash script in cron to remove the PR that is created by
    the weekly CI test driver when all the tests has passed on all the platforms.

    This is done by the script checking if all other labels for all the platforms for the PR
    that has currently been flagged to have run to a successful completion by the check
    ci bash script.

commit 2d64b74a0b0407d01d6f657efa6af9637a131448
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Wed Oct 4 22:33:25 2023 +0000

    CI driver_weekly bugfix deleting new branch if is already on repo (#1899)

    Bugfix and updates to weekly CI test that deletes the new modified branch
    if it is already on the repo but now also makes sure that the intermediary
    branch that creates the PR is coming from emcbot.

commit e4a6c35ae020253f07921ca34a17f19e928b0b6c
Author: Rahul Mahajan <[email protected]>
Date:   Wed Oct 4 09:42:12 2023 -0400

    Fix typo in cice history filename

commit d50938bc4f6705b722338bbea03f925614f953ed
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Oct 3 23:37:39 2023 -0400

    Change metp dependency (#1900)

    MET+ jobs rely on files already having been placed in the local
    archive directory, but the job only depended on post, resulting
    in the job prematurely firing. The dependency is now updated to
    be on the archive job instead.

    Resolves #1756

commit 836642bb201cd2e5e205eda2ae4a28993623355d
Author: Rahul Mahajan <[email protected]>
Date:   Tue Oct 3 14:45:57 2023 -0400

    Use deterministic marine resolutions for ensemble (#1894)

    This PR determines the ensemble resolution for ocean, ice and waves based on the
    deterministic configuration as there is no dual-resolution capability requested for
    these model components.

    For cycled DA, if the deterministic uses a coupled model, the ensemble will also be
    a coupled model.  This can be turned off manually via adding `DO_AERO_ENKF`,
    `DO_OCN_ENKF`, `DO_ICE_ENKF` and `DO_WAVE_ENKF` flags set in `config.base` or
    `config.efcs`.  This is currently handled manually and will be automated when a
    requirement arises for this flexibility.

    Fixes #1730

commit 48ba775909870f0d27275128bd07ec134b92c356
Author: Kate Friedman <[email protected]>
Date:   Mon Oct 2 13:34:02 2023 -0400

    Update vrfy.sh to only run MINMON in cycled mode (#1901)

    Update MINMON if-block in jobs/rocoto/vrfy.sh to only invoke this section when MODE is cycled.

    Refs #1076

commit e65162f3083c34b639854e3216e2355ff6fccc0b
Author: RussTreadon-NOAA <[email protected]>
Date:   Fri Sep 29 19:18:07 2023 -0400

    Update module loads to intel/2022 for jobs running gsi.x and enkf.x (#1882)

    This PR changes the module loads in g-w jobs `anal.sh`, `eobs.sh`, and `eupd.sh`
    to use machine specific modulefiles from `sorc/gsi_enkf.fd/modulefiles`.  This is
    necessary because [NOAA-EMC/GSI#571](https://github.com/NOAA-EMC/GSI/pull/571)
    updated `gsi.x` and `enkf.x` builds to intel/2022 on NOAA RDHPCS machines.

    Resolves #1863

commit cd439d0bf2ae5fb57139fcb9983aa2755fdc9b2c
Author: Rahul Mahajan <[email protected]>
Date:   Fri Sep 29 15:35:54 2023 -0400

    Add coupled forecast-only tests for S2S and S2SW (#1895)

    This PR:
    - replaces the PR C48 S2S forecast-only test with a S2SW configuration
    - adds a weekly C384 S2SWA forecast-only test.

    The C384 S2SWA is a weekly test and will not be triggered/tested in this PR, but will
    be tested on Friday.  See notes on Orion below in the testing section.

    @JessicaMeixner-NOAA kindly provided the details in
    https://github.com/NOAA-EMC/global-workflow/issues/1794#issuecomment-1740768751

commit 02787fe9ba9e5a6881e5ccf9a9e352545eeadb9d
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri Sep 29 18:03:23 2023 +0000

    Ci rename platform scripts (#1896)

    Simply renaming the platform config files in ${HOMEgfs}/ci/platforms to
    config.${MACHINE} so wxflow can read them too in support of up and
    coming functional testing.

commit bb5a58541d6514d16901dca240dfbbc810bd31c8
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Sep 29 13:28:39 2023 -0400

    Merge S2S defaults config back into other configs (#1876)

    When the prototype S2S was first added, we placed some settings in
    a `config.defaults.s2sw` file to avoid interference with existing
    settings. Now that we are moving towards v17 and run S2S regularly,
    it is time to merge these settings back into the other config files.

    The wave output frequency settings are updated to the coarser fre-
    quency as that is more suitable for development. The prior (ops)
    settings are noted as comments.

    There are a couple of settings that control ice fields within FV3.
    These are placed in `config.ice`, so when the ice model is on those
    settings are still used.

    Changes the output frequency from 3 to 6. While we may leave this
    setting as the default for development, it is required right now
    because the ocean frequency is hard-coded to 6 but links are created
    based on `$FHOUT_GFS`. Resolving #1629 should correct this limitation.

    "Gaussian" archive is updated to the former override values.

    Resolves #1606
    Refs #1629

commit 49dc315c1ef6c5f4952a06b0ba70c36e771f128e
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Sep 29 13:25:58 2023 -0400

    Move product functions to separate script (#1891)

    PR #1822 converted some formerly stand-alone scripts and moved them
    inside one of the standard product scripts. However, `trim_rh.sh`
    is also used by gempak and AWIPS, so this change caused those jobs
    to start failing (they are not yet tested by CI).

    Those functions have now been moved into a separate product functions
    script that can be sourced by all the scripts that need the functions.
    A third similar script was also eliminated and converted into a
    function.

    Additionally fixes a base bug in AWIPS and updates some scripts to
    satisfy (or at least mostly satisfy) the linter.

    **AWIPS still failing when creating GRIB1 products.** That will be addressed
    in a future PR (and may need a subject-matter expert).

    Resolves #1890

commit 3e750d10be577106fb269a78e18765b8d2b8030d
Author: Rahul Mahajan <[email protected]>
Date:   Thu Sep 28 16:21:52 2023 -0400

    Fix a few bugs reported by devs (#1893)

    This PR fixes a …
@JessicaMeixner-NOAA
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@aerorahul I wanted to check in on this issue. @jiandewang ran some scout runs with what is now the develop branch with the unstructured grid in prep for HR3. We like to have 3 hourly output for atm model and that meant we manually made updates to run with 6 hours in the diag table with the updates in #2286 our previous work around no longer works. There's likely another simple work around that we can use to move forward, but before investigating that I thought I'd talk to you first about the longer term fix.

@JessicaMeixner-NOAA
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So it looks like we could hard code FHOUT to 6 here: https://github.com/NOAA-EMC/global-workflow/blob/develop/ush/forecast_predet.sh#L250 but then the post jobs are still thinking it's 3 hours if we change FHOUT. So I'm looking for where that's set to see if that could also be temporarily hard coded to 6 for us to run HR3. -- I looked for your branches @aerorahul that you had pointed me to before but they no longer exist.

aerorahul pushed a commit that referenced this issue Feb 21, 2024
This adds functionality to have ocean/ice output frequency be separate from the atm model. One time was created because there's an assumption in the post that these are the same. This could be further modified to remove this assumption.

Refs #1629
@JessicaMeixner-NOAA
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I did not say that PR @2327 closed this issue because of GEFS, but in hindsight with @WalterKolczynski-NOAA updates I think we might be able to close this issue. @aerorahul thoughts?

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@JessicaMeixner-NOAA
I am fine with closing this issue if the solution in #2327 meets the requirements.
We can re-open or open another one if further enhancements are required.

@JessicaMeixner-NOAA
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We meet the acceptance criteria. Closing!

kayeekayee added a commit to kayeekayee/global-workflow that referenced this issue Mar 1, 2024
commit d1e8f33
Merge: e2d88dd 5166593
Author: kayee.wong <[email protected]>
Date:   Fri Mar 1 00:01:58 2024 +0000

    Merge remote-tracking branch 'emcgw/develop' into develop

    remote: https://github.com/NOAA-EMC/global-workflow.git develop (Feb 29, commit 5166593)
    origin: https://github.com/kayeekayee/global-workflow.git gsl_ufs_dev (Feb 29,commit e0c3e4d)

commit 5166593
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Feb 29 20:14:41 2024 +0000

    Move Jenkinsfile into ci subdirectory (NOAA-EMC#2355)

    Just moves the Jenkinsfile into the ci directory

    Co-authored-by: tmcguinness <[email protected]>

commit b7af315
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Feb 28 22:20:58 2024 +0000

    Fix rocoto forecast hour determination for GEFS (NOAA-EMC#2351)

    The function that generates the list of forecast hours for rocoto was
    trying to use variables that are not defined for GEFS, causing workflow
    generation to fail. The function is updated to not try to load these
    variables before loading the ones actually used for GFS/ GEFS.

    Also turns GEFS CI test back on and adds an entry to stage C192 ICs
    (note: these have not been placed in the centralized location.)

commit d3a4927
Author: Cory Martin <[email protected]>
Date:   Wed Feb 28 09:38:49 2024 -0500

    Rename the land DA jobs to snow DA to better reflect what they are doing (NOAA-EMC#2330)

    This PR renames all of the land DA jobs to snow DA to better reflect
    that this is a JEDI-based snow analysis capability and not a more
    generic land surface analysis.

commit 2693810
Author: Jessica Meixner <[email protected]>
Date:   Tue Feb 27 01:25:51 2024 -0500

    Update ufs-waether-model hash (NOAA-EMC#2338)

    Routine update of ufs-weather-model hash.

    Other small updates:
    * removes comment referencing closed issue.
    * Updates the CICE diag frequency to once per day as recommend here:
    NOAA-EMC#1810 (comment)
    * Updated amount of time for C384 gdas forecast as it was running out of
    time
    * Removed unused variable wave_sys_ver

commit 9608852
Author: RussTreadon-NOAA <[email protected]>
Date:   Mon Feb 26 14:10:01 2024 -0500

    Update JEDI ATM to use .nc for obs and generalize x,y layout (NOAA-EMC#2336)

    # Description
    The changes in this PR are twofold
    1. replace `.nc4` suffix for JEDI ATM observation related files with
    `.nc`
    2. use templated variables to specify `{layout_x, layout_y}` for JEDI
    ATM variational and local ensemble apps

    The first change conforms with the Unidata recommendation that netCDF
    files end with the suffix `.nc`. The second change replaces hardwired
    JEDI ATM var and ens `{layout_x, layout_y}` in `config.resources` with a
    more flexible approach.

    Resolves NOAA-EMC#2335

commit c5c8466
Author: Kate Friedman <[email protected]>
Date:   Mon Feb 26 10:18:50 2024 -0500

    Remove FIX* variables for fix subfolders (NOAA-EMC#2337)

    Remove `FIX*` variables for fix subfolders and replace them with the remaining `FIXgfs` variable and the subfolder name (e.g. `${FIXam}` -> `${FIXgfs}/am`).

    The UFS_UTILS and GDASApp repos were similarly updated. This PR includes a new UFS_UTILS hash.
    The updated GDASAPP hash was already committed within the spack-stack/1.6.0 PR NOAA-EMC#2239.

    Resolves NOAA-EMC#2184

commit 950c38a
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri Feb 23 21:15:46 2024 +0000

    Fix several Jenkins issues (NOAA-EMC#2334)

    Jenkins Updates Resolving final kinks:
    - Removed all `git` shell commands and now exclusively use Software Control
    Manger (**scm**) plugin.
    - Add feature for skipping hosts per configuration specified in case yaml files.
    - Solved and tested false positive builds and experiments.
    - Tested archiving of task error log on case fail
    - First case fail quits pipeline and cancels all pending scheduled jobs
    - Duel build per yaml configuration arguments supported
    - All designated case files in PR directory pass on intended host (fully tested
    on Hera)

    Remaining updates:
    - Fist build fail short circuit when building sub-modules and archiving build
    error log.
    - Re-build/no-build built in logic for Replay and Rerunning previously failed
    experiments.

commit c67393a
Merge: 6f9afff 79d305e
Author: David Huber <[email protected]>
Date:   Fri Feb 23 14:18:15 2024 +0000

    Merge pull request NOAA-EMC#2239 from DavidHuber-NOAA/ss160

    Update to spack-stack 1.6.0

    Includes all submodules except the UFS, which will be updated at a later time.

commit 79d305e
Author: David Huber <[email protected]>
Date:   Thu Feb 22 14:53:57 2024 -0600

    Disable snow DA tests

commit 0459203
Author: David Huber <[email protected]>
Date:   Thu Feb 22 12:55:51 2024 -0600

    Update GDASApp hash to current develop

commit 5c96eb2
Author: David Huber <[email protected]>
Date:   Thu Feb 22 12:37:47 2024 -0600

    Update GDAS hash to allow modified snow DA analysis

commit 79144f2
Merge: abbb0b8 6f9afff
Author: DavidHuber <[email protected]>
Date:   Thu Feb 22 15:14:39 2024 +0000

    Merge remote-tracking branch 'origin/develop' into ss160

commit abbb0b8
Merge: 4ad837e 4529e8c
Author: DavidHuber <[email protected]>
Date:   Thu Feb 22 15:11:03 2024 +0000

    Merge remote-tracking branch 'henry/feature/gwdev_issue_2129' into ss160

commit 4ad837e
Merge: 516b2a2 7ca45db
Author: DavidHuber <[email protected]>
Date:   Thu Feb 22 15:10:24 2024 +0000

    Merge remote-tracking branch 'henry/feature/gfsv17_issue_2125' into ss160

commit 516b2a2
Author: DavidHuber <[email protected]>
Date:   Thu Feb 22 14:19:16 2024 +0000

    Updated GDAS to include rocoto/1.3.6 on Hera.

commit 6f9afff
Author: Jessica Meixner <[email protected]>
Date:   Wed Feb 21 13:09:44 2024 -0500

    Add some flexibility for ocean/ice output (NOAA-EMC#2327)

    This adds functionality to have ocean/ice output frequency be separate from the atm model. One time was created because there's an assumption in the post that these are the same. This could be further modified to remove this assumption.

    Refs NOAA-EMC#1629

commit e2d88dd
Merge: 3e6b1e2 a23b7f2
Author: Janet Derrico <[email protected]>
Date:   Tue Feb 20 16:08:46 2024 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit f6d3015
Author: David Huber <[email protected]>
Date:   Tue Feb 20 09:53:08 2024 -0600

    Update GDASApp hash to include SS/1.6.0 support.

commit 0bf340b
Author: David Huber <[email protected]>
Date:   Tue Feb 20 09:07:32 2024 -0600

    Construct SS paths from version variables.

commit 3330cd7
Author: David Huber <[email protected]>
Date:   Tue Feb 20 09:06:19 2024 -0600

    Removed MET/METplus 'not available' comments

commit fdc638c
Author: David Huber <[email protected]>
Date:   Tue Feb 20 08:35:15 2024 -0600

    Move SS module path to version files.

commit d7d28a6
Author: David Huber <[email protected]>
Date:   Tue Feb 20 07:53:15 2024 -0600

    Update comment about METplus support.

commit a812f88
Author: David Huber <[email protected]>
Date:   Tue Feb 20 07:45:45 2024 -0600

    Update verif-global to latest WCOSS2 support.

commit d81f07f
Author: David Huber <[email protected]>
Date:   Tue Feb 20 07:41:38 2024 -0600

    Clean up build_upp.sh.

    -Corrected whitespace (tabs instead of spaces)
    -Removed debug print statement
    -Alphebetized flags

commit ae7eb19
Author: David Huber <[email protected]>
Date:   Fri Feb 16 16:15:40 2024 -0500

    Fix whitespace in build_upp.sh.

    Co-authored-by: Rahul Mahajan <[email protected]>

commit 48b34d0
Author: David Huber <[email protected]>
Date:   Fri Feb 16 20:56:55 2024 +0000

    Added verif-global support back to WCOSS2.

commit 4529e8c
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Fri Feb 16 11:12:01 2024 -0700

    Bug fix.

commit 8e4f94d
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Fri Feb 16 11:04:41 2024 -0700

    Updates requested by reviewer Rahul Mahajan.

commit 4624ce2
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Fri Feb 16 10:52:11 2024 -0700

    Updates requested by reviewer; testing -- DO NOT REVIEW.

commit ed25bbd
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Fri Feb 16 09:33:59 2024 -0700

    Linter corrections.

commit 6a0b7bf
Merge: f9fb64e 2415b7b
Author: David Huber <[email protected]>
Date:   Fri Feb 16 09:50:22 2024 -0600

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit f9fb64e
Merge: 777d97d a23b7f2
Author: David Huber <[email protected]>
Date:   Fri Feb 16 09:49:42 2024 -0600

    Merge remote-tracking branch 'emc/develop' into ss160

commit 7ca45db
Merge: 73bc76b a23b7f2
Author: Henry R. Winterbottom <[email protected]>
Date:   Fri Feb 16 07:46:35 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125

commit eb2ed53
Merge: 9929277 a23b7f2
Author: Henry R. Winterbottom <[email protected]>
Date:   Fri Feb 16 07:46:24 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129

commit a23b7f2
Author: RussTreadon-NOAA <[email protected]>
Date:   Fri Feb 16 09:37:58 2024 -0500

    Add JEDI 3DEnVar atmosphere only CI test stub (NOAA-EMC#2309)

commit cf83885
Author: Jessica Meixner <[email protected]>
Date:   Fri Feb 16 01:55:02 2024 -0500

    Add unstructured grid for HR3/GFS (NOAA-EMC#2230)

    This adds the capability to use unstructured grids in the global workflow,
    which will be used in HR3.  There are new fix files for a low-resolution
    100km grid and a grid closer to our targeted GFSv17 grid which has the
    resolution combined from the older multi_1 and GFSv16 grids.

    The fix file update is here: NOAA-EMC#2229

    Note: This now means that GFS tests need a new build option:
    `./build_all.sh -w` So that PDLIB=ON is turned on for compiling relevant
    UFS and WW3 codes.

    Resolves NOAA-EMC#1547

commit 9929277
Merge: eb8791c 094e3b8
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Feb 15 15:05:50 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129

commit 094e3b8
Author: Cory Martin <[email protected]>
Date:   Thu Feb 15 14:43:55 2024 -0500

    Move IMS remapping files from COM_OBS to FIXgdas (NOAA-EMC#2322)

    * Add in IMS obs fix directory and update submodule for gdas

commit d465ea0
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Feb 15 19:25:02 2024 +0000

    Set HOMEgfs for module_setup in CI driver (NOAA-EMC#2321)

    Hotfixes to  CI Bash system from updates with sourcing
    `detect_machine.sh` in `ush/module-setup.sh` using **HOMEgfs**.

commit 2415b7b
Author: David Huber <[email protected]>
Date:   Thu Feb 15 19:21:17 2024 +0000

    Load default rocoto on Jet.

commit eb8791c
Merge: 60d5ee6 638684e
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Feb 15 11:56:40 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129

commit 777d97d
Author: David Huber <[email protected]>
Date:   Thu Feb 15 12:34:59 2024 -0600

    Fixed Orion cdo version.

commit ef07235
Author: DavidHuber <[email protected]>
Date:   Thu Feb 15 16:29:32 2024 +0000

    Revert UFS hash.

commit 0ce8c0d
Author: DavidHuber <[email protected]>
Date:   Thu Feb 15 14:55:48 2024 +0000

    Fix git version in Hera's gwsetup module.

commit 3080a34
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 20:52:34 2024 +0000

    Fixed xarray version for SS/1.6.0.

commit 49392dd
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 20:29:41 2024 +0000

    Updated GSI-Utils hash to head of develop.

commit c3553f0
Merge: 4568653 638684e
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 20:28:14 2024 +0000

    Merge remote-tracking branch 'origin/develop' into ss160

commit 4568653
Author: David Huber <[email protected]>
Date:   Wed Feb 14 14:22:13 2024 -0600

    Reupgrade Hercules to SS/1.6.0

commit 638684e
Author: Kate Friedman <[email protected]>
Date:   Wed Feb 14 14:55:21 2024 -0500

    Remove `finddate.sh` from system (NOAA-EMC#2308)

    * Retire finddate.sh usage from system
    * Update gfs-utils hash to 7a84c88 - New hash includes removal of finddate.sh

    Refs NOAA-EMC#2279

commit 2b160f8
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 18:31:28 2024 +0000

    Reenable METplus jobs on Hercules.

commit 8f59002
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 18:30:23 2024 +0000

    Update GSI hashes.

commit 73bc76b
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 14 09:27:37 2024 -0700

    Updates based on user request.

commit e4bc674
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 14 08:03:45 2024 -0700

    Corrected based on reviewer review.

commit 60d5ee6
Merge: 40f2cf6 1aaef05
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Feb 13 18:08:33 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129

commit 0330411
Merge: 929b903 1aaef05
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Feb 13 17:58:12 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125

commit 1aaef05
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Feb 13 18:15:59 2024 -0500

    Jenkins Pipeline updates for Canceling Jobs (NOAA-EMC#2307)

    Tuning updates for Jenkins Pipeline :
    - Added short circuit for all parallel runs of cases on error of any
    - Fixed canceling of all scheduled jobs on first case error
    - Added feature to save error log files to Jenkins Archive facility on fail

commit 6404892
Author: Rahul Mahajan <[email protected]>
Date:   Tue Feb 13 14:57:37 2024 -0500

    Ocean/ice product generation for GFS and GEFS (NOAA-EMC#2286)

    This PR does several things:
    1. the model output for ocean and ice in the `COM/` directory are now
        named per EE2 convention for coupled model.
        E.g `gfs.ocean.t12z.6hr_avg.f120.nc` and `gfs.ocean.t12z.daily.f120.nc`
    2. The products are generated using the `ocnicepost.fd` utility developed
        by @DeniseWorthen in https://github.com/NOAA-EMC/gfs-utils and
        converted to grib2 using example scripts provided by @GwenChen-NOAA
        using `wgrib2`.
    3. NetCDF products on the native grid are also generated by subsetting
        variables from  the raw model output.  This is done with `xarray`.
    4. updates the hash of https://github.com/NOAA-EMC/gfs-utils to include
        fixes in `ocnicepost.fd`
    5. removes NCL related scripting that was previously used for ocean/ice
        interpolation and `reg2grb2` used for converting to grib2.
    6. updates archive scripts to accommodate updated file names
    7. removes intermediate ocean processed files such as 2D/3D/xsect data-
        sets
    8. separate jobs are added for ocean and ice product generation.
    9. removes intermediate restarts for the mediator and only saves the medi-
        ator restart at the end of the forecast in `COM`.
    10. Increases memory for offline UPP when run at C768.  The program
          segfaults with an OOM when memory is self allocated based on PEs by
          the scheduler on Hera.
    11. Enables ocean/ice ensemble product generation for GEFS
    12. Some minor clean-ups

    Fixes NOAA-EMC#935
    Fixes NOAA-EMC#1317
    Fixes NOAA-EMC#1864

commit 40f2cf6
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Tue Feb 13 10:18:53 2024 -0700

    Implemented ush/detect_machine.sh for host determination and removed redundant checks for expected file paths.

commit 929b903
Merge: 2d08d01 3f99f70
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Feb 13 08:31:06 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125

commit 3f99f70
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Feb 13 00:57:18 2024 -0500

    Add wave post jobs to GEFS (NOAA-EMC#2292)

    Adds the wave post jobs for gridded and points to GEFS. Boundary
    point jobs are added even though the current GEFS buoy file does
    not contain any (tested by manually subbing in the GFS buoy file).

    Resolves NOAA-EMC#827

commit 842adf3
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Feb 12 12:50:08 2024 -0500

    Added additional test cases to the pr list in Jenkins (NOAA-EMC#2306)

    C48mx500_3DVarAOWCDA, C96C48_hybatmDA, and C96_atmsnowDA
    Co-authored-by: terrance.mcguinness <[email protected]>

commit bb4ca65
Author: CatherineThomas-NOAA <[email protected]>
Date:   Mon Feb 12 14:50:41 2024 +0000

    Redo v16.3 config.base changes for DA increments (NOAA-EMC#2304)

    Include the additional hydrometeors to the
    INCREMENTS_TO_ZERO and INCVARS_ZERO_STRAT
    variables in config.base that were modified
    in v16.3.

    Resolves: NOAA-EMC#2303

commit 061992b
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Sat Feb 10 01:33:36 2024 -0500

    Fix Jenkins success reporting (NOAA-EMC#2302)

    Moving the post section back outside of main Run Experiments
    stage. This allows the system to correctly report the **Success**
    status until after all tests pass.

    _Had originally moved them in attempts to solve "Not an SCM
    GitHub Job" issue and cause the reporting to misbehave._

    Also ran through Jenkins linter and updated some messaging
    that was incorrectly reporting system build type.

commit 28ccf78
Merge: b972f66 54daa31
Author: David Huber <[email protected]>
Date:   Fri Feb 9 14:00:43 2024 -0600

    Merge remote-tracking branch 'emc/develop' into ss160

commit b972f66
Author: David Huber <[email protected]>
Date:   Fri Feb 9 10:47:00 2024 -0600

    Fix SS versions for CI modules.

commit 4b01d8e
Author: David Huber <[email protected]>
Date:   Fri Feb 9 10:44:30 2024 -0600

    Revert Hercules modules to SS/1.5.1.

commit 54daa31
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Feb 8 15:48:38 2024 -0500

    Jenkins Declartive Pipeline for CI with gfs/gefs multibuilds (NOAA-EMC#2246)

    Adding top level Jenkins file for CI tests running on Jenkins Controller:

    - Declarative Multi-branch Pipeline (has enhanced restart capabilities
    on a per section bases)
    - Starts Pipeline from Label PR same as BASH system (for now)
    - Progress and restarts can me managed with CAC Login at [EPIC OAR
    Jenkins](https://jenkins.epic.oarcloud.noaa.gov)
    - Has logic for multi **gfs/gefs** system builds (arguments based on a
    configuration file `ci/casts/yamls/build.yaml`)
      - Any number of **systems** may be added by manual adding an ele-
    ment to the matrix in the Jenkinsfile
      - _It may be possible to dynamic add matrix values with a specialty
    plug-in_
    - Currently only runs on **Orion** and **Hera** using `mterry` account

    Resolves NOAA-EMC#2119
    Resolves NOAA-EMC#2118

commit 43429e2
Author: Rahul Mahajan <[email protected]>
Date:   Thu Feb 8 15:30:28 2024 -0500

    Enable AO WCDA test (NOAA-EMC#1963)

    This PR:
    - adds GSI + SOCA C48 5-deg ocean 3DVar test (courtesy @guillaumevernieres)
    - adds a toggle to optionally disable ocnanalvrfy job.

commit 2d08d01
Merge: 4745d4a f563528
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Feb 8 07:24:54 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125

commit f563528
Author: Kate Friedman <[email protected]>
Date:   Wed Feb 7 15:09:12 2024 -0500

    Update JGLOBAL_FORECAST for octal error (NOAA-EMC#2295)

    Add "10#" to ENSMEM value > 0 check to handle octal errors.

commit 4745d4a
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 7 08:45:49 2024 -0700

    Removed jlogfile references.

commit 5894ca2
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 7 08:32:16 2024 -0700

    Removed dummy variable passed to perl scripts.

commit dae884a
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 7 08:29:49 2024 -0700

    Removed jlogfile and postmsg references within gempak scripts.

commit 801058f
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Feb 7 00:41:59 2024 -0700

    Consolidate `npe_node_max` (NOAA-EMC#2289)

    - The environment variable `npe_node_max` is removed from all
    files beneath `global-workflow/env`;
    - The environment variable `npe_node_max` is removed from
    `parm/config/gefs/config.ufs` and `parm/config/gfs/config.ufs`;
    - The environment variable `npe_node_max` is maintained only
    within `parm/config/gefs/config.resources` and
    `parm/config/gfs/config.resources`.

    Resolves NOAA-EMC#2133

commit b0325e0
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Feb 7 00:40:20 2024 -0700

    Removes files module loading file no longer used by the GW (NOAA-EMC#2281)

    Removes `module-setup.csh.inc` and `module-setup.sh.inc`.

    The module `ush/module-setup.sh` is updated such that it now sources
    `ush/detect_machine.sh` to determine which supported platform the
    global-workflow is being execute on.

    Resolves NOAA-EMC#2130

commit 3e6b1e2
Merge: f4c8e00 1ccc989
Author: Janet Derrico <[email protected]>
Date:   Tue Feb 6 10:43:55 2024 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit 1ccc989
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Feb 5 14:16:07 2024 -0500

    Remove EnKF forecast groups (NOAA-EMC#2280)

    Removes the grouping of EnKF forecasts so each job only runs
    one forecast. Member and MEMDIR are now set at the workflow
    manager (rocoto) level. This change makes much of the system
    simpler (especially dependencies) and allows the elimination of
    the separate efcs scripts.

    Metatask names of updated jobs have been updated to make
    them a little less opaque by using the same name name as its
    constituent tasks (e.g. the forecast metatask is named
    `enkgdasfcst`, not `enkfgdasefcs`). Metatasks that weren't
    updated retain the same names as before for now.

    Resolves NOAA-EMC#2254

commit 9f3383f
Author: Henry R. Winterbottom <[email protected]>
Date:   Mon Feb 5 12:15:13 2024 -0700

    Updated detect_machine.sh using that from UFS WM. (NOAA-EMC#2252)

    Updates `ush/detect_machine.sh` to match the UFS weather-model
    `tests/detect_machine.sh` prepared by @BrianCurtis-NOAA

    Resolves NOAA-EMC#2228

commit 7d68b0b
Author: CatherineThomas-NOAA <[email protected]>
Date:   Sun Feb 4 22:02:41 2024 +0000

    Update global_cycle for fractional grid (NOAA-EMC#2262)

    The hash for ufs_utils is updated to include the changes for
    fractional grid support within global_cycle.  This commit also
    removes the hack to skip global_cycle in cycling mode with
    v17 physics.

    Resolves: NOAA-EMC#1775
    Refs: ufs-community/UFS_UTILS#815
    Refs: ufs-community/UFS_UTILS#891

commit ed592a6
Author: Kate Friedman <[email protected]>
Date:   Sat Feb 3 02:55:14 2024 -0500

    Retire cycle-specific FHMAX_GFS variables (NOAA-EMC#2278)

    This PR retires the `FHMAX_GFS_${cyc}` variables that allowed users to specify
    different gfs forecast lengths for each cycle. This function is no longer supported
    in global-workflow. The `FHMAX_GFS_*` variables will be removed and will no
    longer be checked to set the final `FHMAX_GFS` variable. The same forecast
    length will be set for every cycle.

    This PR also includes a small fix to add new post parm files into the `.gitignore`
    file. This was intended to be included in a different PR but that PR is on hold for
    further testing so it is being included here to get it into `develop` sooner.

    Resolves NOAA-EMC#2218

commit 977e2d6
Author: Henry R. Winterbottom <[email protected]>
Date:   Fri Feb 2 07:49:09 2024 -0700

    New GDASApp hash. (NOAA-EMC#2285)

commit b5f2bd9
Merge: 4d66742 0400e1f
Author: David Huber <[email protected]>
Date:   Tue Jan 30 13:55:00 2024 -0600

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit 0400e1f
Author: David Huber <[email protected]>
Date:   Tue Jan 30 09:57:11 2024 -0600

    Fix gfs_utils Orion spack-stack env path.

commit 6bbe823
Author: DWesl <[email protected]>
Date:   Mon Jan 29 21:15:30 2024 -0500

    Use seq to generate the list of times, instead of a bash for-loop (NOAA-EMC#2264)

    I'm running a year-long forecast, which means I get a large portion of the log file dedicated to these loops.

    `seq ${START} ${STEP} ${STOP}` will generate a sequence going from START to STOP by STEP, including STOP if relevant.  That seems to be the purpose of these loops.  It will by default separate the list with newlines, but `seq -s ' ' ${START} ${STEP} ${STOP}` will separate them with spaces instead, more closely mimicing the previous behavior.

    I would like this to be two lines in the log, rather than a few hundred, and this may also be faster, though probably more for reasons of fewer writes to disk than because bash isn't designed for arithmetic.

commit f4c8e00
Merge: 61975cf d5bee38
Author: Janet Derrico <[email protected]>
Date:   Mon Jan 29 15:38:56 2024 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit d5bee38
Author: Kate Friedman <[email protected]>
Date:   Mon Jan 29 14:35:02 2024 -0500

    Correct typos in GFS config.resources (NOAA-EMC#2267)

    This PR corrects some typos in `parm/config/gfs/config.resources` that were
    introduced in PR NOAA-EMC#2216. The esfc job was failing in tests on WCOSS2 due to
    insufficient memory. This lead to discovering the other typos. The esfc job
    completes without error after its memory is set back to `80GB` from the
    incorrect `8GB`.

    Resolves NOAA-EMC#2266

commit 81557be
Author: David Huber <[email protected]>
Date:   Mon Jan 29 12:13:31 2024 -0600

    Update monitor hash to noaa-emc with SS/1.6.0 support.

commit 2238dd6
Author: DavidHuber <[email protected]>
Date:   Mon Jan 29 13:21:30 2024 +0000

    Update Orion, Hercules, S4 modulefiles.

commit 6ffd94f
Author: DavidHuber <[email protected]>
Date:   Fri Jan 26 16:01:23 2024 +0000

    Update GDAS hash to include SS/1.6.0 support.

commit be11f85
Merge: 56b9680 04e0772
Author: DavidHuber <[email protected]>
Date:   Fri Jan 26 15:34:24 2024 +0000

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit 8ff3448
Author: Rahul Mahajan <[email protected]>
Date:   Fri Jan 26 10:12:18 2024 -0500

    Add a yaml for snow DA testing. (NOAA-EMC#2199)

    - adds a new test yaml C96_atmsnowDA.yaml for 3DVar atmosphere with GSI and Land (Snow) DA with JEDI
    - moves a few yamls from platforms/ to yamls/
    - adds ability to overwrite a previously created experiment as an addition to user input.
    ---------

    Co-authored-by: Cory Martin <[email protected]>

commit 04e0772
Author: David Huber <[email protected]>
Date:   Fri Jan 26 07:16:25 2024 -0600

    Update ufs_utils hash for spack-stack/1.6.0 support.

commit 3d44ff3
Author: Barry Baker <[email protected]>
Date:   Thu Jan 25 14:33:27 2024 -0500

    GOCART ExtData biogenic climatology fix (NOAA-EMC#2253)

    Updates the ExtData for biogenic emissions to be climatology rather than
    for current time.  Fixes an issue which will crash by default for other years.

commit 66f58b8
Author: Guillaume Vernieres <[email protected]>
Date:   Thu Jan 25 13:16:41 2024 -0500

    Added missing container case in gfs/config.resources (NOAA-EMC#2258)

    fixes  NOAA-EMC#2257

commit 553b4f2
Author: WenMeng-NOAA <[email protected]>
Date:   Thu Jan 25 13:00:45 2024 -0500

    Fix post parm links (NOAA-EMC#2243)

    Change symbolic links under parm/post with the latest version of develop branch from UPP repository and enable MERRA2 aerosol fields.

    Resolves NOAA-EMC#2259

commit 4d66742
Merge: 6c05803 afa09e3
Author: David Huber <[email protected]>
Date:   Thu Jan 25 07:49:08 2024 -0600

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit 6c05803
Author: David Huber <[email protected]>
Date:   Thu Jan 25 07:48:42 2024 -0600

    Fix wgrib2/gfs_utils on Hercules.

commit ee6f536
Author: Kate Friedman <[email protected]>
Date:   Thu Jan 25 07:43:13 2024 -0500

    Update GFS version to v16.3.13 in index.rst (NOAA-EMC#2256)

    GFSv16.3.13 WAFS update was implemented

    Refs NOAA-EMC#2013

commit 2445d44
Author: RussTreadon-NOAA <[email protected]>
Date:   Thu Jan 25 06:17:11 2024 -0500

    Simplify and extend load_ufsda_modules to Hercules (NOAA-EMC#2245)

    GDASApp jobs do not run on Hercules because `ush/load_ufsda_modules.sh` does
    not include logic to load the appropriate GDASApp modules on Hercules.  This PR
    extends `load_ufsda_modules.sh` functionality to Hercules, thereby enabling
    GDASApp jobs to run on Hercules.

    Resolves NOAA-EMC#2244

commit 56b9680
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 19:47:34 2024 +0000

    Update hashes (revert WCOSS2 modules).

commit afa09e3
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 18:59:40 2024 +0000

    New (cleaner history) gdas hash.

commit a9eaec2
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 18:52:27 2024 +0000

    Update gdasapp to include ss/1.6.0 support.

commit 5ef8eb2
Merge: 4c46354 e400068
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 17:08:54 2024 +0000

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit 4c46354
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 17:05:12 2024 +0000

    Reenable verif-global support

commit f775755
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 16:59:10 2024 +0000

    Assign fcsthrs for awips_g2 job.

commit e400068
Author: David Huber <[email protected]>
Date:   Mon Jan 22 15:01:07 2024 -0600

    More gsi-addon path fixes.

commit f663d47
Author: David Huber <[email protected]>
Date:   Mon Jan 22 14:41:59 2024 -0600

    Fix gsi-addon paths for hercules, orion, and S4.

commit e304bbe
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:59:34 2024 +0000

    Better optimize build jobs (more ufs jobs).

commit ccc6e2d
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:56:18 2024 +0000

    Reenable verif-global. NOAA-EMC#2195

commit 3ef3411
Merge: 4365f63 f4d187f
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:39:10 2024 +0000

    Merge remote-tracking branch 'origin/develop' into ss160

commit 4365f63
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:37:25 2024 +0000

    Corrected the SS env. name in the version files. NOAA-EMC#2195

commit f4d187f
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Mon Jan 22 12:28:28 2024 -0500

    Converts obsproc to obsprep in prepoceanobs config file (NOAA-EMC#2236)

    Converts obsproc to obsprep in prepoceanobs config file as a compliment to mutually depended GDASApp PR NOAA-EMC/GDASApp#858
    The motivations are explained in refs NOAA-EMC/GDASApp#857

commit 9a09d30
Author: DavidHuber <[email protected]>
Date:   Fri Jan 19 21:23:50 2024 +0000

    Corrected gsi-addon-dev spelling.

commit 21ff645
Author: DavidHuber <[email protected]>
Date:   Fri Jan 19 21:11:34 2024 +0000

    Update modulefiles, submodules to spack-stack 1.6.0. NOAA-EMC#2195

commit d4c55d1
Author: Kate Friedman <[email protected]>
Date:   Fri Jan 19 15:43:37 2024 -0500

    Update typing hint for WCOSS version of python (NOAA-EMC#2238)

    The typing hint `typing.List` was deprecated with python 3.9 in favor
    of using the primitive `list[str]`, but the functional version of python
    on WCOSS2 is <3.9, causing `setup_xml.py` to fail there. This replaces
    `list[str]` as a typing hint with the deprecated form until the supported
    version on WCOSS2 is >=3.9.

commit 61975cf
Merge: 1344313 4919287
Author: Janet Derrico <[email protected]>
Date:   Fri Jan 19 08:38:17 2024 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit 4919287
Author: Barry Baker <[email protected]>
Date:   Thu Jan 18 22:31:27 2024 -0500

    GOCART Emission updates for GEFSv13 and GDAS  (NOAA-EMC#2201)

    This PR addresses several things needed for more recent simulations using
    GOCART2G as well as preparing for the GEFSv13 30 year run.  The main
    updates are:

    - Update CEDS to use monthly emission files instead of daily.  This will
    drastically reduce the number of files needed. No science change
    - Update biogenic MEGAN inputs to use a climatology rather than the
    offline biogenic previously used.  This is needed to deal with simulations
    where the current dataset is not available.
    - Update volcanic SO4 emissions to use degassing emissions only.  This is
    to support the need for more recent simulations where data is not available.

commit 13d25cf
Author: Kate Friedman <[email protected]>
Date:   Thu Jan 18 22:29:43 2024 -0500

    Add `POSTAMBLE_CMD` into preamble postamble (NOAA-EMC#2235)

    This PR adds the ability to run a command at the end of jobs via the
    preamble's postamble function. A new command can be set via
    `POSTAMBLE_CMD` and will be invoked at the end of jobs. Users can
    add the command to the top of an env file to have every job run it or
    it can be placed within a job if-block in the env file to run for just that
    job.

    Resolves NOAA-EMC#1145

commit 7759163
Author: Rahul Mahajan <[email protected]>
Date:   Thu Jan 18 01:13:49 2024 -0500

    Add option to create WGNE atmosphere products (NOAA-EMC#2233)

    Adds option to create WGNE products for the atmosphere.

    Resolves NOAA-EMC#1951
    Resolves NOAA-EMC#2226

commit d95ed85
Author: Rahul Mahajan <[email protected]>
Date:   Wed Jan 17 18:04:56 2024 -0500

    Use ufs.configure, model_configure, MOM_input, data_table, and ice_in templates from UFS-weather-model (NOAA-EMC#2051)

    This PR:
    - links `ufs.configure.*.IN`, `model_configure.IN`, `MOM_input_${OCNRES}.in`,
    `MOM6_data_table.IN`, and `ice_in.IN` from ufs-weather-model into the
    global-workflow `parm/ufs` directory
    - prepares local variables for use in the templates in the respective functions
    for FV3, MOM6, and CICE6
    - uses `atparse.bash` to render these templates into fully formed namelists

    - Work was performed by @DeniseWorthen in the ufs-weather-model to
    templatize several variables that are hard-wired in the ufs-weather-model
    for CICE. See ufs-community/ufs-weather-model/NOAA-EMC#2010

commit 44a66dd
Author: RussTreadon-NOAA <[email protected]>
Date:   Wed Jan 17 13:52:09 2024 -0500

    Update gdas.cd hash to use gsibec tag 1.1.3 (NOAA-EMC#2231) (NOAA-EMC#2234)

commit 9046d97
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Jan 17 10:19:18 2024 -0500

    Add basic atmos products for GEFS and refactor resources (NOAA-EMC#2216)

    * Add basic atmos products for GEFS

    Adds basic atmosphere products for GEFS members (no mean or spread).

    To facilitate the addition of GEFS parameter lists, the existing GFS
    lists are renamed. They are also relocated to `parm/products/` direc
    tory instead of `parm/post/`. GEFS v12 uses different parameter lists
    for different resolutions, but for this implementation, the 0p25 lists
    are used for all resolutions. However, to hedge against the final con-
    figuration, all of the GEFS parameter lists have been added to parm.
    Implementation of different parameter lists for each resolution will
    take additional refactoring of the atmos_products job, as it currently
    assumes all resolutions use the same lists.

    The new GEFS rocoto task is implented as two loops of metatasks (made
    possible by PR NOAA-EMC#2189). The member is set at the rocoto level, so the
    setting in `config.base` had to be updated to accept a pass-through.
    The generation of a forecast hour list is moved up to its own function
    in `rocoto.tasks`, separate from the post groups which are not used.
    This can be used as a model for future metatasks (or refactoring of old
    ones). `rocoto_viewer.py` does function with the nested metatasks,
    though only one level of folding is available and the metatask name
    is that of the lower metatask (though it encompasses the entire outer
    metatask).

    Additionally, the GEFS `config.resources` had diverged from the GFS
    version, which included not having a section for the atm products job.
    This led to the refactoring of the GFS `config.resources`, including
    switching to using a `case` statement instead of sequential `elif`.
    This refactored script was then copied over to GEFS, replacing the old
    one, with all jobs not currently implemented for GEFS removed (except
    wave post, whose inclusion is immenent). New blocks can be copied over
    from GFS as they are added.

    Resolves NOAA-EMC#823

commit fbba174
Author: RussTreadon-NOAA <[email protected]>
Date:   Tue Jan 16 14:05:48 2024 -0500

    Update GDASApp (gdas.cd) hash (NOAA-EMC#2225)

    GDASApp now uses gitsubmodules

commit 1344313
Merge: 4b58891 dddd837
Author: Janet Derrico <[email protected]>
Date:   Tue Jan 16 11:13:59 2024 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit dddd837
Author: Rahul Mahajan <[email protected]>
Date:   Tue Jan 16 12:17:19 2024 -0500

    Fix ocean resolution for the S2SWA test (NOAA-EMC#2223)

commit 83edaf1
Author: David Huber <[email protected]>
Date:   Tue Jan 16 11:07:02 2024 -0500

    Apply fixes to archiving jobs (NOAA-EMC#2221)

    Add checks for potentially missing log/data files and update log names for archiving.

    Missing sflux index files are also added to the products script.

    Resolves NOAA-EMC#2076

commit c590476
Author: Rahul Mahajan <[email protected]>
Date:   Fri Jan 12 19:21:02 2024 -0500

    Update hash to ufs-weather-model. The noahmptable.tbl was reorganized, so update link_workflow.sh to use the same one used in UFSWM RT (NOAA-EMC#2219)

commit c041968
Author: Kate Friedman <[email protected]>
Date:   Fri Jan 12 12:09:35 2024 -0500

    Add ocean resolution to setup_expt invocation and retire/reduce COMROT/ROTDIR usage (NOAA-EMC#2214)

    Two series of updates:

    1) Update setup scripts to now allow users to provide ocean resolution
    2) Housekeeping to retire the `COMROT` variable, replacing it with other variables
    as needed, and reduce the `ROTDIR` variable usage.

    Both updates change options for the workflow setup API.

    Refs NOAA-EMC#2061

commit 997f978
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Fri Jan 12 10:46:36 2024 -0500

    Allow use of ocean obs prep in WCDA cycling and remove R2D2 (NOAA-EMC#2215)

    Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same.
    Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS.
    Replaces the current R2D2 processing.

commit 12a5bb1
Merge: 4cb5802 6492c2d
Author: David Huber <[email protected]>
Date:   Fri Jan 12 09:26:27 2024 -0500

    Merge pull request NOAA-EMC#2217 from DavidHuber-NOAA/update/versions

    Update and clean up version and module files

commit 6492c2d
Author: David Huber <[email protected]>
Date:   Thu Jan 11 11:49:08 2024 -0600

    Update orion module/version files for met/metplus NOAA-EMC#2123

commit 94c9937
Author: DavidHuber <[email protected]>
Date:   Thu Jan 11 17:42:53 2024 +0000

    Comment met/metplus out from Hera modulefile. NOAA-EMC#2123

commit 8c32f8b
Merge: a65e4c6 4cb5802
Author: David Huber <[email protected]>
Date:   Thu Jan 11 11:34:44 2024 -0600

    Merge branch 'develop' of github.com:noaa-emc/global-workflow into develop

commit a65e4c6
Author: David Huber <[email protected]>
Date:   Thu Jan 11 11:34:19 2024 -0600

    Initial update of version/module files NOAA-EMC#2123

commit 4b58891
Merge: a75e73e 4cb5802
Author: Janet Derrico <[email protected]>
Date:   Wed Jan 10 10:15:48 2024 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit 4cb5802
Author: souopgui <[email protected]>
Date:   Wed Jan 10 08:30:22 2024 -0600

    Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh when running MPMD tasks (NOAA-EMC#2212)

    Fix OpenMP over-allocation of resources running MPMD tasks
    Co-authored-by: Innocent Souopgui <[email protected]>

commit b056b53
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Jan 8 17:28:05 2024 -0500

    Add Hercules as valid machine in CI scripts (NOAA-EMC#2207)

    Few updates to CI scripts to include names for hercules that where missed
    the first time.

commit 6574d29
Author: Rahul Mahajan <[email protected]>
Date:   Mon Jan 8 17:25:47 2024 -0500

    Fix invalid GH action and restart file name (NOAA-EMC#2210)

    Resolves a typo that leads to an invalid workflow yaml and fixes the restart filename in restart detection.

    Resolves NOAA-EMC#2205

commit 69605ea
Author: Rahul Mahajan <[email protected]>
Date:   Mon Jan 8 17:00:28 2024 -0500

    Stop attempting to comment link to RTD for non-PRs (NOAA-EMC#2209)

    Adds a check so comments with a link to documentation are only generated
    for PRs.

commit 4e160a8
Author: Rahul Mahajan <[email protected]>
Date:   Mon Jan 8 13:10:15 2024 -0500

    Enable UPP for GOES processing (NOAA-EMC#2203)

    Wnables the creation of special master grib2 files from UPP for
    GOES processing

commit c15875b
Author: David Huber <[email protected]>
Date:   Mon Jan 8 09:56:06 2024 -0500

    Port cycling to Hercules (NOAA-EMC#2196)

    Adds cycled support for Hercules (excluding gsi-monitor).
    Partially resolves NOAA-EMC#1588
    GSI monitoring is disabled on Hercules due to missing Perl modules. That will be enabled in a later PR.

commit ef6827d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Jan 8 09:43:12 2024 -0500

    Refactor rocoto task XML creation (NOAA-EMC#2189)

    Refactors the rocoto task generation to be recursive.
    This will allow nested metatasks to loop over multiple variables, which is needed for GEFS product generation.

    As part of this refactor, there is no longer separate arguments to designate metatasks.
    Instead, task dicts can include a nested 'task_dict' as well as a 'var_dict' containing the variables to loop over.
    The nested task dict can then either have another layer, or be the innermost task.

    To accommodate the new recursive nature, some defaults that were previously defined in create_wf_task() had to be pushed down into the function that creates the innermost task.
    Also, former keywords have been absorbed by the task dict.

    Refs NOAA-EMC#823
    Refs NOAA-EMC#827

commit 2b81cfa
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Jan 8 09:41:03 2024 -0500

    Update fix versions (NOAA-EMC#2198)

    Updates fix versions for a few components:
    - Update cice and mom6 versions to support C96/1p00 marine
    - Update wave to change betamax setting for glo_025 waves

    Resolves NOAA-EMC#2004
    Resolves NOAA-EMC#2107

commit a75e73e
Merge: 5adc47b 9d901db
Author: Janet Derrico <[email protected]>
Date:   Tue Jan 2 12:44:40 2024 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit 5adc47b
Merge: a3ce9db a3c5099
Author: Janet Derrico <[email protected]>
Date:   Tue Dec 26 12:40:08 2023 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit a3ce9db
Merge: 2b1a8e3 a81da33
Author: Janet Derrico <[email protected]>
Date:   Tue Dec 19 09:12:48 2023 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit 2b1a8e3
Merge: 4562dec 9505cb4
Author: Janet Derrico <[email protected]>
Date:   Fri Dec 15 09:50:35 2023 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit 4562dec
Merge: 9f7eeba 29d3417
Author: Janet Derrico <[email protected]>
Date:   Mon Dec 11 12:10:25 2023 -0700

    Merge pull request NOAA-GSL#34 from NOAA-EMC/develop

    Sync develop branch with EMC develop
kayeekayee added a commit to kayeekayee/global-workflow that referenced this issue Mar 15, 2024
   UFS: 21Feb24, 6988662
   FV3: 14Feb24, 0fe9ba3
   UPP: 23Jan23, 945cb2c
   UFS_UTILS: 22Feb24, d805336

Squashed commit of the following:

commit 732a874
Author: Rahul Mahajan <[email protected]>
Date:   Mon Mar 4 16:04:26 2024 -0500

    Reformat snowDA templates to jinja2 (NOAA-EMC#2371)

    # Description
    This PR:
    - replaces use of non-jinja2 templates in the yaml templates.
    Specifically `$( )` in favor of pure jinja2.
    - uses jinja2's built-in capability to include templates within
    templates, thereby allowing to assemble a completely rendered template
    before passing it to for e.g. yaml loader.
    - requires updates to `wxflow` and `gdasapp`
    - Changes in `wxflow` in `parse_j2yaml` are **not** backwards compatible

    Additionally, this PR:
    - renames `config.base.emc.dyn` to `config.base`.  Resolves NOAA-EMC#2347

commit d1fa411
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Sat Mar 2 04:54:26 2024 +0000

    Reduce Jenkins messaging to GitHub (NOAA-EMC#2370)

    This PR updates the Jenkins Pipeline code with safeguards against the
    errors caused when Jenkins fails to authenticate with GitHub to message
    or update a label. This was achieved simply by:

    - Reducing the number out messages sent to the GitHub PR
    - Putting try blocks around most of the update label calls

    Co-authored-by: tmcguinness <[email protected]>

commit 52fa3cb
Author: Henry R. Winterbottom <[email protected]>
Date:   Fri Mar 1 12:36:27 2024 -0700

    Adding debug option for all build scripts (NOAA-EMC#2326)

    This PR addresses issue NOAA-EMC#300 that allows building in `debug` mode.
    Co-authored-by: David Huber <[email protected]>
    Co-authored-by: Rahul Mahajan <[email protected]>

commit 91738cb
Author: DWesl <[email protected]>
Date:   Fri Mar 1 13:46:42 2024 -0500

    Sort list of coupler restart files for restart time determination (NOAA-EMC#2360)

    The loop in the following conditional seems to assume the list is
    sorted, so make that explicit in the array construction.

commit 23c2552
Author: Neil Barton <[email protected]>
Date:   Fri Mar 1 13:45:39 2024 -0500

    Update stage IC to handle ocean perturbations (NOAA-EMC#2364)

    This PR adds the option to stage ocean perturbation files for ensemble
    forecasts. These perturbation files are used in GEFS forecasts.
    A new variable is introduced in config.base to use the ocean
    perturbation files.
    This PR does not include using these perturbation files. A future PR
    will address this.

commit 8efe05f
Author: Jessica Meixner <[email protected]>
Date:   Fri Mar 1 07:41:56 2024 -0500

    Turn on C48mx500_3DVarAOWCDA test on hera (NOAA-EMC#2363)

    This PR activates the C48mx500_3DVarAOWCDA test on hera. This required
    an update of the gdas app.

commit 5166593
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Feb 29 20:14:41 2024 +0000

    Move Jenkinsfile into ci subdirectory (NOAA-EMC#2355)

    Just moves the Jenkinsfile into the ci directory

    Co-authored-by: tmcguinness <[email protected]>

commit b7af315
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Feb 28 22:20:58 2024 +0000

    Fix rocoto forecast hour determination for GEFS (NOAA-EMC#2351)

    The function that generates the list of forecast hours for rocoto was
    trying to use variables that are not defined for GEFS, causing workflow
    generation to fail. The function is updated to not try to load these
    variables before loading the ones actually used for GFS/ GEFS.

    Also turns GEFS CI test back on and adds an entry to stage C192 ICs
    (note: these have not been placed in the centralized location.)

commit d3a4927
Author: Cory Martin <[email protected]>
Date:   Wed Feb 28 09:38:49 2024 -0500

    Rename the land DA jobs to snow DA to better reflect what they are doing (NOAA-EMC#2330)

    This PR renames all of the land DA jobs to snow DA to better reflect
    that this is a JEDI-based snow analysis capability and not a more
    generic land surface analysis.

commit 2693810
Author: Jessica Meixner <[email protected]>
Date:   Tue Feb 27 01:25:51 2024 -0500

    Update ufs-waether-model hash (NOAA-EMC#2338)

    Routine update of ufs-weather-model hash.

    Other small updates:
    * removes comment referencing closed issue.
    * Updates the CICE diag frequency to once per day as recommend here:
    NOAA-EMC#1810 (comment)
    * Updated amount of time for C384 gdas forecast as it was running out of
    time
    * Removed unused variable wave_sys_ver

commit 9608852
Author: RussTreadon-NOAA <[email protected]>
Date:   Mon Feb 26 14:10:01 2024 -0500

    Update JEDI ATM to use .nc for obs and generalize x,y layout (NOAA-EMC#2336)

    # Description
    The changes in this PR are twofold
    1. replace `.nc4` suffix for JEDI ATM observation related files with
    `.nc`
    2. use templated variables to specify `{layout_x, layout_y}` for JEDI
    ATM variational and local ensemble apps

    The first change conforms with the Unidata recommendation that netCDF
    files end with the suffix `.nc`. The second change replaces hardwired
    JEDI ATM var and ens `{layout_x, layout_y}` in `config.resources` with a
    more flexible approach.

    Resolves NOAA-EMC#2335

commit c5c8466
Author: Kate Friedman <[email protected]>
Date:   Mon Feb 26 10:18:50 2024 -0500

    Remove FIX* variables for fix subfolders (NOAA-EMC#2337)

    Remove `FIX*` variables for fix subfolders and replace them with the remaining `FIXgfs` variable and the subfolder name (e.g. `${FIXam}` -> `${FIXgfs}/am`).

    The UFS_UTILS and GDASApp repos were similarly updated. This PR includes a new UFS_UTILS hash.
    The updated GDASAPP hash was already committed within the spack-stack/1.6.0 PR NOAA-EMC#2239.

    Resolves NOAA-EMC#2184

commit 950c38a
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri Feb 23 21:15:46 2024 +0000

    Fix several Jenkins issues (NOAA-EMC#2334)

    Jenkins Updates Resolving final kinks:
    - Removed all `git` shell commands and now exclusively use Software Control
    Manger (**scm**) plugin.
    - Add feature for skipping hosts per configuration specified in case yaml files.
    - Solved and tested false positive builds and experiments.
    - Tested archiving of task error log on case fail
    - First case fail quits pipeline and cancels all pending scheduled jobs
    - Duel build per yaml configuration arguments supported
    - All designated case files in PR directory pass on intended host (fully tested
    on Hera)

    Remaining updates:
    - Fist build fail short circuit when building sub-modules and archiving build
    error log.
    - Re-build/no-build built in logic for Replay and Rerunning previously failed
    experiments.

commit c67393a
Merge: 6f9afff 79d305e
Author: David Huber <[email protected]>
Date:   Fri Feb 23 14:18:15 2024 +0000

    Merge pull request NOAA-EMC#2239 from DavidHuber-NOAA/ss160

    Update to spack-stack 1.6.0

    Includes all submodules except the UFS, which will be updated at a later time.

commit 79d305e
Author: David Huber <[email protected]>
Date:   Thu Feb 22 14:53:57 2024 -0600

    Disable snow DA tests

commit 0459203
Author: David Huber <[email protected]>
Date:   Thu Feb 22 12:55:51 2024 -0600

    Update GDASApp hash to current develop

commit 5c96eb2
Author: David Huber <[email protected]>
Date:   Thu Feb 22 12:37:47 2024 -0600

    Update GDAS hash to allow modified snow DA analysis

commit 79144f2
Merge: abbb0b8 6f9afff
Author: DavidHuber <[email protected]>
Date:   Thu Feb 22 15:14:39 2024 +0000

    Merge remote-tracking branch 'origin/develop' into ss160

commit abbb0b8
Merge: 4ad837e 4529e8c
Author: DavidHuber <[email protected]>
Date:   Thu Feb 22 15:11:03 2024 +0000

    Merge remote-tracking branch 'henry/feature/gwdev_issue_2129' into ss160

commit 4ad837e
Merge: 516b2a2 7ca45db
Author: DavidHuber <[email protected]>
Date:   Thu Feb 22 15:10:24 2024 +0000

    Merge remote-tracking branch 'henry/feature/gfsv17_issue_2125' into ss160

commit 516b2a2
Author: DavidHuber <[email protected]>
Date:   Thu Feb 22 14:19:16 2024 +0000

    Updated GDAS to include rocoto/1.3.6 on Hera.

commit 6f9afff
Author: Jessica Meixner <[email protected]>
Date:   Wed Feb 21 13:09:44 2024 -0500

    Add some flexibility for ocean/ice output (NOAA-EMC#2327)

    This adds functionality to have ocean/ice output frequency be separate from the atm model. One time was created because there's an assumption in the post that these are the same. This could be further modified to remove this assumption.

    Refs NOAA-EMC#1629

commit f6d3015
Author: David Huber <[email protected]>
Date:   Tue Feb 20 09:53:08 2024 -0600

    Update GDASApp hash to include SS/1.6.0 support.

commit 0bf340b
Author: David Huber <[email protected]>
Date:   Tue Feb 20 09:07:32 2024 -0600

    Construct SS paths from version variables.

commit 3330cd7
Author: David Huber <[email protected]>
Date:   Tue Feb 20 09:06:19 2024 -0600

    Removed MET/METplus 'not available' comments

commit fdc638c
Author: David Huber <[email protected]>
Date:   Tue Feb 20 08:35:15 2024 -0600

    Move SS module path to version files.

commit d7d28a6
Author: David Huber <[email protected]>
Date:   Tue Feb 20 07:53:15 2024 -0600

    Update comment about METplus support.

commit a812f88
Author: David Huber <[email protected]>
Date:   Tue Feb 20 07:45:45 2024 -0600

    Update verif-global to latest WCOSS2 support.

commit d81f07f
Author: David Huber <[email protected]>
Date:   Tue Feb 20 07:41:38 2024 -0600

    Clean up build_upp.sh.

    -Corrected whitespace (tabs instead of spaces)
    -Removed debug print statement
    -Alphebetized flags

commit ae7eb19
Author: David Huber <[email protected]>
Date:   Fri Feb 16 16:15:40 2024 -0500

    Fix whitespace in build_upp.sh.

    Co-authored-by: Rahul Mahajan <[email protected]>

commit 48b34d0
Author: David Huber <[email protected]>
Date:   Fri Feb 16 20:56:55 2024 +0000

    Added verif-global support back to WCOSS2.

commit 4529e8c
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Fri Feb 16 11:12:01 2024 -0700

    Bug fix.

commit 8e4f94d
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Fri Feb 16 11:04:41 2024 -0700

    Updates requested by reviewer Rahul Mahajan.

commit 4624ce2
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Fri Feb 16 10:52:11 2024 -0700

    Updates requested by reviewer; testing -- DO NOT REVIEW.

commit ed25bbd
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Fri Feb 16 09:33:59 2024 -0700

    Linter corrections.

commit 6a0b7bf
Merge: f9fb64e 2415b7b
Author: David Huber <[email protected]>
Date:   Fri Feb 16 09:50:22 2024 -0600

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit f9fb64e
Merge: 777d97d a23b7f2
Author: David Huber <[email protected]>
Date:   Fri Feb 16 09:49:42 2024 -0600

    Merge remote-tracking branch 'emc/develop' into ss160

commit 7ca45db
Merge: 73bc76b a23b7f2
Author: Henry R. Winterbottom <[email protected]>
Date:   Fri Feb 16 07:46:35 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125

commit eb2ed53
Merge: 9929277 a23b7f2
Author: Henry R. Winterbottom <[email protected]>
Date:   Fri Feb 16 07:46:24 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129

commit a23b7f2
Author: RussTreadon-NOAA <[email protected]>
Date:   Fri Feb 16 09:37:58 2024 -0500

    Add JEDI 3DEnVar atmosphere only CI test stub (NOAA-EMC#2309)

commit cf83885
Author: Jessica Meixner <[email protected]>
Date:   Fri Feb 16 01:55:02 2024 -0500

    Add unstructured grid for HR3/GFS (NOAA-EMC#2230)

    This adds the capability to use unstructured grids in the global workflow,
    which will be used in HR3.  There are new fix files for a low-resolution
    100km grid and a grid closer to our targeted GFSv17 grid which has the
    resolution combined from the older multi_1 and GFSv16 grids.

    The fix file update is here: NOAA-EMC#2229

    Note: This now means that GFS tests need a new build option:
    `./build_all.sh -w` So that PDLIB=ON is turned on for compiling relevant
    UFS and WW3 codes.

    Resolves NOAA-EMC#1547

commit 9929277
Merge: eb8791c 094e3b8
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Feb 15 15:05:50 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129

commit 094e3b8
Author: Cory Martin <[email protected]>
Date:   Thu Feb 15 14:43:55 2024 -0500

    Move IMS remapping files from COM_OBS to FIXgdas (NOAA-EMC#2322)

    * Add in IMS obs fix directory and update submodule for gdas

commit d465ea0
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Feb 15 19:25:02 2024 +0000

    Set HOMEgfs for module_setup in CI driver (NOAA-EMC#2321)

    Hotfixes to  CI Bash system from updates with sourcing
    `detect_machine.sh` in `ush/module-setup.sh` using **HOMEgfs**.

commit 2415b7b
Author: David Huber <[email protected]>
Date:   Thu Feb 15 19:21:17 2024 +0000

    Load default rocoto on Jet.

commit eb8791c
Merge: 60d5ee6 638684e
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Feb 15 11:56:40 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129

commit 777d97d
Author: David Huber <[email protected]>
Date:   Thu Feb 15 12:34:59 2024 -0600

    Fixed Orion cdo version.

commit ef07235
Author: DavidHuber <[email protected]>
Date:   Thu Feb 15 16:29:32 2024 +0000

    Revert UFS hash.

commit 0ce8c0d
Author: DavidHuber <[email protected]>
Date:   Thu Feb 15 14:55:48 2024 +0000

    Fix git version in Hera's gwsetup module.

commit 3080a34
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 20:52:34 2024 +0000

    Fixed xarray version for SS/1.6.0.

commit 49392dd
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 20:29:41 2024 +0000

    Updated GSI-Utils hash to head of develop.

commit c3553f0
Merge: 4568653 638684e
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 20:28:14 2024 +0000

    Merge remote-tracking branch 'origin/develop' into ss160

commit 4568653
Author: David Huber <[email protected]>
Date:   Wed Feb 14 14:22:13 2024 -0600

    Reupgrade Hercules to SS/1.6.0

commit 638684e
Author: Kate Friedman <[email protected]>
Date:   Wed Feb 14 14:55:21 2024 -0500

    Remove `finddate.sh` from system (NOAA-EMC#2308)

    * Retire finddate.sh usage from system
    * Update gfs-utils hash to 7a84c88 - New hash includes removal of finddate.sh

    Refs NOAA-EMC#2279

commit 2b160f8
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 18:31:28 2024 +0000

    Reenable METplus jobs on Hercules.

commit 8f59002
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 18:30:23 2024 +0000

    Update GSI hashes.

commit 73bc76b
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 14 09:27:37 2024 -0700

    Updates based on user request.

commit e4bc674
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 14 08:03:45 2024 -0700

    Corrected based on reviewer review.

commit 60d5ee6
Merge: 40f2cf6 1aaef05
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Feb 13 18:08:33 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129

commit 0330411
Merge: 929b903 1aaef05
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Feb 13 17:58:12 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125

commit 1aaef05
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Feb 13 18:15:59 2024 -0500

    Jenkins Pipeline updates for Canceling Jobs (NOAA-EMC#2307)

    Tuning updates for Jenkins Pipeline :
    - Added short circuit for all parallel runs of cases on error of any
    - Fixed canceling of all scheduled jobs on first case error
    - Added feature to save error log files to Jenkins Archive facility on fail

commit 6404892
Author: Rahul Mahajan <[email protected]>
Date:   Tue Feb 13 14:57:37 2024 -0500

    Ocean/ice product generation for GFS and GEFS (NOAA-EMC#2286)

    This PR does several things:
    1. the model output for ocean and ice in the `COM/` directory are now
        named per EE2 convention for coupled model.
        E.g `gfs.ocean.t12z.6hr_avg.f120.nc` and `gfs.ocean.t12z.daily.f120.nc`
    2. The products are generated using the `ocnicepost.fd` utility developed
        by @DeniseWorthen in https://github.com/NOAA-EMC/gfs-utils and
        converted to grib2 using example scripts provided by @GwenChen-NOAA
        using `wgrib2`.
    3. NetCDF products on the native grid are also generated by subsetting
        variables from  the raw model output.  This is done with `xarray`.
    4. updates the hash of https://github.com/NOAA-EMC/gfs-utils to include
        fixes in `ocnicepost.fd`
    5. removes NCL related scripting that was previously used for ocean/ice
        interpolation and `reg2grb2` used for converting to grib2.
    6. updates archive scripts to accommodate updated file names
    7. removes intermediate ocean processed files such as 2D/3D/xsect data-
        sets
    8. separate jobs are added for ocean and ice product generation.
    9. removes intermediate restarts for the mediator and only saves the medi-
        ator restart at the end of the forecast in `COM`.
    10. Increases memory for offline UPP when run at C768.  The program
          segfaults with an OOM when memory is self allocated based on PEs by
          the scheduler on Hera.
    11. Enables ocean/ice ensemble product generation for GEFS
    12. Some minor clean-ups

    Fixes NOAA-EMC#935
    Fixes NOAA-EMC#1317
    Fixes NOAA-EMC#1864

commit 40f2cf6
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Tue Feb 13 10:18:53 2024 -0700

    Implemented ush/detect_machine.sh for host determination and removed redundant checks for expected file paths.

commit 929b903
Merge: 2d08d01 3f99f70
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Feb 13 08:31:06 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125

commit 3f99f70
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Feb 13 00:57:18 2024 -0500

    Add wave post jobs to GEFS (NOAA-EMC#2292)

    Adds the wave post jobs for gridded and points to GEFS. Boundary
    point jobs are added even though the current GEFS buoy file does
    not contain any (tested by manually subbing in the GFS buoy file).

    Resolves NOAA-EMC#827

commit 842adf3
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Feb 12 12:50:08 2024 -0500

    Added additional test cases to the pr list in Jenkins (NOAA-EMC#2306)

    C48mx500_3DVarAOWCDA, C96C48_hybatmDA, and C96_atmsnowDA
    Co-authored-by: terrance.mcguinness <[email protected]>

commit bb4ca65
Author: CatherineThomas-NOAA <[email protected]>
Date:   Mon Feb 12 14:50:41 2024 +0000

    Redo v16.3 config.base changes for DA increments (NOAA-EMC#2304)

    Include the additional hydrometeors to the
    INCREMENTS_TO_ZERO and INCVARS_ZERO_STRAT
    variables in config.base that were modified
    in v16.3.

    Resolves: NOAA-EMC#2303

commit 061992b
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Sat Feb 10 01:33:36 2024 -0500

    Fix Jenkins success reporting (NOAA-EMC#2302)

    Moving the post section back outside of main Run Experiments
    stage. This allows the system to correctly report the **Success**
    status until after all tests pass.

    _Had originally moved them in attempts to solve "Not an SCM
    GitHub Job" issue and cause the reporting to misbehave._

    Also ran through Jenkins linter and updated some messaging
    that was incorrectly reporting system build type.

commit 28ccf78
Merge: b972f66 54daa31
Author: David Huber <[email protected]>
Date:   Fri Feb 9 14:00:43 2024 -0600

    Merge remote-tracking branch 'emc/develop' into ss160

commit b972f66
Author: David Huber <[email protected]>
Date:   Fri Feb 9 10:47:00 2024 -0600

    Fix SS versions for CI modules.

commit 4b01d8e
Author: David Huber <[email protected]>
Date:   Fri Feb 9 10:44:30 2024 -0600

    Revert Hercules modules to SS/1.5.1.

commit 54daa31
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Feb 8 15:48:38 2024 -0500

    Jenkins Declartive Pipeline for CI with gfs/gefs multibuilds (NOAA-EMC#2246)

    Adding top level Jenkins file for CI tests running on Jenkins Controller:

    - Declarative Multi-branch Pipeline (has enhanced restart capabilities
    on a per section bases)
    - Starts Pipeline from Label PR same as BASH system (for now)
    - Progress and restarts can me managed with CAC Login at [EPIC OAR
    Jenkins](https://jenkins.epic.oarcloud.noaa.gov)
    - Has logic for multi **gfs/gefs** system builds (arguments based on a
    configuration file `ci/casts/yamls/build.yaml`)
      - Any number of **systems** may be added by manual adding an ele-
    ment to the matrix in the Jenkinsfile
      - _It may be possible to dynamic add matrix values with a specialty
    plug-in_
    - Currently only runs on **Orion** and **Hera** using `mterry` account

    Resolves NOAA-EMC#2119
    Resolves NOAA-EMC#2118

commit 43429e2
Author: Rahul Mahajan <[email protected]>
Date:   Thu Feb 8 15:30:28 2024 -0500

    Enable AO WCDA test (NOAA-EMC#1963)

    This PR:
    - adds GSI + SOCA C48 5-deg ocean 3DVar test (courtesy @guillaumevernieres)
    - adds a toggle to optionally disable ocnanalvrfy job.

commit 2d08d01
Merge: 4745d4a f563528
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Feb 8 07:24:54 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125

commit f563528
Author: Kate Friedman <[email protected]>
Date:   Wed Feb 7 15:09:12 2024 -0500

    Update JGLOBAL_FORECAST for octal error (NOAA-EMC#2295)

    Add "10#" to ENSMEM value > 0 check to handle octal errors.

commit 4745d4a
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 7 08:45:49 2024 -0700

    Removed jlogfile references.

commit 5894ca2
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 7 08:32:16 2024 -0700

    Removed dummy variable passed to perl scripts.

commit dae884a
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 7 08:29:49 2024 -0700

    Removed jlogfile and postmsg references within gempak scripts.

commit 801058f
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Feb 7 00:41:59 2024 -0700

    Consolidate `npe_node_max` (NOAA-EMC#2289)

    - The environment variable `npe_node_max` is removed from all
    files beneath `global-workflow/env`;
    - The environment variable `npe_node_max` is removed from
    `parm/config/gefs/config.ufs` and `parm/config/gfs/config.ufs`;
    - The environment variable `npe_node_max` is maintained only
    within `parm/config/gefs/config.resources` and
    `parm/config/gfs/config.resources`.

    Resolves NOAA-EMC#2133

commit b0325e0
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Feb 7 00:40:20 2024 -0700

    Removes files module loading file no longer used by the GW (NOAA-EMC#2281)

    Removes `module-setup.csh.inc` and `module-setup.sh.inc`.

    The module `ush/module-setup.sh` is updated such that it now sources
    `ush/detect_machine.sh` to determine which supported platform the
    global-workflow is being execute on.

    Resolves NOAA-EMC#2130

commit 1ccc989
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Feb 5 14:16:07 2024 -0500

    Remove EnKF forecast groups (NOAA-EMC#2280)

    Removes the grouping of EnKF forecasts so each job only runs
    one forecast. Member and MEMDIR are now set at the workflow
    manager (rocoto) level. This change makes much of the system
    simpler (especially dependencies) and allows the elimination of
    the separate efcs scripts.

    Metatask names of updated jobs have been updated to make
    them a little less opaque by using the same name name as its
    constituent tasks (e.g. the forecast metatask is named
    `enkgdasfcst`, not `enkfgdasefcs`). Metatasks that weren't
    updated retain the same names as before for now.

    Resolves NOAA-EMC#2254

commit 9f3383f
Author: Henry R. Winterbottom <[email protected]>
Date:   Mon Feb 5 12:15:13 2024 -0700

    Updated detect_machine.sh using that from UFS WM. (NOAA-EMC#2252)

    Updates `ush/detect_machine.sh` to match the UFS weather-model
    `tests/detect_machine.sh` prepared by @BrianCurtis-NOAA

    Resolves NOAA-EMC#2228

commit 7d68b0b
Author: CatherineThomas-NOAA <[email protected]>
Date:   Sun Feb 4 22:02:41 2024 +0000

    Update global_cycle for fractional grid (NOAA-EMC#2262)

    The hash for ufs_utils is updated to include the changes for
    fractional grid support within global_cycle.  This commit also
    removes the hack to skip global_cycle in cycling mode with
    v17 physics.

    Resolves: NOAA-EMC#1775
    Refs: ufs-community/UFS_UTILS#815
    Refs: ufs-community/UFS_UTILS#891

commit ed592a6
Author: Kate Friedman <[email protected]>
Date:   Sat Feb 3 02:55:14 2024 -0500

    Retire cycle-specific FHMAX_GFS variables (NOAA-EMC#2278)

    This PR retires the `FHMAX_GFS_${cyc}` variables that allowed users to specify
    different gfs forecast lengths for each cycle. This function is no longer supported
    in global-workflow. The `FHMAX_GFS_*` variables will be removed and will no
    longer be checked to set the final `FHMAX_GFS` variable. The same forecast
    length will be set for every cycle.

    This PR also includes a small fix to add new post parm files into the `.gitignore`
    file. This was intended to be included in a different PR but that PR is on hold for
    further testing so it is being included here to get it into `develop` sooner.

    Resolves NOAA-EMC#2218

commit 977e2d6
Author: Henry R. Winterbottom <[email protected]>
Date:   Fri Feb 2 07:49:09 2024 -0700

    New GDASApp hash. (NOAA-EMC#2285)

commit b5f2bd9
Merge: 4d66742 0400e1f
Author: David Huber <[email protected]>
Date:   Tue Jan 30 13:55:00 2024 -0600

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit 0400e1f
Author: David Huber <[email protected]>
Date:   Tue Jan 30 09:57:11 2024 -0600

    Fix gfs_utils Orion spack-stack env path.

commit 6bbe823
Author: DWesl <[email protected]>
Date:   Mon Jan 29 21:15:30 2024 -0500

    Use seq to generate the list of times, instead of a bash for-loop (NOAA-EMC#2264)

    I'm running a year-long forecast, which means I get a large portion of the log file dedicated to these loops.

    `seq ${START} ${STEP} ${STOP}` will generate a sequence going from START to STOP by STEP, including STOP if relevant.  That seems to be the purpose of these loops.  It will by default separate the list with newlines, but `seq -s ' ' ${START} ${STEP} ${STOP}` will separate them with spaces instead, more closely mimicing the previous behavior.

    I would like this to be two lines in the log, rather than a few hundred, and this may also be faster, though probably more for reasons of fewer writes to disk than because bash isn't designed for arithmetic.

commit d5bee38
Author: Kate Friedman <[email protected]>
Date:   Mon Jan 29 14:35:02 2024 -0500

    Correct typos in GFS config.resources (NOAA-EMC#2267)

    This PR corrects some typos in `parm/config/gfs/config.resources` that were
    introduced in PR NOAA-EMC#2216. The esfc job was failing in tests on WCOSS2 due to
    insufficient memory. This lead to discovering the other typos. The esfc job
    completes without error after its memory is set back to `80GB` from the
    incorrect `8GB`.

    Resolves NOAA-EMC#2266

commit 81557be
Author: David Huber <[email protected]>
Date:   Mon Jan 29 12:13:31 2024 -0600

    Update monitor hash to noaa-emc with SS/1.6.0 support.

commit 2238dd6
Author: DavidHuber <[email protected]>
Date:   Mon Jan 29 13:21:30 2024 +0000

    Update Orion, Hercules, S4 modulefiles.

commit 6ffd94f
Author: DavidHuber <[email protected]>
Date:   Fri Jan 26 16:01:23 2024 +0000

    Update GDAS hash to include SS/1.6.0 support.

commit be11f85
Merge: 56b9680 04e0772
Author: DavidHuber <[email protected]>
Date:   Fri Jan 26 15:34:24 2024 +0000

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit 8ff3448
Author: Rahul Mahajan <[email protected]>
Date:   Fri Jan 26 10:12:18 2024 -0500

    Add a yaml for snow DA testing. (NOAA-EMC#2199)

    - adds a new test yaml C96_atmsnowDA.yaml for 3DVar atmosphere with GSI and Land (Snow) DA with JEDI
    - moves a few yamls from platforms/ to yamls/
    - adds ability to overwrite a previously created experiment as an addition to user input.
    ---------

    Co-authored-by: Cory Martin <[email protected]>

commit 04e0772
Author: David Huber <[email protected]>
Date:   Fri Jan 26 07:16:25 2024 -0600

    Update ufs_utils hash for spack-stack/1.6.0 support.

commit 3d44ff3
Author: Barry Baker <[email protected]>
Date:   Thu Jan 25 14:33:27 2024 -0500

    GOCART ExtData biogenic climatology fix (NOAA-EMC#2253)

    Updates the ExtData for biogenic emissions to be climatology rather than
    for current time.  Fixes an issue which will crash by default for other years.

commit 66f58b8
Author: Guillaume Vernieres <[email protected]>
Date:   Thu Jan 25 13:16:41 2024 -0500

    Added missing container case in gfs/config.resources (NOAA-EMC#2258)

    fixes  NOAA-EMC#2257

commit 553b4f2
Author: WenMeng-NOAA <[email protected]>
Date:   Thu Jan 25 13:00:45 2024 -0500

    Fix post parm links (NOAA-EMC#2243)

    Change symbolic links under parm/post with the latest version of develop branch from UPP repository and enable MERRA2 aerosol fields.

    Resolves NOAA-EMC#2259

commit 4d66742
Merge: 6c05803 afa09e3
Author: David Huber <[email protected]>
Date:   Thu Jan 25 07:49:08 2024 -0600

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit 6c05803
Author: David Huber <[email protected]>
Date:   Thu Jan 25 07:48:42 2024 -0600

    Fix wgrib2/gfs_utils on Hercules.

commit ee6f536
Author: Kate Friedman <[email protected]>
Date:   Thu Jan 25 07:43:13 2024 -0500

    Update GFS version to v16.3.13 in index.rst (NOAA-EMC#2256)

    GFSv16.3.13 WAFS update was implemented

    Refs NOAA-EMC#2013

commit 2445d44
Author: RussTreadon-NOAA <[email protected]>
Date:   Thu Jan 25 06:17:11 2024 -0500

    Simplify and extend load_ufsda_modules to Hercules (NOAA-EMC#2245)

    GDASApp jobs do not run on Hercules because `ush/load_ufsda_modules.sh` does
    not include logic to load the appropriate GDASApp modules on Hercules.  This PR
    extends `load_ufsda_modules.sh` functionality to Hercules, thereby enabling
    GDASApp jobs to run on Hercules.

    Resolves NOAA-EMC#2244

commit 56b9680
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 19:47:34 2024 +0000

    Update hashes (revert WCOSS2 modules).

commit afa09e3
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 18:59:40 2024 +0000

    New (cleaner history) gdas hash.

commit a9eaec2
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 18:52:27 2024 +0000

    Update gdasapp to include ss/1.6.0 support.

commit 5ef8eb2
Merge: 4c46354 e400068
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 17:08:54 2024 +0000

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit 4c46354
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 17:05:12 2024 +0000

    Reenable verif-global support

commit f775755
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 16:59:10 2024 +0000

    Assign fcsthrs for awips_g2 job.

commit e400068
Author: David Huber <[email protected]>
Date:   Mon Jan 22 15:01:07 2024 -0600

    More gsi-addon path fixes.

commit f663d47
Author: David Huber <[email protected]>
Date:   Mon Jan 22 14:41:59 2024 -0600

    Fix gsi-addon paths for hercules, orion, and S4.

commit e304bbe
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:59:34 2024 +0000

    Better optimize build jobs (more ufs jobs).

commit ccc6e2d
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:56:18 2024 +0000

    Reenable verif-global. NOAA-EMC#2195

commit 3ef3411
Merge: 4365f63 f4d187f
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:39:10 2024 +0000

    Merge remote-tracking branch 'origin/develop' into ss160

commit 4365f63
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:37:25 2024 +0000

    Corrected the SS env. name in the version files. NOAA-EMC#2195

commit f4d187f
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Mon Jan 22 12:28:28 2024 -0500

    Converts obsproc to obsprep in prepoceanobs config file (NOAA-EMC#2236)

    Converts obsproc to obsprep in prepoceanobs config file as a compliment to mutually depended GDASApp PR NOAA-EMC/GDASApp#858
    The motivations are explained in refs NOAA-EMC/GDASApp#857

commit 9a09d30
Author: DavidHuber <[email protected]>
Date:   Fri Jan 19 21:23:50 2024 +0000

    Corrected gsi-addon-dev spelling.

commit 21ff645
Author: DavidHuber <[email protected]>
Date:   Fri Jan 19 21:11:34 2024 +0000

    Update modulefiles, submodules to spack-stack 1.6.0. NOAA-EMC#2195

commit d4c55d1
Author: Kate Friedman <[email protected]>
Date:   Fri Jan 19 15:43:37 2024 -0500

    Update typing hint for WCOSS version of python (NOAA-EMC#2238)

    The typing hint `typing.List` was deprecated with python 3.9 in favor
    of using the primitive `list[str]`, but the functional version of python
    on WCOSS2 is <3.9, causing `setup_xml.py` to fail there. This replaces
    `list[str]` as a typing hint with the deprecated form until the supported
    version on WCOSS2 is >=3.9.

commit 4919287
Author: Barry Baker <[email protected]>
Date:   Thu Jan 18 22:31:27 2024 -0500

    GOCART Emission updates for GEFSv13 and GDAS  (NOAA-EMC#2201)

    This PR addresses several things needed for more recent simulations using
    GOCART2G as well as preparing for the GEFSv13 30 year run.  The main
    updates are:

    - Update CEDS to use monthly emission files instead of daily.  This will
    drastically reduce the number of files needed. No science change
    - Update biogenic MEGAN inputs to use a climatology rather than the
    offline biogenic previously used.  This is needed to deal with simulations
    where the current dataset is not available.
    - Update volcanic SO4 emissions to use degassing emissions only.  This is
    to support the need for more recent simulations where data is not available.

commit 13d25cf
Author: Kate Friedman <[email protected]>
Date:   Thu Jan 18 22:29:43 2024 -0500

    Add `POSTAMBLE_CMD` into preamble postamble (NOAA-EMC#2235)

    This PR adds the ability to run a command at the end of jobs via the
    preamble's postamble function. A new command can be set via
    `POSTAMBLE_CMD` and will be invoked at the end of jobs. Users can
    add the command to the top of an env file to have every job run it or
    it can be placed within a job if-block in the env file to run for just that
    job.

    Resolves NOAA-EMC#1145

commit 7759163
Author: Rahul Mahajan <[email protected]>
Date:   Thu Jan 18 01:13:49 2024 -0500

    Add option to create WGNE atmosphere products (NOAA-EMC#2233)

    Adds option to create WGNE products for the atmosphere.

    Resolves NOAA-EMC#1951
    Resolves NOAA-EMC#2226

commit d95ed85
Author: Rahul Mahajan <[email protected]>
Date:   Wed Jan 17 18:04:56 2024 -0500

    Use ufs.configure, model_configure, MOM_input, data_table, and ice_in templates from UFS-weather-model (NOAA-EMC#2051)

    This PR:
    - links `ufs.configure.*.IN`, `model_configure.IN`, `MOM_input_${OCNRES}.in`,
    `MOM6_data_table.IN`, and `ice_in.IN` from ufs-weather-model into the
    global-workflow `parm/ufs` directory
    - prepares local variables for use in the templates in the respective functions
    for FV3, MOM6, and CICE6
    - uses `atparse.bash` to render these templates into fully formed namelists

    - Work was performed by @DeniseWorthen in the ufs-weather-model to
    templatize several variables that are hard-wired in the ufs-weather-model
    for CICE. See ufs-community/ufs-weather-model/NOAA-EMC#2010

commit 44a66dd
Author: RussTreadon-NOAA <[email protected]>
Date:   Wed Jan 17 13:52:09 2024 -0500

    Update gdas.cd hash to use gsibec tag 1.1.3 (NOAA-EMC#2231) (NOAA-EMC#2234)

commit 9046d97
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Jan 17 10:19:18 2024 -0500

    Add basic atmos products for GEFS and refactor resources (NOAA-EMC#2216)

    * Add basic atmos products for GEFS

    Adds basic atmosphere products for GEFS members (no mean or spread).

    To facilitate the addition of GEFS parameter lists, the existing GFS
    lists are renamed. They are also relocated to `parm/products/` direc
    tory instead of `parm/post/`. GEFS v12 uses different parameter lists
    for different resolutions, but for this implementation, the 0p25 lists
    are used for all resolutions. However, to hedge against the final con-
    figuration, all of the GEFS parameter lists have been added to parm.
    Implementation of different parameter lists for each resolution will
    take additional refactoring of the atmos_products job, as it currently
    assumes all resolutions use the same lists.

    The new GEFS rocoto task is implented as two loops of metatasks (made
    possible by PR NOAA-EMC#2189). The member is set at the rocoto level, so the
    setting in `config.base` had to be updated to accept a pass-through.
    The generation of a forecast hour list is moved up to its own function
    in `rocoto.tasks`, separate from the post groups which are not used.
    This can be used as a model for future metatasks (or refactoring of old
    ones). `rocoto_viewer.py` does function with the nested metatasks,
    though only one level of folding is available and the metatask name
    is that of the lower metatask (though it encompasses the entire outer
    metatask).

    Additionally, the GEFS `config.resources` had diverged from the GFS
    version, which included not having a section for the atm products job.
    This led to the refactoring of the GFS `config.resources`, including
    switching to using a `case` statement instead of sequential `elif`.
    This refactored script was then copied over to GEFS, replacing the old
    one, with all jobs not currently implemented for GEFS removed (except
    wave post, whose inclusion is immenent). New blocks can be copied over
    from GFS as they are added.

    Resolves NOAA-EMC#823

commit fbba174
Author: RussTreadon-NOAA <[email protected]>
Date:   Tue Jan 16 14:05:48 2024 -0500

    Update GDASApp (gdas.cd) hash (NOAA-EMC#2225)

    GDASApp now uses gitsubmodules

commit dddd837
Author: Rahul Mahajan <[email protected]>
Date:   Tue Jan 16 12:17:19 2024 -0500

    Fix ocean resolution for the S2SWA test (NOAA-EMC#2223)

commit 83edaf1
Author: David Huber <[email protected]>
Date:   Tue Jan 16 11:07:02 2024 -0500

    Apply fixes to archiving jobs (NOAA-EMC#2221)

    Add checks for potentially missing log/data files and update log names for archiving.

    Missing sflux index files are also added to the products script.

    Resolves NOAA-EMC#2076

commit c590476
Author: Rahul Mahajan <[email protected]>
Date:   Fri Jan 12 19:21:02 2024 -0500

    Update hash to ufs-weather-model. The noahmptable.tbl was reorganized, so update link_workflow.sh to use the same one used in UFSWM RT (NOAA-EMC#2219)

commit c041968
Author: Kate Friedman <[email protected]>
Date:   Fri Jan 12 12:09:35 2024 -0500

    Add ocean resolution to setup_expt invocation and retire/reduce COMROT/ROTDIR usage (NOAA-EMC#2214)

    Two series of updates:

    1) Update setup scripts to now allow users to provide ocean resolution
    2) Housekeeping to retire the `COMROT` variable, replacing it with other variables
    as needed, and reduce the `ROTDIR` variable usage.

    Both updates change options for the workflow setup API.

    Refs NOAA-EMC#2061

commit 997f978
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Fri Jan 12 10:46:36 2024 -0500

    Allow use of ocean obs prep in WCDA cycling and remove R2D2 (NOAA-EMC#2215)

    Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same.
    Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS.
    Replaces the current R2D2 processing.

commit 12a5bb1
Merge: 4cb5802 6492c2d
Author: David Huber <[email protected]>
Date:   Fri Jan 12 09:26:27 2024 -0500

    Merge pull request NOAA-EMC#2217 from DavidHuber-NOAA/update/versions

    Update and clean up version and module files

commit 6492c2d
Author: David Huber <[email protected]>
Date:   Thu Jan 11 11:49:08 2024 -0600

    Update orion module/version files for met/metplus NOAA-EMC#2123

commit 94c9937
Author: DavidHuber <[email protected]>
Date:   Thu Jan 11 17:42:53 2024 +0000

    Comment met/metplus out from Hera modulefile. NOAA-EMC#2123

commit 8c32f8b
Merge: a65e4c6 4cb5802
Author: David Huber <[email protected]>
Date:   Thu Jan 11 11:34:44 2024 -0600

    Merge branch 'develop' of github.com:noaa-emc/global-workflow into develop

commit a65e4c6
Author: David Huber <[email protected]>
Date:   Thu Jan 11 11:34:19 2024 -0600

    Initial update of version/module files NOAA-EMC#2123

commit 4cb5802
Author: souopgui <[email protected]>
Date:   Wed Jan 10 08:30:22 2024 -0600

    Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh when running MPMD tasks (NOAA-EMC#2212)

    Fix OpenMP over-allocation of resources running MPMD tasks
    Co-authored-by: Innocent Souopgui <[email protected]>

commit b056b53
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Jan 8 17:28:05 2024 -0500

    Add Hercules as valid machine in CI scripts (NOAA-EMC#2207)

    Few updates to CI scripts to include names for hercules that where missed
    the first time.

commit 6574d29
Author: Rahul Mahajan <[email protected]>
Date:   Mon Jan 8 17:25:47 2024 -0500

    Fix invalid GH action and restart file name (NOAA-EMC#2210)

    Resolves a typo that leads to an invalid workflow yaml and fixes the restart filename in restart detection.

    Resolves NOAA-EMC#2205

commit 69605ea
Author: Rahul Mahajan <[email protected]>
Date:   Mon Jan 8 17:00:28 2024 -0500

    Stop attempting to comment link to RTD for non-PRs (NOAA-EMC#2209)

    Adds a check so comments with a link to documentation are only generated
    for PRs.

commit 4e160a8
Author: Rahul Mahajan <[email protected]>
Date:   Mon Jan 8 13:10:15 2024 -0500

    Enable UPP for GOES processing (NOAA-EMC#2203)

    Wnables the creation of special master grib2 files from UPP for
    GOES processing

commit c15875b
Author: David Huber <[email protected]>
Date:   Mon Jan 8 09:56:06 2024 -0500

    Port cycling to Hercules (NOAA-EMC#2196)

    Adds cycled support for Hercules (excluding gsi-monitor).
    Partially resolves NOAA-EMC#1588
    GSI monitoring is disabled on Hercules due to missing Perl modules. That will be enabled in a later PR.

commit ef6827d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Jan 8 09:43:12 2024 -0500

    Refactor rocoto task XML creation (NOAA-EMC#2189)

    Refactors the rocoto task generation to be recursive.
    This will allow nested metatasks to loop over multiple variables, which is needed for GEFS product generation.

    As part of this refactor, there is no longer separate arguments to designate metatasks.
    Instead, task dicts can include a nested 'task_dict' as well as a 'var_dict' containing the variables to loop over.
    The nested task dict can then either have another layer, or be the innermost task.

    To accommodate the new recursive nature, some defaults that were previously defined in create_wf_task() had to be pushed down into the function that creates the innermost task.
    Also, former keywords have been absorbed by the task dict.

    Refs NOAA-EMC#823
    Refs NOAA-EMC#827

commit 2b81cfa
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Jan 8 09:41:03 2024 -0500

    Update fix versions (NOAA-EMC#2198)

    Updates fix versions for a few components:
    - Update cice and mom6 versions to support C96/1p00 marine
    - Update wave to change betamax setting for glo_025 waves

    Resolves NOAA-EMC#2004
    Resolves NOAA-EMC#2107
kayeekayee added a commit to kayeekayee/global-workflow that referenced this issue Apr 11, 2024
Squashed commit of the following:

commit c54fe98c4fe8d811907366d4ba6ff16347bf174c
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Apr 2 15:58:49 2024 -0400

    Move bash utility functions out of preamble (#2447)

    The preamble was accumulating a bunch of utility functions. These
    functions are now moved to a separate file that is sourced by the
    preamble. The only functions remaining in the preamble are those related
    to script control and logging (`set_trace()`, `set_strict()`,
    `postamble()`).

    Resolves #2346

commit 4a39c8afc0555a8f2d621efb55589b9b309a416c
Author: David Huber <[email protected]>
Date:   Tue Apr 2 18:00:21 2024 +0000

    Reenable the minimization monitor on Hera (#2446)

    This allows the minimization monitor to run on Hera Rocky 8.

    A missing perl module was added (List/MoreUtils.pm), but had to be
    installed under the perl/5.38.0 installation, thus that module needs to
    be loaded.

    Resolves #2439

commit 0eaa53771b5e8d476d3b5feabd3181c8dc48629a
Author: Travis Elless <[email protected]>
Date:   Tue Apr 2 00:31:14 2024 -0400

    Fix rotating member bugs (#2443)

    When PR #2427 introduced the rotating subset of member guess states for
    the early-cycle EnKF, the rotating member calculation function was
    omitted from the DOSFCANL_ENKF if block in the enkf surface script. This
    PR adds this feature to this section. This PR also removes hard coded
    values that were included in this function and are replaced with a
    variable equal to the number of late cycle members.

    Resolves #2441

commit 39ba9d720c38ac85239a1eb1696c78df82396644
Author: CatherineThomas-NOAA <[email protected]>
Date:   Mon Apr 1 17:48:42 2024 -0400

    Remove the reset of upper layer humidity (#2449)

    # Description
    The parameter "nudge_qv" resets the upper layer humidity to HALOE
    climatology when cold starting. This parameter has been set to ".true."
    but is no longer needed using v16+ ICs and will now be set to ".false."
    by default.

    Resolves: #2448

commit 7f6bf216566e92bbe072ebe4b64d26cc60fb53f1
Author: Jiarui Dong <[email protected]>
Date:   Mon Apr 1 13:08:33 2024 -0400

    Archive the snow DA analysis into HPSS (#2414)

    This PR adds the capabilities to archive the snow analysis output into
    HPSS. Changes are made to archive the snow stats, letkfoi yaml file and
    snow analysis into HPSS.

commit c1b11a2559e618f61866498b5dad503ba74d8332
Author: Neil Barton <[email protected]>
Date:   Mon Apr 1 13:05:57 2024 -0400

    Add GEFS ENS Atmos options (#2392)

    This PR adds the FV3 atmos perturbation options when running GEFS. This
    is needed for GEFS reforecasts and GEFS operational forecasts.

    This PR continues to address the below issues
    #1720
    #1921

    Co-authored-by: Rahul Mahajan <[email protected]>
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
    Co-authored-by: Bing Fu <[email protected]>

commit 834ce31348a627e14d448cdbe33d4ec0dabe99e4
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Mar 29 13:17:08 2024 -0400

    Refactor gempak jobs for new COM and style (#2374)

    Updates the gempak jobs to fit the new COM structure while also
    refactoring them some to improve the style. Despite these technical
    changes, the overall structure is left unchanged for most scripts,
    though some have been rewritten to make the needed changes easier. Some
    of these scripts had already been updated some in the original COM
    refactor and thus needed fewer updates.

    Style updates includes converting all gempak scripts to bash, making
    them shellcheck compliant, and removing trailing whitespace. Further
    refactoring to improve maintainability will be needed in the future (see
    #2341, #2342, #2343, #2348).

    The GFS gif scripts were identical except the forecast hour, so they are
    collapsed down into two: one for f000 and one for other forecast hours.

    The gempak executables have short path limits. To get around this
    without having the gempak module recompiled, target directories (mostly
    relevant for the gempak meta jobs) are symlinked into the working
    directory to drasticly reduce the path lengths.

    Part of this update includes replacing existing MPMD calls with the new
    standard `ush/run_mpmd.sh` script.

    A new function, `wait_for_file()`, is introduced to standardize waiting
    for a file to be available.

    Gempak forecast hours are often hard-coded within scripts. In addition
    to issues with maintainability, this causes problems for shorter
    forecasts, such as we typically run for testing purposes. For now, we
    simply check the values against the forecast length and reduce if
    necessary. Future work (#2348) will be needed to remove these hard-coded
    values with variables set in the config file (or just use update gempak
    products to match standard output time variables).

    One-degree gempak files have been updated to include `1p00` in the
    filename.

    Several gempak job dependencies are corrected.

    Fake gempak data for external models is being staged on tier-1 machines
    to allow testing.

    **Output has not been verified.** Future PRs will likely be needed to
    bring full functionality online.

    Resolves #2158
    Resolves #2152
    Resolves #2151
    Resolves #2249
    Resolves #2247
    Refs #2157
    Refs #2348

commit 20635b0639656769842218d544ec7ce2436337c5
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri Mar 29 08:15:29 2024 +0000

    Turn GEFS CI test on for Hera (#2442)

    Re-enabling gefs case to test gefs system builds in Jenkins on Hera.

    Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>
    Co-authored-by: terrance.mcguinness <[email protected]>
    Co-authored-by: Walter.Kolczynski <[email protected]>

commit ba6a9d5fa6a079b1e3fdd424a493252bbf499c5d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Mar 28 17:34:22 2024 -0400

    Modify APP based on RUN (#2413)

    There is a need to change which coupled components are on depending on
    the current `RUN`. To facilitate this, the `APP` is modified prior to
    the setting of the `DO_<component>` variables based on `RUN`, turning
    off components as desired.

    This new system also replaces the `DO_<component>_ENKF` switches that
    were formerly used to turn components off for the ensemble.

    Also expands allows apps for cycled to include S2SWA.

    Resolves #2318

commit 3ff7a92c25564ddf984cb09cb5667ae8fafe01a0
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Mar 28 17:48:00 2024 +0000

    Fix post log arg check and don't create build semaphore (#2440)

    Two Hot Fixes to Jenkins latest updates:

    1. Logic fixed in checking for mutually exclusive use of gists and repo
    for publishing error files
    2. Removed creation of build success file semaphore forcing complete
    rebuild as the default behavior for rerun/restarts

    Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>
    Co-authored-by: terrance.mcguinness <[email protected]>

commit d6be3b5c3a1b8fd025a303b40e0660e2914906a7
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Mar 27 20:56:18 2024 -0600

    Update global-workflow and subcomponents to Hera/Rocky 8 partition (#2421)

    This PR addresses issue #2329. The following is accomplished:

    - All submodule RDHPCS Hera stacks are updated to be compatible with the
    Rocky-8 distro spack-stack;
    - The global-workflow version files `versions/build.hera.ver` and
    `versions/run.hera.ver` are updated for Rocky-8;
    - All submodule hashes have been updated to be compliant with the
    Rocky-8 distro spack-stack (see the reference PRs below);
    - Update to `parm/config/config.base` is made for not yet compliant
    packages;
    - Relevant updates are made to `modulefiles/module_base.hera.lua` and
    `modulefiles/module_gwsetup.lua`.

      Resolves #2329
      Refs: [#958](https://github.com/NOAA-EMC/GDASApp/issues/958)
               [#49](https://github.com/NOAA-EMC/gfs-utils/issues/49)
               [#124](https://github.com/NOAA-EMC/GSI-Monitor/issues/124)
               [#31](https://github.com/NOAA-EMC/GSI-utils/issues/31)
    [#2167](https://github.com/ufs-community/ufs-weather-model/issues/2167)
    [#2143](https://github.com/ufs-community/ufs-weather-model/issues/2143)
               [#913](https://github.com/ufs-community/UFS_UTILS/issues/913)

    Co-authored-by: Rahul Mahajan <[email protected]>
    Co-authored-by: David Huber <[email protected]>

commit 47302153f13f6b23539be841b78ed78664599c08
Author: Travis Elless <[email protected]>
Date:   Wed Mar 27 21:14:57 2024 -0400

    Add a rotating subset of members for early-cycle enkf (#2427)

    The early-cycle EnKF needs the ability to run with fewer members than
    the late-cycle due to operational resource constraints. Because of this
    requirement, the introduction of a rotating subset of member first-guess
    states used by the early-cycle ensemble is also needed in order to
    preserve the rotating member initial condition functionality currently
    used by the GEFS.

    Co-authored-by: Travis J Elless <[email protected]>
    Co-authored-by: travis elless <[email protected]>

commit 94c282ef6fdcd47076e932bcadb5bdd55236aa05
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Wed Mar 27 20:28:15 2024 +0000

    Uploading error logs to GitHub from Jenkins CI Runs (#2429)

    This PR enhances the user experience within GitHub for when errors occur
    during build and running of CI cases from within the PR messages. This
    is done by uploading the error logs to GitHub Gists and then publishing
    the links to them along with the full paths of the logs on disk.

    This PR adds the python Class **GitHubPR** in
    `${HOMEgfs}/ci/scripts/utils/githubpr.py` by inhearting the GitHub Class
    from **pyGitHub**. We use this module to introduce a helper python
    utility that can publish a list of log files into a GitHub Gist and/or
    the designated branch **error_logs** in the **emcbot** repo
    **ci-global-workflows** for storing error log files for review from any
    git configured terminal. This upload feature will also create
    persistence of errors over time.

    Also the `build_all.sh -k` script has been updated to support a "quick
    kill" feature (thanks David) that stops the parallel builds whenever one
    fails and creates an error_log file that has the paths to the error
    files that are also uploaded and published in the PR messages in GitHub.

    Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>
    Co-authored-by: terrance.mcguinness <[email protected]>
    Co-authored-by: DavidHuber <[email protected]>
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

commit 6c5065e2e83a45b14505e7575aa4500482ef7452
Author: Rahul Mahajan <[email protected]>
Date:   Wed Mar 27 03:39:16 2024 -0400

    Add option to use traditional threading in the UFS (#2384)

    # Description
    This PR:
    - adds the option of running the ufs-weather-model with traditional
    threading in addition to ESMF-managed threading. See new toggle
    `USE_ESMF_THREADING=YES|NO` set in `config.fcst`
    - does not change the current default of using ESMF-managed threading.
    Traditional threading use might need a little more fine tuning for the
    job-card specification. This will be achieved when the UFSWM RT
    completely switches over to traditional threading
    - updates the hash of the ufs-weather-model to the PR
    https://github.com/ufs-community/ufs-weather-model/pull/2172

    Resolves #2277

    In addition to the above stated objectives, this PR also addresses open
    issues. In particular, this PR:
    - adds a newline at the end of `diag_table_aod`. Fixes #2407
    @zhanglikate
    - reserves more memory on WCOSS2 for offline UPP when running at C768.
    Fixes #2408 @WenMeng-NOAA

    Co-authored-by: David Huber <[email protected]>

commit bc1c46dfd7393c5164abcdc2dfa76a9c4bc834b8
Author: RussTreadon-NOAA <[email protected]>
Date:   Tue Mar 26 22:27:30 2024 -0400

    Correct GDASApp paths (#2435)

    The changes in this PR
    - account for changes in GDASApp directory structure
    - generalize how the path to the GDASApp python ioda library is
    specified

    Resolves #2434

commit f0b912be6f2cf2fac590272253f19cb082fbf5f2
Author: David Huber <[email protected]>
Date:   Mon Mar 25 21:46:32 2024 +0000

    Fix *earc jobs where the number of members isn't a multiple of 10 (#2424)

    This limits the earc search for ensemble members to the maximum number
    of members, which prevents attempting to send non-existent members to
    HPSS if the number of ensemble members is not a multiple of 10.

    Resolves #2390s

commit daeb0c855017f8ffd6f06870744b825b276097f3
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri Mar 22 17:40:04 2024 +0000

    hotfix to update full path to error logs on CI case fail (#2425)

    This hotfix PR prepends the full path to the error logs on disk to be
    communitated correctly to the GitHub message to the PR that is being
    processed when there is a failure in from a case.

commit 50f75526549245f2b5d984cdb44e402852e086ec
Author: YaliMao-NOAA <[email protected]>
Date:   Thu Mar 21 16:58:25 2024 +0000

    Add WAFS jobs, scripts and ush to GFS v17 workflow repository (#2412)

    # Description
    This PR adds WAFS jobs, scripts and ush to GFS v17 workflow repository

    ---------

    Co-authored-by: yali mao <[email protected]>
    Co-authored-by: Rahul Mahajan <[email protected]>
    Co-authored-by: yali mao <[email protected]>

commit 03ba78ae3df589211d2776254c6e8584ecdc226f
Author: David Huber <[email protected]>
Date:   Thu Mar 21 13:33:50 2024 +0000

    Hotfix: send the correct number of build jobs for the UFS (#2423)

    This fixes a bug in build_ufs.sh that was causing the UFS to always
    build with 8 jobs (except on the cloud).

commit 4d1bf5266f00b35778ea47896f438e3ef612628d
Author: Kate Friedman <[email protected]>
Date:   Wed Mar 20 14:00:31 2024 -0400

    Updates to RTD documentation (#2418)

    Updates to the RTD documentation include:

    - Textual updates
    - Better definition of GDA subfolder structure
    - Added note about GDAur having been discontinued
    - Adjust copyright and author information
    - Fix Git version table and update its contents
    - Add "Table of Contents" header before table of contents on front page
    - Add AWS ICs path to init page
    - Add link to UFS_UTILS gdas_init RTD documentation
    - Add note about bash to `gw_setup.sh` section and added a warning block

    Refs #2395

commit afe874ee8b28942e459796cd1005ec598458a5b7
Author: Neil Barton <[email protected]>
Date:   Tue Mar 19 14:35:02 2024 -0400

    Add GEFS Ocean Perturbation Options (#2385)

    This PR adds the MOM6 ocean perturbation options when running GEFS. This
    is needed for GEFS reforecasts and GEFS operational forecasts.

    This PR continues to address the below issues
    https://github.com/NOAA-EMC/global-workflow/issues/1720
    https://github.com/NOAA-EMC/global-workflow/issues/1921

    Fixes #2403

commit fa855baa851b0cb635edd1b9ae1bfed5112d41e5
Author: Clara Draper <[email protected]>
Date:   Mon Mar 18 12:49:14 2024 -0600

    Add initial GSI-based soil analysis capability (#2263)

    First set of changes for adding the new soil analysis, from the
    assimilation of screen-level T and q. The changes here enable the
    screen-level observations to be assimilated in the Hybrid (Var and EnKF)
    update, and the soil temperature and soil moisture updates to be made in
    the EnKF only. The functionality is turned on by setting GSI_SOILANAL to
    YES in config.base.

    Resolves #1479

commit e9700d84b521907ee23e1584712f80e25e60f08e
Author: Jessica Meixner <[email protected]>
Date:   Mon Mar 18 09:32:13 2024 -0400

    re-enable ci/cases/pr/C48mx500_3DVarAOWCDA.yaml (#2405)

    Updates to re-enable C48mx500_3DVarAOWCDA CI test after it was disabled
    in https://github.com/NOAA-EMC/global-workflow/pull/2371

    Fixes github.com/NOAA-EMC/global-workflow/issues/2404

commit 3ccffeee120340ab580fc9d96b552970c9f42a8f
Author: Rahul Mahajan <[email protected]>
Date:   Mon Mar 18 09:30:35 2024 -0400

    Parse jediyaml only once (#2387)

    `JEDIYAML` was being parsed 3 times; once in `get_obs_dict`, second in
    `get_bias_dict` and a third time in `initialize` for the specific
    component analysis task.

    This PR:
    - eliminates the duplications and constructs the `jedi_config`
    dictionary just once. The dictionary is written out before calling the
    executable.
    - updates hash to gdasapp
    - updates configs for snow, aerosol, atmvar and atmens JEDI-DA to
    include `JEDI_FIX_YAML` and `CRTM_FIX_YAML` . This allows greater
    flexibility and control over the contents of these fix data sets to be
    copied into the run directory.
    - Combines snowDA and aerosolDA into a single test

    Co-authored-by: Cory Martin <[email protected]>
    Co-authored-by: David Huber <[email protected]>

commit a5f24951c5bef142747c6f6cc6abd474f0b53ac2
Author: CatherineThomas-NOAA <[email protected]>
Date:   Fri Mar 15 14:47:54 2024 -0400

    Fix ensemble archive groups to include all members (#2402)

    The number of groups used in the ensemble archive step (earc) needs to
    include a task for the ensemble stat files such as the mean and the
    spread, resulting in `n_groups+1` tasks for `earc`.

    Resolves: #2390

commit 056cfdca9e7fd7426a315fcbffc38d8ee2891212
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri Mar 15 18:30:23 2024 +0000

    GitHub message error paths (#2401)

    Add feature to message paths to error logs of failed experiments to
    GitHub Messaging the PR from Jenkins.

commit d897ee4936d62160811d936248c8555187f81b65
Author: Rahul Mahajan <[email protected]>
Date:   Thu Mar 14 12:37:49 2024 -0400

    Missed a comma from the hotfix this AM (#2399)

    This PR is a hotfix to the hotfix from earlier this AM. A comma was
    missing.

commit 906540acacf1b2ce4c0489d0d9d4913f53a4e8ad
Author: Rahul Mahajan <[email protected]>
Date:   Thu Mar 14 10:40:03 2024 -0400

    Fix KeyError issue in ocean/ice postprocessing job. (#2398)

    The jjob for ocean and ice pp, only defines the component specific
    history and grib directory. This causes an error in the exscript trying
    to pull keys for both ocean and ice. Fix this. Surprised this has not
    caused failures before today

    Co-authored-by: David Huber <[email protected]>

commit c27f243ce24c60261718f15628f6ab30d7b09f7b
Author: Rahul Mahajan <[email protected]>
Date:   Wed Mar 13 13:31:57 2024 -0400

    Remove documentation about generating ICs using global-workflow (#2397)

    Removes instructions on generating ics using global-workflow and
    directs the user to use ufs-utils.

commit 0edbdc197441582f9c402da0f3a7f144b88960c7
Author: DavidNew-NOAA <[email protected]>
Date:   Tue Mar 12 16:30:45 2024 -0400

    Changed config.atmanl to allow non-hybrid background error yamls (#2394)

    # Description

    Makes change so that if DOHYBVAR equals "NO", then the JEDI background
    error yaml is set to staticb_${STATICB_TYPE}.yaml.j2 rather than
    hybvar_${STATICB_TYPE}.yaml.j2. This allows GDAS to run without hybvar,
    which may be necessary for development purposes.

    This is all accomplished by a simple switch in config.atmanl.

commit ccb1f528489e740bb2adc4958146552323dd8709
Author: RussTreadon-NOAA <[email protected]>
Date:   Tue Mar 12 10:45:39 2024 -0400

    Add JEDI atmosphere only CI (#2357)

    The PR contains a minimal set of changes to enable JEDI atmospheric DA
    CI testing. Prototype JEDI atmospheric cycling has begun. The JEDI
    atmosphere DA CI case provides an automated way to see if future PRs
    impact JEDI atmospheric cycling.

    Resolves #2294
    Dependency: GDASApp PR
    [#937](https://github.com/NOAA-EMC/GDASApp/pull/937)

commit b96f5ebbb1968bd539336652b87a2faa8ce68fd4
Author: Kate Friedman <[email protected]>
Date:   Tue Mar 12 07:58:40 2024 -0400

    Add switch to control `debug=true` on WCOSS2 for development testing (#2388)

    Adds a switch (`DEBUG_POSTSCRIPT`) to control whether
    `debug=true` is set when submitting development rocoto jobs to PBS
    schedulers (currently just WCOSS2).

    There isn't an equivalent flag to set for SLURM on the RDHPCS.

    Have added this new switch to documentation.

    Refs #619

commit 02d650500353663d0b193ef14003897daa5dd86c
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Mar 11 21:51:16 2024 +0000

    Rewrote pr_list_database.py to use wxflow's SQLiteDB Class (#2376)

    This PR updates the `pr_list_database.py` code to use **wxflow**
    SQLiteDB Class

    - Improved code's readability
    - Uses better code style matching project's software culture
    - Better docstring standards

    Co-authored-by: tmcguinness <[email protected]>
    Co-authored-by: Rahul Mahajan <[email protected]>
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

commit a3374607d01fbdabbec0660afb82b5eb3677b4af
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Fri Mar 8 16:08:42 2024 -0500

    Return ocnanalrun npes resource setting back to previous value (#2386)

    Variable `npes` in `ocnanalrun` entry of `config.resources` was
    erroneously changed in
    https://github.com/NOAA-EMC/global-workflow/pull/2299 and this PR
    changes it back.

    Resolves https://github.com/NOAA-EMC/GDASApp/issues/962

commit d7e9bde84aebe922039589bd2bcd65832c1074eb
Author: BoCui-NOAA <[email protected]>
Date:   Thu Mar 7 16:14:28 2024 -0500

    Add new BUFR table file parm/product/bufr_ij9km.txt for GFSv17 C1152 (#2383)

    This PR will add a new table file parm/product/bufr_ij9km.txt, and
    modify ush/gfs_bufr.sh to choose the different bufr table files based on
    the GFSv17 run resolution, i.e. use file bufr_ij9km.txt for C1152 or
    bufr_ij13km.txt, for C768.

      Resolves #2382

commit 4a525bef3bbed2ea60a71f71b3740c82df125c36
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Thu Mar 7 16:12:31 2024 -0500

    Add global-workflow infrastructure for ocean analysis recentering task (#2299)

    Adds jjob, rocoto script, config file, and basic `config.resources`
    entry for ocean analysis recentering task

    This PR is a dependency for further work on the associated issue within
    global-workflow and GDASApp

    Refs https://github.com/NOAA-EMC/GDASApp/issues/912

commit f83d17a937006add55241ed453e42f4fcbae50aa
Author: Kate Friedman <[email protected]>
Date:   Thu Mar 7 09:29:14 2024 -0500

    Clean out non-gfs top level variables (#2366)

    Clean out non-gfs top level variables that are duplicates or no longer needed.
    Also standardize how we set these variables in scripts.

    Refs #2332

commit c7b306e052497aef0022cd53550a168d2c5b6e5b
Author: Guillaume Vernieres <[email protected]>
Date:   Wed Mar 6 16:16:08 2024 -0500

    Forgotten templated  DO_VRFY_OCEANDA (#2379)

    # Description
    This PR adds the possibility to use the switch for the ocean and sea-ice
    DA verify task from the yaml configuration.

    - fixes
    [GDASApp/issues/954](https://github.com/NOAA-EMC/GDASApp/issues/954)

commit ba6a4fdf6e245b57530f2b20e6f0ccf567115720
Author: David Huber <[email protected]>
Date:   Tue Mar 5 19:09:48 2024 +0000

    Add Hercules support for the GSI monitor (#2373)

    # Description
    This updates the GSI monitor hash and updates the modulefiles to add
    support for the monitor on Hercules.

commit 732a874a2c6793296f136afb23545fab9869b181
Author: Rahul Mahajan <[email protected]>
Date:   Mon Mar 4 16:04:26 2024 -0500

    Reformat snowDA templates to jinja2 (#2371)

    # Description
    This PR:
    - replaces use of non-jinja2 templates in the yaml templates.
    Specifically `$( )` in favor of pure jinja2.
    - uses jinja2's built-in capability to include templates within
    templates, thereby allowing to assemble a completely rendered template
    before passing it to for e.g. yaml loader.
    - requires updates to `wxflow` and `gdasapp`
    - Changes in `wxflow` in `parse_j2yaml` are **not** backwards compatible

    Additionally, this PR:
    - renames `config.base.emc.dyn` to `config.base`.  Resolves #2347

commit d1fa41106e991556606b0f62a15bf45f469f4f79
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Sat Mar 2 04:54:26 2024 +0000

    Reduce Jenkins messaging to GitHub (#2370)

    This PR updates the Jenkins Pipeline code with safeguards against the
    errors caused when Jenkins fails to authenticate with GitHub to message
    or update a label. This was achieved simply by:

    - Reducing the number out messages sent to the GitHub PR
    - Putting try blocks around most of the update label calls

    Co-authored-by: tmcguinness <[email protected]>

commit 52fa3cb32d8b50e47f391b82ea8901435fc88aff
Author: Henry R. Winterbottom <[email protected]>
Date:   Fri Mar 1 12:36:27 2024 -0700

    Adding debug option for all build scripts (#2326)

    This PR addresses issue #300 that allows building in `debug` mode.
    Co-authored-by: David Huber <[email protected]>
    Co-authored-by: Rahul Mahajan <[email protected]>

commit 91738cbf871d8cdce46912e2c11e304d567a2aae
Author: DWesl <[email protected]>
Date:   Fri Mar 1 13:46:42 2024 -0500

    Sort list of coupler restart files for restart time determination (#2360)

    The loop in the following conditional seems to assume the list is
    sorted, so make that explicit in the array construction.

commit 23c25527ad2a62275cd9105bd103b8520a28e573
Author: Neil Barton <[email protected]>
Date:   Fri Mar 1 13:45:39 2024 -0500

    Update stage IC to handle ocean perturbations (#2364)

    This PR adds the option to stage ocean perturbation files for ensemble
    forecasts. These perturbation files are used in GEFS forecasts.
    A new variable is introduced in config.base to use the ocean
    perturbation files.
    This PR does not include using these perturbation files. A future PR
    will address this.

commit 8efe05f475b81e7cf6376745d5f1ce31987cb4eb
Author: Jessica Meixner <[email protected]>
Date:   Fri Mar 1 07:41:56 2024 -0500

    Turn on C48mx500_3DVarAOWCDA test on hera (#2363)

    This PR activates the C48mx500_3DVarAOWCDA test on hera. This required
    an update of the gdas app.

commit 5166593945e9ecc04dfa3409752576c08797d09f
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Feb 29 20:14:41 2024 +0000

    Move Jenkinsfile into ci subdirectory (#2355)

    Just moves the Jenkinsfile into the ci directory

    Co-authored-by: tmcguinness <[email protected]>

commit b7af315bb9dea77b37c6d030b71060b87bedf33e
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Feb 28 22:20:58 2024 +0000

    Fix rocoto forecast hour determination for GEFS (#2351)

    The function that generates the list of forecast hours for rocoto was
    trying to use variables that are not defined for GEFS, causing workflow
    generation to fail. The function is updated to not try to load these
    variables before loading the ones actually used for GFS/ GEFS.

    Also turns GEFS CI test back on and adds an entry to stage C192 ICs
    (note: these have not been placed in the centralized location.)

commit d3a49271b6c3816a9feeb7f6fb474797bacf1d7e
Author: Cory Martin <[email protected]>
Date:   Wed Feb 28 09:38:49 2024 -0500

    Rename the land DA jobs to snow DA to better reflect what they are doing (#2330)

    This PR renames all of the land DA jobs to snow DA to better reflect
    that this is a JEDI-based snow analysis capability and not a more
    generic land surface analysis.

commit 2693810d6ea9d9b20090777ff3a98e3d072c76d7
Author: Jessica Meixner <[email protected]>
Date:   Tue Feb 27 01:25:51 2024 -0500

    Update ufs-waether-model hash (#2338)

    Routine update of ufs-weather-model hash.

    Other small updates:
    * removes comment referencing closed issue.
    * Updates the CICE diag frequency to once per day as recommend here:
    https://github.com/NOAA-EMC/global-workflow/issues/1810#issuecomment-1686278925
    * Updated amount of time for C384 gdas forecast as it was running out of
    time
    * Removed unused variable wave_sys_ver

commit 9608852784871ebf03d92b53bde891b6dcab8684
Author: RussTreadon-NOAA <[email protected]>
Date:   Mon Feb 26 14:10:01 2024 -0500

    Update JEDI ATM to use .nc for obs and generalize x,y layout (#2336)

    # Description
    The changes in this PR are twofold
    1. replace `.nc4` suffix for JEDI ATM observation related files with
    `.nc`
    2. use templated variables to specify `{layout_x, layout_y}` for JEDI
    ATM variational and local ensemble apps

    The first change conforms with the Unidata recommendation that netCDF
    files end with the suffix `.nc`. The second change replaces hardwired
    JEDI ATM var and ens `{layout_x, layout_y}` in `config.resources` with a
    more flexible approach.

    Resolves #2335

commit c5c84660f10f0ef9ce939231b2f7fda498b39a29
Author: Kate Friedman <[email protected]>
Date:   Mon Feb 26 10:18:50 2024 -0500

    Remove FIX* variables for fix subfolders (#2337)

    Remove `FIX*` variables for fix subfolders and replace them with the remaining `FIXgfs` variable and the subfolder name (e.g. `${FIXam}` -> `${FIXgfs}/am`).

    The UFS_UTILS and GDASApp repos were similarly updated. This PR includes a new UFS_UTILS hash.
    The updated GDASAPP hash was already committed within the spack-stack/1.6.0 PR #2239.

    Resolves #2184

commit 950c38a093c6a4e2b67e18c76390280d8bfbaef7
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri Feb 23 21:15:46 2024 +0000

    Fix several Jenkins issues (#2334)

    Jenkins Updates Resolving final kinks:
    - Removed all `git` shell commands and now exclusively use Software Control
    Manger (**scm**) plugin.
    - Add feature for skipping hosts per configuration specified in case yaml files.
    - Solved and tested false positive builds and experiments.
    - Tested archiving of task error log on case fail
    - First case fail quits pipeline and cancels all pending scheduled jobs
    - Duel build per yaml configuration arguments supported
    - All designated case files in PR directory pass on intended host (fully tested
    on Hera)

    Remaining updates:
    - Fist build fail short circuit when building sub-modules and archiving build
    error log.
    - Re-build/no-build built in logic for Replay and Rerunning previously failed
    experiments.

commit c67393a203285792b852da0d83fd10fa47155669
Merge: 6f9afff07 79d305e8c
Author: David Huber <[email protected]>
Date:   Fri Feb 23 14:18:15 2024 +0000

    Merge pull request #2239 from DavidHuber-NOAA/ss160

    Update to spack-stack 1.6.0

    Includes all submodules except the UFS, which will be updated at a later time.

commit 79d305e8cbc339208ea6fe0475ddc56af94a285b
Author: David Huber <[email protected]>
Date:   Thu Feb 22 14:53:57 2024 -0600

    Disable snow DA tests

commit 0459203e97211b041520b39e93a188951396ba33
Author: David Huber <[email protected]>
Date:   Thu Feb 22 12:55:51 2024 -0600

    Update GDASApp hash to current develop

commit 5c96eb2272fe6117f9e4a4c0c790db58e4870d46
Author: David Huber <[email protected]>
Date:   Thu Feb 22 12:37:47 2024 -0600

    Update GDAS hash to allow modified snow DA analysis

commit 79144f2403a33d08140577cc3e8a61d6c4924403
Merge: abbb0b8a7 6f9afff07
Author: DavidHuber <[email protected]>
Date:   Thu Feb 22 15:14:39 2024 +0000

    Merge remote-tracking branch 'origin/develop' into ss160

commit abbb0b8a76b39d34433802fd4e3d7973fb9f0a39
Merge: 4ad837ea1 4529e8cf3
Author: DavidHuber <[email protected]>
Date:   Thu Feb 22 15:11:03 2024 +0000

    Merge remote-tracking branch 'henry/feature/gwdev_issue_2129' into ss160

commit 4ad837ea157b98d2bd173cb696c4d30d142e5540
Merge: 516b2a270 7ca45db8f
Author: DavidHuber <[email protected]>
Date:   Thu Feb 22 15:10:24 2024 +0000

    Merge remote-tracking branch 'henry/feature/gfsv17_issue_2125' into ss160

commit 516b2a270234bdab5714ef2705c83dd3835b134d
Author: DavidHuber <[email protected]>
Date:   Thu Feb 22 14:19:16 2024 +0000

    Updated GDAS to include rocoto/1.3.6 on Hera.

commit 6f9afff073dd589096f992a3448fb7f0e62c9804
Author: Jessica Meixner <[email protected]>
Date:   Wed Feb 21 13:09:44 2024 -0500

    Add some flexibility for ocean/ice output (#2327)

    This adds functionality to have ocean/ice output frequency be separate from the atm model. One time was created because there's an assumption in the post that these are the same. This could be further modified to remove this assumption.

    Refs #1629

commit f6d3015ab9f9fd23ce0081baa2edbc5d9f5f3e16
Author: David Huber <[email protected]>
Date:   Tue Feb 20 09:53:08 2024 -0600

    Update GDASApp hash to include SS/1.6.0 support.

commit 0bf340bce2f865c582e5305f0c5984cd3affe74e
Author: David Huber <[email protected]>
Date:   Tue Feb 20 09:07:32 2024 -0600

    Construct SS paths from version variables.

commit 3330cd7310bde8090b68720c225656074676d6b2
Author: David Huber <[email protected]>
Date:   Tue Feb 20 09:06:19 2024 -0600

    Removed MET/METplus 'not available' comments

commit fdc638ca1616b347912caec77e5abc2d3e6f18af
Author: David Huber <[email protected]>
Date:   Tue Feb 20 08:35:15 2024 -0600

    Move SS module path to version files.

commit d7d28a6b65b84c8d821abd2c13d0c068bd5ad6d8
Author: David Huber <[email protected]>
Date:   Tue Feb 20 07:53:15 2024 -0600

    Update comment about METplus support.

commit a812f88af3fc043d57494840e81a7527723858e4
Author: David Huber <[email protected]>
Date:   Tue Feb 20 07:45:45 2024 -0600

    Update verif-global to latest WCOSS2 support.

commit d81f07fbf53666a37ab01bd463152e10252869ae
Author: David Huber <[email protected]>
Date:   Tue Feb 20 07:41:38 2024 -0600

    Clean up build_upp.sh.

    -Corrected whitespace (tabs instead of spaces)
    -Removed debug print statement
    -Alphebetized flags

commit ae7eb194cbe2213e564807dd7bc03a28d493eff2
Author: David Huber <[email protected]>
Date:   Fri Feb 16 16:15:40 2024 -0500

    Fix whitespace in build_upp.sh.

    Co-authored-by: Rahul Mahajan <[email protected]>

commit 48b34d0f388a398bb91f7c3b1e5f8338f4beb7b9
Author: David Huber <[email protected]>
Date:   Fri Feb 16 20:56:55 2024 +0000

    Added verif-global support back to WCOSS2.

commit 4529e8cf3736ffbacf615a27e99f4d1beec391aa
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Fri Feb 16 11:12:01 2024 -0700

    Bug fix.

commit 8e4f94d13d32849b2862a9d59aa070f4103c61ae
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Fri Feb 16 11:04:41 2024 -0700

    Updates requested by reviewer Rahul Mahajan.

commit 4624ce21c99ab303afa10c1dd8ddcce7b6f715ca
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Fri Feb 16 10:52:11 2024 -0700

    Updates requested by reviewer; testing -- DO NOT REVIEW.

commit ed25bbd0b26a893d32ce4a10b368dec2bb722424
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Fri Feb 16 09:33:59 2024 -0700

    Linter corrections.

commit 6a0b7bf214815c13eec98a93bd3abe9978de04e4
Merge: f9fb64ef8 2415b7b4f
Author: David Huber <[email protected]>
Date:   Fri Feb 16 09:50:22 2024 -0600

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit f9fb64ef802b683d7b369f8e8268d423ab581481
Merge: 777d97d3a a23b7f2fd
Author: David Huber <[email protected]>
Date:   Fri Feb 16 09:49:42 2024 -0600

    Merge remote-tracking branch 'emc/develop' into ss160

commit 7ca45db8fa32c84ef117ff2938a650822c81a786
Merge: 73bc76bfd a23b7f2fd
Author: Henry R. Winterbottom <[email protected]>
Date:   Fri Feb 16 07:46:35 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125

commit eb2ed53857eb3387735488a1ce5d701ff680e3db
Merge: 9929277dc a23b7f2fd
Author: Henry R. Winterbottom <[email protected]>
Date:   Fri Feb 16 07:46:24 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129

commit a23b7f2fdca5be700d257e28052a0104f2173a0f
Author: RussTreadon-NOAA <[email protected]>
Date:   Fri Feb 16 09:37:58 2024 -0500

    Add JEDI 3DEnVar atmosphere only CI test stub (#2309)

commit cf83885548bb3a6740c033f42479ce2ad283a4a9
Author: Jessica Meixner <[email protected]>
Date:   Fri Feb 16 01:55:02 2024 -0500

    Add unstructured grid for HR3/GFS (#2230)

    This adds the capability to use unstructured grids in the global workflow,
    which will be used in HR3.  There are new fix files for a low-resolution
    100km grid and a grid closer to our targeted GFSv17 grid which has the
    resolution combined from the older multi_1 and GFSv16 grids.

    The fix file update is here: NOAA-EMC/global-workflow#2229

    Note: This now means that GFS tests need a new build option:
    `./build_all.sh -w` So that PDLIB=ON is turned on for compiling relevant
    UFS and WW3 codes.

    Resolves NOAA-EMC/global-workflow#1547

commit 9929277dc7d0ad90f5366faf4b5f2278969a0aa2
Merge: eb8791ccb 094e3b86d
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Feb 15 15:05:50 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129

commit 094e3b86da44f1d3fc1d99f68f6fdfcd36deb09f
Author: Cory Martin <[email protected]>
Date:   Thu Feb 15 14:43:55 2024 -0500

    Move IMS remapping files from COM_OBS to FIXgdas (#2322)

    * Add in IMS obs fix directory and update submodule for gdas

commit d465ea06e8b2a8f3a5eb1120647c1e2ce5197d66
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Feb 15 19:25:02 2024 +0000

    Set HOMEgfs for module_setup in CI driver (#2321)

    Hotfixes to  CI Bash system from updates with sourcing
    `detect_machine.sh` in `ush/module-setup.sh` using **HOMEgfs**.

commit 2415b7b4f3e6c376aca27707510001141cc9dd92
Author: David Huber <[email protected]>
Date:   Thu Feb 15 19:21:17 2024 +0000

    Load default rocoto on Jet.

commit eb8791ccbe684828dc529d0e553551969274fc22
Merge: 60d5ee64b 638684e0b
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Feb 15 11:56:40 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129

commit 777d97d3a1c9f5ec5e8af3ca40a41224ec7099a1
Author: David Huber <[email protected]>
Date:   Thu Feb 15 12:34:59 2024 -0600

    Fixed Orion cdo version.

commit ef0723503c72f295de93521c7102c43e75c47417
Author: DavidHuber <[email protected]>
Date:   Thu Feb 15 16:29:32 2024 +0000

    Revert UFS hash.

commit 0ce8c0dbc13227884fef1c637e93616a28c68d34
Author: DavidHuber <[email protected]>
Date:   Thu Feb 15 14:55:48 2024 +0000

    Fix git version in Hera's gwsetup module.

commit 3080a34253e8e24105bf2be72b6a872b1c072935
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 20:52:34 2024 +0000

    Fixed xarray version for SS/1.6.0.

commit 49392dd47ff84b6586052aeae6879d7d8050b746
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 20:29:41 2024 +0000

    Updated GSI-Utils hash to head of develop.

commit c3553f0d8e6a05c6234e7c14a179983aa44fd6f3
Merge: 4568653a6 638684e0b
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 20:28:14 2024 +0000

    Merge remote-tracking branch 'origin/develop' into ss160

commit 4568653a67aa37c902379db628fb10f69fe7190f
Author: David Huber <[email protected]>
Date:   Wed Feb 14 14:22:13 2024 -0600

    Reupgrade Hercules to SS/1.6.0

commit 638684e0bfcd06700cc8695f09824891a0a1eee1
Author: Kate Friedman <[email protected]>
Date:   Wed Feb 14 14:55:21 2024 -0500

    Remove `finddate.sh` from system (#2308)

    * Retire finddate.sh usage from system
    * Update gfs-utils hash to 7a84c88 - New hash includes removal of finddate.sh

    Refs #2279

commit 2b160f8470bed16c513ca4a5665e2b6d4448c50e
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 18:31:28 2024 +0000

    Reenable METplus jobs on Hercules.

commit 8f5900265a31e894060bbe9c89b262f4df0b1760
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 18:30:23 2024 +0000

    Update GSI hashes.

commit 73bc76bfd47f2cff54df55e15d9ed8969683367d
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 14 09:27:37 2024 -0700

    Updates based on user request.

commit e4bc674cf3b2df10e0b0dfd50a8ecb0f4f7825d8
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 14 08:03:45 2024 -0700

    Corrected based on reviewer review.

commit 60d5ee64bda7a16c1f2dc20c8badcd7c8fc4e592
Merge: 40f2cf6cd 1aaef05d3
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Feb 13 18:08:33 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129

commit 03304112347a673b7a0fcc404703bb10960bc47a
Merge: 929b90330 1aaef05d3
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Feb 13 17:58:12 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125

commit 1aaef05d317cd1eec548ef2b9842679c531cef8b
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Feb 13 18:15:59 2024 -0500

    Jenkins Pipeline updates for Canceling Jobs (#2307)

    Tuning updates for Jenkins Pipeline :
    - Added short circuit for all parallel runs of cases on error of any
    - Fixed canceling of all scheduled jobs on first case error
    - Added feature to save error log files to Jenkins Archive facility on fail

commit 64048926627f8c9edb087de286095e3b93a214c2
Author: Rahul Mahajan <[email protected]>
Date:   Tue Feb 13 14:57:37 2024 -0500

    Ocean/ice product generation for GFS and GEFS (#2286)

    This PR does several things:
    1. the model output for ocean and ice in the `COM/` directory are now
        named per EE2 convention for coupled model.
        E.g `gfs.ocean.t12z.6hr_avg.f120.nc` and `gfs.ocean.t12z.daily.f120.nc`
    2. The products are generated using the `ocnicepost.fd` utility developed
        by @DeniseWorthen in https://github.com/NOAA-EMC/gfs-utils and
        converted to grib2 using example scripts provided by @GwenChen-NOAA
        using `wgrib2`.
    3. NetCDF products on the native grid are also generated by subsetting
        variables from  the raw model output.  This is done with `xarray`.
    4. updates the hash of https://github.com/NOAA-EMC/gfs-utils to include
        fixes in `ocnicepost.fd`
    5. removes NCL related scripting that was previously used for ocean/ice
        interpolation and `reg2grb2` used for converting to grib2.
    6. updates archive scripts to accommodate updated file names
    7. removes intermediate ocean processed files such as 2D/3D/xsect data-
        sets
    8. separate jobs are added for ocean and ice product generation.
    9. removes intermediate restarts for the mediator and only saves the medi-
        ator restart at the end of the forecast in `COM`.
    10. Increases memory for offline UPP when run at C768.  The program
          segfaults with an OOM when memory is self allocated based on PEs by
          the scheduler on Hera.
    11. Enables ocean/ice ensemble product generation for GEFS
    12. Some minor clean-ups

    Fixes #935
    Fixes #1317
    Fixes #1864

commit 40f2cf6cd70ac94e01babc96982f37ae1b0c7e79
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Tue Feb 13 10:18:53 2024 -0700

    Implemented ush/detect_machine.sh for host determination and removed redundant checks for expected file paths.

commit 929b90330c7eb345011c2c850915e0004ca26b11
Merge: 2d08d015a 3f99f700c
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Feb 13 08:31:06 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125

commit 3f99f700c987526c8eb754b3f4c7b698b3e9b1dc
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Feb 13 00:57:18 2024 -0500

    Add wave post jobs to GEFS (#2292)

    Adds the wave post jobs for gridded and points to GEFS. Boundary
    point jobs are added even though the current GEFS buoy file does
    not contain any (tested by manually subbing in the GFS buoy file).

    Resolves #827

commit 842adf38087aec9f1c0bca9567e4b11d494e14c7
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Feb 12 12:50:08 2024 -0500

    Added additional test cases to the pr list in Jenkins (#2306)

    C48mx500_3DVarAOWCDA, C96C48_hybatmDA, and C96_atmsnowDA
    Co-authored-by: terrance.mcguinness <[email protected]>

commit bb4ca65fe5524f76e40b97346339f1dda6680ce1
Author: CatherineThomas-NOAA <[email protected]>
Date:   Mon Feb 12 14:50:41 2024 +0000

    Redo v16.3 config.base changes for DA increments (#2304)

    Include the additional hydrometeors to the
    INCREMENTS_TO_ZERO and INCVARS_ZERO_STRAT
    variables in config.base that were modified
    in v16.3.

    Resolves: #2303

commit 061992bb6160554430cf688adf6184f01b732098
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Sat Feb 10 01:33:36 2024 -0500

    Fix Jenkins success reporting (#2302)

    Moving the post section back outside of main Run Experiments
    stage. This allows the system to correctly report the **Success**
    status until after all tests pass.

    _Had originally moved them in attempts to solve "Not an SCM
    GitHub Job" issue and cause the reporting to misbehave._

    Also ran through Jenkins linter and updated some messaging
    that was incorrectly reporting system build type.

commit 28ccf78073a20ba1e4d3b379d164109b54ff6708
Merge: b972f66fc 54daa31ce
Author: David Huber <[email protected]>
Date:   Fri Feb 9 14:00:43 2024 -0600

    Merge remote-tracking branch 'emc/develop' into ss160

commit b972f66fc924790c48f38d395e7141fa78ef9d90
Author: David Huber <[email protected]>
Date:   Fri Feb 9 10:47:00 2024 -0600

    Fix SS versions for CI modules.

commit 4b01d8eeca26c3b3d843a4b1e7b1618f281de68f
Author: David Huber <[email protected]>
Date:   Fri Feb 9 10:44:30 2024 -0600

    Revert Hercules modules to SS/1.5.1.

commit 54daa31ce0a3c23d4d74def5e54436a39a899ed4
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Feb 8 15:48:38 2024 -0500

    Jenkins Declartive Pipeline for CI with gfs/gefs multibuilds (#2246)

    Adding top level Jenkins file for CI tests running on Jenkins Controller:

    - Declarative Multi-branch Pipeline (has enhanced restart capabilities
    on a per section bases)
    - Starts Pipeline from Label PR same as BASH system (for now)
    - Progress and restarts can me managed with CAC Login at [EPIC OAR
    Jenkins](https://jenkins.epic.oarcloud.noaa.gov)
    - Has logic for multi **gfs/gefs** system builds (arguments based on a
    configuration file `ci/casts/yamls/build.yaml`)
      - Any number of **systems** may be added by manual adding an ele-
    ment to the matrix in the Jenkinsfile
      - _It may be possible to dynamic add matrix values with a specialty
    plug-in_
    - Currently only runs on **Orion** and **Hera** using `mterry` account

    Resolves #2119
    Resolves #2118

commit 43429e23c12c1f2050b3a3f356abdec98dc73ea0
Author: Rahul Mahajan <[email protected]>
Date:   Thu Feb 8 15:30:28 2024 -0500

    Enable AO WCDA test (#1963)

    This PR:
    - adds GSI + SOCA C48 5-deg ocean 3DVar test (courtesy @guillaumevernieres)
    - adds a toggle to optionally disable ocnanalvrfy job.

commit 2d08d015afb9c850577efd9754add16b10c45ae6
Merge: 4745d4a06 f56352874
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Feb 8 07:24:54 2024 -0700

    Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125

commit f56352874d6dc133a4f1181f77c8f91ca38a6416
Author: Kate Friedman <[email protected]>
Date:   Wed Feb 7 15:09:12 2024 -0500

    Update JGLOBAL_FORECAST for octal error (#2295)

    Add "10#" to ENSMEM value > 0 check to handle octal errors.

commit 4745d4a06148cc6c702c647e12ede4875e3a5862
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 7 08:45:49 2024 -0700

    Removed jlogfile references.

commit 5894ca2bf11e8ab7910c69781a9fbe51352a7e8c
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 7 08:32:16 2024 -0700

    Removed dummy variable passed to perl scripts.

commit dae884a7c48b4a30c1844685c3d0ef50c9b78344
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 7 08:29:49 2024 -0700

    Removed jlogfile and postmsg references within gempak scripts.

commit 801058ffb0cbbfe101fd5b686aed79c5bf7538c1
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Feb 7 00:41:59 2024 -0700

    Consolidate `npe_node_max` (#2289)

    - The environment variable `npe_node_max` is removed from all
    files beneath `global-workflow/env`;
    - The environment variable `npe_node_max` is removed from
    `parm/config/gefs/config.ufs` and `parm/config/gfs/config.ufs`;
    - The environment variable `npe_node_max` is maintained only
    within `parm/config/gefs/config.resources` and
    `parm/config/gfs/config.resources`.

    Resolves #2133

commit b0325e0157598702cbba6c3cc09af0120881e2b4
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Feb 7 00:40:20 2024 -0700

    Removes files module loading file no longer used by the GW (#2281)

    Removes `module-setup.csh.inc` and `module-setup.sh.inc`.

    The module `ush/module-setup.sh` is updated such that it now sources
    `ush/detect_machine.sh` to determine which supported platform the
    global-workflow is being execute on.

    Resolves #2130

commit 1ccc9896b361f2aaef8e6e7592a06ae4cfb7c491
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Feb 5 14:16:07 2024 -0500

    Remove EnKF forecast groups (#2280)

    Removes the grouping of EnKF forecasts so each job only runs
    one forecast. Member and MEMDIR are now set at the workflow
    manager (rocoto) level. This change makes much of the system
    simpler (especially dependencies) and allows the elimination of
    the separate efcs scripts.

    Metatask names of updated jobs have been updated to make
    them a little less opaque by using the same name name as its
    constituent tasks (e.g. the forecast metatask is named
    `enkgdasfcst`, not `enkfgdasefcs`). Metatasks that weren't
    updated retain the same names as before for now.

    Resolves #2254

commit 9f3383fd8d8322428a40b94764a172a16872995e
Author: Henry R. Winterbottom <[email protected]>
Date:   Mon Feb 5 12:15:13 2024 -0700

    Updated detect_machine.sh using that from UFS WM. (#2252)

    Updates `ush/detect_machine.sh` to match the UFS weather-model
    `tests/detect_machine.sh` prepared by @BrianCurtis-NOAA

    Resolves #2228

commit 7d68b0b164f0ffcd56867ae4fdab67905d9589eb
Author: CatherineThomas-NOAA <[email protected]>
Date:   Sun Feb 4 22:02:41 2024 +0000

    Update global_cycle for fractional grid (#2262)

    The hash for ufs_utils is updated to include the changes for
    fractional grid support within global_cycle.  This commit also
    removes the hack to skip global_cycle in cycling mode with
    v17 physics.

    Resolves: #1775
    Refs: ufs-community/UFS_UTILS#815
    Refs: ufs-community/UFS_UTILS#891

commit ed592a6ecfabc0d0b64a6e276531b7bc5ae3b8ea
Author: Kate Friedman <[email protected]>
Date:   Sat Feb 3 02:55:14 2024 -0500

    Retire cycle-specific FHMAX_GFS variables (#2278)

    This PR retires the `FHMAX_GFS_${cyc}` variables that allowed users to specify
    different gfs forecast lengths for each cycle. This function is no longer supported
    in global-workflow. The `FHMAX_GFS_*` variables will be removed and will no
    longer be checked to set the final `FHMAX_GFS` variable. The same forecast
    length will be set for every cycle.

    This PR also includes a small fix to add new post parm files into the `.gitignore`
    file. This was intended to be included in a different PR but that PR is on hold for
    further testing so it is being included here to get it into `develop` sooner.

    Resolves #2218

commit 977e2d67b268477321aa26fc56073dd373e4f979
Author: Henry R. Winterbottom <[email protected]>
Date:   Fri Feb 2 07:49:09 2024 -0700

    New GDASApp hash. (#2285)

commit b5f2bd9ec5632c4be43004604eed0e130dfe1735
Merge: 4d667421d 0400e1f35
Author: David Huber <[email protected]>
Date:   Tue Jan 30 13:55:00 2024 -0600

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit 0400e1f3558be8e34c1298d32e14999c9dd46f8c
Author: David Huber <[email protected]>
Date:   Tue Jan 30 09:57:11 2024 -0600

    Fix gfs_utils Orion spack-stack env path.

commit 6bbe823e729291db326d108765d3a92a99552a58
Author: DWesl <[email protected]>
Date:   Mon Jan 29 21:15:30 2024 -0500

    Use seq to generate the list of times, instead of a bash for-loop (#2264)

    I'm running a year-long forecast, which means I get a large portion of the log file dedicated to these loops.

    `seq ${START} ${STEP} ${STOP}` will generate a sequence going from START to STOP by STEP, including STOP if relevant.  That seems to be the purpose of these loops.  It will by default separate the list with newlines, but `seq -s ' ' ${START} ${STEP} ${STOP}` will separate them with spaces instead, more closely mimicing the previous behavior.

    I would like this to be two lines in the log, rather than a few hundred, and this may also be faster, though probably more for reasons of fewer writes to disk than because bash isn't designed for arithmetic.

commit d5bee38979cde547861261d1cd150f3a61601d4b
Author: Kate Friedman <[email protected]>
Date:   Mon Jan 29 14:35:02 2024 -0500

    Correct typos in GFS config.resources (#2267)

    This PR corrects some typos in `parm/config/gfs/config.resources` that were
    introduced in PR #2216. The esfc job was failing in tests on WCOSS2 due to
    insufficient memory. This lead to discovering the other typos. The esfc job
    completes without error after its memory is set back to `80GB` from the
    incorrect `8GB`.

    Resolves #2266

commit 81557beca9eecd878e7b25b3822e30a4276f4a16
Author: David Huber <[email protected]>
Date:   Mon Jan 29 12:13:31 2024 -0600

    Update monitor hash to noaa-emc with SS/1.6.0 support.

commit 2238dd6ac0094ba2ff5e1027e964ef29ad33352c
Author: DavidHuber <[email protected]>
Date:   Mon Jan 29 13:21:30 2024 +0000

    Update Orion, Hercules, S4 modulefiles.

commit 6ffd94fd95f54ceb940f0c9201774ad73fbb055b
Author: DavidHuber <[email protected]>
Date:   Fri Jan 26 16:01:23 2024 +0000

    Update GDAS hash to include SS/1.6.0 support.

commit be11f85f28cf832e5fbb390fdd387f1bdecb5f82
Merge: 56b968080 04e0772d9
Author: DavidHuber <[email protected]>
Date:   Fri Jan 26 15:34:24 2024 +0000

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit 8ff344844e28c3b2d03a0356f88b14635f318c12
Author: Rahul Mahajan <[email protected]>
Date:   Fri Jan 26 10:12:18 2024 -0500

    Add a yaml for snow DA testing. (#2199)

    - adds a new test yaml C96_atmsnowDA.yaml for 3DVar atmosphere with GSI and Land (Snow) DA with JEDI
    - moves a few yamls from platforms/ to yamls/
    - adds ability to overwrite a previously created experiment as an addition to user input.
    ---------

    Co-authored-by: Cory Martin <[email protected]>

commit 04e0772d9d3e77ac5a24ce4570d48cb41424a08b
Author: David Huber <[email protected]>
Date:   Fri Jan 26 07:16:25 2024 -0600

    Update ufs_utils hash for spack-stack/1.6.0 support.

commit 3d44ff38c5c3324c22fc104fe3259b4ac864c6d6
Author: Barry Baker <[email protected]>
Date:   Thu Jan 25 14:33:27 2024 -0500

    GOCART ExtData biogenic climatology fix (#2253)

    Updates the ExtData for biogenic emissions to be climatology rather than
    for current time.  Fixes an issue which will crash by default for other years.

commit 66f58b8ab1a9524d6be95271f27a06c2f32e5f78
Author: Guillaume Vernieres <[email protected]>
Date:   Thu Jan 25 13:16:41 2024 -0500

    Added missing container case in gfs/config.resources (#2258)

    fixes  #2257

commit 553b4f2e74ef610115436b75f7f6df100babd8dd
Author: WenMeng-NOAA <[email protected]>
Date:   Thu Jan 25 13:00:45 2024 -0500

    Fix post parm links (#2243)

    Change symbolic links under parm/post with the latest version of develop branch from UPP repository and enable MERRA2 aerosol fields.

    Resolves #2259

commit 4d667421d5eefea2347ea1dd8097e39e167d7201
Merge: 6c058039e afa09e356
Author: David Huber <[email protected]>
Date:   Thu Jan 25 07:49:08 2024 -0600

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit 6c058039e209c67ea477d37d2d6f76b7a2fa68ac
Author: David Huber <[email protected]>
Date:   Thu Jan 25 07:48:42 2024 -0600

    Fix wgrib2/gfs_utils on Hercules.

commit ee6f536ea0228c60f5a8bec4037cd6f7ea63b816
Author: Kate Friedman <[email protected]>
Date:   Thu Jan 25 07:43:13 2024 -0500

    Update GFS version to v16.3.13 in index.rst (#2256)

    GFSv16.3.13 WAFS update was implemented

    Refs #2013

commit 2445d44d0d66f35512080b0bd5867501660793bb
Author: RussTreadon-NOAA <[email protected]>
Date:   Thu Jan 25 06:17:11 2024 -0500

    Simplify and extend load_ufsda_modules to Hercules (#2245)

    GDASApp jobs do not run on Hercules because `ush/load_ufsda_modules.sh` does
    not include logic to load the appropriate GDASApp modules on Hercules.  This PR
    extends `load_ufsda_modules.sh` functionality to Hercules, thereby enabling
    GDASApp jobs to run on Hercules.

    Resolves #2244

commit 56b9680803f109720f6439276a0e5783a9c49352
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 19:47:34 2024 +0000

    Update hashes (revert WCOSS2 modules).

commit afa09e356503f1befc162df9a79dc9ce7414dc22
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 18:59:40 2024 +0000

    New (cleaner history) gdas hash.

commit a9eaec23d5103ea766342ff81d77df8e0f6d9a58
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 18:52:27 2024 +0000

    Update gdasapp to include ss/1.6.0 support.

commit 5ef8eb24eeaeaff9c9a03767d929f2114fd4840f
Merge: 4c463548b e400068a2
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 17:08:54 2024 +0000

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit 4c463548b0c38f36c13c01716fa0b1e91544e440
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 17:05:12 2024 +0000

    Reenable verif-global support

commit f775755df5f1579edfafbce9a7b47034907d023f
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 16:59:10 2024 +0000

    Assign fcsthrs for awips_g2 job.

commit e400068a2951e5fa3b130369861b4a60ece01491
Author: David Huber <[email protected]>
Date:   Mon Jan 22 15:01:07 2024 -0600

    More gsi-addon path fixes.

commit f663d4786f226f8164d348d403e8d105cc3d801b
Author: David Huber <[email protected]>
Date:   Mon Jan 22 14:41:59 2024 -0600

    Fix gsi-addon paths for hercules, orion, and S4.

commit e304bbeb364067e411fb50801796d000b44d9147
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:59:34 2024 +0000

    Better optimize build jobs (more ufs jobs).

commit ccc6e2d445d4c2e2f44fb907c7bc972b1e69f6ff
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:56:18 2024 +0000

    Reenable verif-global. #2195

commit 3ef3411f856b0c5a9cf51686f3a51a2252596690
Merge: 4365f63e5 f4d187f4e
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:39:10 2024 +0000

    Merge remote-tracking branch 'origin/develop' into ss160

commit 4365f63e54e2ddb9b88e768a6e88a92504b5d482
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:37:25 2024 +0000

    Corrected the SS env. name in the version files. #2195

commit f4d187f4e45fe89583d18987d68a883490827104
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Mon Jan 22 12:28:28 2024 -0500

    Converts obsproc to obsprep in prepoceanobs config file (#2236)

    Converts obsproc to obsprep in prepoceanobs config file as a compliment to mutually depended GDASApp PR NOAA-EMC/GDASApp#858
    The motivations are explained in refs NOAA-EMC/GDASApp#857

commit 9a09d3082208ad206cf6e7103a53bfb7c4946f4a
Author: DavidHuber <[email protected]>
Date:   Fri Jan 19 21:23:50 2024 +0000

    Corrected gsi-addon-dev spelling.

commit 21ff6458aac9372b26cc223f6a114953a137067e
Author: DavidHuber <[email protected]>
Date:   Fri Jan 19 21:11:34 2024 +0000

    Update modulefiles, submodules to spack-stack 1.6.0. #2195

commit d4c55d1011f8b0385d25b62ac04710837ed8413e
Author: Kate Friedman <[email protected]>
Date:   Fri Jan 19 15:43:37 2024 -0500

    Update typing hint for WCOSS version of python (#2238)

    The typing hint `typing.List` was deprecated with python 3.9 in favor
    of using the primitive `list[str]`, but the functional version of python
    on WCOSS2 is <3.9, causing `setup_xml.py` to fail there. This replaces
    `list[str]` as a typing hint with the deprecated form until the supported
    version on WCOSS2 is >=3.9.

commit 491928712ae1dabac62750450c9cad8f538c2a3e
Author: Barry Baker <[email protected]>
Date:   Thu Jan 18 22:31:27 2024 -0500

    GOCART Emission updates for GEFSv13 and GDAS  (#2201)

    This PR addresses several things needed for more recent simulations using
    GOCART2G as well as preparing for the GEFSv13 30 year run.  The main
    updates are:

    - Update CEDS to use monthly emission files instead of daily.  This will
    drastically reduce the number of files needed. No science change
    - Update biogenic MEGAN inputs to use a climatology rather than the
    offline biogenic previously used.  This is needed to deal with simulations
    where the current dataset is not available.
    - Update volcanic SO4 emissions to use degassing emissions only.  This is
    to support the need for more recent simulations where data is not available.

commit 13d25cfc3614de978bfd4b7f273d1f13cb820878
Author: Kate Friedman <[email protected]>
Date:   Thu Jan 18 22:29:43 2024 -0500

    Add `POSTAMBLE_CMD` into preamble postamble (#2235)

    This PR adds the ability to run a command at the end of jobs via the
    preamble's postamble function. A new command can be set via
    `POSTAMBLE_CMD` and will be invoked at the end of jobs. Users can
    add the command to the top of an env file to have every job run it or
    it can be placed within a job if-block in the env file to run for just that
    job.

    Resolves #1145

commit 7759163c668eb6ccc11dc1ecd39c0dc5d433cdc1
Author: Rahul Mahajan <[email protected]>
Date:   Thu Jan 18 01:13:49 2024 -0500

    Add option to…
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This issue has come up for GEFS in PR #2561. In the GEFS reforecast, FHOUT_OCNICE_GFS needs to be 24 and FHOUT_GFS needs to be 6 (the goal is to set this to 3 for first 240 lead hours). After some modifications to gefs_tasks.py and tasks.py, this issue has mostly been resolved for GEFS.

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