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Support multiple APP for GFSv17 #2318

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JessicaMeixner-NOAA opened this issue Feb 15, 2024 · 3 comments · Fixed by #2413
Closed

Support multiple APP for GFSv17 #2318

JessicaMeixner-NOAA opened this issue Feb 15, 2024 · 3 comments · Fixed by #2413
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@DavidHuber-NOAA
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@JessicaMeixner-NOAA
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JessicaMeixner-NOAA commented Feb 15, 2024 •
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What new functionality do you need?

Be able to use different values of APP for different forecast jobs.

What are the requirements for the new functionality?

Currently for GFSv17 the plan is to have 3 different apps for different forecasts:

gfs forecast APP=S2SW
gdas forecast APP=S2SWA
enkfgdas forecast APP=S2S

While all these apps can use the same executable, we will need to configure each of these forecasts to run with different components.

Acceptance Criteria

Be able to configure and run with three different apps for the various forecat jobs.

Suggest a solution (optional)

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@JessicaMeixner-NOAA JessicaMeixner-NOAA added feature New feature or request triage Issues that are triage labels Feb 15, 2024
@CoryMartin-NOAA
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Just as a follow up requirement:

Currently the aerosol analysis runs dependent on the 'app' chosen. But we will need a GDAS aero analysis and a GFS aero analysis (to initialize the GEFS) even if the GFS forecast app is not S2SWA. So we will need some sort of switch that says:
if APPgdas has aero, gfs cycle has aero analysis...

@WalterKolczynski-NOAA WalterKolczynski-NOAA removed the triage Issues that are triage label Feb 26, 2024
@JessicaMeixner-NOAA JessicaMeixner-NOAA mentioned this issue Feb 29, 2024
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@CoryMartin-NOAA CoryMartin-NOAA mentioned this issue Mar 1, 2024
Closed
7 tasks
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Mar 20, 2024
@WalterKolczynski-NOAA
Modify APP based on RUN
27b85ef 
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.

Resolves NOAA-EMC#2318
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Mar 20, 2024
@WalterKolczynski-NOAA
Modify APP based on RUN
45f6430 
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.

Resolves NOAA-EMC#2318
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Mar 20, 2024
@WalterKolczynski-NOAA
Modify APP based on RUN
62bae5d 
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.

Resolves NOAA-EMC#2318
Merged
7 tasks
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Mar 20, 2024
@WalterKolczynski-NOAA
Modify APP based on RUN
613418b 
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.

Resolves NOAA-EMC#2318
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Mar 28, 2024
@WalterKolczynski-NOAA
Modify APP based on RUN
3cc5794 
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.

Resolves NOAA-EMC#2318
WalterKolczynski-NOAA added a commit that referenced this issue Mar 28, 2024
@WalterKolczynski-NOAA
Modify APP based on RUN (#2413)
ba6a9d5 
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
kayeekayee added a commit to kayeekayee/global-workflow that referenced this issue Apr 11, 2024
@kayeekayee
Merge to 2024 Apr 2 NOAA-EMC/develop (c54fe98)
5f5727a 
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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…
@DavidHuber-NOAA
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As is, aerosol analyses/forecasts are not being run if APP includes "A". This is because setup_xml.py sources config.base with RUN=gfs, causing the A to be trimmed by

global-workflow/parm/config/gfs/config.base

Lines 165 to 168 in a005244

case "${RUN}" in
gfs) # Turn off aerosols
APP="${APP/%A}"
;;

A sample test case of C96_atmaerosnowDA is available in /scratch1/NCEPDEV/global/David.Huber/noscrub/test_snow. test_snow.xml does not contain any aerosol jobs.

First reported by @CoryMartin-NOAA here.

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I'm going to try and fix this as part of #2491, though it may need to be handled separately if there are any issues with the aerosol jobs.

@DavidHuber-NOAA DavidHuber-NOAA self-assigned this May 3, 2024
@DavidHuber-NOAA DavidHuber-NOAA mentioned this issue May 3, 2024
Merged
13 tasks
kayeekayee added a commit to kayeekayee/global-workflow that referenced this issue Aug 28, 2024
@kayeekayee
Merge to 2024 Aug 05 NOAA-EMC/develop (d599fff) and update to 2024 Ju…
f92292c 
…l 19 UFS (c127601)

Squashed commit of the following:

commit d599fff4aedd41ae587dbe02226acb12ff48efc1
Author: HelinWei-NOAA <[email protected]>
Date:   Mon Aug 5 05:31:31 2024 -0400

    Change land surface for HR4 (#2787)

    Resets the default value of opt_diag to 2 corresponding to the land
    surface upgrades in ufs-weather-model for HR4.

    Resolves #2786

commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb
Author: David Huber <[email protected]>
Date:   Fri Aug 2 15:41:29 2024 -0400

    Run METplus serially and correct the name of prod tasks (#2804)

    Adds 2 hot fixes:

    - METplus v9.1.3 has a bug in it that sometimes attempts to create
    multiple copies of the same directory when running in parallel, causing
    a Python error and downstream problems. This PR makes METplus run in
    serial mode, preventing such issues.
    - Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in
    workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod)

commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri Aug 2 15:03:45 2024 -0400

    Update Java Agent launching script for Jenkins connections (#2762)

    Made updates to the Jenkins Launching Script for robustness and less
    ambiguous documentation:
    - Clearer distinction between required user token for the remote api and
    the systems token for launching
    - Added pre-checks: `gh` is authenticating, named compliant token and
    secret file exists
    - More robust Jason based parser of the remote api response for checking
    the state of the Node connection
    - For `cron` use a 5 minute pause and recheck was added before
    re-launching of the java agent
    - Added concise header documentation of requirements and purpose
    ---------

    Co-authored-by: David Huber <[email protected]>
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

commit b73b1fd203496db97f8067652659573a632bcc67
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Aug 2 07:59:06 2024 -0400

    Fix erroneous cdump addition (#2803)

commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3
Author: Rahul Mahajan <[email protected]>
Date:   Thu Aug 1 20:26:13 2024 -0400

    Update ocean post-processing triggers (#2784)

    This PR:
    - replaces `check_netcdf.sh` checker for ocean post-processing with with
    ocean output at the next forecast hour or finishing of the forecast job
    for ocean prod
    - removes no longer needed `ush/check_netcdf.sh`

commit aa2af1ca8d59424a60a1730722bf528775d9e606
Author: GeorgeGayno-NOAA <[email protected]>
Date:   Thu Aug 1 16:46:10 2024 -0400

    Update the gfs_utils repository hash (#2801)

    # Description
    Point to the latest hash of the gfs-utils repository, which contains the
    bug fix to gaussian_sfcanl.

    Resolves #2669.
    Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73

commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8
Author: David Huber <[email protected]>
Date:   Thu Aug 1 08:12:14 2024 -0400

    Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791)

    Changes how METplus jobs run so that they run on the last GFS cycle for
    a given `PDY`.

    This is a departure from operations where the METplus jobs run on the
    00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through
    `${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on
    `${PDY}18` for cycles 00-18. See
    https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details.

commit 1cf8b448af562dbb7af198399c78c585977e81da
Author: David Huber <[email protected]>
Date:   Tue Jul 30 10:38:49 2024 -0400

    Simplify resource-related variables, remove CDUMP where unneeded (#2727)

    This overhauls resource-related variables to use a common set of
    variables for each job. In the process, this also removed the use of
    CDUMP in most cases.

    Resolves #1299 #2693

commit 61875f25c9e971f82ae499b5b612d7f095deebd4
Author: Eric Sinsky - NOAA <[email protected]>
Date:   Mon Jul 29 14:40:03 2024 -0400

    Remove f000 from atmos rocoto tasks for replay cases (#2778)

    The main purpose of this PR is to remove the f000 from
    atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In
    cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater
    than `0`, it becomes necessary to have the first lead hour set to
    `OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For
    example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead
    time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and
    the minimum lead time for the ocean_prod rocoto task needs to be 6
    (assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up
    possible by removing 0 from fhrs for atmosphere-related tasks in
    `gefs_tasks.py` when replaying.

    This PR also moves where f000 is being removed for the ocean_prod and
    ice_prod tasks. The if-block that performs this f000 removal has been
    moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`.

    ---------

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

commit f156a7894d639f177e3e2588f98eec1f6f59aa68
Author: Jessica Meixner <[email protected]>
Date:   Fri Jul 26 14:18:32 2024 -0500

    HR4 GWD update (#2732)

    This update is a combination of the gravity wave drag (GWD) versions
    from the NOAA/GSL and NOAA/PSL

commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891
Author: David Huber <[email protected]>
Date:   Thu Jul 25 14:26:52 2024 -0400

    Temporarily disable METplus jobs (#2796)

commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2
Author: Guillaume Vernieres <[email protected]>
Date:   Wed Jul 24 15:00:35 2024 -0400

    Refactoring of the marine B-matrix job (#2749)

    Refactor the functionality of B-matrix generation from the GDASApp

    Resolves #2743

commit 65a7ab75dc0e4baba06a02e11ed0455787056a68
Author: David Huber <[email protected]>
Date:   Tue Jul 23 08:35:48 2024 -0400

    Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775)

    Removes the namespace-based construction of EnKF member COM directories
    in the enkf archive template.

commit c45b9611f3e701b819bd33dc5af29033f060bb91
Author: Eric Sinsky - NOAA <[email protected]>
Date:   Tue Jul 23 00:33:16 2024 -0400

    Add task to process reforecast variables to save on WCOSS2 (#2680)

    # Description
    This PR adds an optional task to the global-workflow to process a subset
    of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for
    the GEFSv13 reforecast. This task is designed to process GEFS variables
    so that specific reforecast product requirements are met. A new variable
    in `config.base` called `DO_EXTRACTVARS` enables this task, which is
    currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by
    default and is specifically a task designed to be executed for the
    GEFSv13 reforecast.

    Refs #1878

    # Type of change
    - New feature (adds functionality)

    # Change characteristics
    - Is this a breaking change (a change in existing functionality)? NO
    - Does this change require a documentation update? NO

    # How has this been tested?
    This has been cloned and tested on WCOSS2. This will need to be tested
    on Hera and other platforms on which the reforecast may be running.

    # Checklist
    - [ ] Any dependent changes have been merged and published
    - [x] My code follows the style guidelines of this project
    - [x] I have performed a self-review of my own code
    - [ ] I have commented my code, particularly in hard-to-understand areas
    - [x] My changes generate no new warnings
    - [x] New and existing tests pass with my changes
    - [ ] I have made corresponding changes to the documentation if
    necessary

    ---------

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

commit 71dc33c6ca991c16ce743760d99feaaf60f2218a
Author: David Huber <[email protected]>
Date:   Mon Jul 22 14:51:53 2024 -0400

    Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774)

    Fix metp* resources and check that they completed properly; add support for Orion Rocky 9

commit 56df67a90fe090c425199f1285e5aac722c398b1
Author: David Huber <[email protected]>
Date:   Mon Jul 22 09:28:18 2024 -0400

    Hotfix: Update jcb to avoid git-lfs files (#2782)

    Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to
    be cloned on Hera.

    This hotfix points to a non-authoritative branch of the GDASApp
    (https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and
    should be updated ASAP back to the authoritative repository.

commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd
Author: Rahul Mahajan <[email protected]>
Date:   Tue Jul 16 09:44:00 2024 -0400

    Address issues in creating XML for GFS forecast-only with app S2SWA (#2757)

    This bugfix PR:
    - fixes an issue where a user is unable to generate the XML for a GFS
    forecast-only experiment with APP=S2SWA

    Specifically, the changes are related to defining `aero_fcst_cdumps`.
    Following `setup_expt.py`, the user will have to set
    `AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in
    `config.base`.

commit e0878dba0e53706a7f53429b61aee2936e2c21bf
Author: Kate Friedman <[email protected]>
Date:   Mon Jul 15 10:25:11 2024 -0400

    Updated prepobs and fit2obs versions for Orion Rocky9 (#2758)

    Update prepobs to v1.0.2 and fit2obs to v1.1.2

    These versions now support Orion Rocky9. Updates are included
    for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet.

commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Jul 11 17:48:47 2024 +0000

    CI maintenance updates and adding CI Unit Tests (#2740)

    This PR has a few maintenance updates to the CI pipeline and adds a test
    directory with Unit Tests
    **Major Maintenance updates:**
    - Added try blocks with appropriate messaging to GitHub PR of failure
    for:
    - - **scm** checkout
    - - build fail (with error logs sent as gists)
    - - create experiment fails with `stderr` sent to GitHub PR messaging
    - Pre-stage FAILS from the above are now captured these fails allow
    FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state
    labels in GitHub - see image below)
    **Minor Maintenance updates:**
    - Fix for STALLED cases reviled from PR 2700 (just needed a lambda
    specifier)
    - Fixed path to experiment directory in PR message (had dropped EXPDIR
    in path)
    - Needed `latin-1` decoder in reading log files for publishing
    **Added python Unit Tests for CI functionality:**
    - Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI
    utility codes
    - Cashed the install of Rocoto in the GitHub Runners to greatly reduce
    stetup time for running the unit tests
    - Unit Tests Python scripts added
    - `test_rocostat.py`: rocoto_statcount() rocoto_summary()
    rocoto_stalled()
      - `test_setup.py`: setup_expt() test_setup_xml()
      - `test_create_experment`: test_create_experiment()
      - - Runs all PR cases that do not have ICs in the GItHub Runner
    - Reporting mechanism in the Actions tab for Python Unit Testing results
    - Test case data for STALLED and RUNNING stored on S3 and pulled using
    wget during runtime of tests

commit 5ef4db74649b8be03402c17aa29c024e71699a7b
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Thu Jul 11 08:59:24 2024 -0400

    Adds contents of constructor and initialize methods to marine LETKF class (#2635)

    Adds contents of constructor and initialize methods to marine LETKF class

    Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091
    ---------

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

commit 8998ec7b74123e953b97a93fa14cc78d471a1aee
Author: David Huber <[email protected]>
Date:   Tue Jul 9 08:31:57 2024 -0400

    Fix GDAS group B restart archiving (#2735)

    Archives the GDAS restartb dataset at a 6-hour offset from restarta

    This allows cycled experiments to restart from the archives.
    The tabbing for the master archive templates was also added to
    improve readability.

    Resolves #2722

commit 3ca74771255727033b9dc043c652ac585178629c
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Tue Jul 9 08:28:54 2024 -0400

    Add fcst dependency to ocnanalprep (#2728)

    Add previous cycle's `fcst` as a dependency to `ocnanalprep`

    This ensures that the availability of restart files to the latter. This addresses a
    seldomly-encountered race condition where `ocnanalprep` fails due to the
    lack of the files.

commit 58fca1668aecd6fb1afd12a441256ad35900e075
Author: Rahul Mahajan <[email protected]>
Date:   Fri Jul 5 15:02:23 2024 -0400

    Update (partially) global-workflow for orion+rocky9 (#2741)

    This PR:
    - updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils,
    GFS-utils) to include recent update to their modulefiles for
    Orion+Rocky9 upgrade
    - updates the modulefiles in global-workflow to load modules from
    Orion+Rocky9 paths
    - updates modulefiles for `gwsetup` and `gwci` as well.
    - removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not
    installed.
    - adds `parm/config.gfs/config.resources.ORION` to address GSI
    performance degradation after Rocky 9 upgrade.

    This PR:
    - does not update the build for UPP. Standalone UPP is not available via
    ufs-weather-model as of #2729
    - will need a follow-up update for `prepobs` and `fit2obs` updated
    locations when they are installed in `glopara` space on Orion.

    # Type of change
    - Maintenance (code refactor, clean-up, new CI test, etc.)

    # Change characteristics
    - Is this a breaking change (a change in existing functionality)? NO
    - Does this change require a documentation update? NO

    # How has this been tested?
    This PR is not sufficient for Orion.
    This PR must be tested on other platforms (Hera, WCOSS2) as this PR
    updates submodules.

    # Checklist
    - [ ] Any dependent changes have been merged and published
    - [ ] My code follows the style guidelines of this project
    - [ ] I have performed a self-review of my own code
    - [ ] I have commented my code, particularly in hard-to-understand areas
    - [ ] My changes generate no new warnings
    - [ ] New and existing tests pass with my changes
    - [ ] I have made corresponding changes to the documentation if
    necessary

    ---------

    Co-authored-by: Kate Friedman <[email protected]>

commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a
Author: Jessica Meixner <[email protected]>
Date:   Wed Jul 3 21:07:49 2024 -0400

    Update ufs model hash to 20240625 (#2729)

    Updates UFS weather model hash to hash from 2024-06-24 which has orion
    porting updates + a few namelist updates.

commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85
Author: David Huber <[email protected]>
Date:   Wed Jul 3 11:32:40 2024 -0400

    Hotfix for undefined CLUSTERS (#2748)

    Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses
    the native `dict` `get` method to prevent grabbing an unset entry.

commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf
Author: GwenChen-NOAA <[email protected]>
Date:   Wed Jul 3 09:56:08 2024 -0400

    Update gempak job to run one fcst hour per task (#2671)

    This PR updates gempak jobs (gfs, gdas, and goes) from processing all
    forecast hours at once to one forecast hour at a time. This will reduce
    the job runtime to less than 5 min, so restart capability is not needed.

    Resolves #1250
    Ref #2666 #2667
    ---------

    Co-authored-by: Walter.Kolczynski <[email protected]>

commit 8215ae654202186a4f753c3abe937b7b9b91a9c7
Author: Rahul Mahajan <[email protected]>
Date:   Tue Jul 2 16:22:11 2024 -0400

    Hotfix for clusters from #2701 (#2747)

    Fixes an issue created from #2701 that added `CLUSTERS` to the
    `gaea.yaml`.

commit 11943e36ba12b3df49c51942da780698fab02d38
Author: DavidBurrows-NCO <[email protected]>
Date:   Tue Jul 2 12:58:10 2024 -0400

    Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701)

    This PR sets up the ability on Gaea for auto generation of a clean xml
    file, i.e., an xml file that does not need any alterations before
    running rocoto.
    Refs #2572
    Refs #2664

commit de8706702ead0630beb54d868f83aa2cb23f8f79
Author: RussTreadon-NOAA <[email protected]>
Date:   Mon Jul 1 09:29:14 2024 -0400

    Update for JCB policies and stage DA job files with Jinja2-templates (#2700)

    This PR updates the `gdas.cd` hash to bring in new JCB conventions.
    Resolves #2699

    From #2654
    This PR will move much of the staging code that take place in the python
    initialization subroutines of the variational and ensemble DA jobs into
    Jinja2-templated YAML files to be passed into the wxflow file handler.
    Much of the staging has already been done this way, but this PR simply
    expands that strategy.

    The old Python routines that were doing this staging are now removed.
    This is part of a broader refactoring of the pygfs tasking.

    wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a
    companion to this PR.

    Co-authored-by: danholdaway <[email protected]>
    Co-authored-by: DavidNew-NOAA <[email protected]>
    Co-authored-by: DavidNew-NOAA <[email protected]>
    Co-authored-by: Dan Holdaway <[email protected]>

commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b
Author: Rahul Mahajan <[email protected]>
Date:   Fri Jun 28 14:56:19 2024 -0400

    Revert PR 2681 (#2739)

    This PR:
    - reverts #2681 in part
    - keeps some changes for `RUN`.
    - is a hotfix
    - should be merged ASAP after consensus w/ @guillaumevernieres
    @CatherineThomas-NOAA @WalterKolczynski-NOAA

commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Wed Jun 26 15:46:08 2024 -0400

    updated Finalize in Jenkinsfile and added try block around scm checkout (#2692)

    We are updating the Jenkins Pipeline with a try block around checkout to
    capture errors for the user.
    Also cleaned up Finalize and added section to clean out workspace on
    success.

commit 968568f682bac7564095440bdb7813abefd76821
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Jun 26 13:27:19 2024 -0400

    Activate snow DA test on WCOSS (#2720)

    Activate the snow DA test on WCOSS.

commit 7706760bb8adbdf78cb640b02739023c886e7699
Author: Rahul Mahajan <[email protected]>
Date:   Wed Jun 26 10:02:22 2024 -0400

    Cleanup of stale RUNDIRS from an experiment (#2719)

    This PR:
    - removes stale temporary scratch run directories from `$DATAROOT/`
    every 3 days.
    - should help to scrub failed attempts.
    - removes an unused variable `RUNDIR` defined in `config.base`

commit 8962991691b5f0857b813bddfd28aa1034d4bd2b
Author: Jessica Meixner <[email protected]>
Date:   Wed Jun 26 09:43:48 2024 -0400

    Update logic for MOM6 number of layers/exception values (#2681)

    Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine
    how many layers and sets the exception value for MOM6 to be 1e-34 for
    all scenarios. Note, we will no longer have zeros in the ocean grib
    output and the DA will also run without issues.

    Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615

commit 12431f76bdce807067929415007592cffc8a2457
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Wed Jun 26 07:42:35 2024 -0600

    Update wave jobs to use COMIN/COMOUT (#2643)

    NCO has requested that each COM variable specify whether it is an input
    or an output.
    This completes that process for the global-workflow wave
    model and products tasks.
    Refs #2451

commit b902c0bac126c323a07186ad8881384b032b6fda
Author: David Huber <[email protected]>
Date:   Tue Jun 25 07:48:46 2024 -0400

    Assign machine- and RUN-specific resources (#2672)

    Redefine resource variables based explicitly on RUN or CDUMP

    Additionally, machine-specific resources are moved out of
    config.resources and placed in respective config.resources.{machine}
    files.

    Resolves #177 #2672

commit 4e1b937b67ed220120e81925c4507f03b9b8965f
Author: David Huber <[email protected]>
Date:   Mon Jun 24 10:50:52 2024 -0400

    Add minimum software requirements (#2712)

    Adds a table to HPC documentation stating the minimum support versions

commit f43a86276aaef91efa28faadc71a3cf50e749efe
Author: David Huber <[email protected]>
Date:   Fri Jun 21 13:44:29 2024 -0400

    Fix and simplify online archiving and reenable METplus jobs (#2687)

    This fixes the online archiving portion of the `*arch` and `*earc00`
    jobs, a prerequisite for running METplus.  This also reenables
    METplus by default.

    The approach previously taken created `FileHandler` dictionaries at
    varying levels within the resulting yaml, which was not properly parsed
    by `exglobal_archive.py`. This approach creates a single `FileHandler`
    dictionary and is much less complicated overall.

    Resolves #2673 #2647

commit 8993b42cb91144c0ab0501dc7841ea8d675c4701
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Jun 19 21:51:22 2024 -0400

    Eliminate post groups (#2667)

    Eliminates the post groups used for upp and products jobs so that each
    task only processes one forecast hour. This is more efficient and
    greatly simplifies downstream dependencies that depend on a specific
    forecast hour.

    Resolves #2666
    Refs #2642

commit 0b810c888239853fedd0e4584fe62536c6aaacdf
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Tue Jun 18 20:32:48 2024 -0600

    Removes misleading "No such file or directory" syntax errors from output files (#2688)

    This PR addresses issue #1252. The following is accomplished:

    - Prior to removing files, the existence of a file is checked prior to
    attempting to remove; this is performed as noted
    [here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369);
    this PR only addresses the the `chgrp` issue.

    Refs #1252

    ---------

    Co-authored-by: David Huber <[email protected]>

commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Tue Jun 18 12:17:59 2024 -0600

    Hotfix for bug in template names. (#2697)

    This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/`
    template.
    Resolves #2696
    Refs #2451

commit 35d4d99eaac669721add9ddcc793153e5ab3b30a
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Tue Jun 18 08:06:53 2024 -0600

    Update archive job to use COMIN/COMOUT (#2668)

    NCO has requested that each COM variable specify whether it is an input
    or an output. This completes that process for the global-workflow
    archive task.

    Refs #2451
    ---------

    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
    Co-authored-by: Rahul Mahajan <[email protected]>
    Co-authored-by: David Huber <[email protected]>

commit 47b3a581c8257fa24411fb400df8bb0e1e04972a
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Jun 17 22:55:38 2024 -0400

    Turn on high-frequency output in extended test (#2679)

    Turns on high-frequency (hourly) output in the extended products test to
    exercise that aspect of the code. This test only runs on WCOSS.

    Also adds the hooks to optionally turn on the metplus jobs, but that is
    deferred as they are not currently working correctly.

commit 38f2df9fb0c074b1f80d3c637080be79be693161
Author: David Huber <[email protected]>
Date:   Mon Jun 17 17:12:55 2024 +0000

    Optimize wavepostpnt (#2657)

    Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs

    This is done by
    1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by
    - performing operations on all files at once instead of looping over
    each file
        - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`)
        - combining `sed` and `grep` calls when possible
        - adding logic to `awk` calls instead of handling that logic in bash
    2) minimizing as much as possible the amount of data on disk that has to
    be read in (e.g. limiting sed to read only the line numbers it needs)
    ---------

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

commit 5af325a6a4e0a14d180514a418603ca79fada487
Author: Dan Holdaway <[email protected]>
Date:   Fri Jun 14 18:05:23 2024 -0400

    Update GDASapp hash to move JCB into GDASapp (#2665)

    This PR moves JCB into GDASapp. The PR
    also bumps up the hash of GDASapp to what is in `feature/move_jcb`,
    which at time of writing is develop plus the absorption of JCB into
    GDASapp.
    Note that I also took the changes from
    https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the
    testing @RussTreadon-NOAA has done.

commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b
Author: Yaping Wang <[email protected]>
Date:   Fri Jun 14 10:18:17 2024 -0500

    Add observation preparation job for aerosols DA to workflow (#2624)

    Add a prepaeroobs job to prepare aerosol obs files for DA.

    This job does quality control of the VIIRS aerosol raw observations and
    convert them to ioda format.

    Resolves #2623
    ---------

    Co-authored-by: ypwang19 <[email protected]>
    Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>
    Co-authored-by: Cory Martin <[email protected]>
    Co-authored-by: David Huber <[email protected]>

commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4
Author: Jessica Meixner <[email protected]>
Date:   Fri Jun 14 11:04:41 2024 -0400

    Remove ocean daily files (#2689)

    This PR removes the ocn_daily files that are produced by the ocean
    component. These files can be recreated by averaging data that exists in
    the 6 hour aveaged files if needed.

    Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675
    Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by
    removing them and making this obsolete)

commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Jun 13 12:22:03 2024 -0400

    Update Jenkinsfile

    needed a comma

commit dc21eac6c3941d7f30803891d91d82f4cc1f8183
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Jun 13 11:41:14 2024 -0400

    Add Hercules-EMC to the Jenkins configurable parameter list (#2685)

    This quick-fix PR is to update the Jenkins Pipeline's configurable
    parameter list to include the **Hercules-EMC** node.
    This allows Jenkins users to restart Jobs in the controller when no
    updates have been made.

commit ebacebfbe458634b8c80af6a735d6b6d01e4e406
Author: RussTreadon-NOAA <[email protected]>
Date:   Thu Jun 13 11:20:24 2024 -0400

    Update gdas.cd and gsi_utils hashes (#2641)

    This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The
    updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea
    build for gsi_utils.

    Resolves #2640

commit 34155fb4767769600a1ff95f0a65e37081addc2a
Author: Neil Barton <[email protected]>
Date:   Thu Jun 13 11:18:22 2024 -0400

    Add ability to use GEFS replay ICs (#2559)

    The PR allows the use of ICs from PSL's replay analysis. These replay
    ICs will be used for GEFS reforecasting and SFS. Two main changes are
    associated with these updates: (1) replay ICs being valid at 3Z, and (2)
    the use of warm starts.

    Resolves #1838

    ---------

    Co-authored-by: Jessica Meixner <[email protected]>
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
    Co-authored-by: Rahul Mahajan <[email protected]>

commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Wed Jun 12 19:25:42 2024 -0600

    Replace `sleep` with `wait_for_file` (#2586)

    This PR addresses issue #2444. The following is accomplished:

    - All `sleep` statements are replaced with `wait_for_file` for the
    relevant scripts beneath `scripts` and `ush`;
    - Indentation and shell-norms are updated where applicable.

    Note: The WAFS scripts are not updated as per @aerorahul direction.

    Resolves #2444

    ---------

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

commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Jun 12 13:31:55 2024 -0400

    Add COM template for JEDI obs (#2678)

    Adds a COM template to define a path to store obs processed for JEDI.
    This will allow UFSDA to stop writing to COM_OBS, which should be
    read-only as it belongs to obsproc in operations.

    No functional change yet.

commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed
Author: Guoqing Ge <[email protected]>
Date:   Wed Jun 12 09:06:23 2024 -0600

    Link both global-nest fix files and non-nest ones at the same time (#2632)

    This PR enables linking both global-nest fix files and non-nest ones at
    the same time and users can run both nesting and non-nesting experiments
    at the same time without worries about what fix files to be linked.

    Resolves #2631

commit 61de004d4f9e9edf8a31bb173f2719b46451a36a
Author: Jessica Meixner <[email protected]>
Date:   Wed Jun 12 11:03:13 2024 -0400

    Update ufs-weather-model  (#2663)

    Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack
    allowing some temporary fixes to be reverted.
    * removes upp submodule
    * uses upp from the ufs-weather-model
    * restores the build and link that were hacked during the Hera Rocky 8
    transition to allow for UPP submodule
    * Removes forecast directories in clean-up

    Resolves #2617
    Resolves #2437

    ---------

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

commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d
Author: Eric Sinsky - NOAA <[email protected]>
Date:   Wed Jun 12 01:15:37 2024 -0400

    Add ability to process ocean/ice products specific to GEFS (#2561)

    This PR begins to add the capability to produce GEFSv13 ocean and ice
    products in the global-workflow according to stakeholder requirements.
    The following features are added.

    - An oceanice prod yaml file has been added to address the ocean and ice
    products specific to GEFSv13.
    - The rocoto dependencies and config.base for GEFS have also been
    modified to allow for 24-hour averaged ocean and ice output.
    - Various scripts have been modified to allow for ocean and ice output
    frequencies of 24 hours.
    - `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN`
    and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`.

    Refs #1878

commit 6691e7489650e0b738c176fbd096109288dc09b6
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Tue Jun 11 21:15:07 2024 -0600

    Update cleanup job to use COMIN/COMOUT (#2649)

    NCO has requested that each COM variable specify whether it is an input
    or an output. This completes that process for the global-workflow
    clean-up task.

    Refs #2451

    ---------

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

commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Jun 11 16:17:25 2024 -0400

    Add overwrite to creat experiment in BASH CI (#2676)

    This is a quick hotfix to the CI BASH driver script adding `--overwrite`
    to create experiment script to avoid errors from restarting an
    experiment.

commit e7909af8d9e1f34140388a3f8556d8e582c58fe5
Author: emilyhcliu <[email protected]>
Date:   Mon Jun 10 15:11:27 2024 -0400

    Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py  (#2645)

    This PR proposes updates for the following two scripts:

    1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select
    CRTM cloud optical table based on cloud microphysical scheme indicated
    by `imp_physics'
    The default scheme in the GFS forecast model is Thompson scheme
    (imp_physics = 8).

    2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in
    the script due to increased variables to interplate increments and
    calculate analysis in the netcdf_io routines in GSI-utils.
    Here is the related [PR #46 for
    GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46).

    ---------

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

commit 9caa51de8fb7be07d2e61775da01937d576964f6
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Thu Jun 6 22:15:23 2024 -0600

    Update RDHPCS Hera resource for `eupd` task (#2636)

    As per @wx20jjung, the resource for the `eupd` task have been updated
    for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job
    fails.

    Resolves #2454

    ---------

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

commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b
Author: DavidNew-NOAA <[email protected]>
Date:   Thu Jun 6 11:49:03 2024 -0400

    Parameterize some things in config.atmanl and config.atmensanl (#2661)

    This PR adds some parameters in config.atmanl and config.atmensanl that
    can be altered with the defaults.yaml. The motivation is to make these
    files match those in the GDASApp JJOB tests (example:
    https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl),
    so we can just use the Global Workflow config.atmanl and
    config.atmensanl in the tests rather than custom ones in GDASApp that
    have to be separately updated every time the ones in the Global Workflow
    are updated.

commit 54ea0b73a07921be5fbb07fe41e976888bd3e549
Author: Guillaume Vernieres <[email protected]>
Date:   Thu Jun 6 01:36:02 2024 -0400

    Add links to the ocean insitu obs processing tools (#2644)

    Add links to the marine bufr to ioda converters for the marine insitu
    observations.

    - fixes https://github.com/NOAA-EMC/GDASApp/issues/1106
    - waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135

commit 205d0c2b13e2d7755cec75bf8c978ab20d453862
Author: David Huber <[email protected]>
Date:   Wed Jun 5 17:31:30 2024 +0000

    Update S4 point of contact in docs (#2660)

    Update the point of contact for global workflow issues on S4.

commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262
Author: RussTreadon-NOAA <[email protected]>
Date:   Wed Jun 5 12:50:14 2024 -0400

    Enable wcoss2 ufsda build and module load (#2620)

    This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2.

    Resolves #2602
    Resolves #2579

commit 67b833e0c7bc390865d453588b4609a1a7ede981
Author: Jessica Meixner <[email protected]>
Date:   Tue Jun 4 13:33:43 2024 -0400

    Update ufs-weather-model  (#2646)

    Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6
    This should resolve the issue and allow C768 runs on Hera and allow for CICE
    to run on WCOSS2 (due to library updates to allow linking).

    From what I can tell, all updates needed were done by
    @HenryWinterbottom-NOAA which were updates for CICE

    Fixes #2490

commit c44d0ac86cfdf78eb87492431bf6d825e8bae637
Author: GwenChen-NOAA <[email protected]>
Date:   Tue Jun 4 10:29:49 2024 -0400

    Update wmo parm files to fix WMO header (#2652)

    This PR updates wmo parm files to switch WMO header of precipitation
    type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to
    instantaneous.

    Resolves #2566

commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60
Author: Cory Martin <[email protected]>
Date:   Tue Jun 4 13:55:33 2024 +0000

    Add IAU to snow DA (and its test) (#2610)

    This PR enables IAU for the snow DA which is necessary for GFSv17.

    A snow analysis is created for the center of the window regardless, and
    an additional at the beginning of the window is added if IAU is on. The
    former is needed for UPP and the latter, to initialize the model.

    The increment is valid throughout the window for 3DVar, so the same
    increment is added to both forecasts.

    Additionally, the input file that goes into global_cycle has been
    updated to be the output of the JEDI snow analysis instead of the
    forecast (@jiaruidong2017 I recall discussing this, can you confirm this
    is right or am I mistaken)

    This PR also makes the CI test for snow DA (and aerosol DA) include IAU
    rather than without IAU,.

    ---------

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

commit c92bf415060750127c9c05a62a1d2851c489551a
Author: David Huber <[email protected]>
Date:   Sat Jun 1 05:11:07 2024 +0000

    Archiving cleanup (#2621)

    1) Adds a lot of comments to the jinja templates for archiving
    2) Rearranges the gdas and enkf templates to a more logical order
    3) Fixes a couple of bugs in the enkf archiving of increments and
    analyses
    4) Disables archiving for the half cycle
    5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`,
    instead relying on `DO_FIT2OBS`
    6) Updates wxflow to add the option to not allow undefined variables
    when parsing jinja templates and invokes this feature when running
    archives

    Resolves #2612

commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri May 31 04:57:08 2024 -0400

    Switch to Rocky 9 built external packages on Hercules (#2608)

    The workflow was updated to use modules built on Rocky 9, but the
    external packages (like prepobs) were still pointing to the versions
    built on CentOS (Orion). This transitions to packages built on Rocky 9.

    Updating of the tracker package has been deferred until later. As such,
    the tracker jobs have been disabled by returning immediately if they are
    on Hercules. Since these jobs are small, resource-wise, it should not
    meaningfully impact turnover time.

commit 4422550c01c9214a2b3b8890bdcc898123ee216a
Author: Guoqing Ge <[email protected]>
Date:   Thu May 30 08:05:23 2024 -0600

    Add the capability to use slurm reservation nodes (#2627)

    Add the capability to use slurm reservation nodes
    Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE

    Resolves #2626

commit a54153fd9d26126206bc07a1da4e80f50c0c5910
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed May 29 23:24:07 2024 -0400

    Update forecast job to use COMIN/COMOUT (#2622)

    NCO has requested that each COM variable specify whether it is an input
    or an output. This completes that process for the forecast job.

    Refs #2451

    ---------

    Co-authored-by: David Huber <[email protected]>

commit d69a8af95d492982b918670322ed5c41ab074335
Author: Jessica Meixner <[email protected]>
Date:   Wed May 29 21:29:03 2024 -0400

    Update to add 1-deg global wave grid (#2619)

    This PR adds options to use a global 1 deg grid, intended for testing
    with the SFS application.

    Requires new fix file changes NOAA-EMC/global-workflow#2618

commit 0b4670ecf83b99b72835c8380573b2bca7cf5324
Author: Jessica Meixner <[email protected]>
Date:   Wed May 29 17:17:21 2024 -0400

    Add C384mx025_3DVarAOWCDA yamls (#2625)

    Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder.

commit 2e885d05c64b947f00a3cf055a1277fbfac195c9
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Wed May 29 13:00:51 2024 -0400

    Script to keep Jenkins Agent persistent from cron (#2634)

    This "persistent" Java Agent launch script can be ran from a cron job:

    - Uses Jenkins Remote API to check the status of the Node connection
    using curl for a given machine.
    - If it is not connected a new agent is launched for that node.

    Resolves #2633

commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5
Author: GwenChen-NOAA <[email protected]>
Date:   Tue May 28 17:17:11 2024 -0400

    Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611)

    Based on users' feedback, this PR do the following:
    1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF
    2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD,
      and VOGRD) from "%g m below water surface" to "%g m below sea level"
    3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m)

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

commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31
Author: DavidNew-NOAA <[email protected]>
Date:   Tue May 28 17:16:23 2024 -0400

    Add atmensanlfv3inc job (#2592)

    This PR creates the atmensanlfv3inc job, the ensemble version of
    atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is
    #[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS
    companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3).

commit 50c2b8951b29a3c883a778becbf8582f9519eb48
Author: Anil Kumar <[email protected]>
Date:   Tue May 28 13:23:53 2024 -0400

    Global-workflow (AR) Generic updates for Gaea C5 (#2515)

    - Port global-workflow’s build and run capability to Gaea-C5
    - Building global-workflow on Gaea-C5
    - Setting up experiments with global-workflow on Gaea-C5

    ---------

    Co-authored-by: AnilKumar-NOAA <[email protected]>
    Co-authored-by: DavidBurrows-NCO <[email protected]>

commit b6ca771a0c584cbfcbbf9be739765d5f3815df97
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri May 24 10:52:45 2024 -0400

    Update STMP and PTMP settings in host file for Orion and Hercules  (#2614)

    - Updating STMP and PTMP settings in host file for Orion and Hercules
    because they are cross mounted.
    - Also took the opportunity to finally update **SLURM_ACCOUNT** to
    **HPC_ACCOUT** in CI over rides.
    - Added a refactor of the `rocotostat.py` tool that is more pythonic and
    as a execute retry feature because the `rocotostat` utility on Orion has
    been failing sometimes.

commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f
Author: Guillaume Vernieres <[email protected]>
Date:   Tue May 21 23:50:50 2024 -0400

    Sea-ice analysis insertion (#2584)

    Allows cycling and restarting CICE with the sea-ice analysis if the
    marine DA is switched on.

    Resolves #2568
    Resolves NOAA-EMC/GDASApp#1103

commit 5369a1ff3a3969149fcf32810fad0e50216752b7
Author: David Huber <[email protected]>
Date:   Tue May 21 22:12:29 2024 +0000

    Refactored archiving (#2491)

    This provides a new pygfs task, archive.py, that provides all of the
    tools necessary to archive data to the local (`ARCDIR`) and backup
    (`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to
    define the file to be archived or tarred to replace the
    `hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts
    and make it easier to add new data and explicitly handle optional and
    required files.

    For `ATARDIR` archiving, a master jinja template is provided for each
    `RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2,
    master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both
    `enkfgdas` and `enkfgfs` `RUN`s. These templates then include the
    appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on
    experiment, cycle, and coupled parameters. Each of these templates
    corresponds to a single tarball to populate and are tabbed 4 spaces so
    they are defined within the master `datasets` dictionary.

    Future developers should not have to make modifications to archive.py
    unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then
    only a single `elif` needs to be added to the configure method to
    specify the master `ATARDIR` template to archive (e.g.
    `master_gefs.yaml.j2`). If a new component is coming online that needs
    to be archived to `ATARDIR` (e.g. SNOW), then create a new template for
    each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`)
    and reference the template in the appropriate master templates, e.g.

    `master_gdas.yaml:`
    ```jinja
    {% if DO_SNOW %}
    {% include "gdassnow.yaml.j2" %}
    {% endif %}
    ```

    A few other issues were addressed along the way:
    1. Aerosols have been reenabled. Aerosol forecasts should only be
    performed during gdas cycles, but analyses can be performed for both gfs
    and gdas cycles. This was accomplished by setting separate
    `AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs.
    2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`.
    This prevented restarts from being used for cice-enable experiments.
    This feature was not tested.
    3. Create a temporary fix for the `wgrib` utility. For spack-stack
    1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is
    open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in
    existing installations. Once complete, this temporary fix should be
    removed.
    4. The number of `earc` jobs has been reduced for lower resolution
    experiments. Both C48 and C96 experiments will now only have two earc
    jobs (one for the non-member files to archive and another for the member
    files). C192 will have up to 3 earc jobs (one non-member, one for
    members 1-40 and another for members 41-80, if needed).

    Resolves #2345
    Resolves #2318

    ---------

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

commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri May 17 12:57:59 2024 -0400

     Add remove RUNDIRS step in CI before creating experements (#2607)

    As had been done in Bash CI we need to remove the RUNDIR in Jenkins
    before a creating an experiment in the event that case had beem
    previously ran.

commit bb930050b3cd51d28ecba6b231c8675f6d11856c
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Thu May 16 12:28:30 2024 -0400

    Adds jjob and other necessities for marine LETKF task (#2564)

    Adds jjob, rocoto script, config file, and other necessities for new
    marine LETKF task.

    Partially addresses NOAA-EMC/GDASApp#1091

commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu May 16 12:12:06 2024 -0400

    Updating CI Machine configs with redundant PTMP (#2605)

    Quick fix adding PTMP as STMP in Machine configs for CI for completeness

commit ef340ff33a6f89adf70838206ba3fd56a953fa7a
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu May 16 11:37:30 2024 -0400

    Fix race condition in CI between Orion and Hercules (#2604)

    Hotfix to solve race conditions in the CI system due to cross-mounted
    file systems between Orion and Hercules

commit e8b17e27f719df280170dc3f5bd9f19917cefaf2
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Wed May 15 17:16:30 2024 -0400

    Remove existing EXPDIRs and COMROTs when CI is re-run (#2601)

    Quick hotfix for having default for re-runing jobs to start clean with
    new EXPDIRs and COMROTs

commit b5d113efb1970ede5cd1d3d4dff8d96320519c41
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Wed May 15 16:52:49 2024 -0400

    Moving logic for skipping hosts in pr cases (#2573)

    This PR removes the logic of skipping hosts for pr cases from
    `create_experiment.py` and moves it to a test in the cron bash driver
    using a `parse_yaml.py` python tool.

    The Jenkins pipeline was not effected as it uses the
    `get_host_case_list.py` utility to form the cases on a per host bases.

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

commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916
Author: RussTreadon-NOAA <[email protected]>
Date:   Wed May 15 13:13:30 2024 -0400

    Update gsi_utils.fd hash (#2598)

    This PR updates the `gsi_utils.fd` hash to bring in updates which add
    safeguards to
    -
    `src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90`
    - `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90`

    The safeguards are described in GSI-utils PR
    [#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated
    issue.

    Resolves #2597

commit d5366c66bd67f89d118b18956fe230207cbf0aea
Author: Kate Friedman <[email protected]>
Date:   Wed May 15 13:12:56 2024 -0400

    Update CICE and MOM6 fix versions (#2600)

    This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions
    to the newer `20240416` timestamps, which includes updates and fixes to
    the `100` (1-deg) resolution files.

    Resolves #2480
    Resolves #2483
    Resolves #2595

commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b
Author: David Huber <[email protected]>
Date:   Mon May 13 22:57:38 2024 +0000

    Limit gfswavepostpnt to 40 PEs/node (#2588)

    This fixes the slow runtime of the gfswavepostpnt job on Hercules. The
    job is very I/O intensive and does not scale well to large nodes, so
    limit the number of jobs/node to 40.

    Resolves #2587

commit 4fb7c12c325702a47f27c802a5067efd33d0327c
Author: Fanglin Yang <[email protected]>
Date:   Mon May 13 16:37:51 2024 -0400

    Update damping and time-step (#2575)

    Updates the model to use explicit Rayleigh damping for u/v and implicit
    damping to w. This improves model stability and allows for longer
    timesteps. Also unifies the GDAS and GFS to use the same damping.

    Results from a test at the C1152 resolution (coupled model) can be found
    at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/

    Resolves #2574

    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
    Co-authored-by: Lisa Bengtsson <[email protected]>
    Co-authored-by: Rahul Mahajan <[email protected]>

commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri May 10 14:17:13 2024 -0400

    Do not use BUILT_semphore to force rebuilds when re-run (#2593)

    Remove the placement of the `BUILT_semaphore` file after the build in
    the Jenkins Pipeline and force it to rebuild any changes after a PR is
    re-ran.

commit 2346c6161f75ae02369cbf30f30c6150d3e12b66
Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com>
Date:   Thu May 9 21:17:06 2024 -0500

    Migration to Rocky8 spack-stack installations on Jet (#2458)

    # Description
    Migrates Global Workflow to Rocky8 spack-stack installations on Jet.
    Jet has moved from CentOS7 to Rocky8.

    Resolves #2377
    Refs NOAA-EMC/UPP#919
    Refs NOAA-EMC/gfs-utils#60
    Refs NOAA-EMC/GSI#732
    Refs NOAA-EMC/GSI-Monitor#130
    Refs NOAA-EMC/GSI-utils#33

commit c7b3973014480a20dd8e24edaeb83a9e9e68159f
Author: Jessica Meixner <[email protected]>
Date:   Thu May 9 11:36:58 2024 -0400

    Updates for cold start half cycle, then continuing with IAU for WCDA (#2560)

    This PR allows us to run C384 S2S with IAU, but starting with the first
    half-cycle as a cold-start. This will be necessary for cycled testing as
    we build towards the full system for GFSv17. This updates the copying of
    the restarts for RUN=gdas for both ocean and ice copying what the atm
    model is doing. It also reduced the amount of restart files from 4 to 3.

    Other updates:
    * Add DOJEDI ocean triggers for archiving certain files update from:
    @CatherineThomas-NOAA
    * Adds COPY_FINAL_RESTARTS option to turn on/off copying the last
    restart file to COM. Defaults to off...
    * Defines model_start_date_current_cycle & model_start_date_next_cycle
    to help with knowing which IC to grab.

    Refs #2546

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

commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2
Author: Dan Holdaway <[email protected]>
Date:   Wed May 8 20:52:48 2024 -0400

    Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477)

    Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI
    Configuration Builder (JCB) tool so that YAMLs can be made more portable
    and invoke the observation chronicle mechanism.

    Resolves #2476

    Co-authored-by: danholdaway <[email protected]>
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed May 8 02:04:16 2024 -0400

    Add CI test for products (#2567)

    Adds a new version of the atm3DVar test that runs the full forecast
    length and produces most of the secondary products. For now, this test
    will only run on WCOSS due to gempak failures on other machines as well
    as computational needs. On other machines, the original version will run
    (the original version will not run on WCOSS). AWIPS remains off for now
    in this extended test due to a bug involving tocgrib2 and the convective
    precip fields (see #2566).

    The new test runs for 4½ cycles and the full 384-hr forecast length to
    ensure all gempak scripts are exercised. Since the cycle throttle is 3
    and the bulk of the time is in the free forecast, the cycles run mostly
    concurrently so it doesn't extend the total test time too much beyond
    that of a single 384-hr forecast.

    Fixes a bug in NPOESS that was introduced when the post filenames were
    reverted to the previous format for the GOES products until the final
    filenames are determined (#2499).

    Also removes the AWIPS g2 job from the rocoto mesh to complete the
    retirement of grib1 products.

    Resolves #2132
    Resolves #2445

commit 9b6f8404ac4507d14adc404b77cfdf002b55e832
Author: Rahul Mahajan <[email protected]>
Date:   Tue May 7 00:14:36 2024 -0400

    Add task to prepare emissions for GEFS (#2562)

    This PR:
    - introduces a task to prepare emissions for a forecast into the GEFS
    application.
    - adds configuration, j-job, rocoto job, ex-script and the python class
    for this job
    - updates GEFS workflow to be able to generate the XML to call this job.
    - updates the `fcst` and `efcs` job dependencies in the GEFS application
    to depend on `prep_emissions` if aerosols are turned ON.
    - provides a placeholder for @bbakernoaa to work on the details for
    preparing emissions.

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

commit 233c18815d2e8e6b344f161fd0c102a4fbdfb66d
Author: Dan Holdaway <[email protected]>
Date:   Mon May 6 18:11:35 2024 -0400

    Single Executable for main GDAS JEDI applications (#2565)

    Changes that accompany GDAS PR (NOAA-EMC/GDASApp/pull/1075) that allows
    building of a single gdas executable, which should be more compliant
    with NCO requirements.

    Addresses https://github.com/NOAA-EMC/GDASApp/issues/1085

commit a005244bbfb2f1c525bca60d966f8095aa1acb8e
Author: Guoqing Ge <[email protected]>
Date:   Thu May 2 20:32:53 2024 -0600

    Add nest capability (#2545)

    This PR adds the global nesting capability to the global workflow so
    that one can run a regional domain nested in a global run.

    Resolves #2544

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

commit cb87daaced9fddd17f8370a1842d7e4ddab24e8f
Author: DavidBurrows-NCO <[email protected]>
Date:   Thu May 2 15:30:53 2024 -0400

    Update gfs_utils for Gaea (#2556)

    What: add build capability to the gfs_utils submod within the global
    workflow on Gaea

    Refs #2535

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

commit 707a1cc5124bcd8e006839a17f76ceb88f45f902
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Wed May 1 18:13:02 2024 -0600

    Updated GEMPAK version and APRUN launcher. (#2555)

    This PR addresses issue #2248 and #2513. The following is accomplished:

    - Updates the parallel executable for GEMPAK applications;
    - Updates the GEMPAK version for RDHPCS Hera.

    Describe your changes. Focus on the *what* and *why*. The *how* will be
    evident from the changes. In particular, be sure to note any interface
    changes, such as command line syntax, that will need to be communicated
    to users.

    At the end of your description, please be sure to add the issue this PR
    solves using the word "Resolves". If there are any issues that are
    related but not yet resolved (including in other repos), you may use
    "Refs".

    Resolves #2248
    Resolves #2513

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

commit f151cbf394e998ca0fdae893ca174499468d0c85
Author: Travis Elless <[email protected]>
Date:   Wed May 1 11:01:18 2024 -0400

    Utilize scale-dependent localization for atmospheric analysis (#2542)

    The plan for GFSv17 is to use a scale-dependent localization for the
    atmospheric analysis. This PR adds the necessary parameters to allow
    this feature to be used by default.

commit 53b6764392cb4c0f3b4506ccd3f8cba5c5d2c56e
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Apr 30 16:37:54 2024 -0400

    Remove implicit symlink names (#2527)

    Lustre has a defect under Rocky 9 that results in symlink sometimes
    failing when the link name is not explicit. This updates all link
    creation to use explicit names.

    `config.base` is updated to turn off two monitor jobs on Hercules
    because the executables are not yet built there. This, combined with the
    previous change, should make workflow available for use on Hercules.

    Also removes the redundant utility names for NCP, NLN, etc. in the gdas
    scripts that are already defined in `config.base`.

    Resolves #2131
    Resolves #2522

commit 762f040a2045db17cdacd9026df9c4b8fd520156
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Mon Apr 29 22:26:28 2024 -0400

    Fixes sea ice archiving (#2541)

    Removes/changes sea ice output files that are failing to be added to
    list for archiving, causing `gdasarch` to fail in WCDA cycling.

    Resolves https://github.com/NOAA-EMC/GDASApp/issues/1044

commit 2ecf4f86e0cbe59407ba2c4e105ee7292f1eda01
Author: RussTreadon-NOAA <[email protected]>
Date:   Mon Apr 29 22:25:57 2024 -0400

    Link ensemble analysis increment files to COMROOT for warm_start (#2553)

    Scripting is added to `setup_expt.py` to link ensemble analysis
    increment files to COMROOT for warm_start experiments.

    Resolves #2552

commit 3a7abe1d63c573006e0e656237f1220002c3f579
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Apr 30 02:25:28 2024 +0000

    Launch Multiple Platforms to Jenkins with polling (#2548)

    When launching Jenkins CI Tests all requested RDHPCS machines can now be
    selected via the Ready label at once.
    This is all that is required sense polling also works now on the
    controller end.

    Killing the jobs still needs to be done directly on the Jenkins
    Controller.
    Do not try to update the CI process using Labels. It is for launching
    only.
    Jenkins will update the labels as the states change.

    NOTE: When a case fails the label will be update to a **Fail** for that
    system but will continue to report failures of subsequent cases until
    otherwise stopped in the Jenkins Controller directly.

    Do not update any labels to **Ready** until a push has been made to the
    repo of the PR, and
    The job has been completed or stopped directly on the controller first.
    You can do this at anytime without having to wait until the other
    machines are completed.

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

commit 4b96c1237c562b67650c2d2fa015984c95b228eb
Author: Jessica Meixner <[email protected]>
Date:   Sat Apr 27 19:03:26 2024 -0400

    Turn C48mx500_3DVarAOWCDA back on  (#2543)

    This PR turns the C48mx500_3DVarAOWCDA test back on. This required a few
    bugfixes in GDAS app which have now been merged.

    Resolves #2438
    Resolves #2528

    co-authors: @guillaumevernieres and @aerorahul who provided the bug
    fixes.

commit 48489b4e7758e80660941279652431e49fdd3cfa
Author: Guoqing Ge <[email protected]>
Date:   Sat Apr 27 00:23:00 2024 -0600

    Add option to link different orog/ugwd fix files for global nest (#2532)

    The global nest runs use a different set of tiles and need a different
    set of orog and ugwd fix files.
    The PR add an option to link correct fix files for global nest.

    Resolves #2530
    Resolves #2529

commit 7911f12ef0213f487a0681b260e4c982c946c17c
Author: GwenChen-NOAA <[email protected]>
Date:   Fri Apr 26 16:20:44 2024 -0400

    Retire AWIPS GRIB1 products (#2547)

    This PR retires AWIPS GRIB1 products by deleting the files that are responsible for it.
    This PR does not remove the awips_g2 tasks from rocoto task list.  It will be addressed in a follow up PR by workflow developers
      Refs #2445

commit 93c853d464908a88222d5a6eeca686cd1a413c0e
Author: James Jung <[email protected]>
Date:   Fri Apr 26 13:16:47 2024 -0400

    Add CADS use flexibility (#2540)

    The current design requires a script change to turn CADS on/off for
    specific instruments. The new design moves the on/off (true/false) flags
    to the config.anal file.

    Resolves #2538

commit 11bf141319ef2a29398742007a29d79bbf4439d5
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Apr 25 23:35:57 2024 +0000

    Hot fix for bash CI on WCOSS2 (#2536)

    A couple of minor hotfixes need for bash CI to work on WCOSS2.
    PR tested in bash on WCOSS with these changes

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

commit f11bf3dc2bc062c070b901ce3aa808bd6b69a007
Author: Walter Kolczynski - NOAA <Walter…
kayeekayee added a commit to kayeekayee/global-workflow that referenced this issue Sep 2, 2024
@kayeekayee
Update realtime branch, gsl_ufs_rt
d5c49a4 
 - based on gsl_ufs_dev from KaYee's fork
   global-workflow: 07Aug24,37c53ac [dev_07Aug2024_37c53ac]
   UFS: 19Jul24, c127601
   FV3: 19Jul24, 2527c11
   UPP: 23Apr24, be0410e
   CCPP-PHYSICS: 19Jul24, 46df080
   UFS_UTILS: 26Jun24, 3ef2e6b

Squashed commit of the following:

commit 70b557836379bb7e545fcc6642e28d66cfc17735
Merge: 5edbd123e 37c53ac69
Author: Janet Derrico <[email protected]>
Date:   Wed Aug 7 11:02:24 2024 -0600

    Merge branch 'NOAA-EMC:develop' into develop

commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04
Author: Kate Friedman <[email protected]>
Date:   Wed Aug 7 08:11:21 2024 -0400

    Revert MSU FIX_DIRs back to glopara (#2811)

commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Aug 6 14:47:36 2024 -0400

    Bugfix for updating label states in Jenkins (#2808)

    Quick bug fix for updating state labels in CI during finalize.
    (did not reference GitHub CLI executable correctly in the pipeline
    script)

commit 8fee36f0307b0c08080e3a8fa8fa6703e7da5fce
Author: Rahul Mahajan <[email protected]>
Date:   Tue Aug 6 11:02:45 2024 -0400

    Clean-up temporary rundirs - take 2. (#2753)

    This PR:
    - is a follow-up to a previous PR that aggressively pruned run
    directories.
    - removes run directories for the current cycle in the clean-up if the
    cycle is successful. If the cycle is not successful, cleanup is not
    called and all run directories for the cycle are safe from being purged.
    - also updates the PR template to list/query for any updates to
    submodules.

    ---------

    Co-authored-by: David Huber <[email protected]>
    Co-authored-by: David Huber <[email protected]>
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

commit d599fff4aedd41ae587dbe02226acb12ff48efc1
Author: HelinWei-NOAA <[email protected]>
Date:   Mon Aug 5 05:31:31 2024 -0400

    Change land surface for HR4 (#2787)

    Resets the default value of opt_diag to 2 corresponding to the land
    surface upgrades in ufs-weather-model for HR4.

    Resolves #2786

commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb
Author: David Huber <[email protected]>
Date:   Fri Aug 2 15:41:29 2024 -0400

    Run METplus serially and correct the name of prod tasks (#2804)

    Adds 2 hot fixes:

    - METplus v9.1.3 has a bug in it that sometimes attempts to create
    multiple copies of the same directory when running in parallel, causing
    a Python error and downstream problems. This PR makes METplus run in
    serial mode, preventing such issues.
    - Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in
    workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod)

commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri Aug 2 15:03:45 2024 -0400

    Update Java Agent launching script for Jenkins connections (#2762)

    Made updates to the Jenkins Launching Script for robustness and less
    ambiguous documentation:
    - Clearer distinction between required user token for the remote api and
    the systems token for launching
    - Added pre-checks: `gh` is authenticating, named compliant token and
    secret file exists
    - More robust Jason based parser of the remote api response for checking
    the state of the Node connection
    - For `cron` use a 5 minute pause and recheck was added before
    re-launching of the java agent
    - Added concise header documentation of requirements and purpose
    ---------

    Co-authored-by: David Huber <[email protected]>
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

commit b73b1fd203496db97f8067652659573a632bcc67
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Aug 2 07:59:06 2024 -0400

    Fix erroneous cdump addition (#2803)

commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3
Author: Rahul Mahajan <[email protected]>
Date:   Thu Aug 1 20:26:13 2024 -0400

    Update ocean post-processing triggers (#2784)

    This PR:
    - replaces `check_netcdf.sh` checker for ocean post-processing with with
    ocean output at the next forecast hour or finishing of the forecast job
    for ocean prod
    - removes no longer needed `ush/check_netcdf.sh`

commit aa2af1ca8d59424a60a1730722bf528775d9e606
Author: GeorgeGayno-NOAA <[email protected]>
Date:   Thu Aug 1 16:46:10 2024 -0400

    Update the gfs_utils repository hash (#2801)

    # Description
    Point to the latest hash of the gfs-utils repository, which contains the
    bug fix to gaussian_sfcanl.

    Resolves #2669.
    Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73

commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8
Author: David Huber <[email protected]>
Date:   Thu Aug 1 08:12:14 2024 -0400

    Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791)

    Changes how METplus jobs run so that they run on the last GFS cycle for
    a given `PDY`.

    This is a departure from operations where the METplus jobs run on the
    00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through
    `${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on
    `${PDY}18` for cycles 00-18. See
    https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details.

commit 1cf8b448af562dbb7af198399c78c585977e81da
Author: David Huber <[email protected]>
Date:   Tue Jul 30 10:38:49 2024 -0400

    Simplify resource-related variables, remove CDUMP where unneeded (#2727)

    This overhauls resource-related variables to use a common set of
    variables for each job. In the process, this also removed the use of
    CDUMP in most cases.

    Resolves #1299 #2693

commit 61875f25c9e971f82ae499b5b612d7f095deebd4
Author: Eric Sinsky - NOAA <[email protected]>
Date:   Mon Jul 29 14:40:03 2024 -0400

    Remove f000 from atmos rocoto tasks for replay cases (#2778)

    The main purpose of this PR is to remove the f000 from
    atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In
    cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater
    than `0`, it becomes necessary to have the first lead hour set to
    `OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For
    example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead
    time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and
    the minimum lead time for the ocean_prod rocoto task needs to be 6
    (assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up
    possible by removing 0 from fhrs for atmosphere-related tasks in
    `gefs_tasks.py` when replaying.

    This PR also moves where f000 is being removed for the ocean_prod and
    ice_prod tasks. The if-block that performs this f000 removal has been
    moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`.

    ---------

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

commit f156a7894d639f177e3e2588f98eec1f6f59aa68
Author: Jessica Meixner <[email protected]>
Date:   Fri Jul 26 14:18:32 2024 -0500

    HR4 GWD update (#2732)

    This update is a combination of the gravity wave drag (GWD) versions
    from the NOAA/GSL and NOAA/PSL

commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891
Author: David Huber <[email protected]>
Date:   Thu Jul 25 14:26:52 2024 -0400

    Temporarily disable METplus jobs (#2796)

commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2
Author: Guillaume Vernieres <[email protected]>
Date:   Wed Jul 24 15:00:35 2024 -0400

    Refactoring of the marine B-matrix job (#2749)

    Refactor the functionality of B-matrix generation from the GDASApp

    Resolves #2743

commit 65a7ab75dc0e4baba06a02e11ed0455787056a68
Author: David Huber <[email protected]>
Date:   Tue Jul 23 08:35:48 2024 -0400

    Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775)

    Removes the namespace-based construction of EnKF member COM directories
    in the enkf archive template.

commit c45b9611f3e701b819bd33dc5af29033f060bb91
Author: Eric Sinsky - NOAA <[email protected]>
Date:   Tue Jul 23 00:33:16 2024 -0400

    Add task to process reforecast variables to save on WCOSS2 (#2680)

    # Description
    This PR adds an optional task to the global-workflow to process a subset
    of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for
    the GEFSv13 reforecast. This task is designed to process GEFS variables
    so that specific reforecast product requirements are met. A new variable
    in `config.base` called `DO_EXTRACTVARS` enables this task, which is
    currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by
    default and is specifically a task designed to be executed for the
    GEFSv13 reforecast.

    Refs #1878

    # Type of change
    - New feature (adds functionality)

    # Change characteristics
    - Is this a breaking change (a change in existing functionality)? NO
    - Does this change require a documentation update? NO

    # How has this been tested?
    This has been cloned and tested on WCOSS2. This will need to be tested
    on Hera and other platforms on which the reforecast may be running.

    # Checklist
    - [ ] Any dependent changes have been merged and published
    - [x] My code follows the style guidelines of this project
    - [x] I have performed a self-review of my own code
    - [ ] I have commented my code, particularly in hard-to-understand areas
    - [x] My changes generate no new warnings
    - [x] New and existing tests pass with my changes
    - [ ] I have made corresponding changes to the documentation if
    necessary

    ---------

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

commit 71dc33c6ca991c16ce743760d99feaaf60f2218a
Author: David Huber <[email protected]>
Date:   Mon Jul 22 14:51:53 2024 -0400

    Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774)

    Fix metp* resources and check that they completed properly; add support for Orion Rocky 9

commit 56df67a90fe090c425199f1285e5aac722c398b1
Author: David Huber <[email protected]>
Date:   Mon Jul 22 09:28:18 2024 -0400

    Hotfix: Update jcb to avoid git-lfs files (#2782)

    Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to
    be cloned on Hera.

    This hotfix points to a non-authoritative branch of the GDASApp
    (https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and
    should be updated ASAP back to the authoritative repository.

commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd
Author: Rahul Mahajan <[email protected]>
Date:   Tue Jul 16 09:44:00 2024 -0400

    Address issues in creating XML for GFS forecast-only with app S2SWA (#2757)

    This bugfix PR:
    - fixes an issue where a user is unable to generate the XML for a GFS
    forecast-only experiment with APP=S2SWA

    Specifically, the changes are related to defining `aero_fcst_cdumps`.
    Following `setup_expt.py`, the user will have to set
    `AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in
    `config.base`.

commit e0878dba0e53706a7f53429b61aee2936e2c21bf
Author: Kate Friedman <[email protected]>
Date:   Mon Jul 15 10:25:11 2024 -0400

    Updated prepobs and fit2obs versions for Orion Rocky9 (#2758)

    Update prepobs to v1.0.2 and fit2obs to v1.1.2

    These versions now support Orion Rocky9. Updates are included
    for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet.

commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Jul 11 17:48:47 2024 +0000

    CI maintenance updates and adding CI Unit Tests (#2740)

    This PR has a few maintenance updates to the CI pipeline and adds a test
    directory with Unit Tests
    **Major Maintenance updates:**
    - Added try blocks with appropriate messaging to GitHub PR of failure
    for:
    - - **scm** checkout
    - - build fail (with error logs sent as gists)
    - - create experiment fails with `stderr` sent to GitHub PR messaging
    - Pre-stage FAILS from the above are now captured these fails allow
    FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state
    labels in GitHub - see image below)
    **Minor Maintenance updates:**
    - Fix for STALLED cases reviled from PR 2700 (just needed a lambda
    specifier)
    - Fixed path to experiment directory in PR message (had dropped EXPDIR
    in path)
    - Needed `latin-1` decoder in reading log files for publishing
    **Added python Unit Tests for CI functionality:**
    - Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI
    utility codes
    - Cashed the install of Rocoto in the GitHub Runners to greatly reduce
    stetup time for running the unit tests
    - Unit Tests Python scripts added
    - `test_rocostat.py`: rocoto_statcount() rocoto_summary()
    rocoto_stalled()
      - `test_setup.py`: setup_expt() test_setup_xml()
      - `test_create_experment`: test_create_experiment()
      - - Runs all PR cases that do not have ICs in the GItHub Runner
    - Reporting mechanism in the Actions tab for Python Unit Testing results
    - Test case data for STALLED and RUNNING stored on S3 and pulled using
    wget during runtime of tests

commit 5ef4db74649b8be03402c17aa29c024e71699a7b
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Thu Jul 11 08:59:24 2024 -0400

    Adds contents of constructor and initialize methods to marine LETKF class (#2635)

    Adds contents of constructor and initialize methods to marine LETKF class

    Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091
    ---------

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

commit 8998ec7b74123e953b97a93fa14cc78d471a1aee
Author: David Huber <[email protected]>
Date:   Tue Jul 9 08:31:57 2024 -0400

    Fix GDAS group B restart archiving (#2735)

    Archives the GDAS restartb dataset at a 6-hour offset from restarta

    This allows cycled experiments to restart from the archives.
    The tabbing for the master archive templates was also added to
    improve readability.

    Resolves #2722

commit 3ca74771255727033b9dc043c652ac585178629c
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Tue Jul 9 08:28:54 2024 -0400

    Add fcst dependency to ocnanalprep (#2728)

    Add previous cycle's `fcst` as a dependency to `ocnanalprep`

    This ensures that the availability of restart files to the latter. This addresses a
    seldomly-encountered race condition where `ocnanalprep` fails due to the
    lack of the files.

commit 58fca1668aecd6fb1afd12a441256ad35900e075
Author: Rahul Mahajan <[email protected]>
Date:   Fri Jul 5 15:02:23 2024 -0400

    Update (partially) global-workflow for orion+rocky9 (#2741)

    This PR:
    - updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils,
    GFS-utils) to include recent update to their modulefiles for
    Orion+Rocky9 upgrade
    - updates the modulefiles in global-workflow to load modules from
    Orion+Rocky9 paths
    - updates modulefiles for `gwsetup` and `gwci` as well.
    - removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not
    installed.
    - adds `parm/config.gfs/config.resources.ORION` to address GSI
    performance degradation after Rocky 9 upgrade.

    This PR:
    - does not update the build for UPP. Standalone UPP is not available via
    ufs-weather-model as of #2729
    - will need a follow-up update for `prepobs` and `fit2obs` updated
    locations when they are installed in `glopara` space on Orion.

    # Type of change
    - Maintenance (code refactor, clean-up, new CI test, etc.)

    # Change characteristics
    - Is this a breaking change (a change in existing functionality)? NO
    - Does this change require a documentation update? NO

    # How has this been tested?
    This PR is not sufficient for Orion.
    This PR must be tested on other platforms (Hera, WCOSS2) as this PR
    updates submodules.

    # Checklist
    - [ ] Any dependent changes have been merged and published
    - [ ] My code follows the style guidelines of this project
    - [ ] I have performed a self-review of my own code
    - [ ] I have commented my code, particularly in hard-to-understand areas
    - [ ] My changes generate no new warnings
    - [ ] New and existing tests pass with my changes
    - [ ] I have made corresponding changes to the documentation if
    necessary

    ---------

    Co-authored-by: Kate Friedman <[email protected]>

commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a
Author: Jessica Meixner <[email protected]>
Date:   Wed Jul 3 21:07:49 2024 -0400

    Update ufs model hash to 20240625 (#2729)

    Updates UFS weather model hash to hash from 2024-06-24 which has orion
    porting updates + a few namelist updates.

commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85
Author: David Huber <[email protected]>
Date:   Wed Jul 3 11:32:40 2024 -0400

    Hotfix for undefined CLUSTERS (#2748)

    Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses
    the native `dict` `get` method to prevent grabbing an unset entry.

commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf
Author: GwenChen-NOAA <[email protected]>
Date:   Wed Jul 3 09:56:08 2024 -0400

    Update gempak job to run one fcst hour per task (#2671)

    This PR updates gempak jobs (gfs, gdas, and goes) from processing all
    forecast hours at once to one forecast hour at a time. This will reduce
    the job runtime to less than 5 min, so restart capability is not needed.

    Resolves #1250
    Ref #2666 #2667
    ---------

    Co-authored-by: Walter.Kolczynski <[email protected]>

commit 8215ae654202186a4f753c3abe937b7b9b91a9c7
Author: Rahul Mahajan <[email protected]>
Date:   Tue Jul 2 16:22:11 2024 -0400

    Hotfix for clusters from #2701 (#2747)

    Fixes an issue created from #2701 that added `CLUSTERS` to the
    `gaea.yaml`.

commit 11943e36ba12b3df49c51942da780698fab02d38
Author: DavidBurrows-NCO <[email protected]>
Date:   Tue Jul 2 12:58:10 2024 -0400

    Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701)

    This PR sets up the ability on Gaea for auto generation of a clean xml
    file, i.e., an xml file that does not need any alterations before
    running rocoto.
    Refs #2572
    Refs #2664

commit de8706702ead0630beb54d868f83aa2cb23f8f79
Author: RussTreadon-NOAA <[email protected]>
Date:   Mon Jul 1 09:29:14 2024 -0400

    Update for JCB policies and stage DA job files with Jinja2-templates (#2700)

    This PR updates the `gdas.cd` hash to bring in new JCB conventions.
    Resolves #2699

    From #2654
    This PR will move much of the staging code that take place in the python
    initialization subroutines of the variational and ensemble DA jobs into
    Jinja2-templated YAML files to be passed into the wxflow file handler.
    Much of the staging has already been done this way, but this PR simply
    expands that strategy.

    The old Python routines that were doing this staging are now removed.
    This is part of a broader refactoring of the pygfs tasking.

    wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a
    companion to this PR.

    Co-authored-by: danholdaway <[email protected]>
    Co-authored-by: DavidNew-NOAA <[email protected]>
    Co-authored-by: DavidNew-NOAA <[email protected]>
    Co-authored-by: Dan Holdaway <[email protected]>

commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b
Author: Rahul Mahajan <[email protected]>
Date:   Fri Jun 28 14:56:19 2024 -0400

    Revert PR 2681 (#2739)

    This PR:
    - reverts #2681 in part
    - keeps some changes for `RUN`.
    - is a hotfix
    - should be merged ASAP after consensus w/ @guillaumevernieres
    @CatherineThomas-NOAA @WalterKolczynski-NOAA

commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Wed Jun 26 15:46:08 2024 -0400

    updated Finalize in Jenkinsfile and added try block around scm checkout (#2692)

    We are updating the Jenkins Pipeline with a try block around checkout to
    capture errors for the user.
    Also cleaned up Finalize and added section to clean out workspace on
    success.

commit 968568f682bac7564095440bdb7813abefd76821
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Jun 26 13:27:19 2024 -0400

    Activate snow DA test on WCOSS (#2720)

    Activate the snow DA test on WCOSS.

commit 7706760bb8adbdf78cb640b02739023c886e7699
Author: Rahul Mahajan <[email protected]>
Date:   Wed Jun 26 10:02:22 2024 -0400

    Cleanup of stale RUNDIRS from an experiment (#2719)

    This PR:
    - removes stale temporary scratch run directories from `$DATAROOT/`
    every 3 days.
    - should help to scrub failed attempts.
    - removes an unused variable `RUNDIR` defined in `config.base`

commit 8962991691b5f0857b813bddfd28aa1034d4bd2b
Author: Jessica Meixner <[email protected]>
Date:   Wed Jun 26 09:43:48 2024 -0400

    Update logic for MOM6 number of layers/exception values (#2681)

    Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine
    how many layers and sets the exception value for MOM6 to be 1e-34 for
    all scenarios. Note, we will no longer have zeros in the ocean grib
    output and the DA will also run without issues.

    Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615

commit 12431f76bdce807067929415007592cffc8a2457
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Wed Jun 26 07:42:35 2024 -0600

    Update wave jobs to use COMIN/COMOUT (#2643)

    NCO has requested that each COM variable specify whether it is an input
    or an output.
    This completes that process for the global-workflow wave
    model and products tasks.
    Refs #2451

commit b902c0bac126c323a07186ad8881384b032b6fda
Author: David Huber <[email protected]>
Date:   Tue Jun 25 07:48:46 2024 -0400

    Assign machine- and RUN-specific resources (#2672)

    Redefine resource variables based explicitly on RUN or CDUMP

    Additionally, machine-specific resources are moved out of
    config.resources and placed in respective config.resources.{machine}
    files.

    Resolves #177 #2672

commit 5edbd123e2878a07f5cce8e3c7ea6147f286633a
Merge: 09333c01d 4e1b937b6
Author: Janet Derrico <[email protected]>
Date:   Mon Jun 24 12:44:05 2024 -0600

    Merge branch 'NOAA-EMC:develop' into develop

commit 4e1b937b67ed220120e81925c4507f03b9b8965f
Author: David Huber <[email protected]>
Date:   Mon Jun 24 10:50:52 2024 -0400

    Add minimum software requirements (#2712)

    Adds a table to HPC documentation stating the minimum support versions

commit f43a86276aaef91efa28faadc71a3cf50e749efe
Author: David Huber <[email protected]>
Date:   Fri Jun 21 13:44:29 2024 -0400

    Fix and simplify online archiving and reenable METplus jobs (#2687)

    This fixes the online archiving portion of the `*arch` and `*earc00`
    jobs, a prerequisite for running METplus.  This also reenables
    METplus by default.

    The approach previously taken created `FileHandler` dictionaries at
    varying levels within the resulting yaml, which was not properly parsed
    by `exglobal_archive.py`. This approach creates a single `FileHandler`
    dictionary and is much less complicated overall.

    Resolves #2673 #2647

commit 8993b42cb91144c0ab0501dc7841ea8d675c4701
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Jun 19 21:51:22 2024 -0400

    Eliminate post groups (#2667)

    Eliminates the post groups used for upp and products jobs so that each
    task only processes one forecast hour. This is more efficient and
    greatly simplifies downstream dependencies that depend on a specific
    forecast hour.

    Resolves #2666
    Refs #2642

commit 0b810c888239853fedd0e4584fe62536c6aaacdf
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Tue Jun 18 20:32:48 2024 -0600

    Removes misleading "No such file or directory" syntax errors from output files (#2688)

    This PR addresses issue #1252. The following is accomplished:

    - Prior to removing files, the existence of a file is checked prior to
    attempting to remove; this is performed as noted
    [here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369);
    this PR only addresses the the `chgrp` issue.

    Refs #1252

    ---------

    Co-authored-by: David Huber <[email protected]>

commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Tue Jun 18 12:17:59 2024 -0600

    Hotfix for bug in template names. (#2697)

    This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/`
    template.
    Resolves #2696
    Refs #2451

commit 35d4d99eaac669721add9ddcc793153e5ab3b30a
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Tue Jun 18 08:06:53 2024 -0600

    Update archive job to use COMIN/COMOUT (#2668)

    NCO has requested that each COM variable specify whether it is an input
    or an output. This completes that process for the global-workflow
    archive task.

    Refs #2451
    ---------

    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
    Co-authored-by: Rahul Mahajan <[email protected]>
    Co-authored-by: David Huber <[email protected]>

commit 47b3a581c8257fa24411fb400df8bb0e1e04972a
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Jun 17 22:55:38 2024 -0400

    Turn on high-frequency output in extended test (#2679)

    Turns on high-frequency (hourly) output in the extended products test to
    exercise that aspect of the code. This test only runs on WCOSS.

    Also adds the hooks to optionally turn on the metplus jobs, but that is
    deferred as they are not currently working correctly.

commit 38f2df9fb0c074b1f80d3c637080be79be693161
Author: David Huber <[email protected]>
Date:   Mon Jun 17 17:12:55 2024 +0000

    Optimize wavepostpnt (#2657)

    Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs

    This is done by
    1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by
    - performing operations on all files at once instead of looping over
    each file
        - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`)
        - combining `sed` and `grep` calls when possible
        - adding logic to `awk` calls instead of handling that logic in bash
    2) minimizing as much as possible the amount of data on disk that has to
    be read in (e.g. limiting sed to read only the line numbers it needs)
    ---------

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

commit 5af325a6a4e0a14d180514a418603ca79fada487
Author: Dan Holdaway <[email protected]>
Date:   Fri Jun 14 18:05:23 2024 -0400

    Update GDASapp hash to move JCB into GDASapp (#2665)

    This PR moves JCB into GDASapp. The PR
    also bumps up the hash of GDASapp to what is in `feature/move_jcb`,
    which at time of writing is develop plus the absorption of JCB into
    GDASapp.
    Note that I also took the changes from
    https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the
    testing @RussTreadon-NOAA has done.

commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b
Author: Yaping Wang <[email protected]>
Date:   Fri Jun 14 10:18:17 2024 -0500

    Add observation preparation job for aerosols DA to workflow (#2624)

    Add a prepaeroobs job to prepare aerosol obs files for DA.

    This job does quality control of the VIIRS aerosol raw observations and
    convert them to ioda format.

    Resolves #2623
    ---------

    Co-authored-by: ypwang19 <[email protected]>
    Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>
    Co-authored-by: Cory Martin <[email protected]>
    Co-authored-by: David Huber <[email protected]>

commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4
Author: Jessica Meixner <[email protected]>
Date:   Fri Jun 14 11:04:41 2024 -0400

    Remove ocean daily files (#2689)

    This PR removes the ocn_daily files that are produced by the ocean
    component. These files can be recreated by averaging data that exists in
    the 6 hour aveaged files if needed.

    Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675
    Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by
    removing them and making this obsolete)

commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Jun 13 12:22:03 2024 -0400

    Update Jenkinsfile

    needed a comma

commit dc21eac6c3941d7f30803891d91d82f4cc1f8183
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Jun 13 11:41:14 2024 -0400

    Add Hercules-EMC to the Jenkins configurable parameter list (#2685)

    This quick-fix PR is to update the Jenkins Pipeline's configurable
    parameter list to include the **Hercules-EMC** node.
    This allows Jenkins users to restart Jobs in the controller when no
    updates have been made.

commit ebacebfbe458634b8c80af6a735d6b6d01e4e406
Author: RussTreadon-NOAA <[email protected]>
Date:   Thu Jun 13 11:20:24 2024 -0400

    Update gdas.cd and gsi_utils hashes (#2641)

    This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The
    updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea
    build for gsi_utils.

    Resolves #2640

commit 34155fb4767769600a1ff95f0a65e37081addc2a
Author: Neil Barton <[email protected]>
Date:   Thu Jun 13 11:18:22 2024 -0400

    Add ability to use GEFS replay ICs (#2559)

    The PR allows the use of ICs from PSL's replay analysis. These replay
    ICs will be used for GEFS reforecasting and SFS. Two main changes are
    associated with these updates: (1) replay ICs being valid at 3Z, and (2)
    the use of warm starts.

    Resolves #1838

    ---------

    Co-authored-by: Jessica Meixner <[email protected]>
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
    Co-authored-by: Rahul Mahajan <[email protected]>

commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Wed Jun 12 19:25:42 2024 -0600

    Replace `sleep` with `wait_for_file` (#2586)

    This PR addresses issue #2444. The following is accomplished:

    - All `sleep` statements are replaced with `wait_for_file` for the
    relevant scripts beneath `scripts` and `ush`;
    - Indentation and shell-norms are updated where applicable.

    Note: The WAFS scripts are not updated as per @aerorahul direction.

    Resolves #2444

    ---------

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

commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Jun 12 13:31:55 2024 -0400

    Add COM template for JEDI obs (#2678)

    Adds a COM template to define a path to store obs processed for JEDI.
    This will allow UFSDA to stop writing to COM_OBS, which should be
    read-only as it belongs to obsproc in operations.

    No functional change yet.

commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed
Author: Guoqing Ge <[email protected]>
Date:   Wed Jun 12 09:06:23 2024 -0600

    Link both global-nest fix files and non-nest ones at the same time (#2632)

    This PR enables linking both global-nest fix files and non-nest ones at
    the same time and users can run both nesting and non-nesting experiments
    at the same time without worries about what fix files to be linked.

    Resolves #2631

commit 61de004d4f9e9edf8a31bb173f2719b46451a36a
Author: Jessica Meixner <[email protected]>
Date:   Wed Jun 12 11:03:13 2024 -0400

    Update ufs-weather-model  (#2663)

    Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack
    allowing some temporary fixes to be reverted.
    * removes upp submodule
    * uses upp from the ufs-weather-model
    * restores the build and link that were hacked during the Hera Rocky 8
    transition to allow for UPP submodule
    * Removes forecast directories in clean-up

    Resolves #2617
    Resolves #2437

    ---------

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

commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d
Author: Eric Sinsky - NOAA <[email protected]>
Date:   Wed Jun 12 01:15:37 2024 -0400

    Add ability to process ocean/ice products specific to GEFS (#2561)

    This PR begins to add the capability to produce GEFSv13 ocean and ice
    products in the global-workflow according to stakeholder requirements.
    The following features are added.

    - An oceanice prod yaml file has been added to address the ocean and ice
    products specific to GEFSv13.
    - The rocoto dependencies and config.base for GEFS have also been
    modified to allow for 24-hour averaged ocean and ice output.
    - Various scripts have been modified to allow for ocean and ice output
    frequencies of 24 hours.
    - `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN`
    and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`.

    Refs #1878

commit 6691e7489650e0b738c176fbd096109288dc09b6
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Tue Jun 11 21:15:07 2024 -0600

    Update cleanup job to use COMIN/COMOUT (#2649)

    NCO has requested that each COM variable specify whether it is an input
    or an output. This completes that process for the global-workflow
    clean-up task.

    Refs #2451

    ---------

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

commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Jun 11 16:17:25 2024 -0400

    Add overwrite to creat experiment in BASH CI (#2676)

    This is a quick hotfix to the CI BASH driver script adding `--overwrite`
    to create experiment script to avoid errors from restarting an
    experiment.

commit e7909af8d9e1f34140388a3f8556d8e582c58fe5
Author: emilyhcliu <[email protected]>
Date:   Mon Jun 10 15:11:27 2024 -0400

    Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py  (#2645)

    This PR proposes updates for the following two scripts:

    1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select
    CRTM cloud optical table based on cloud microphysical scheme indicated
    by `imp_physics'
    The default scheme in the GFS forecast model is Thompson scheme
    (imp_physics = 8).

    2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in
    the script due to increased variables to interplate increments and
    calculate analysis in the netcdf_io routines in GSI-utils.
    Here is the related [PR #46 for
    GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46).

    ---------

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

commit 9caa51de8fb7be07d2e61775da01937d576964f6
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Thu Jun 6 22:15:23 2024 -0600

    Update RDHPCS Hera resource for `eupd` task (#2636)

    As per @wx20jjung, the resource for the `eupd` task have been updated
    for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job
    fails.

    Resolves #2454

    ---------

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

commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b
Author: DavidNew-NOAA <[email protected]>
Date:   Thu Jun 6 11:49:03 2024 -0400

    Parameterize some things in config.atmanl and config.atmensanl (#2661)

    This PR adds some parameters in config.atmanl and config.atmensanl that
    can be altered with the defaults.yaml. The motivation is to make these
    files match those in the GDASApp JJOB tests (example:
    https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl),
    so we can just use the Global Workflow config.atmanl and
    config.atmensanl in the tests rather than custom ones in GDASApp that
    have to be separately updated every time the ones in the Global Workflow
    are updated.

commit 54ea0b73a07921be5fbb07fe41e976888bd3e549
Author: Guillaume Vernieres <[email protected]>
Date:   Thu Jun 6 01:36:02 2024 -0400

    Add links to the ocean insitu obs processing tools (#2644)

    Add links to the marine bufr to ioda converters for the marine insitu
    observations.

    - fixes https://github.com/NOAA-EMC/GDASApp/issues/1106
    - waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135

commit 205d0c2b13e2d7755cec75bf8c978ab20d453862
Author: David Huber <[email protected]>
Date:   Wed Jun 5 17:31:30 2024 +0000

    Update S4 point of contact in docs (#2660)

    Update the point of contact for global workflow issues on S4.

commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262
Author: RussTreadon-NOAA <[email protected]>
Date:   Wed Jun 5 12:50:14 2024 -0400

    Enable wcoss2 ufsda build and module load (#2620)

    This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2.

    Resolves #2602
    Resolves #2579

commit 67b833e0c7bc390865d453588b4609a1a7ede981
Author: Jessica Meixner <[email protected]>
Date:   Tue Jun 4 13:33:43 2024 -0400

    Update ufs-weather-model  (#2646)

    Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6
    This should resolve the issue and allow C768 runs on Hera and allow for CICE
    to run on WCOSS2 (due to library updates to allow linking).

    From what I can tell, all updates needed were done by
    @HenryWinterbottom-NOAA which were updates for CICE

    Fixes #2490

commit c44d0ac86cfdf78eb87492431bf6d825e8bae637
Author: GwenChen-NOAA <[email protected]>
Date:   Tue Jun 4 10:29:49 2024 -0400

    Update wmo parm files to fix WMO header (#2652)

    This PR updates wmo parm files to switch WMO header of precipitation
    type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to
    instantaneous.

    Resolves #2566

commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60
Author: Cory Martin <[email protected]>
Date:   Tue Jun 4 13:55:33 2024 +0000

    Add IAU to snow DA (and its test) (#2610)

    This PR enables IAU for the snow DA which is necessary for GFSv17.

    A snow analysis is created for the center of the window regardless, and
    an additional at the beginning of the window is added if IAU is on. The
    former is needed for UPP and the latter, to initialize the model.

    The increment is valid throughout the window for 3DVar, so the same
    increment is added to both forecasts.

    Additionally, the input file that goes into global_cycle has been
    updated to be the output of the JEDI snow analysis instead of the
    forecast (@jiaruidong2017 I recall discussing this, can you confirm this
    is right or am I mistaken)

    This PR also makes the CI test for snow DA (and aerosol DA) include IAU
    rather than without IAU,.

    ---------

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

commit c92bf415060750127c9c05a62a1d2851c489551a
Author: David Huber <[email protected]>
Date:   Sat Jun 1 05:11:07 2024 +0000

    Archiving cleanup (#2621)

    1) Adds a lot of comments to the jinja templates for archiving
    2) Rearranges the gdas and enkf templates to a more logical order
    3) Fixes a couple of bugs in the enkf archiving of increments and
    analyses
    4) Disables archiving for the half cycle
    5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`,
    instead relying on `DO_FIT2OBS`
    6) Updates wxflow to add the option to not allow undefined variables
    when parsing jinja templates and invokes this feature when running
    archives

    Resolves #2612

commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri May 31 04:57:08 2024 -0400

    Switch to Rocky 9 built external packages on Hercules (#2608)

    The workflow was updated to use modules built on Rocky 9, but the
    external packages (like prepobs) were still pointing to the versions
    built on CentOS (Orion). This transitions to packages built on Rocky 9.

    Updating of the tracker package has been deferred until later. As such,
    the tracker jobs have been disabled by returning immediately if they are
    on Hercules. Since these jobs are small, resource-wise, it should not
    meaningfully impact turnover time.

commit 4422550c01c9214a2b3b8890bdcc898123ee216a
Author: Guoqing Ge <[email protected]>
Date:   Thu May 30 08:05:23 2024 -0600

    Add the capability to use slurm reservation nodes (#2627)

    Add the capability to use slurm reservation nodes
    Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE

    Resolves #2626

commit a54153fd9d26126206bc07a1da4e80f50c0c5910
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed May 29 23:24:07 2024 -0400

    Update forecast job to use COMIN/COMOUT (#2622)

    NCO has requested that each COM variable specify whether it is an input
    or an output. This completes that process for the forecast job.

    Refs #2451

    ---------

    Co-authored-by: David Huber <[email protected]>

commit d69a8af95d492982b918670322ed5c41ab074335
Author: Jessica Meixner <[email protected]>
Date:   Wed May 29 21:29:03 2024 -0400

    Update to add 1-deg global wave grid (#2619)

    This PR adds options to use a global 1 deg grid, intended for testing
    with the SFS application.

    Requires new fix file changes NOAA-EMC/global-workflow#2618

commit 0b4670ecf83b99b72835c8380573b2bca7cf5324
Author: Jessica Meixner <[email protected]>
Date:   Wed May 29 17:17:21 2024 -0400

    Add C384mx025_3DVarAOWCDA yamls (#2625)

    Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder.

commit 2e885d05c64b947f00a3cf055a1277fbfac195c9
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Wed May 29 13:00:51 2024 -0400

    Script to keep Jenkins Agent persistent from cron (#2634)

    This "persistent" Java Agent launch script can be ran from a cron job:

    - Uses Jenkins Remote API to check the status of the Node connection
    using curl for a given machine.
    - If it is not connected a new agent is launched for that node.

    Resolves #2633

commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5
Author: GwenChen-NOAA <[email protected]>
Date:   Tue May 28 17:17:11 2024 -0400

    Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611)

    Based on users' feedback, this PR do the following:
    1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF
    2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD,
      and VOGRD) from "%g m below water surface" to "%g m below sea level"
    3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m)

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

commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31
Author: DavidNew-NOAA <[email protected]>
Date:   Tue May 28 17:16:23 2024 -0400

    Add atmensanlfv3inc job (#2592)

    This PR creates the atmensanlfv3inc job, the ensemble version of
    atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is
    #[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS
    companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3).

commit 50c2b8951b29a3c883a778becbf8582f9519eb48
Author: Anil Kumar <[email protected]>
Date:   Tue May 28 13:23:53 2024 -0400

    Global-workflow (AR) Generic updates for Gaea C5 (#2515)

    - Port global-workflow’s build and run capability to Gaea-C5
    - Building global-workflow on Gaea-C5
    - Setting up experiments with global-workflow on Gaea-C5

    ---------

    Co-authored-by: AnilKumar-NOAA <[email protected]>
    Co-authored-by: DavidBurrows-NCO <[email protected]>

commit b6ca771a0c584cbfcbbf9be739765d5f3815df97
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri May 24 10:52:45 2024 -0400

    Update STMP and PTMP settings in host file for Orion and Hercules  (#2614)

    - Updating STMP and PTMP settings in host file for Orion and Hercules
    because they are cross mounted.
    - Also took the opportunity to finally update **SLURM_ACCOUNT** to
    **HPC_ACCOUT** in CI over rides.
    - Added a refactor of the `rocotostat.py` tool that is more pythonic and
    as a execute retry feature because the `rocotostat` utility on Orion has
    been failing sometimes.

commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f
Author: Guillaume Vernieres <[email protected]>
Date:   Tue May 21 23:50:50 2024 -0400

    Sea-ice analysis insertion (#2584)

    Allows cycling and restarting CICE with the sea-ice analysis if the
    marine DA is switched on.

    Resolves #2568
    Resolves NOAA-EMC/GDASApp#1103

commit 5369a1ff3a3969149fcf32810fad0e50216752b7
Author: David Huber <[email protected]>
Date:   Tue May 21 22:12:29 2024 +0000

    Refactored archiving (#2491)

    This provides a new pygfs task, archive.py, that provides all of the
    tools necessary to archive data to the local (`ARCDIR`) and backup
    (`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to
    define the file to be archived or tarred to replace the
    `hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts
    and make it easier to add new data and explicitly handle optional and
    required files.

    For `ATARDIR` archiving, a master jinja template is provided for each
    `RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2,
    master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both
    `enkfgdas` and `enkfgfs` `RUN`s. These templates then include the
    appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on
    experiment, cycle, and coupled parameters. Each of these templates
    corresponds to a single tarball to populate and are tabbed 4 spaces so
    they are defined within the master `datasets` dictionary.

    Future developers should not have to make modifications to archive.py
    unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then
    only a single `elif` needs to be added to the configure method to
    specify the master `ATARDIR` template to archive (e.g.
    `master_gefs.yaml.j2`). If a new component is coming online that needs
    to be archived to `ATARDIR` (e.g. SNOW), then create a new template for
    each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`)
    and reference the template in the appropriate master templates, e.g.

    `master_gdas.yaml:`
    ```jinja
    {% if DO_SNOW %}
    {% include "gdassnow.yaml.j2" %}
    {% endif %}
    ```

    A few other issues were addressed along the way:
    1. Aerosols have been reenabled. Aerosol forecasts should only be
    performed during gdas cycles, but analyses can be performed for both gfs
    and gdas cycles. This was accomplished by setting separate
    `AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs.
    2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`.
    This prevented restarts from being used for cice-enable experiments.
    This feature was not tested.
    3. Create a temporary fix for the `wgrib` utility. For spack-stack
    1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is
    open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in
    existing installations. Once complete, this temporary fix should be
    removed.
    4. The number of `earc` jobs has been reduced for lower resolution
    experiments. Both C48 and C96 experiments will now only have two earc
    jobs (one for the non-member files to archive and another for the member
    files). C192 will have up to 3 earc jobs (one non-member, one for
    members 1-40 and another for members 41-80, if needed).

    Resolves #2345
    Resolves #2318

    ---------

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

commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri May 17 12:57:59 2024 -0400

     Add remove RUNDIRS step in CI before creating experements (#2607)

    As had been done in Bash CI we need to remove the RUNDIR in Jenkins
    before a creating an experiment in the event that case had beem
    previously ran.

commit 09333c01dbafddb2d2fe7e181b479af3cc6d3621
Merge: f7e9f4489 bb930050b
Author: Janet Derrico <[email protected]>
Date:   Thu May 16 14:33:19 2024 -0600

    Merge branch 'NOAA-EMC:develop' into develop

commit bb930050b3cd51d28ecba6b231c8675f6d11856c
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Thu May 16 12:28:30 2024 -0400

    Adds jjob and other necessities for marine LETKF task (#2564)

    Adds jjob, rocoto script, config file, and other necessities for new
    marine LETKF task.

    Partially addresses NOAA-EMC/GDASApp#1091

commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu May 16 12:12:06 2024 -0400

    Updating CI Machine configs with redundant PTMP (#2605)

    Quick fix adding PTMP as STMP in Machine configs for CI for completeness

commit ef340ff33a6f89adf70838206ba3fd56a953fa7a
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu May 16 11:37:30 2024 -0400

    Fix race condition in CI between Orion and Hercules (#2604)

    Hotfix to solve race conditions in the CI system due to cross-mounted
    file systems between Orion and Hercules

commit e8b17e27f719df280170dc3f5bd9f19917cefaf2
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Wed May 15 17:16:30 2024 -0400

    Remove existing EXPDIRs and COMROTs when CI is re-run (#2601)

    Quick hotfix for having default for re-runing jobs to start clean with
    new EXPDIRs and COMROTs

commit b5d113efb1970ede5cd1d3d4dff8d96320519c41
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Wed May 15 16:52:49 2024 -0400

    Moving logic for skipping hosts in pr cases (#2573)

    This PR removes the logic of skipping hosts for pr cases from
    `create_experiment.py` and moves it to a test in the cron bash driver
    using a `parse_yaml.py` python tool.

    The Jenkins pipeline was not effected as it uses the
    `get_host_case_list.py` utility to form the cases on a per host bases.

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

commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916
Author: RussTreadon-NOAA <[email protected]>
Date:   Wed May 15 13:13:30 2024 -0400

    Update gsi_utils.fd hash (#2598)

    This PR updates the `gsi_utils.fd` hash to bring in updates which add
    safeguards to
    -
    `src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90`
    - `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90`

    The safeguards are described in GSI-utils PR
    [#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated
    issue.

    Resolves #2597

commit d5366c66bd67f89d118b18956fe230207cbf0aea
Author: Kate Friedman <[email protected]>
Date:   Wed May 15 13:12:56 2024 -0400

    Update CICE and MOM6 fix versions (#2600)

    This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions
    to the newer `20240416` timestamps, which includes updates and fixes to
    the `100` (1-deg) resolution files.

    Resolves #2480
    Resolves #2483
    Resolves #2595

commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b
Author: David Huber <[email protected]>
Date:   Mon May 13 22:57:38 2024 +0000

    Limit gfswavepostpnt to 40 PEs/node (#2588)

    This fixes the slow runtime of the gfswavepostpnt job on Hercules. The
    job is very I/O intensive and does not scale well to large nodes, so
    limit the number of jobs/node to 40.

    Resolves #2587

commit 4fb7c12c325702a47f27c802a5067efd33d0327c
Author: Fanglin Yang <[email protected]>
Date:   Mon May 13 16:37:51 2024 -0400

    Update damping and time-step (#2575)

    Updates the model to use explicit Rayleigh damping for u/v and implicit
    damping to w. This improves model stability and allows for longer
    timesteps. Also unifies the GDAS and GFS to use the same damping.

    Results from a test at the C1152 resolution (coupled model) can be found
    at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/

    Resolves #2574

    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
    Co-authored-by: Lisa Bengtsson <[email protected]>
    Co-authored-by: Rahul Mahajan <[email protected]>

commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri May 10 14:17:13 2024 -0400

    Do not use BUILT_semphore to force rebuilds when re-run (#2593)

    Remove the placement of the `BUILT_semaphore` file after the build in
    the Jenkins Pipeline and force it to rebuild any changes after a PR is
    re-ran.

commit 2346c6161f75ae02369cbf30f30c6150d3e12b66
Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com>
Date:   Thu May 9 21:17:06 2024 -0500

    Migration to Rocky8 spack-stack installations on Jet (#2458)

    # Description
    Migrates Global Workflow to Rocky8 spack-stack installations on Jet.
    Jet has moved from CentOS7 to Rocky8.

    Resolves #2377
    Refs NOAA-EMC/UPP#919
    Refs NOAA-EMC/gfs-utils#60
    Refs NOAA-EMC/GSI#732
    Refs NOAA-EMC/GSI-Monitor#130
    Refs NOAA-EMC/GSI-utils#33

commit c7b3973014480a20dd8e24edaeb83a9e9e68159f
Author: Jessica Meixner <[email protected]>
Date:   Thu May 9 11:36:58 2024 -0400

    Updates for cold start half cycle, then continuing with IAU for WCDA (#2560)

    This PR allows us to run C384 S2S with IAU, but starting with the first
    half-cycle as a cold-start. This will be necessary for cycled testing as
    we build towards the full system for GFSv17. This updates the copying of
    the restarts for RUN=gdas for both ocean and ice copying what the atm
    model is doing. It also reduced the amount of restart files from 4 to 3.

    Other updates:
    * Add DOJEDI ocean triggers for archiving certain files update from:
    @CatherineThomas-NOAA
    * Adds COPY_FINAL_RESTARTS option to turn on/off copying the last
    restart file to COM. Defaults to off...
    * Defines model_start_date_current_cycle & model_start_date_next_cycle
    to help with knowing which IC to grab.

    Refs #2546

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

commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2
Author: Dan Holdaway <[email protected]>
Date:   Wed May 8 20:52:48 2024 -0400

    Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477)

    Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI
    Configuration Builder (JCB) tool so that YAMLs can be made more portable
    and invoke the observation chronicle mechanism.

    Resolves #2476

    Co-authored-by: danholdaway <[email protected]>
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed May 8 02:04:16 2024 -0400

    Add CI test for products (#2567)

    Adds a new version of the atm3DVar test that runs the full forecast
    length and produces most of the secondary products. For now, this test
    will only run on WCOSS due to gempak failures on other machines as well
    as computational needs. On other machines, the original version will run
    (the original version will not run on WCOSS). AWIPS remains off for now
    in this extended test due to a bug involving tocgrib2 and the convective
    precip fields (see #2566).

    The new test runs for 4½ cycles and the full 384-hr forecast length to
    ensure all gempak scripts are exercised. Since the cycle throttle is 3
    and the bulk of the time is in the free forecast, the cycles run mostly
    concurrently so it doesn't extend the total test time too much beyond
    that of a single 384-hr forecast.

    Fixes a bug in NPOESS that was introduced when the post filenames were
    reverted to the previous format for the GOES products until the final
    filenames are determined (#2499).

    Also removes the AWIPS g2 job from the rocoto mesh to complete the
    retirement of grib1 products.

    Resolves #2132
    Resolves #2445

commit 9b6f8404ac4507d14adc404b77cfdf002b55e832
Author: Rahul Mahajan <[email protected]>
Date:   Tue May 7 00:14:36 2024 -0400

    Add task to prepare emissions for GEFS (#2562)

    This PR:
    - introduces a task to prepare emissions for a forecast into the GEFS
    application.
    - adds configuration, j-job, rocoto job, ex-script and the python class
    for this job
    - updates GEFS workflow to be able to generate the XML to call this job.
    - updates the `fcst` and `efcs` job dependencies in the GEFS application
    to depend on `prep_emissions` if aerosols are turned ON.
    - provides a placeholder for @bbakernoaa to work on the details for
    preparing emissions.

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

commit 233c18815d2e8e6b344f161fd0c102a4fbdfb66d
Author: Dan Holdaway <[email protected]>
Date:   Mon May 6 18:11:35 2024 -0400

    Single Executable for main GDAS JEDI applications (#2565)

    Changes that accompany GDAS PR (NOAA-EMC/GDASApp/pull/1075) that allows
    building of a single gdas executable, which should be more compliant
    with NCO requirements.

    Addresses https://github.com/NOAA-EMC/GDASApp/issues/1085

commit a005244bbfb2f1c525bca60d966f8095aa1acb8e
Author: Guoqing Ge <[email protected]>
Date:   Thu May 2 20:32:53 2024 -0600

    Add nest capability (#2545)

    This PR adds the global nesting capability to the global workflow so
    that one can run a regional domain nested in a global run.

    Resolves #2544

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

commit cb87daaced9fddd17f8370a1842d7e4ddab24e8f
Author: DavidBurrows-NCO <[email protected]>
Date:   Thu May 2 15:30:53 2024 -0400

    Update gfs_utils for Gaea (#2556)

    What: add build capability to the gfs_utils submod within the global
    workflow on Gaea

    Refs #2535

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

commit 707a1cc5124bcd8e006839a17f76ceb88f45f902
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Wed May 1 18:13:02 2024 -0600

    Updated GEMPAK version and APRUN launcher. (#2555)

    This PR addresses issue #2248 and #2513. The following is accomplished:

    - Updates the parallel executable for GEMPAK applications;
    - Updates the GEMPAK version for RDHPCS Hera.

    Describe your changes. Focus on the *what* and *why*. The *how* will be
    evident from the changes. In particular, be sure to note any interface
    changes, such as command line syntax, that will need to be communicated
    to users.

    At the end of your description, please be sure to add the issue this PR
    solves using the word "Resolves". If there are any issues that are
    related but not yet resolved (including in other repos), you may use
    "Refs".

    Resolves #2248
    Resolves #2513

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

commit f151cbf394e998ca0fdae893ca174499468d0c85
Author: Travis Elless <[email protected]>
Date:   Wed May 1 11:01:18 2024 -0400

    Utilize scale-dependent localization for atmospheric analysis (#2542)

    The plan for GFSv17 is to use a scale-dependent localization for the
    atmospheric analysis. This PR adds the necessary parameters to allow
    this feature to be used by default.

commit 53b6764392cb4c0f3b4506ccd3f8cba5c5d2c56e
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Apr 30 16:37:54 2024 -0400

    Remove implicit symlink names (#2527)

    Lustre has a defect under Rocky 9 that results in symlink sometimes
    failing when the link name is not explicit. This updates all link
    creation to use explicit names.

    `config.base` is updated to turn off two monitor jobs on Hercules
    because the executables are not yet built there. This, combined with the
    previous change, should make workflow available for use on Hercules.

    Also removes the redundant utility names for NCP, NLN, etc. in the gdas
    scripts that are already defined in `config.base`.

    Resolves #2131
    Resolves #2522

commit f7e9f4489fc0b10830f621fdf149e8e3149d6a51
Merge: 67a4810c4 762f040a2
Author: Janet Derrico <[email protected]>
Date:   Tue Apr 30 12:24:48 2024 -0600

    Merge branch 'NOAA-EMC:develop' into develop

commit 762f040a2045db17cdacd9026df9c4b8fd520156
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Mon Apr 29 22:26:28 2024 -0400

    Fixes sea ice archiving (#2541)

    Removes/changes sea ice output files that are failing to be added to
    list for archiving, causing `gdasarch` to fail in WCDA cycling.

    Resolves https://github.com/NOAA-EMC/GDASApp/issues/1044

commit 2ecf4f86e0cbe59407ba2c4e105ee7292f1eda01
Author: RussTreadon-NOAA <[email protected]>
Date:   Mon Apr 29 22:25:57 2024 -0400

    Link ensemble analysis increment files to COMROOT for warm_start (#2553)

    Scripting is added to `setup_expt.py` to link ensemble analysis
    increment files to COMROOT for warm_start experiments.

    Resolves #2552

commit 3a7abe1d63c573006e0e656237f1220002c3f579
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Apr 30 02:25:28 2024 +0000

    Launch Multiple Platforms to Jenkins with polling (#2548)

    When launching Jenkins CI Tests all requested RDHPCS machines can now be
    selected via the Ready label at once.
    This is all that is required sense polling also works now on the
    controller end.

    Killing the jobs still needs to be done directly on the Jenkins
    Controller.
    Do not try to update the CI process using Labels. It is for launching
    only.
    Jenkins will update the labels as the states change.

    NOTE: When a case fails the label will be update to a **Fail** for that
    system but will continue to report failures of subsequent cases until
    otherwise stopped in the Jenkins Controller directly.

    Do not update any labels to …
kayeekayee added a commit to kayeekayee/global-workflow that referenced this issue Sep 18, 2024
@kayeekayee
Update develop branch, gsl_ufs_dev
32bf790 
 - based on gsl_ufs_dev from KaYee's fork
   global-workflow: 07Aug24,37c53ac [develop_07Aug2024_37c53ac]
   UFS: 19Jul24, c127601
   FV3: 19Jul24, 2527c11
   UPP: 23Apr24, be0410e
   CCPP-PHYSICS: 19Jul24, 46df080
   UFS_UTILS: 26Jun24, 3ef2e6b

Squashed commit of the following:

commit 70b557836379bb7e545fcc6642e28d66cfc17735
Merge: 5edbd123e 37c53ac69
Author: Janet Derrico <[email protected]>
Date:   Wed Aug 7 11:02:24 2024 -0600

    Merge branch 'NOAA-EMC:develop' into develop

commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04
Author: Kate Friedman <[email protected]>
Date:   Wed Aug 7 08:11:21 2024 -0400

    Revert MSU FIX_DIRs back to glopara (#2811)

commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Aug 6 14:47:36 2024 -0400

    Bugfix for updating label states in Jenkins (#2808)

    Quick bug fix for updating state labels in CI during finalize.
    (did not reference GitHub CLI executable correctly in the pipeline
    script)

commit 8fee36f0307b0c08080e3a8fa8fa6703e7da5fce
Author: Rahul Mahajan <[email protected]>
Date:   Tue Aug 6 11:02:45 2024 -0400

    Clean-up temporary rundirs - take 2. (#2753)

    This PR:
    - is a follow-up to a previous PR that aggressively pruned run
    directories.
    - removes run directories for the current cycle in the clean-up if the
    cycle is successful. If the cycle is not successful, cleanup is not
    called and all run directories for the cycle are safe from being purged.
    - also updates the PR template to list/query for any updates to
    submodules.

    ---------

    Co-authored-by: David Huber <[email protected]>
    Co-authored-by: David Huber <[email protected]>
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

commit d599fff4aedd41ae587dbe02226acb12ff48efc1
Author: HelinWei-NOAA <[email protected]>
Date:   Mon Aug 5 05:31:31 2024 -0400

    Change land surface for HR4 (#2787)

    Resets the default value of opt_diag to 2 corresponding to the land
    surface upgrades in ufs-weather-model for HR4.

    Resolves #2786

commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb
Author: David Huber <[email protected]>
Date:   Fri Aug 2 15:41:29 2024 -0400

    Run METplus serially and correct the name of prod tasks (#2804)

    Adds 2 hot fixes:

    - METplus v9.1.3 has a bug in it that sometimes attempts to create
    multiple copies of the same directory when running in parallel, causing
    a Python error and downstream problems. This PR makes METplus run in
    serial mode, preventing such issues.
    - Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in
    workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod)

commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri Aug 2 15:03:45 2024 -0400

    Update Java Agent launching script for Jenkins connections (#2762)

    Made updates to the Jenkins Launching Script for robustness and less
    ambiguous documentation:
    - Clearer distinction between required user token for the remote api and
    the systems token for launching
    - Added pre-checks: `gh` is authenticating, named compliant token and
    secret file exists
    - More robust Jason based parser of the remote api response for checking
    the state of the Node connection
    - For `cron` use a 5 minute pause and recheck was added before
    re-launching of the java agent
    - Added concise header documentation of requirements and purpose
    ---------

    Co-authored-by: David Huber <[email protected]>
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

commit b73b1fd203496db97f8067652659573a632bcc67
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Aug 2 07:59:06 2024 -0400

    Fix erroneous cdump addition (#2803)

commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3
Author: Rahul Mahajan <[email protected]>
Date:   Thu Aug 1 20:26:13 2024 -0400

    Update ocean post-processing triggers (#2784)

    This PR:
    - replaces `check_netcdf.sh` checker for ocean post-processing with with
    ocean output at the next forecast hour or finishing of the forecast job
    for ocean prod
    - removes no longer needed `ush/check_netcdf.sh`

commit aa2af1ca8d59424a60a1730722bf528775d9e606
Author: GeorgeGayno-NOAA <[email protected]>
Date:   Thu Aug 1 16:46:10 2024 -0400

    Update the gfs_utils repository hash (#2801)

    # Description
    Point to the latest hash of the gfs-utils repository, which contains the
    bug fix to gaussian_sfcanl.

    Resolves #2669.
    Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73

commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8
Author: David Huber <[email protected]>
Date:   Thu Aug 1 08:12:14 2024 -0400

    Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791)

    Changes how METplus jobs run so that they run on the last GFS cycle for
    a given `PDY`.

    This is a departure from operations where the METplus jobs run on the
    00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through
    `${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on
    `${PDY}18` for cycles 00-18. See
    https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details.

commit 1cf8b448af562dbb7af198399c78c585977e81da
Author: David Huber <[email protected]>
Date:   Tue Jul 30 10:38:49 2024 -0400

    Simplify resource-related variables, remove CDUMP where unneeded (#2727)

    This overhauls resource-related variables to use a common set of
    variables for each job. In the process, this also removed the use of
    CDUMP in most cases.

    Resolves #1299 #2693

commit 61875f25c9e971f82ae499b5b612d7f095deebd4
Author: Eric Sinsky - NOAA <[email protected]>
Date:   Mon Jul 29 14:40:03 2024 -0400

    Remove f000 from atmos rocoto tasks for replay cases (#2778)

    The main purpose of this PR is to remove the f000 from
    atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In
    cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater
    than `0`, it becomes necessary to have the first lead hour set to
    `OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For
    example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead
    time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and
    the minimum lead time for the ocean_prod rocoto task needs to be 6
    (assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up
    possible by removing 0 from fhrs for atmosphere-related tasks in
    `gefs_tasks.py` when replaying.

    This PR also moves where f000 is being removed for the ocean_prod and
    ice_prod tasks. The if-block that performs this f000 removal has been
    moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`.

    ---------

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

commit f156a7894d639f177e3e2588f98eec1f6f59aa68
Author: Jessica Meixner <[email protected]>
Date:   Fri Jul 26 14:18:32 2024 -0500

    HR4 GWD update (#2732)

    This update is a combination of the gravity wave drag (GWD) versions
    from the NOAA/GSL and NOAA/PSL

commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891
Author: David Huber <[email protected]>
Date:   Thu Jul 25 14:26:52 2024 -0400

    Temporarily disable METplus jobs (#2796)

commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2
Author: Guillaume Vernieres <[email protected]>
Date:   Wed Jul 24 15:00:35 2024 -0400

    Refactoring of the marine B-matrix job (#2749)

    Refactor the functionality of B-matrix generation from the GDASApp

    Resolves #2743

commit 65a7ab75dc0e4baba06a02e11ed0455787056a68
Author: David Huber <[email protected]>
Date:   Tue Jul 23 08:35:48 2024 -0400

    Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775)

    Removes the namespace-based construction of EnKF member COM directories
    in the enkf archive template.

commit c45b9611f3e701b819bd33dc5af29033f060bb91
Author: Eric Sinsky - NOAA <[email protected]>
Date:   Tue Jul 23 00:33:16 2024 -0400

    Add task to process reforecast variables to save on WCOSS2 (#2680)

    # Description
    This PR adds an optional task to the global-workflow to process a subset
    of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for
    the GEFSv13 reforecast. This task is designed to process GEFS variables
    so that specific reforecast product requirements are met. A new variable
    in `config.base` called `DO_EXTRACTVARS` enables this task, which is
    currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by
    default and is specifically a task designed to be executed for the
    GEFSv13 reforecast.

    Refs #1878

    # Type of change
    - New feature (adds functionality)

    # Change characteristics
    - Is this a breaking change (a change in existing functionality)? NO
    - Does this change require a documentation update? NO

    # How has this been tested?
    This has been cloned and tested on WCOSS2. This will need to be tested
    on Hera and other platforms on which the reforecast may be running.

    # Checklist
    - [ ] Any dependent changes have been merged and published
    - [x] My code follows the style guidelines of this project
    - [x] I have performed a self-review of my own code
    - [ ] I have commented my code, particularly in hard-to-understand areas
    - [x] My changes generate no new warnings
    - [x] New and existing tests pass with my changes
    - [ ] I have made corresponding changes to the documentation if
    necessary

    ---------

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

commit 71dc33c6ca991c16ce743760d99feaaf60f2218a
Author: David Huber <[email protected]>
Date:   Mon Jul 22 14:51:53 2024 -0400

    Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774)

    Fix metp* resources and check that they completed properly; add support for Orion Rocky 9

commit 56df67a90fe090c425199f1285e5aac722c398b1
Author: David Huber <[email protected]>
Date:   Mon Jul 22 09:28:18 2024 -0400

    Hotfix: Update jcb to avoid git-lfs files (#2782)

    Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to
    be cloned on Hera.

    This hotfix points to a non-authoritative branch of the GDASApp
    (https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and
    should be updated ASAP back to the authoritative repository.

commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd
Author: Rahul Mahajan <[email protected]>
Date:   Tue Jul 16 09:44:00 2024 -0400

    Address issues in creating XML for GFS forecast-only with app S2SWA (#2757)

    This bugfix PR:
    - fixes an issue where a user is unable to generate the XML for a GFS
    forecast-only experiment with APP=S2SWA

    Specifically, the changes are related to defining `aero_fcst_cdumps`.
    Following `setup_expt.py`, the user will have to set
    `AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in
    `config.base`.

commit e0878dba0e53706a7f53429b61aee2936e2c21bf
Author: Kate Friedman <[email protected]>
Date:   Mon Jul 15 10:25:11 2024 -0400

    Updated prepobs and fit2obs versions for Orion Rocky9 (#2758)

    Update prepobs to v1.0.2 and fit2obs to v1.1.2

    These versions now support Orion Rocky9. Updates are included
    for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet.

commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Jul 11 17:48:47 2024 +0000

    CI maintenance updates and adding CI Unit Tests (#2740)

    This PR has a few maintenance updates to the CI pipeline and adds a test
    directory with Unit Tests
    **Major Maintenance updates:**
    - Added try blocks with appropriate messaging to GitHub PR of failure
    for:
    - - **scm** checkout
    - - build fail (with error logs sent as gists)
    - - create experiment fails with `stderr` sent to GitHub PR messaging
    - Pre-stage FAILS from the above are now captured these fails allow
    FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state
    labels in GitHub - see image below)
    **Minor Maintenance updates:**
    - Fix for STALLED cases reviled from PR 2700 (just needed a lambda
    specifier)
    - Fixed path to experiment directory in PR message (had dropped EXPDIR
    in path)
    - Needed `latin-1` decoder in reading log files for publishing
    **Added python Unit Tests for CI functionality:**
    - Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI
    utility codes
    - Cashed the install of Rocoto in the GitHub Runners to greatly reduce
    stetup time for running the unit tests
    - Unit Tests Python scripts added
    - `test_rocostat.py`: rocoto_statcount() rocoto_summary()
    rocoto_stalled()
      - `test_setup.py`: setup_expt() test_setup_xml()
      - `test_create_experment`: test_create_experiment()
      - - Runs all PR cases that do not have ICs in the GItHub Runner
    - Reporting mechanism in the Actions tab for Python Unit Testing results
    - Test case data for STALLED and RUNNING stored on S3 and pulled using
    wget during runtime of tests

commit 5ef4db74649b8be03402c17aa29c024e71699a7b
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Thu Jul 11 08:59:24 2024 -0400

    Adds contents of constructor and initialize methods to marine LETKF class (#2635)

    Adds contents of constructor and initialize methods to marine LETKF class

    Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091
    ---------

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

commit 8998ec7b74123e953b97a93fa14cc78d471a1aee
Author: David Huber <[email protected]>
Date:   Tue Jul 9 08:31:57 2024 -0400

    Fix GDAS group B restart archiving (#2735)

    Archives the GDAS restartb dataset at a 6-hour offset from restarta

    This allows cycled experiments to restart from the archives.
    The tabbing for the master archive templates was also added to
    improve readability.

    Resolves #2722

commit 3ca74771255727033b9dc043c652ac585178629c
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Tue Jul 9 08:28:54 2024 -0400

    Add fcst dependency to ocnanalprep (#2728)

    Add previous cycle's `fcst` as a dependency to `ocnanalprep`

    This ensures that the availability of restart files to the latter. This addresses a
    seldomly-encountered race condition where `ocnanalprep` fails due to the
    lack of the files.

commit 58fca1668aecd6fb1afd12a441256ad35900e075
Author: Rahul Mahajan <[email protected]>
Date:   Fri Jul 5 15:02:23 2024 -0400

    Update (partially) global-workflow for orion+rocky9 (#2741)

    This PR:
    - updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils,
    GFS-utils) to include recent update to their modulefiles for
    Orion+Rocky9 upgrade
    - updates the modulefiles in global-workflow to load modules from
    Orion+Rocky9 paths
    - updates modulefiles for `gwsetup` and `gwci` as well.
    - removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not
    installed.
    - adds `parm/config.gfs/config.resources.ORION` to address GSI
    performance degradation after Rocky 9 upgrade.

    This PR:
    - does not update the build for UPP. Standalone UPP is not available via
    ufs-weather-model as of #2729
    - will need a follow-up update for `prepobs` and `fit2obs` updated
    locations when they are installed in `glopara` space on Orion.

    # Type of change
    - Maintenance (code refactor, clean-up, new CI test, etc.)

    # Change characteristics
    - Is this a breaking change (a change in existing functionality)? NO
    - Does this change require a documentation update? NO

    # How has this been tested?
    This PR is not sufficient for Orion.
    This PR must be tested on other platforms (Hera, WCOSS2) as this PR
    updates submodules.

    # Checklist
    - [ ] Any dependent changes have been merged and published
    - [ ] My code follows the style guidelines of this project
    - [ ] I have performed a self-review of my own code
    - [ ] I have commented my code, particularly in hard-to-understand areas
    - [ ] My changes generate no new warnings
    - [ ] New and existing tests pass with my changes
    - [ ] I have made corresponding changes to the documentation if
    necessary

    ---------

    Co-authored-by: Kate Friedman <[email protected]>

commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a
Author: Jessica Meixner <[email protected]>
Date:   Wed Jul 3 21:07:49 2024 -0400

    Update ufs model hash to 20240625 (#2729)

    Updates UFS weather model hash to hash from 2024-06-24 which has orion
    porting updates + a few namelist updates.

commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85
Author: David Huber <[email protected]>
Date:   Wed Jul 3 11:32:40 2024 -0400

    Hotfix for undefined CLUSTERS (#2748)

    Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses
    the native `dict` `get` method to prevent grabbing an unset entry.

commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf
Author: GwenChen-NOAA <[email protected]>
Date:   Wed Jul 3 09:56:08 2024 -0400

    Update gempak job to run one fcst hour per task (#2671)

    This PR updates gempak jobs (gfs, gdas, and goes) from processing all
    forecast hours at once to one forecast hour at a time. This will reduce
    the job runtime to less than 5 min, so restart capability is not needed.

    Resolves #1250
    Ref #2666 #2667
    ---------

    Co-authored-by: Walter.Kolczynski <[email protected]>

commit 8215ae654202186a4f753c3abe937b7b9b91a9c7
Author: Rahul Mahajan <[email protected]>
Date:   Tue Jul 2 16:22:11 2024 -0400

    Hotfix for clusters from #2701 (#2747)

    Fixes an issue created from #2701 that added `CLUSTERS` to the
    `gaea.yaml`.

commit 11943e36ba12b3df49c51942da780698fab02d38
Author: DavidBurrows-NCO <[email protected]>
Date:   Tue Jul 2 12:58:10 2024 -0400

    Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701)

    This PR sets up the ability on Gaea for auto generation of a clean xml
    file, i.e., an xml file that does not need any alterations before
    running rocoto.
    Refs #2572
    Refs #2664

commit de8706702ead0630beb54d868f83aa2cb23f8f79
Author: RussTreadon-NOAA <[email protected]>
Date:   Mon Jul 1 09:29:14 2024 -0400

    Update for JCB policies and stage DA job files with Jinja2-templates (#2700)

    This PR updates the `gdas.cd` hash to bring in new JCB conventions.
    Resolves #2699

    From #2654
    This PR will move much of the staging code that take place in the python
    initialization subroutines of the variational and ensemble DA jobs into
    Jinja2-templated YAML files to be passed into the wxflow file handler.
    Much of the staging has already been done this way, but this PR simply
    expands that strategy.

    The old Python routines that were doing this staging are now removed.
    This is part of a broader refactoring of the pygfs tasking.

    wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a
    companion to this PR.

    Co-authored-by: danholdaway <[email protected]>
    Co-authored-by: DavidNew-NOAA <[email protected]>
    Co-authored-by: DavidNew-NOAA <[email protected]>
    Co-authored-by: Dan Holdaway <[email protected]>

commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b
Author: Rahul Mahajan <[email protected]>
Date:   Fri Jun 28 14:56:19 2024 -0400

    Revert PR 2681 (#2739)

    This PR:
    - reverts #2681 in part
    - keeps some changes for `RUN`.
    - is a hotfix
    - should be merged ASAP after consensus w/ @guillaumevernieres
    @CatherineThomas-NOAA @WalterKolczynski-NOAA

commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Wed Jun 26 15:46:08 2024 -0400

    updated Finalize in Jenkinsfile and added try block around scm checkout (#2692)

    We are updating the Jenkins Pipeline with a try block around checkout to
    capture errors for the user.
    Also cleaned up Finalize and added section to clean out workspace on
    success.

commit 968568f682bac7564095440bdb7813abefd76821
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Jun 26 13:27:19 2024 -0400

    Activate snow DA test on WCOSS (#2720)

    Activate the snow DA test on WCOSS.

commit 7706760bb8adbdf78cb640b02739023c886e7699
Author: Rahul Mahajan <[email protected]>
Date:   Wed Jun 26 10:02:22 2024 -0400

    Cleanup of stale RUNDIRS from an experiment (#2719)

    This PR:
    - removes stale temporary scratch run directories from `$DATAROOT/`
    every 3 days.
    - should help to scrub failed attempts.
    - removes an unused variable `RUNDIR` defined in `config.base`

commit 8962991691b5f0857b813bddfd28aa1034d4bd2b
Author: Jessica Meixner <[email protected]>
Date:   Wed Jun 26 09:43:48 2024 -0400

    Update logic for MOM6 number of layers/exception values (#2681)

    Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine
    how many layers and sets the exception value for MOM6 to be 1e-34 for
    all scenarios. Note, we will no longer have zeros in the ocean grib
    output and the DA will also run without issues.

    Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615

commit 12431f76bdce807067929415007592cffc8a2457
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Wed Jun 26 07:42:35 2024 -0600

    Update wave jobs to use COMIN/COMOUT (#2643)

    NCO has requested that each COM variable specify whether it is an input
    or an output.
    This completes that process for the global-workflow wave
    model and products tasks.
    Refs #2451

commit b902c0bac126c323a07186ad8881384b032b6fda
Author: David Huber <[email protected]>
Date:   Tue Jun 25 07:48:46 2024 -0400

    Assign machine- and RUN-specific resources (#2672)

    Redefine resource variables based explicitly on RUN or CDUMP

    Additionally, machine-specific resources are moved out of
    config.resources and placed in respective config.resources.{machine}
    files.

    Resolves #177 #2672

commit 5edbd123e2878a07f5cce8e3c7ea6147f286633a
Merge: 09333c01d 4e1b937b6
Author: Janet Derrico <[email protected]>
Date:   Mon Jun 24 12:44:05 2024 -0600

    Merge branch 'NOAA-EMC:develop' into develop

commit 4e1b937b67ed220120e81925c4507f03b9b8965f
Author: David Huber <[email protected]>
Date:   Mon Jun 24 10:50:52 2024 -0400

    Add minimum software requirements (#2712)

    Adds a table to HPC documentation stating the minimum support versions

commit f43a86276aaef91efa28faadc71a3cf50e749efe
Author: David Huber <[email protected]>
Date:   Fri Jun 21 13:44:29 2024 -0400

    Fix and simplify online archiving and reenable METplus jobs (#2687)

    This fixes the online archiving portion of the `*arch` and `*earc00`
    jobs, a prerequisite for running METplus.  This also reenables
    METplus by default.

    The approach previously taken created `FileHandler` dictionaries at
    varying levels within the resulting yaml, which was not properly parsed
    by `exglobal_archive.py`. This approach creates a single `FileHandler`
    dictionary and is much less complicated overall.

    Resolves #2673 #2647

commit 8993b42cb91144c0ab0501dc7841ea8d675c4701
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Jun 19 21:51:22 2024 -0400

    Eliminate post groups (#2667)

    Eliminates the post groups used for upp and products jobs so that each
    task only processes one forecast hour. This is more efficient and
    greatly simplifies downstream dependencies that depend on a specific
    forecast hour.

    Resolves #2666
    Refs #2642

commit 0b810c888239853fedd0e4584fe62536c6aaacdf
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Tue Jun 18 20:32:48 2024 -0600

    Removes misleading "No such file or directory" syntax errors from output files (#2688)

    This PR addresses issue #1252. The following is accomplished:

    - Prior to removing files, the existence of a file is checked prior to
    attempting to remove; this is performed as noted
    [here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369);
    this PR only addresses the the `chgrp` issue.

    Refs #1252

    ---------

    Co-authored-by: David Huber <[email protected]>

commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Tue Jun 18 12:17:59 2024 -0600

    Hotfix for bug in template names. (#2697)

    This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/`
    template.
    Resolves #2696
    Refs #2451

commit 35d4d99eaac669721add9ddcc793153e5ab3b30a
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Tue Jun 18 08:06:53 2024 -0600

    Update archive job to use COMIN/COMOUT (#2668)

    NCO has requested that each COM variable specify whether it is an input
    or an output. This completes that process for the global-workflow
    archive task.

    Refs #2451
    ---------

    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
    Co-authored-by: Rahul Mahajan <[email protected]>
    Co-authored-by: David Huber <[email protected]>

commit 47b3a581c8257fa24411fb400df8bb0e1e04972a
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Jun 17 22:55:38 2024 -0400

    Turn on high-frequency output in extended test (#2679)

    Turns on high-frequency (hourly) output in the extended products test to
    exercise that aspect of the code. This test only runs on WCOSS.

    Also adds the hooks to optionally turn on the metplus jobs, but that is
    deferred as they are not currently working correctly.

commit 38f2df9fb0c074b1f80d3c637080be79be693161
Author: David Huber <[email protected]>
Date:   Mon Jun 17 17:12:55 2024 +0000

    Optimize wavepostpnt (#2657)

    Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs

    This is done by
    1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by
    - performing operations on all files at once instead of looping over
    each file
        - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`)
        - combining `sed` and `grep` calls when possible
        - adding logic to `awk` calls instead of handling that logic in bash
    2) minimizing as much as possible the amount of data on disk that has to
    be read in (e.g. limiting sed to read only the line numbers it needs)
    ---------

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

commit 5af325a6a4e0a14d180514a418603ca79fada487
Author: Dan Holdaway <[email protected]>
Date:   Fri Jun 14 18:05:23 2024 -0400

    Update GDASapp hash to move JCB into GDASapp (#2665)

    This PR moves JCB into GDASapp. The PR
    also bumps up the hash of GDASapp to what is in `feature/move_jcb`,
    which at time of writing is develop plus the absorption of JCB into
    GDASapp.
    Note that I also took the changes from
    https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the
    testing @RussTreadon-NOAA has done.

commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b
Author: Yaping Wang <[email protected]>
Date:   Fri Jun 14 10:18:17 2024 -0500

    Add observation preparation job for aerosols DA to workflow (#2624)

    Add a prepaeroobs job to prepare aerosol obs files for DA.

    This job does quality control of the VIIRS aerosol raw observations and
    convert them to ioda format.

    Resolves #2623
    ---------

    Co-authored-by: ypwang19 <[email protected]>
    Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>
    Co-authored-by: Cory Martin <[email protected]>
    Co-authored-by: David Huber <[email protected]>

commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4
Author: Jessica Meixner <[email protected]>
Date:   Fri Jun 14 11:04:41 2024 -0400

    Remove ocean daily files (#2689)

    This PR removes the ocn_daily files that are produced by the ocean
    component. These files can be recreated by averaging data that exists in
    the 6 hour aveaged files if needed.

    Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675
    Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by
    removing them and making this obsolete)

commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Jun 13 12:22:03 2024 -0400

    Update Jenkinsfile

    needed a comma

commit dc21eac6c3941d7f30803891d91d82f4cc1f8183
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Jun 13 11:41:14 2024 -0400

    Add Hercules-EMC to the Jenkins configurable parameter list (#2685)

    This quick-fix PR is to update the Jenkins Pipeline's configurable
    parameter list to include the **Hercules-EMC** node.
    This allows Jenkins users to restart Jobs in the controller when no
    updates have been made.

commit ebacebfbe458634b8c80af6a735d6b6d01e4e406
Author: RussTreadon-NOAA <[email protected]>
Date:   Thu Jun 13 11:20:24 2024 -0400

    Update gdas.cd and gsi_utils hashes (#2641)

    This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The
    updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea
    build for gsi_utils.

    Resolves #2640

commit 34155fb4767769600a1ff95f0a65e37081addc2a
Author: Neil Barton <[email protected]>
Date:   Thu Jun 13 11:18:22 2024 -0400

    Add ability to use GEFS replay ICs (#2559)

    The PR allows the use of ICs from PSL's replay analysis. These replay
    ICs will be used for GEFS reforecasting and SFS. Two main changes are
    associated with these updates: (1) replay ICs being valid at 3Z, and (2)
    the use of warm starts.

    Resolves #1838

    ---------

    Co-authored-by: Jessica Meixner <[email protected]>
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
    Co-authored-by: Rahul Mahajan <[email protected]>

commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Wed Jun 12 19:25:42 2024 -0600

    Replace `sleep` with `wait_for_file` (#2586)

    This PR addresses issue #2444. The following is accomplished:

    - All `sleep` statements are replaced with `wait_for_file` for the
    relevant scripts beneath `scripts` and `ush`;
    - Indentation and shell-norms are updated where applicable.

    Note: The WAFS scripts are not updated as per @aerorahul direction.

    Resolves #2444

    ---------

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

commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Jun 12 13:31:55 2024 -0400

    Add COM template for JEDI obs (#2678)

    Adds a COM template to define a path to store obs processed for JEDI.
    This will allow UFSDA to stop writing to COM_OBS, which should be
    read-only as it belongs to obsproc in operations.

    No functional change yet.

commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed
Author: Guoqing Ge <[email protected]>
Date:   Wed Jun 12 09:06:23 2024 -0600

    Link both global-nest fix files and non-nest ones at the same time (#2632)

    This PR enables linking both global-nest fix files and non-nest ones at
    the same time and users can run both nesting and non-nesting experiments
    at the same time without worries about what fix files to be linked.

    Resolves #2631

commit 61de004d4f9e9edf8a31bb173f2719b46451a36a
Author: Jessica Meixner <[email protected]>
Date:   Wed Jun 12 11:03:13 2024 -0400

    Update ufs-weather-model  (#2663)

    Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack
    allowing some temporary fixes to be reverted.
    * removes upp submodule
    * uses upp from the ufs-weather-model
    * restores the build and link that were hacked during the Hera Rocky 8
    transition to allow for UPP submodule
    * Removes forecast directories in clean-up

    Resolves #2617
    Resolves #2437

    ---------

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

commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d
Author: Eric Sinsky - NOAA <[email protected]>
Date:   Wed Jun 12 01:15:37 2024 -0400

    Add ability to process ocean/ice products specific to GEFS (#2561)

    This PR begins to add the capability to produce GEFSv13 ocean and ice
    products in the global-workflow according to stakeholder requirements.
    The following features are added.

    - An oceanice prod yaml file has been added to address the ocean and ice
    products specific to GEFSv13.
    - The rocoto dependencies and config.base for GEFS have also been
    modified to allow for 24-hour averaged ocean and ice output.
    - Various scripts have been modified to allow for ocean and ice output
    frequencies of 24 hours.
    - `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN`
    and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`.

    Refs #1878

commit 6691e7489650e0b738c176fbd096109288dc09b6
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Tue Jun 11 21:15:07 2024 -0600

    Update cleanup job to use COMIN/COMOUT (#2649)

    NCO has requested that each COM variable specify whether it is an input
    or an output. This completes that process for the global-workflow
    clean-up task.

    Refs #2451

    ---------

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

commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Jun 11 16:17:25 2024 -0400

    Add overwrite to creat experiment in BASH CI (#2676)

    This is a quick hotfix to the CI BASH driver script adding `--overwrite`
    to create experiment script to avoid errors from restarting an
    experiment.

commit e7909af8d9e1f34140388a3f8556d8e582c58fe5
Author: emilyhcliu <[email protected]>
Date:   Mon Jun 10 15:11:27 2024 -0400

    Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py  (#2645)

    This PR proposes updates for the following two scripts:

    1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select
    CRTM cloud optical table based on cloud microphysical scheme indicated
    by `imp_physics'
    The default scheme in the GFS forecast model is Thompson scheme
    (imp_physics = 8).

    2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in
    the script due to increased variables to interplate increments and
    calculate analysis in the netcdf_io routines in GSI-utils.
    Here is the related [PR #46 for
    GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46).

    ---------

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

commit 9caa51de8fb7be07d2e61775da01937d576964f6
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Thu Jun 6 22:15:23 2024 -0600

    Update RDHPCS Hera resource for `eupd` task (#2636)

    As per @wx20jjung, the resource for the `eupd` task have been updated
    for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job
    fails.

    Resolves #2454

    ---------

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

commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b
Author: DavidNew-NOAA <[email protected]>
Date:   Thu Jun 6 11:49:03 2024 -0400

    Parameterize some things in config.atmanl and config.atmensanl (#2661)

    This PR adds some parameters in config.atmanl and config.atmensanl that
    can be altered with the defaults.yaml. The motivation is to make these
    files match those in the GDASApp JJOB tests (example:
    https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl),
    so we can just use the Global Workflow config.atmanl and
    config.atmensanl in the tests rather than custom ones in GDASApp that
    have to be separately updated every time the ones in the Global Workflow
    are updated.

commit 54ea0b73a07921be5fbb07fe41e976888bd3e549
Author: Guillaume Vernieres <[email protected]>
Date:   Thu Jun 6 01:36:02 2024 -0400

    Add links to the ocean insitu obs processing tools (#2644)

    Add links to the marine bufr to ioda converters for the marine insitu
    observations.

    - fixes https://github.com/NOAA-EMC/GDASApp/issues/1106
    - waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135

commit 205d0c2b13e2d7755cec75bf8c978ab20d453862
Author: David Huber <[email protected]>
Date:   Wed Jun 5 17:31:30 2024 +0000

    Update S4 point of contact in docs (#2660)

    Update the point of contact for global workflow issues on S4.

commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262
Author: RussTreadon-NOAA <[email protected]>
Date:   Wed Jun 5 12:50:14 2024 -0400

    Enable wcoss2 ufsda build and module load (#2620)

    This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2.

    Resolves #2602
    Resolves #2579

commit 67b833e0c7bc390865d453588b4609a1a7ede981
Author: Jessica Meixner <[email protected]>
Date:   Tue Jun 4 13:33:43 2024 -0400

    Update ufs-weather-model  (#2646)

    Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6
    This should resolve the issue and allow C768 runs on Hera and allow for CICE
    to run on WCOSS2 (due to library updates to allow linking).

    From what I can tell, all updates needed were done by
    @HenryWinterbottom-NOAA which were updates for CICE

    Fixes #2490

commit c44d0ac86cfdf78eb87492431bf6d825e8bae637
Author: GwenChen-NOAA <[email protected]>
Date:   Tue Jun 4 10:29:49 2024 -0400

    Update wmo parm files to fix WMO header (#2652)

    This PR updates wmo parm files to switch WMO header of precipitation
    type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to
    instantaneous.

    Resolves #2566

commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60
Author: Cory Martin <[email protected]>
Date:   Tue Jun 4 13:55:33 2024 +0000

    Add IAU to snow DA (and its test) (#2610)

    This PR enables IAU for the snow DA which is necessary for GFSv17.

    A snow analysis is created for the center of the window regardless, and
    an additional at the beginning of the window is added if IAU is on. The
    former is needed for UPP and the latter, to initialize the model.

    The increment is valid throughout the window for 3DVar, so the same
    increment is added to both forecasts.

    Additionally, the input file that goes into global_cycle has been
    updated to be the output of the JEDI snow analysis instead of the
    forecast (@jiaruidong2017 I recall discussing this, can you confirm this
    is right or am I mistaken)

    This PR also makes the CI test for snow DA (and aerosol DA) include IAU
    rather than without IAU,.

    ---------

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

commit c92bf415060750127c9c05a62a1d2851c489551a
Author: David Huber <[email protected]>
Date:   Sat Jun 1 05:11:07 2024 +0000

    Archiving cleanup (#2621)

    1) Adds a lot of comments to the jinja templates for archiving
    2) Rearranges the gdas and enkf templates to a more logical order
    3) Fixes a couple of bugs in the enkf archiving of increments and
    analyses
    4) Disables archiving for the half cycle
    5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`,
    instead relying on `DO_FIT2OBS`
    6) Updates wxflow to add the option to not allow undefined variables
    when parsing jinja templates and invokes this feature when running
    archives

    Resolves #2612

commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri May 31 04:57:08 2024 -0400

    Switch to Rocky 9 built external packages on Hercules (#2608)

    The workflow was updated to use modules built on Rocky 9, but the
    external packages (like prepobs) were still pointing to the versions
    built on CentOS (Orion). This transitions to packages built on Rocky 9.

    Updating of the tracker package has been deferred until later. As such,
    the tracker jobs have been disabled by returning immediately if they are
    on Hercules. Since these jobs are small, resource-wise, it should not
    meaningfully impact turnover time.

commit 4422550c01c9214a2b3b8890bdcc898123ee216a
Author: Guoqing Ge <[email protected]>
Date:   Thu May 30 08:05:23 2024 -0600

    Add the capability to use slurm reservation nodes (#2627)

    Add the capability to use slurm reservation nodes
    Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE

    Resolves #2626

commit a54153fd9d26126206bc07a1da4e80f50c0c5910
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed May 29 23:24:07 2024 -0400

    Update forecast job to use COMIN/COMOUT (#2622)

    NCO has requested that each COM variable specify whether it is an input
    or an output. This completes that process for the forecast job.

    Refs #2451

    ---------

    Co-authored-by: David Huber <[email protected]>

commit d69a8af95d492982b918670322ed5c41ab074335
Author: Jessica Meixner <[email protected]>
Date:   Wed May 29 21:29:03 2024 -0400

    Update to add 1-deg global wave grid (#2619)

    This PR adds options to use a global 1 deg grid, intended for testing
    with the SFS application.

    Requires new fix file changes NOAA-EMC/global-workflow#2618

commit 0b4670ecf83b99b72835c8380573b2bca7cf5324
Author: Jessica Meixner <[email protected]>
Date:   Wed May 29 17:17:21 2024 -0400

    Add C384mx025_3DVarAOWCDA yamls (#2625)

    Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder.

commit 2e885d05c64b947f00a3cf055a1277fbfac195c9
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Wed May 29 13:00:51 2024 -0400

    Script to keep Jenkins Agent persistent from cron (#2634)

    This "persistent" Java Agent launch script can be ran from a cron job:

    - Uses Jenkins Remote API to check the status of the Node connection
    using curl for a given machine.
    - If it is not connected a new agent is launched for that node.

    Resolves #2633

commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5
Author: GwenChen-NOAA <[email protected]>
Date:   Tue May 28 17:17:11 2024 -0400

    Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611)

    Based on users' feedback, this PR do the following:
    1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF
    2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD,
      and VOGRD) from "%g m below water surface" to "%g m below sea level"
    3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m)

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

commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31
Author: DavidNew-NOAA <[email protected]>
Date:   Tue May 28 17:16:23 2024 -0400

    Add atmensanlfv3inc job (#2592)

    This PR creates the atmensanlfv3inc job, the ensemble version of
    atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is
    #[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS
    companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3).

commit 50c2b8951b29a3c883a778becbf8582f9519eb48
Author: Anil Kumar <[email protected]>
Date:   Tue May 28 13:23:53 2024 -0400

    Global-workflow (AR) Generic updates for Gaea C5 (#2515)

    - Port global-workflow’s build and run capability to Gaea-C5
    - Building global-workflow on Gaea-C5
    - Setting up experiments with global-workflow on Gaea-C5

    ---------

    Co-authored-by: AnilKumar-NOAA <[email protected]>
    Co-authored-by: DavidBurrows-NCO <[email protected]>

commit b6ca771a0c584cbfcbbf9be739765d5f3815df97
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri May 24 10:52:45 2024 -0400

    Update STMP and PTMP settings in host file for Orion and Hercules  (#2614)

    - Updating STMP and PTMP settings in host file for Orion and Hercules
    because they are cross mounted.
    - Also took the opportunity to finally update **SLURM_ACCOUNT** to
    **HPC_ACCOUT** in CI over rides.
    - Added a refactor of the `rocotostat.py` tool that is more pythonic and
    as a execute retry feature because the `rocotostat` utility on Orion has
    been failing sometimes.

commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f
Author: Guillaume Vernieres <[email protected]>
Date:   Tue May 21 23:50:50 2024 -0400

    Sea-ice analysis insertion (#2584)

    Allows cycling and restarting CICE with the sea-ice analysis if the
    marine DA is switched on.

    Resolves #2568
    Resolves NOAA-EMC/GDASApp#1103

commit 5369a1ff3a3969149fcf32810fad0e50216752b7
Author: David Huber <[email protected]>
Date:   Tue May 21 22:12:29 2024 +0000

    Refactored archiving (#2491)

    This provides a new pygfs task, archive.py, that provides all of the
    tools necessary to archive data to the local (`ARCDIR`) and backup
    (`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to
    define the file to be archived or tarred to replace the
    `hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts
    and make it easier to add new data and explicitly handle optional and
    required files.

    For `ATARDIR` archiving, a master jinja template is provided for each
    `RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2,
    master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both
    `enkfgdas` and `enkfgfs` `RUN`s. These templates then include the
    appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on
    experiment, cycle, and coupled parameters. Each of these templates
    corresponds to a single tarball to populate and are tabbed 4 spaces so
    they are defined within the master `datasets` dictionary.

    Future developers should not have to make modifications to archive.py
    unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then
    only a single `elif` needs to be added to the configure method to
    specify the master `ATARDIR` template to archive (e.g.
    `master_gefs.yaml.j2`). If a new component is coming online that needs
    to be archived to `ATARDIR` (e.g. SNOW), then create a new template for
    each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`)
    and reference the template in the appropriate master templates, e.g.

    `master_gdas.yaml:`
    ```jinja
    {% if DO_SNOW %}
    {% include "gdassnow.yaml.j2" %}
    {% endif %}
    ```

    A few other issues were addressed along the way:
    1. Aerosols have been reenabled. Aerosol forecasts should only be
    performed during gdas cycles, but analyses can be performed for both gfs
    and gdas cycles. This was accomplished by setting separate
    `AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs.
    2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`.
    This prevented restarts from being used for cice-enable experiments.
    This feature was not tested.
    3. Create a temporary fix for the `wgrib` utility. For spack-stack
    1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is
    open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in
    existing installations. Once complete, this temporary fix should be
    removed.
    4. The number of `earc` jobs has been reduced for lower resolution
    experiments. Both C48 and C96 experiments will now only have two earc
    jobs (one for the non-member files to archive and another for the member
    files). C192 will have up to 3 earc jobs (one non-member, one for
    members 1-40 and another for members 41-80, if needed).

    Resolves #2345
    Resolves #2318

    ---------

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

commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri May 17 12:57:59 2024 -0400

     Add remove RUNDIRS step in CI before creating experements (#2607)

    As had been done in Bash CI we need to remove the RUNDIR in Jenkins
    before a creating an experiment in the event that case had beem
    previously ran.

commit 09333c01dbafddb2d2fe7e181b479af3cc6d3621
Merge: f7e9f4489 bb930050b
Author: Janet Derrico <[email protected]>
Date:   Thu May 16 14:33:19 2024 -0600

    Merge branch 'NOAA-EMC:develop' into develop

commit bb930050b3cd51d28ecba6b231c8675f6d11856c
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Thu May 16 12:28:30 2024 -0400

    Adds jjob and other necessities for marine LETKF task (#2564)

    Adds jjob, rocoto script, config file, and other necessities for new
    marine LETKF task.

    Partially addresses NOAA-EMC/GDASApp#1091

commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu May 16 12:12:06 2024 -0400

    Updating CI Machine configs with redundant PTMP (#2605)

    Quick fix adding PTMP as STMP in Machine configs for CI for completeness

commit ef340ff33a6f89adf70838206ba3fd56a953fa7a
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu May 16 11:37:30 2024 -0400

    Fix race condition in CI between Orion and Hercules (#2604)

    Hotfix to solve race conditions in the CI system due to cross-mounted
    file systems between Orion and Hercules

commit e8b17e27f719df280170dc3f5bd9f19917cefaf2
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Wed May 15 17:16:30 2024 -0400

    Remove existing EXPDIRs and COMROTs when CI is re-run (#2601)

    Quick hotfix for having default for re-runing jobs to start clean with
    new EXPDIRs and COMROTs

commit b5d113efb1970ede5cd1d3d4dff8d96320519c41
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Wed May 15 16:52:49 2024 -0400

    Moving logic for skipping hosts in pr cases (#2573)

    This PR removes the logic of skipping hosts for pr cases from
    `create_experiment.py` and moves it to a test in the cron bash driver
    using a `parse_yaml.py` python tool.

    The Jenkins pipeline was not effected as it uses the
    `get_host_case_list.py` utility to form the cases on a per host bases.

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

commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916
Author: RussTreadon-NOAA <[email protected]>
Date:   Wed May 15 13:13:30 2024 -0400

    Update gsi_utils.fd hash (#2598)

    This PR updates the `gsi_utils.fd` hash to bring in updates which add
    safeguards to
    -
    `src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90`
    - `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90`

    The safeguards are described in GSI-utils PR
    [#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated
    issue.

    Resolves #2597

commit d5366c66bd67f89d118b18956fe230207cbf0aea
Author: Kate Friedman <[email protected]>
Date:   Wed May 15 13:12:56 2024 -0400

    Update CICE and MOM6 fix versions (#2600)

    This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions
    to the newer `20240416` timestamps, which includes updates and fixes to
    the `100` (1-deg) resolution files.

    Resolves #2480
    Resolves #2483
    Resolves #2595

commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b
Author: David Huber <[email protected]>
Date:   Mon May 13 22:57:38 2024 +0000

    Limit gfswavepostpnt to 40 PEs/node (#2588)

    This fixes the slow runtime of the gfswavepostpnt job on Hercules. The
    job is very I/O intensive and does not scale well to large nodes, so
    limit the number of jobs/node to 40.

    Resolves #2587

commit 4fb7c12c325702a47f27c802a5067efd33d0327c
Author: Fanglin Yang <[email protected]>
Date:   Mon May 13 16:37:51 2024 -0400

    Update damping and time-step (#2575)

    Updates the model to use explicit Rayleigh damping for u/v and implicit
    damping to w. This improves model stability and allows for longer
    timesteps. Also unifies the GDAS and GFS to use the same damping.

    Results from a test at the C1152 resolution (coupled model) can be found
    at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/

    Resolves #2574

    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
    Co-authored-by: Lisa Bengtsson <[email protected]>
    Co-authored-by: Rahul Mahajan <[email protected]>

commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri May 10 14:17:13 2024 -0400

    Do not use BUILT_semphore to force rebuilds when re-run (#2593)

    Remove the placement of the `BUILT_semaphore` file after the build in
    the Jenkins Pipeline and force it to rebuild any changes after a PR is
    re-ran.

commit 2346c6161f75ae02369cbf30f30c6150d3e12b66
Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com>
Date:   Thu May 9 21:17:06 2024 -0500

    Migration to Rocky8 spack-stack installations on Jet (#2458)

    # Description
    Migrates Global Workflow to Rocky8 spack-stack installations on Jet.
    Jet has moved from CentOS7 to Rocky8.

    Resolves #2377
    Refs NOAA-EMC/UPP#919
    Refs NOAA-EMC/gfs-utils#60
    Refs NOAA-EMC/GSI#732
    Refs NOAA-EMC/GSI-Monitor#130
    Refs NOAA-EMC/GSI-utils#33

commit c7b3973014480a20dd8e24edaeb83a9e9e68159f
Author: Jessica Meixner <[email protected]>
Date:   Thu May 9 11:36:58 2024 -0400

    Updates for cold start half cycle, then continuing with IAU for WCDA (#2560)

    This PR allows us to run C384 S2S with IAU, but starting with the first
    half-cycle as a cold-start. This will be necessary for cycled testing as
    we build towards the full system for GFSv17. This updates the copying of
    the restarts for RUN=gdas for both ocean and ice copying what the atm
    model is doing. It also reduced the amount of restart files from 4 to 3.

    Other updates:
    * Add DOJEDI ocean triggers for archiving certain files update from:
    @CatherineThomas-NOAA
    * Adds COPY_FINAL_RESTARTS option to turn on/off copying the last
    restart file to COM. Defaults to off...
    * Defines model_start_date_current_cycle & model_start_date_next_cycle
    to help with knowing which IC to grab.

    Refs #2546

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

commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2
Author: Dan Holdaway <[email protected]>
Date:   Wed May 8 20:52:48 2024 -0400

    Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477)

    Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI
    Configuration Builder (JCB) tool so that YAMLs can be made more portable
    and invoke the observation chronicle mechanism.

    Resolves #2476

    Co-authored-by: danholdaway <[email protected]>
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed May 8 02:04:16 2024 -0400

    Add CI test for products (#2567)

    Adds a new version of the atm3DVar test that runs the full forecast
    length and produces most of the secondary products. For now, this test
    will only run on WCOSS due to gempak failures on other machines as well
    as computational needs. On other machines, the original version will run
    (the original version will not run on WCOSS). AWIPS remains off for now
    in this extended test due to a bug involving tocgrib2 and the convective
    precip fields (see #2566).

    The new test runs for 4½ cycles and the full 384-hr forecast length to
    ensure all gempak scripts are exercised. Since the cycle throttle is 3
    and the bulk of the time is in the free forecast, the cycles run mostly
    concurrently so it doesn't extend the total test time too much beyond
    that of a single 384-hr forecast.

    Fixes a bug in NPOESS that was introduced when the post filenames were
    reverted to the previous format for the GOES products until the final
    filenames are determined (#2499).

    Also removes the AWIPS g2 job from the rocoto mesh to complete the
    retirement of grib1 products.

    Resolves #2132
    Resolves #2445

commit 9b6f8404ac4507d14adc404b77cfdf002b55e832
Author: Rahul Mahajan <[email protected]>
Date:   Tue May 7 00:14:36 2024 -0400

    Add task to prepare emissions for GEFS (#2562)

    This PR:
    - introduces a task to prepare emissions for a forecast into the GEFS
    application.
    - adds configuration, j-job, rocoto job, ex-script and the python class
    for this job
    - updates GEFS workflow to be able to generate the XML to call this job.
    - updates the `fcst` and `efcs` job dependencies in the GEFS application
    to depend on `prep_emissions` if aerosols are turned ON.
    - provides a placeholder for @bbakernoaa to work on the details for
    preparing emissions.

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

commit 233c18815d2e8e6b344f161fd0c102a4fbdfb66d
Author: Dan Holdaway <[email protected]>
Date:   Mon May 6 18:11:35 2024 -0400

    Single Executable for main GDAS JEDI applications (#2565)

    Changes that accompany GDAS PR (NOAA-EMC/GDASApp/pull/1075) that allows
    building of a single gdas executable, which should be more compliant
    with NCO requirements.

    Addresses https://github.com/NOAA-EMC/GDASApp/issues/1085

commit a005244bbfb2f1c525bca60d966f8095aa1acb8e
Author: Guoqing Ge <[email protected]>
Date:   Thu May 2 20:32:53 2024 -0600

    Add nest capability (#2545)

    This PR adds the global nesting capability to the global workflow so
    that one can run a regional domain nested in a global run.

    Resolves #2544

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

commit cb87daaced9fddd17f8370a1842d7e4ddab24e8f
Author: DavidBurrows-NCO <[email protected]>
Date:   Thu May 2 15:30:53 2024 -0400

    Update gfs_utils for Gaea (#2556)

    What: add build capability to the gfs_utils submod within the global
    workflow on Gaea

    Refs #2535

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

commit 707a1cc5124bcd8e006839a17f76ceb88f45f902
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date:   Wed May 1 18:13:02 2024 -0600

    Updated GEMPAK version and APRUN launcher. (#2555)

    This PR addresses issue #2248 and #2513. The following is accomplished:

    - Updates the parallel executable for GEMPAK applications;
    - Updates the GEMPAK version for RDHPCS Hera.

    Describe your changes. Focus on the *what* and *why*. The *how* will be
    evident from the changes. In particular, be sure to note any interface
    changes, such as command line syntax, that will need to be communicated
    to users.

    At the end of your description, please be sure to add the issue this PR
    solves using the word "Resolves". If there are any issues that are
    related but not yet resolved (including in other repos), you may use
    "Refs".

    Resolves #2248
    Resolves #2513

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

commit f151cbf394e998ca0fdae893ca174499468d0c85
Author: Travis Elless <[email protected]>
Date:   Wed May 1 11:01:18 2024 -0400

    Utilize scale-dependent localization for atmospheric analysis (#2542)

    The plan for GFSv17 is to use a scale-dependent localization for the
    atmospheric analysis. This PR adds the necessary parameters to allow
    this feature to be used by default.

commit 53b6764392cb4c0f3b4506ccd3f8cba5c5d2c56e
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Apr 30 16:37:54 2024 -0400

    Remove implicit symlink names (#2527)

    Lustre has a defect under Rocky 9 that results in symlink sometimes
    failing when the link name is not explicit. This updates all link
    creation to use explicit names.

    `config.base` is updated to turn off two monitor jobs on Hercules
    because the executables are not yet built there. This, combined with the
    previous change, should make workflow available for use on Hercules.

    Also removes the redundant utility names for NCP, NLN, etc. in the gdas
    scripts that are already defined in `config.base`.

    Resolves #2131
    Resolves #2522

commit f7e9f4489fc0b10830f621fdf149e8e3149d6a51
Merge: 67a4810c4 762f040a2
Author: Janet Derrico <[email protected]>
Date:   Tue Apr 30 12:24:48 2024 -0600

    Merge branch 'NOAA-EMC:develop' into develop

commit 762f040a2045db17cdacd9026df9c4b8fd520156
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Mon Apr 29 22:26:28 2024 -0400

    Fixes sea ice archiving (#2541)

    Removes/changes sea ice output files that are failing to be added to
    list for archiving, causing `gdasarch` to fail in WCDA cycling.

    Resolves https://github.com/NOAA-EMC/GDASApp/issues/1044

commit 2ecf4f86e0cbe59407ba2c4e105ee7292f1eda01
Author: RussTreadon-NOAA <[email protected]>
Date:   Mon Apr 29 22:25:57 2024 -0400

    Link ensemble analysis increment files to COMROOT for warm_start (#2553)

    Scripting is added to `setup_expt.py` to link ensemble analysis
    increment files to COMROOT for warm_start experiments.

    Resolves #2552

commit 3a7abe1d63c573006e0e656237f1220002c3f579
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Apr 30 02:25:28 2024 +0000

    Launch Multiple Platforms to Jenkins with polling (#2548)

    When launching Jenkins CI Tests all requested RDHPCS machines can now be
    selected via the Ready label at once.
    This is all that is required sense polling also works now on the
    controller end.

    Killing the jobs still needs to be done directly on the Jenkins
    Controller.
    Do not try to update the CI process using Labels. It is for launching
    only.
    Jenkins will update the labels as the states change.

    NOTE: When a case fails the label will be update to a **Fail** for that
    system but will continue to report failures of subsequent cases until
    otherwise stopped in the Jenkins Controller directly.

    Do not update any labels…
kayeekayee added a commit to kayeekayee/global-workflow that referenced this issue Sep 18, 2024
@kayeekayee
Update realtime branch, gsl_ufs_rt.
8997be6 
Squashed commit of the following:

commit 4e0a81f7acf5ccba5de8d3bdf7ab19cae80812cb
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 18:37:50 2024 +0000

    Fix typos/links/dependancy.

commit d5fdcbf8d6e987dbdfcd6b4da34d0934c8d82c3b
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 07:37:52 2024 +0000

    Fixed missing config.base files.

commit c6239f925369b20fd8488e8537969e2f4f9e7725
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 06:53:47 2024 +0000

    Update submodule hashs.

commit 32bf790f67b818ff50a7f6b74388fb81ed175b3a
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 06:09:41 2024 +0000

    Update develop branch, gsl_ufs_dev
     - based on gsl_ufs_dev from KaYee's fork
       global-workflow: 07Aug24,37c53ac [develop_07Aug2024_37c53ac]
       UFS: 19Jul24, c127601
       FV3: 19Jul24, 2527c11
       UPP: 23Apr24, be0410e
       CCPP-PHYSICS: 19Jul24, 46df080
       UFS_UTILS: 26Jun24, 3ef2e6b

    Squashed commit of the following:

    commit 70b557836379bb7e545fcc6642e28d66cfc17735
    Merge: 5edbd123e 37c53ac69
    Author: Janet Derrico <[email protected]>
    Date:   Wed Aug 7 11:02:24 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04
    Author: Kate Friedman <[email protected]>
    Date:   Wed Aug 7 08:11:21 2024 -0400

        Revert MSU FIX_DIRs back to glopara (#2811)

    commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Tue Aug 6 14:47:36 2024 -0400

        Bugfix for updating label states in Jenkins (#2808)

        Quick bug fix for updating state labels in CI during finalize.
        (did not reference GitHub CLI executable correctly in the pipeline
        script)

    commit 8fee36f0307b0c08080e3a8fa8fa6703e7da5fce
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Aug 6 11:02:45 2024 -0400

        Clean-up temporary rundirs - take 2. (#2753)

        This PR:
        - is a follow-up to a previous PR that aggressively pruned run
        directories.
        - removes run directories for the current cycle in the clean-up if the
        cycle is successful. If the cycle is not successful, cleanup is not
        called and all run directories for the cycle are safe from being purged.
        - also updates the PR template to list/query for any updates to
        submodules.

        ---------

        Co-authored-by: David Huber <[email protected]>
        Co-authored-by: David Huber <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

    commit d599fff4aedd41ae587dbe02226acb12ff48efc1
    Author: HelinWei-NOAA <[email protected]>
    Date:   Mon Aug 5 05:31:31 2024 -0400

        Change land surface for HR4 (#2787)

        Resets the default value of opt_diag to 2 corresponding to the land
        surface upgrades in ufs-weather-model for HR4.

        Resolves #2786

    commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb
    Author: David Huber <[email protected]>
    Date:   Fri Aug 2 15:41:29 2024 -0400

        Run METplus serially and correct the name of prod tasks (#2804)

        Adds 2 hot fixes:

        - METplus v9.1.3 has a bug in it that sometimes attempts to create
        multiple copies of the same directory when running in parallel, causing
        a Python error and downstream problems. This PR makes METplus run in
        serial mode, preventing such issues.
        - Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in
        workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod)

    commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri Aug 2 15:03:45 2024 -0400

        Update Java Agent launching script for Jenkins connections (#2762)

        Made updates to the Jenkins Launching Script for robustness and less
        ambiguous documentation:
        - Clearer distinction between required user token for the remote api and
        the systems token for launching
        - Added pre-checks: `gh` is authenticating, named compliant token and
        secret file exists
        - More robust Jason based parser of the remote api response for checking
        the state of the Node connection
        - For `cron` use a 5 minute pause and recheck was added before
        re-launching of the java agent
        - Added concise header documentation of requirements and purpose
        ---------

        Co-authored-by: David Huber <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

    commit b73b1fd203496db97f8067652659573a632bcc67
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri Aug 2 07:59:06 2024 -0400

        Fix erroneous cdump addition (#2803)

    commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3
    Author: Rahul Mahajan <[email protected]>
    Date:   Thu Aug 1 20:26:13 2024 -0400

        Update ocean post-processing triggers (#2784)

        This PR:
        - replaces `check_netcdf.sh` checker for ocean post-processing with with
        ocean output at the next forecast hour or finishing of the forecast job
        for ocean prod
        - removes no longer needed `ush/check_netcdf.sh`

    commit aa2af1ca8d59424a60a1730722bf528775d9e606
    Author: GeorgeGayno-NOAA <[email protected]>
    Date:   Thu Aug 1 16:46:10 2024 -0400

        Update the gfs_utils repository hash (#2801)

        # Description
        Point to the latest hash of the gfs-utils repository, which contains the
        bug fix to gaussian_sfcanl.

        Resolves #2669.
        Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73

    commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8
    Author: David Huber <[email protected]>
    Date:   Thu Aug 1 08:12:14 2024 -0400

        Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791)

        Changes how METplus jobs run so that they run on the last GFS cycle for
        a given `PDY`.

        This is a departure from operations where the METplus jobs run on the
        00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through
        `${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on
        `${PDY}18` for cycles 00-18. See
        https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details.

    commit 1cf8b448af562dbb7af198399c78c585977e81da
    Author: David Huber <[email protected]>
    Date:   Tue Jul 30 10:38:49 2024 -0400

        Simplify resource-related variables, remove CDUMP where unneeded (#2727)

        This overhauls resource-related variables to use a common set of
        variables for each job. In the process, this also removed the use of
        CDUMP in most cases.

        Resolves #1299 #2693

    commit 61875f25c9e971f82ae499b5b612d7f095deebd4
    Author: Eric Sinsky - NOAA <[email protected]>
    Date:   Mon Jul 29 14:40:03 2024 -0400

        Remove f000 from atmos rocoto tasks for replay cases (#2778)

        The main purpose of this PR is to remove the f000 from
        atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In
        cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater
        than `0`, it becomes necessary to have the first lead hour set to
        `OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For
        example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead
        time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and
        the minimum lead time for the ocean_prod rocoto task needs to be 6
        (assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up
        possible by removing 0 from fhrs for atmosphere-related tasks in
        `gefs_tasks.py` when replaying.

        This PR also moves where f000 is being removed for the ocean_prod and
        ice_prod tasks. The if-block that performs this f000 removal has been
        moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`.

        ---------

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

    commit f156a7894d639f177e3e2588f98eec1f6f59aa68
    Author: Jessica Meixner <[email protected]>
    Date:   Fri Jul 26 14:18:32 2024 -0500

        HR4 GWD update (#2732)

        This update is a combination of the gravity wave drag (GWD) versions
        from the NOAA/GSL and NOAA/PSL

    commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891
    Author: David Huber <[email protected]>
    Date:   Thu Jul 25 14:26:52 2024 -0400

        Temporarily disable METplus jobs (#2796)

    commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2
    Author: Guillaume Vernieres <[email protected]>
    Date:   Wed Jul 24 15:00:35 2024 -0400

        Refactoring of the marine B-matrix job (#2749)

        Refactor the functionality of B-matrix generation from the GDASApp

        Resolves #2743

    commit 65a7ab75dc0e4baba06a02e11ed0455787056a68
    Author: David Huber <[email protected]>
    Date:   Tue Jul 23 08:35:48 2024 -0400

        Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775)

        Removes the namespace-based construction of EnKF member COM directories
        in the enkf archive template.

    commit c45b9611f3e701b819bd33dc5af29033f060bb91
    Author: Eric Sinsky - NOAA <[email protected]>
    Date:   Tue Jul 23 00:33:16 2024 -0400

        Add task to process reforecast variables to save on WCOSS2 (#2680)

        # Description
        This PR adds an optional task to the global-workflow to process a subset
        of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for
        the GEFSv13 reforecast. This task is designed to process GEFS variables
        so that specific reforecast product requirements are met. A new variable
        in `config.base` called `DO_EXTRACTVARS` enables this task, which is
        currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by
        default and is specifically a task designed to be executed for the
        GEFSv13 reforecast.

        Refs #1878

        # Type of change
        - New feature (adds functionality)

        # Change characteristics
        - Is this a breaking change (a change in existing functionality)? NO
        - Does this change require a documentation update? NO

        # How has this been tested?
        This has been cloned and tested on WCOSS2. This will need to be tested
        on Hera and other platforms on which the reforecast may be running.

        # Checklist
        - [ ] Any dependent changes have been merged and published
        - [x] My code follows the style guidelines of this project
        - [x] I have performed a self-review of my own code
        - [ ] I have commented my code, particularly in hard-to-understand areas
        - [x] My changes generate no new warnings
        - [x] New and existing tests pass with my changes
        - [ ] I have made corresponding changes to the documentation if
        necessary

        ---------

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

    commit 71dc33c6ca991c16ce743760d99feaaf60f2218a
    Author: David Huber <[email protected]>
    Date:   Mon Jul 22 14:51:53 2024 -0400

        Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774)

        Fix metp* resources and check that they completed properly; add support for Orion Rocky 9

    commit 56df67a90fe090c425199f1285e5aac722c398b1
    Author: David Huber <[email protected]>
    Date:   Mon Jul 22 09:28:18 2024 -0400

        Hotfix: Update jcb to avoid git-lfs files (#2782)

        Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to
        be cloned on Hera.

        This hotfix points to a non-authoritative branch of the GDASApp
        (https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and
        should be updated ASAP back to the authoritative repository.

    commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jul 16 09:44:00 2024 -0400

        Address issues in creating XML for GFS forecast-only with app S2SWA (#2757)

        This bugfix PR:
        - fixes an issue where a user is unable to generate the XML for a GFS
        forecast-only experiment with APP=S2SWA

        Specifically, the changes are related to defining `aero_fcst_cdumps`.
        Following `setup_expt.py`, the user will have to set
        `AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in
        `config.base`.

    commit e0878dba0e53706a7f53429b61aee2936e2c21bf
    Author: Kate Friedman <[email protected]>
    Date:   Mon Jul 15 10:25:11 2024 -0400

        Updated prepobs and fit2obs versions for Orion Rocky9 (#2758)

        Update prepobs to v1.0.2 and fit2obs to v1.1.2

        These versions now support Orion Rocky9. Updates are included
        for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet.

    commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu Jul 11 17:48:47 2024 +0000

        CI maintenance updates and adding CI Unit Tests (#2740)

        This PR has a few maintenance updates to the CI pipeline and adds a test
        directory with Unit Tests
        **Major Maintenance updates:**
        - Added try blocks with appropriate messaging to GitHub PR of failure
        for:
        - - **scm** checkout
        - - build fail (with error logs sent as gists)
        - - create experiment fails with `stderr` sent to GitHub PR messaging
        - Pre-stage FAILS from the above are now captured these fails allow
        FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state
        labels in GitHub - see image below)
        **Minor Maintenance updates:**
        - Fix for STALLED cases reviled from PR 2700 (just needed a lambda
        specifier)
        - Fixed path to experiment directory in PR message (had dropped EXPDIR
        in path)
        - Needed `latin-1` decoder in reading log files for publishing
        **Added python Unit Tests for CI functionality:**
        - Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI
        utility codes
        - Cashed the install of Rocoto in the GitHub Runners to greatly reduce
        stetup time for running the unit tests
        - Unit Tests Python scripts added
        - `test_rocostat.py`: rocoto_statcount() rocoto_summary()
        rocoto_stalled()
          - `test_setup.py`: setup_expt() test_setup_xml()
          - `test_create_experment`: test_create_experiment()
          - - Runs all PR cases that do not have ICs in the GItHub Runner
        - Reporting mechanism in the Actions tab for Python Unit Testing results
        - Test case data for STALLED and RUNNING stored on S3 and pulled using
        wget during runtime of tests

    commit 5ef4db74649b8be03402c17aa29c024e71699a7b
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Thu Jul 11 08:59:24 2024 -0400

        Adds contents of constructor and initialize methods to marine LETKF class (#2635)

        Adds contents of constructor and initialize methods to marine LETKF class

        Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091
        ---------

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

    commit 8998ec7b74123e953b97a93fa14cc78d471a1aee
    Author: David Huber <[email protected]>
    Date:   Tue Jul 9 08:31:57 2024 -0400

        Fix GDAS group B restart archiving (#2735)

        Archives the GDAS restartb dataset at a 6-hour offset from restarta

        This allows cycled experiments to restart from the archives.
        The tabbing for the master archive templates was also added to
        improve readability.

        Resolves #2722

    commit 3ca74771255727033b9dc043c652ac585178629c
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Tue Jul 9 08:28:54 2024 -0400

        Add fcst dependency to ocnanalprep (#2728)

        Add previous cycle's `fcst` as a dependency to `ocnanalprep`

        This ensures that the availability of restart files to the latter. This addresses a
        seldomly-encountered race condition where `ocnanalprep` fails due to the
        lack of the files.

    commit 58fca1668aecd6fb1afd12a441256ad35900e075
    Author: Rahul Mahajan <[email protected]>
    Date:   Fri Jul 5 15:02:23 2024 -0400

        Update (partially) global-workflow for orion+rocky9 (#2741)

        This PR:
        - updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils,
        GFS-utils) to include recent update to their modulefiles for
        Orion+Rocky9 upgrade
        - updates the modulefiles in global-workflow to load modules from
        Orion+Rocky9 paths
        - updates modulefiles for `gwsetup` and `gwci` as well.
        - removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not
        installed.
        - adds `parm/config.gfs/config.resources.ORION` to address GSI
        performance degradation after Rocky 9 upgrade.

        This PR:
        - does not update the build for UPP. Standalone UPP is not available via
        ufs-weather-model as of #2729
        - will need a follow-up update for `prepobs` and `fit2obs` updated
        locations when they are installed in `glopara` space on Orion.

        # Type of change
        - Maintenance (code refactor, clean-up, new CI test, etc.)

        # Change characteristics
        - Is this a breaking change (a change in existing functionality)? NO
        - Does this change require a documentation update? NO

        # How has this been tested?
        This PR is not sufficient for Orion.
        This PR must be tested on other platforms (Hera, WCOSS2) as this PR
        updates submodules.

        # Checklist
        - [ ] Any dependent changes have been merged and published
        - [ ] My code follows the style guidelines of this project
        - [ ] I have performed a self-review of my own code
        - [ ] I have commented my code, particularly in hard-to-understand areas
        - [ ] My changes generate no new warnings
        - [ ] New and existing tests pass with my changes
        - [ ] I have made corresponding changes to the documentation if
        necessary

        ---------

        Co-authored-by: Kate Friedman <[email protected]>

    commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jul 3 21:07:49 2024 -0400

        Update ufs model hash to 20240625 (#2729)

        Updates UFS weather model hash to hash from 2024-06-24 which has orion
        porting updates + a few namelist updates.

    commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85
    Author: David Huber <[email protected]>
    Date:   Wed Jul 3 11:32:40 2024 -0400

        Hotfix for undefined CLUSTERS (#2748)

        Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses
        the native `dict` `get` method to prevent grabbing an unset entry.

    commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf
    Author: GwenChen-NOAA <[email protected]>
    Date:   Wed Jul 3 09:56:08 2024 -0400

        Update gempak job to run one fcst hour per task (#2671)

        This PR updates gempak jobs (gfs, gdas, and goes) from processing all
        forecast hours at once to one forecast hour at a time. This will reduce
        the job runtime to less than 5 min, so restart capability is not needed.

        Resolves #1250
        Ref #2666 #2667
        ---------

        Co-authored-by: Walter.Kolczynski <[email protected]>

    commit 8215ae654202186a4f753c3abe937b7b9b91a9c7
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jul 2 16:22:11 2024 -0400

        Hotfix for clusters from #2701 (#2747)

        Fixes an issue created from #2701 that added `CLUSTERS` to the
        `gaea.yaml`.

    commit 11943e36ba12b3df49c51942da780698fab02d38
    Author: DavidBurrows-NCO <[email protected]>
    Date:   Tue Jul 2 12:58:10 2024 -0400

        Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701)

        This PR sets up the ability on Gaea for auto generation of a clean xml
        file, i.e., an xml file that does not need any alterations before
        running rocoto.
        Refs #2572
        Refs #2664

    commit de8706702ead0630beb54d868f83aa2cb23f8f79
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Mon Jul 1 09:29:14 2024 -0400

        Update for JCB policies and stage DA job files with Jinja2-templates (#2700)

        This PR updates the `gdas.cd` hash to bring in new JCB conventions.
        Resolves #2699

        From #2654
        This PR will move much of the staging code that take place in the python
        initialization subroutines of the variational and ensemble DA jobs into
        Jinja2-templated YAML files to be passed into the wxflow file handler.
        Much of the staging has already been done this way, but this PR simply
        expands that strategy.

        The old Python routines that were doing this staging are now removed.
        This is part of a broader refactoring of the pygfs tasking.

        wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a
        companion to this PR.

        Co-authored-by: danholdaway <[email protected]>
        Co-authored-by: DavidNew-NOAA <[email protected]>
        Co-authored-by: DavidNew-NOAA <[email protected]>
        Co-authored-by: Dan Holdaway <[email protected]>

    commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b
    Author: Rahul Mahajan <[email protected]>
    Date:   Fri Jun 28 14:56:19 2024 -0400

        Revert PR 2681 (#2739)

        This PR:
        - reverts #2681 in part
        - keeps some changes for `RUN`.
        - is a hotfix
        - should be merged ASAP after consensus w/ @guillaumevernieres
        @CatherineThomas-NOAA @WalterKolczynski-NOAA

    commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed Jun 26 15:46:08 2024 -0400

        updated Finalize in Jenkinsfile and added try block around scm checkout (#2692)

        We are updating the Jenkins Pipeline with a try block around checkout to
        capture errors for the user.
        Also cleaned up Finalize and added section to clean out workspace on
        success.

    commit 968568f682bac7564095440bdb7813abefd76821
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 26 13:27:19 2024 -0400

        Activate snow DA test on WCOSS (#2720)

        Activate the snow DA test on WCOSS.

    commit 7706760bb8adbdf78cb640b02739023c886e7699
    Author: Rahul Mahajan <[email protected]>
    Date:   Wed Jun 26 10:02:22 2024 -0400

        Cleanup of stale RUNDIRS from an experiment (#2719)

        This PR:
        - removes stale temporary scratch run directories from `$DATAROOT/`
        every 3 days.
        - should help to scrub failed attempts.
        - removes an unused variable `RUNDIR` defined in `config.base`

    commit 8962991691b5f0857b813bddfd28aa1034d4bd2b
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jun 26 09:43:48 2024 -0400

        Update logic for MOM6 number of layers/exception values (#2681)

        Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine
        how many layers and sets the exception value for MOM6 to be 1e-34 for
        all scenarios. Note, we will no longer have zeros in the ocean grib
        output and the DA will also run without issues.

        Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615

    commit 12431f76bdce807067929415007592cffc8a2457
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Wed Jun 26 07:42:35 2024 -0600

        Update wave jobs to use COMIN/COMOUT (#2643)

        NCO has requested that each COM variable specify whether it is an input
        or an output.
        This completes that process for the global-workflow wave
        model and products tasks.
        Refs #2451

    commit b902c0bac126c323a07186ad8881384b032b6fda
    Author: David Huber <[email protected]>
    Date:   Tue Jun 25 07:48:46 2024 -0400

        Assign machine- and RUN-specific resources (#2672)

        Redefine resource variables based explicitly on RUN or CDUMP

        Additionally, machine-specific resources are moved out of
        config.resources and placed in respective config.resources.{machine}
        files.

        Resolves #177 #2672

    commit 5edbd123e2878a07f5cce8e3c7ea6147f286633a
    Merge: 09333c01d 4e1b937b6
    Author: Janet Derrico <[email protected]>
    Date:   Mon Jun 24 12:44:05 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit 4e1b937b67ed220120e81925c4507f03b9b8965f
    Author: David Huber <[email protected]>
    Date:   Mon Jun 24 10:50:52 2024 -0400

        Add minimum software requirements (#2712)

        Adds a table to HPC documentation stating the minimum support versions

    commit f43a86276aaef91efa28faadc71a3cf50e749efe
    Author: David Huber <[email protected]>
    Date:   Fri Jun 21 13:44:29 2024 -0400

        Fix and simplify online archiving and reenable METplus jobs (#2687)

        This fixes the online archiving portion of the `*arch` and `*earc00`
        jobs, a prerequisite for running METplus.  This also reenables
        METplus by default.

        The approach previously taken created `FileHandler` dictionaries at
        varying levels within the resulting yaml, which was not properly parsed
        by `exglobal_archive.py`. This approach creates a single `FileHandler`
        dictionary and is much less complicated overall.

        Resolves #2673 #2647

    commit 8993b42cb91144c0ab0501dc7841ea8d675c4701
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 19 21:51:22 2024 -0400

        Eliminate post groups (#2667)

        Eliminates the post groups used for upp and products jobs so that each
        task only processes one forecast hour. This is more efficient and
        greatly simplifies downstream dependencies that depend on a specific
        forecast hour.

        Resolves #2666
        Refs #2642

    commit 0b810c888239853fedd0e4584fe62536c6aaacdf
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 18 20:32:48 2024 -0600

        Removes misleading "No such file or directory" syntax errors from output files (#2688)

        This PR addresses issue #1252. The following is accomplished:

        - Prior to removing files, the existence of a file is checked prior to
        attempting to remove; this is performed as noted
        [here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369);
        this PR only addresses the the `chgrp` issue.

        Refs #1252

        ---------

        Co-authored-by: David Huber <[email protected]>

    commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 18 12:17:59 2024 -0600

        Hotfix for bug in template names. (#2697)

        This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/`
        template.
        Resolves #2696
        Refs #2451

    commit 35d4d99eaac669721add9ddcc793153e5ab3b30a
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 18 08:06:53 2024 -0600

        Update archive job to use COMIN/COMOUT (#2668)

        NCO has requested that each COM variable specify whether it is an input
        or an output. This completes that process for the global-workflow
        archive task.

        Refs #2451
        ---------

        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>
        Co-authored-by: David Huber <[email protected]>

    commit 47b3a581c8257fa24411fb400df8bb0e1e04972a
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jun 17 22:55:38 2024 -0400

        Turn on high-frequency output in extended test (#2679)

        Turns on high-frequency (hourly) output in the extended products test to
        exercise that aspect of the code. This test only runs on WCOSS.

        Also adds the hooks to optionally turn on the metplus jobs, but that is
        deferred as they are not currently working correctly.

    commit 38f2df9fb0c074b1f80d3c637080be79be693161
    Author: David Huber <[email protected]>
    Date:   Mon Jun 17 17:12:55 2024 +0000

        Optimize wavepostpnt (#2657)

        Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs

        This is done by
        1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by
        - performing operations on all files at once instead of looping over
        each file
            - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`)
            - combining `sed` and `grep` calls when possible
            - adding logic to `awk` calls instead of handling that logic in bash
        2) minimizing as much as possible the amount of data on disk that has to
        be read in (e.g. limiting sed to read only the line numbers it needs)
        ---------

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

    commit 5af325a6a4e0a14d180514a418603ca79fada487
    Author: Dan Holdaway <[email protected]>
    Date:   Fri Jun 14 18:05:23 2024 -0400

        Update GDASapp hash to move JCB into GDASapp (#2665)

        This PR moves JCB into GDASapp. The PR
        also bumps up the hash of GDASapp to what is in `feature/move_jcb`,
        which at time of writing is develop plus the absorption of JCB into
        GDASapp.
        Note that I also took the changes from
        https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the
        testing @RussTreadon-NOAA has done.

    commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b
    Author: Yaping Wang <[email protected]>
    Date:   Fri Jun 14 10:18:17 2024 -0500

        Add observation preparation job for aerosols DA to workflow (#2624)

        Add a prepaeroobs job to prepare aerosol obs files for DA.

        This job does quality control of the VIIRS aerosol raw observations and
        convert them to ioda format.

        Resolves #2623
        ---------

        Co-authored-by: ypwang19 <[email protected]>
        Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>
        Co-authored-by: Cory Martin <[email protected]>
        Co-authored-by: David Huber <[email protected]>

    commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4
    Author: Jessica Meixner <[email protected]>
    Date:   Fri Jun 14 11:04:41 2024 -0400

        Remove ocean daily files (#2689)

        This PR removes the ocn_daily files that are produced by the ocean
        component. These files can be recreated by averaging data that exists in
        the 6 hour aveaged files if needed.

        Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675
        Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by
        removing them and making this obsolete)

    commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu Jun 13 12:22:03 2024 -0400

        Update Jenkinsfile

        needed a comma

    commit dc21eac6c3941d7f30803891d91d82f4cc1f8183
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu Jun 13 11:41:14 2024 -0400

        Add Hercules-EMC to the Jenkins configurable parameter list (#2685)

        This quick-fix PR is to update the Jenkins Pipeline's configurable
        parameter list to include the **Hercules-EMC** node.
        This allows Jenkins users to restart Jobs in the controller when no
        updates have been made.

    commit ebacebfbe458634b8c80af6a735d6b6d01e4e406
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Thu Jun 13 11:20:24 2024 -0400

        Update gdas.cd and gsi_utils hashes (#2641)

        This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The
        updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea
        build for gsi_utils.

        Resolves #2640

    commit 34155fb4767769600a1ff95f0a65e37081addc2a
    Author: Neil Barton <[email protected]>
    Date:   Thu Jun 13 11:18:22 2024 -0400

        Add ability to use GEFS replay ICs (#2559)

        The PR allows the use of ICs from PSL's replay analysis. These replay
        ICs will be used for GEFS reforecasting and SFS. Two main changes are
        associated with these updates: (1) replay ICs being valid at 3Z, and (2)
        the use of warm starts.

        Resolves #1838

        ---------

        Co-authored-by: Jessica Meixner <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>

    commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Wed Jun 12 19:25:42 2024 -0600

        Replace `sleep` with `wait_for_file` (#2586)

        This PR addresses issue #2444. The following is accomplished:

        - All `sleep` statements are replaced with `wait_for_file` for the
        relevant scripts beneath `scripts` and `ush`;
        - Indentation and shell-norms are updated where applicable.

        Note: The WAFS scripts are not updated as per @aerorahul direction.

        Resolves #2444

        ---------

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

    commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 12 13:31:55 2024 -0400

        Add COM template for JEDI obs (#2678)

        Adds a COM template to define a path to store obs processed for JEDI.
        This will allow UFSDA to stop writing to COM_OBS, which should be
        read-only as it belongs to obsproc in operations.

        No functional change yet.

    commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed
    Author: Guoqing Ge <[email protected]>
    Date:   Wed Jun 12 09:06:23 2024 -0600

        Link both global-nest fix files and non-nest ones at the same time (#2632)

        This PR enables linking both global-nest fix files and non-nest ones at
        the same time and users can run both nesting and non-nesting experiments
        at the same time without worries about what fix files to be linked.

        Resolves #2631

    commit 61de004d4f9e9edf8a31bb173f2719b46451a36a
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jun 12 11:03:13 2024 -0400

        Update ufs-weather-model  (#2663)

        Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack
        allowing some temporary fixes to be reverted.
        * removes upp submodule
        * uses upp from the ufs-weather-model
        * restores the build and link that were hacked during the Hera Rocky 8
        transition to allow for UPP submodule
        * Removes forecast directories in clean-up

        Resolves #2617
        Resolves #2437

        ---------

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

    commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d
    Author: Eric Sinsky - NOAA <[email protected]>
    Date:   Wed Jun 12 01:15:37 2024 -0400

        Add ability to process ocean/ice products specific to GEFS (#2561)

        This PR begins to add the capability to produce GEFSv13 ocean and ice
        products in the global-workflow according to stakeholder requirements.
        The following features are added.

        - An oceanice prod yaml file has been added to address the ocean and ice
        products specific to GEFSv13.
        - The rocoto dependencies and config.base for GEFS have also been
        modified to allow for 24-hour averaged ocean and ice output.
        - Various scripts have been modified to allow for ocean and ice output
        frequencies of 24 hours.
        - `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN`
        and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`.

        Refs #1878

    commit 6691e7489650e0b738c176fbd096109288dc09b6
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 11 21:15:07 2024 -0600

        Update cleanup job to use COMIN/COMOUT (#2649)

        NCO has requested that each COM variable specify whether it is an input
        or an output. This completes that process for the global-workflow
        clean-up task.

        Refs #2451

        ---------

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

    commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Tue Jun 11 16:17:25 2024 -0400

        Add overwrite to creat experiment in BASH CI (#2676)

        This is a quick hotfix to the CI BASH driver script adding `--overwrite`
        to create experiment script to avoid errors from restarting an
        experiment.

    commit e7909af8d9e1f34140388a3f8556d8e582c58fe5
    Author: emilyhcliu <[email protected]>
    Date:   Mon Jun 10 15:11:27 2024 -0400

        Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py  (#2645)

        This PR proposes updates for the following two scripts:

        1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select
        CRTM cloud optical table based on cloud microphysical scheme indicated
        by `imp_physics'
        The default scheme in the GFS forecast model is Thompson scheme
        (imp_physics = 8).

        2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in
        the script due to increased variables to interplate increments and
        calculate analysis in the netcdf_io routines in GSI-utils.
        Here is the related [PR #46 for
        GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46).

        ---------

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

    commit 9caa51de8fb7be07d2e61775da01937d576964f6
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Thu Jun 6 22:15:23 2024 -0600

        Update RDHPCS Hera resource for `eupd` task (#2636)

        As per @wx20jjung, the resource for the `eupd` task have been updated
        for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job
        fails.

        Resolves #2454

        ---------

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

    commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b
    Author: DavidNew-NOAA <[email protected]>
    Date:   Thu Jun 6 11:49:03 2024 -0400

        Parameterize some things in config.atmanl and config.atmensanl (#2661)

        This PR adds some parameters in config.atmanl and config.atmensanl that
        can be altered with the defaults.yaml. The motivation is to make these
        files match those in the GDASApp JJOB tests (example:
        https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl),
        so we can just use the Global Workflow config.atmanl and
        config.atmensanl in the tests rather than custom ones in GDASApp that
        have to be separately updated every time the ones in the Global Workflow
        are updated.

    commit 54ea0b73a07921be5fbb07fe41e976888bd3e549
    Author: Guillaume Vernieres <[email protected]>
    Date:   Thu Jun 6 01:36:02 2024 -0400

        Add links to the ocean insitu obs processing tools (#2644)

        Add links to the marine bufr to ioda converters for the marine insitu
        observations.

        - fixes https://github.com/NOAA-EMC/GDASApp/issues/1106
        - waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135

    commit 205d0c2b13e2d7755cec75bf8c978ab20d453862
    Author: David Huber <[email protected]>
    Date:   Wed Jun 5 17:31:30 2024 +0000

        Update S4 point of contact in docs (#2660)

        Update the point of contact for global workflow issues on S4.

    commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Wed Jun 5 12:50:14 2024 -0400

        Enable wcoss2 ufsda build and module load (#2620)

        This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2.

        Resolves #2602
        Resolves #2579

    commit 67b833e0c7bc390865d453588b4609a1a7ede981
    Author: Jessica Meixner <[email protected]>
    Date:   Tue Jun 4 13:33:43 2024 -0400

        Update ufs-weather-model  (#2646)

        Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6
        This should resolve the issue and allow C768 runs on Hera and allow for CICE
        to run on WCOSS2 (due to library updates to allow linking).

        From what I can tell, all updates needed were done by
        @HenryWinterbottom-NOAA which were updates for CICE

        Fixes #2490

    commit c44d0ac86cfdf78eb87492431bf6d825e8bae637
    Author: GwenChen-NOAA <[email protected]>
    Date:   Tue Jun 4 10:29:49 2024 -0400

        Update wmo parm files to fix WMO header (#2652)

        This PR updates wmo parm files to switch WMO header of precipitation
        type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to
        instantaneous.

        Resolves #2566

    commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60
    Author: Cory Martin <[email protected]>
    Date:   Tue Jun 4 13:55:33 2024 +0000

        Add IAU to snow DA (and its test) (#2610)

        This PR enables IAU for the snow DA which is necessary for GFSv17.

        A snow analysis is created for the center of the window regardless, and
        an additional at the beginning of the window is added if IAU is on. The
        former is needed for UPP and the latter, to initialize the model.

        The increment is valid throughout the window for 3DVar, so the same
        increment is added to both forecasts.

        Additionally, the input file that goes into global_cycle has been
        updated to be the output of the JEDI snow analysis instead of the
        forecast (@jiaruidong2017 I recall discussing this, can you confirm this
        is right or am I mistaken)

        This PR also makes the CI test for snow DA (and aerosol DA) include IAU
        rather than without IAU,.

        ---------

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

    commit c92bf415060750127c9c05a62a1d2851c489551a
    Author: David Huber <[email protected]>
    Date:   Sat Jun 1 05:11:07 2024 +0000

        Archiving cleanup (#2621)

        1) Adds a lot of comments to the jinja templates for archiving
        2) Rearranges the gdas and enkf templates to a more logical order
        3) Fixes a couple of bugs in the enkf archiving of increments and
        analyses
        4) Disables archiving for the half cycle
        5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`,
        instead relying on `DO_FIT2OBS`
        6) Updates wxflow to add the option to not allow undefined variables
        when parsing jinja templates and invokes this feature when running
        archives

        Resolves #2612

    commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri May 31 04:57:08 2024 -0400

        Switch to Rocky 9 built external packages on Hercules (#2608)

        The workflow was updated to use modules built on Rocky 9, but the
        external packages (like prepobs) were still pointing to the versions
        built on CentOS (Orion). This transitions to packages built on Rocky 9.

        Updating of the tracker package has been deferred until later. As such,
        the tracker jobs have been disabled by returning immediately if they are
        on Hercules. Since these jobs are small, resource-wise, it should not
        meaningfully impact turnover time.

    commit 4422550c01c9214a2b3b8890bdcc898123ee216a
    Author: Guoqing Ge <[email protected]>
    Date:   Thu May 30 08:05:23 2024 -0600

        Add the capability to use slurm reservation nodes (#2627)

        Add the capability to use slurm reservation nodes
        Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE

        Resolves #2626

    commit a54153fd9d26126206bc07a1da4e80f50c0c5910
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed May 29 23:24:07 2024 -0400

        Update forecast job to use COMIN/COMOUT (#2622)

        NCO has requested that each COM variable specify whether it is an input
        or an output. This completes that process for the forecast job.

        Refs #2451

        ---------

        Co-authored-by: David Huber <[email protected]>

    commit d69a8af95d492982b918670322ed5c41ab074335
    Author: Jessica Meixner <[email protected]>
    Date:   Wed May 29 21:29:03 2024 -0400

        Update to add 1-deg global wave grid (#2619)

        This PR adds options to use a global 1 deg grid, intended for testing
        with the SFS application.

        Requires new fix file changes NOAA-EMC/global-workflow#2618

    commit 0b4670ecf83b99b72835c8380573b2bca7cf5324
    Author: Jessica Meixner <[email protected]>
    Date:   Wed May 29 17:17:21 2024 -0400

        Add C384mx025_3DVarAOWCDA yamls (#2625)

        Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder.

    commit 2e885d05c64b947f00a3cf055a1277fbfac195c9
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed May 29 13:00:51 2024 -0400

        Script to keep Jenkins Agent persistent from cron (#2634)

        This "persistent" Java Agent launch script can be ran from a cron job:

        - Uses Jenkins Remote API to check the status of the Node connection
        using curl for a given machine.
        - If it is not connected a new agent is launched for that node.

        Resolves #2633

    commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5
    Author: GwenChen-NOAA <[email protected]>
    Date:   Tue May 28 17:17:11 2024 -0400

        Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611)

        Based on users' feedback, this PR do the following:
        1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF
        2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD,
          and VOGRD) from "%g m below water surface" to "%g m below sea level"
        3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m)

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

    commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31
    Author: DavidNew-NOAA <[email protected]>
    Date:   Tue May 28 17:16:23 2024 -0400

        Add atmensanlfv3inc job (#2592)

        This PR creates the atmensanlfv3inc job, the ensemble version of
        atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is
        #[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS
        companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3).

    commit 50c2b8951b29a3c883a778becbf8582f9519eb48
    Author: Anil Kumar <[email protected]>
    Date:   Tue May 28 13:23:53 2024 -0400

        Global-workflow (AR) Generic updates for Gaea C5 (#2515)

        - Port global-workflow’s build and run capability to Gaea-C5
        - Building global-workflow on Gaea-C5
        - Setting up experiments with global-workflow on Gaea-C5

        ---------

        Co-authored-by: AnilKumar-NOAA <[email protected]>
        Co-authored-by: DavidBurrows-NCO <[email protected]>

    commit b6ca771a0c584cbfcbbf9be739765d5f3815df97
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri May 24 10:52:45 2024 -0400

        Update STMP and PTMP settings in host file for Orion and Hercules  (#2614)

        - Updating STMP and PTMP settings in host file for Orion and Hercules
        because they are cross mounted.
        - Also took the opportunity to finally update **SLURM_ACCOUNT** to
        **HPC_ACCOUT** in CI over rides.
        - Added a refactor of the `rocotostat.py` tool that is more pythonic and
        as a execute retry feature because the `rocotostat` utility on Orion has
        been failing sometimes.

    commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f
    Author: Guillaume Vernieres <[email protected]>
    Date:   Tue May 21 23:50:50 2024 -0400

        Sea-ice analysis insertion (#2584)

        Allows cycling and restarting CICE with the sea-ice analysis if the
        marine DA is switched on.

        Resolves #2568
        Resolves NOAA-EMC/GDASApp#1103

    commit 5369a1ff3a3969149fcf32810fad0e50216752b7
    Author: David Huber <[email protected]>
    Date:   Tue May 21 22:12:29 2024 +0000

        Refactored archiving (#2491)

        This provides a new pygfs task, archive.py, that provides all of the
        tools necessary to archive data to the local (`ARCDIR`) and backup
        (`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to
        define the file to be archived or tarred to replace the
        `hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts
        and make it easier to add new data and explicitly handle optional and
        required files.

        For `ATARDIR` archiving, a master jinja template is provided for each
        `RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2,
        master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both
        `enkfgdas` and `enkfgfs` `RUN`s. These templates then include the
        appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on
        experiment, cycle, and coupled parameters. Each of these templates
        corresponds to a single tarball to populate and are tabbed 4 spaces so
        they are defined within the master `datasets` dictionary.

        Future developers should not have to make modifications to archive.py
        unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then
        only a single `elif` needs to be added to the configure method to
        specify the master `ATARDIR` template to archive (e.g.
        `master_gefs.yaml.j2`). If a new component is coming online that needs
        to be archived to `ATARDIR` (e.g. SNOW), then create a new template for
        each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`)
        and reference the template in the appropriate master templates, e.g.

        `master_gdas.yaml:`
        ```jinja
        {% if DO_SNOW %}
        {% include "gdassnow.yaml.j2" %}
        {% endif %}
        ```

        A few other issues were addressed along the way:
        1. Aerosols have been reenabled. Aerosol forecasts should only be
        performed during gdas cycles, but analyses can be performed for both gfs
        and gdas cycles. This was accomplished by setting separate
        `AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs.
        2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`.
        This prevented restarts from being used for cice-enable experiments.
        This feature was not tested.
        3. Create a temporary fix for the `wgrib` utility. For spack-stack
        1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is
        open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in
        existing installations. Once complete, this temporary fix should be
        removed.
        4. The number of `earc` jobs has been reduced for lower resolution
        experiments. Both C48 and C96 experiments will now only have two earc
        jobs (one for the non-member files to archive and another for the member
        files). C192 will have up to 3 earc jobs (one non-member, one for
        members 1-40 and another for members 41-80, if needed).

        Resolves #2345
        Resolves #2318

        ---------

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

    commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri May 17 12:57:59 2024 -0400

         Add remove RUNDIRS step in CI before creating experements (#2607)

        As had been done in Bash CI we need to remove the RUNDIR in Jenkins
        before a creating an experiment in the event that case had beem
        previously ran.

    commit 09333c01dbafddb2d2fe7e181b479af3cc6d3621
    Merge: f7e9f4489 bb930050b
    Author: Janet Derrico <[email protected]>
    Date:   Thu May 16 14:33:19 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit bb930050b3cd51d28ecba6b231c8675f6d11856c
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Thu May 16 12:28:30 2024 -0400

        Adds jjob and other necessities for marine LETKF task (#2564)

        Adds jjob, rocoto script, config file, and other necessities for new
        marine LETKF task.

        Partially addresses NOAA-EMC/GDASApp#1091

    commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu May 16 12:12:06 2024 -0400

        Updating CI Machine configs with redundant PTMP (#2605)

        Quick fix adding PTMP as STMP in Machine configs for CI for completeness

    commit ef340ff33a6f89adf70838206ba3fd56a953fa7a
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu May 16 11:37:30 2024 -0400

        Fix race condition in CI between Orion and Hercules (#2604)

        Hotfix to solve race conditions in the CI system due to cross-mounted
        file systems between Orion and Hercules

    commit e8b17e27f719df280170dc3f5bd9f19917cefaf2
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed May 15 17:16:30 2024 -0400

        Remove existing EXPDIRs and COMROTs when CI is re-run (#2601)

        Quick hotfix for having default for re-runing jobs to start clean with
        new EXPDIRs and COMROTs

    commit b5d113efb1970ede5cd1d3d4dff8d96320519c41
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed May 15 16:52:49 2024 -0400

        Moving logic for skipping hosts in pr cases (#2573)

        This PR removes the logic of skipping hosts for pr cases from
        `create_experiment.py` and moves it to a test in the cron bash driver
        using a `parse_yaml.py` python tool.

        The Jenkins pipeline was not effected as it uses the
        `get_host_case_list.py` utility to form the cases on a per host bases.

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

    commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Wed May 15 13:13:30 2024 -0400

        Update gsi_utils.fd hash (#2598)

        This PR updates the `gsi_utils.fd` hash to bring in updates which add
        safeguards to
        -
        `src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90`
        - `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90`

        The safeguards are described in GSI-utils PR
        [#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated
        issue.

        Resolves #2597

    commit d5366c66bd67f89d118b18956fe230207cbf0aea
    Author: Kate Friedman <[email protected]>
    Date:   Wed May 15 13:12:56 2024 -0400

        Update CICE and MOM6 fix versions (#2600)

        This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions
        to the newer `20240416` timestamps, which includes updates and fixes to
        the `100` (1-deg) resolution files.

        Resolves #2480
        Resolves #2483
        Resolves #2595

    commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b
    Author: David Huber <[email protected]>
    Date:   Mon May 13 22:57:38 2024 +0000

        Limit gfswavepostpnt to 40 PEs/node (#2588)

        This fixes the slow runtime of the gfswavepostpnt job on Hercules. The
        job is very I/O intensive and does not scale well to large nodes, so
        limit the number of jobs/node to 40.

        Resolves #2587

    commit 4fb7c12c325702a47f27c802a5067efd33d0327c
    Author: Fanglin Yang <[email protected]>
    Date:   Mon May 13 16:37:51 2024 -0400

        Update damping and time-step (#2575)

        Updates the model to use explicit Rayleigh damping for u/v and implicit
        damping to w. This improves model stability and allows for longer
        timesteps. Also unifies the GDAS and GFS to use the same damping.

        Results from a test at the C1152 resolution (coupled model) can be found
        at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/

        Resolves #2574

        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
        Co-authored-by: Lisa Bengtsson <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>

    commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri May 10 14:17:13 2024 -0400

        Do not use BUILT_semphore to force rebuilds when re-run (#2593)

        Remove the placement of the `BUILT_semaphore` file after the build in
        the Jenkins Pipeline and force it to rebuild any changes after a PR is
        re-ran.

    commit 2346c6161f75ae02369cbf30f30c6150d3e12b66
    Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com>
    Date:   Thu May 9 21:17:06 2024 -0500

        Migration to Rocky8 spack-stack installations on Jet (#2458)

        # Description
        Migrates Global Workflow to Rocky8 spack-stack installations on Jet.
        Jet has moved from CentOS7 to Rocky8.

        Resolves #2377
        Refs NOAA-EMC/UPP#919
        Refs NOAA-EMC/gfs-utils#60
        Refs NOAA-EMC/GSI#732
        Refs NOAA-EMC/GSI-Monitor#130
        Refs NOAA-EMC/GSI-utils#33

    commit c7b3973014480a20dd8e24edaeb83a9e9e68159f
    Author: Jessica Meixner <[email protected]>
    Date:   Thu May 9 11:36:58 2024 -0400

        Updates for cold start half cycle, then continuing with IAU for WCDA (#2560)

        This PR allows us to run C384 S2S with IAU, but starting with the first
        half-cycle as a cold-start. This will be necessary for cycled testing as
        we build towards the full system for GFSv17. This updates the copying of
        the restarts for RUN=gdas for both ocean and ice copying what the atm
        model is doing. It also reduced the amount of restart files from 4 to 3.

        Other updates:
        * Add DOJEDI ocean triggers for archiving certain files update from:
        @CatherineThomas-NOAA
        * Adds COPY_FINAL_RESTARTS option to turn on/off copying the last
        restart file to COM. Defaults to off...
        * Defines model_start_date_current_cycle & model_start_date_next_cycle
        to help with knowing which IC to grab.

        Refs #2546

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

    commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2
    Author: Dan Holdaway <[email protected]>
    Date:   Wed May 8 20:52:48 2024 -0400

        Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477)

        Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI
        Configuration Builder (JCB) tool so that YAMLs can be made more portable
        and invoke the observation chronicle mechanism.

        Resolves #2476

        Co-authored-by: danholdaway <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

    commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed May 8 02:04:16 2024 -0400

        Add CI test for products (#2567)

        Adds a new version of the atm3DVar test that runs the full forecast
        length and produces most of the secondary products. For now, this test
        will only run on WCOSS due to gempak failures on other machines as well
        as computational needs. On other machines, the original version will run
        (the original version will not run on WCOSS). AWIPS remains off for now
        in this extended test due to a bug involving tocgrib2 and the convective
        precip fields (see #2566).

        The new test runs for 4½ cycles and the full 384-hr forecast length to
        ensure all gempak scripts are exercised. Since the cycle throttle is 3
        and the bulk of the time is in the free forecast, the cycles run mostly
        concurrently so it doesn't extend the total test time too much beyond
        that of a single 384-hr forecast.

        Fixes a bug in NPOESS that was introduced when the post filenames were
        reverted to the previous format for the GOES products until the final
        filenames are determined (#2499).

        Also removes the AWIPS g2 job from the rocoto mesh to complete the
        retirement of grib1 products.

        Resolves #2132
        Resolves #2445

    commit 9b6f8404ac4507d14adc404b77cfdf002b55e832
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue May 7 00:14:36 2024 -0400

        Add task to prepare emissions for GEFS (#2562)

        This PR:
        - introduces a task to prepare emissions for a forecast into the GEFS
        application.
        - adds configuration, j-job, rocoto job, ex-script and the python class
        for this job
        - updates GEFS workflow to be able to generate the XML to call this job.
        - updates the `fcst` and `efcs` job dependencies in the GEFS application
        to depend on `prep_emissions` if aerosols are turned ON.
        - provides a placeholder for @bbakernoaa to work on the details for
        preparing emissions.

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

    commit 233c18815d2e8e6b344f161fd0c102a4fbdfb66d
    Author: Dan Holdaway <[email protected]>
    Date:   Mon May 6 18:11:35 2024 -0400

        Single Executable for main GDAS JEDI applications (#2565)

        Changes that accompany GDAS PR (NOAA-EMC/GDASApp/pull/1075) that allow…
kayeekayee added a commit to kayeekayee/global-workflow that referenced this issue Sep 19, 2024
@kayeekayee
Update realtime branch, gsl_ufs_rtdev1.
69d54ea 
Squashed commit of the following:

commit 4e0a81f7acf5ccba5de8d3bdf7ab19cae80812cb
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 18:37:50 2024 +0000

    Fix typos/links/dependancy.

commit d5fdcbf8d6e987dbdfcd6b4da34d0934c8d82c3b
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 07:37:52 2024 +0000

    Fixed missing config.base files.

commit c6239f925369b20fd8488e8537969e2f4f9e7725
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 06:53:47 2024 +0000

    Update submodule hashs.

commit 32bf790f67b818ff50a7f6b74388fb81ed175b3a
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 06:09:41 2024 +0000

    Update develop branch, gsl_ufs_dev
     - based on gsl_ufs_dev from KaYee's fork
       global-workflow: 07Aug24,37c53ac [develop_07Aug2024_37c53ac]
       UFS: 19Jul24, c127601
       FV3: 19Jul24, 2527c11
       UPP: 23Apr24, be0410e
       CCPP-PHYSICS: 19Jul24, 46df080
       UFS_UTILS: 26Jun24, 3ef2e6b

    Squashed commit of the following:

    commit 70b557836379bb7e545fcc6642e28d66cfc17735
    Merge: 5edbd123e 37c53ac69
    Author: Janet Derrico <[email protected]>
    Date:   Wed Aug 7 11:02:24 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04
    Author: Kate Friedman <[email protected]>
    Date:   Wed Aug 7 08:11:21 2024 -0400

        Revert MSU FIX_DIRs back to glopara (#2811)

    commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Tue Aug 6 14:47:36 2024 -0400

        Bugfix for updating label states in Jenkins (#2808)

        Quick bug fix for updating state labels in CI during finalize.
        (did not reference GitHub CLI executable correctly in the pipeline
        script)

    commit 8fee36f0307b0c08080e3a8fa8fa6703e7da5fce
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Aug 6 11:02:45 2024 -0400

        Clean-up temporary rundirs - take 2. (#2753)

        This PR:
        - is a follow-up to a previous PR that aggressively pruned run
        directories.
        - removes run directories for the current cycle in the clean-up if the
        cycle is successful. If the cycle is not successful, cleanup is not
        called and all run directories for the cycle are safe from being purged.
        - also updates the PR template to list/query for any updates to
        submodules.

        ---------

        Co-authored-by: David Huber <[email protected]>
        Co-authored-by: David Huber <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

    commit d599fff4aedd41ae587dbe02226acb12ff48efc1
    Author: HelinWei-NOAA <[email protected]>
    Date:   Mon Aug 5 05:31:31 2024 -0400

        Change land surface for HR4 (#2787)

        Resets the default value of opt_diag to 2 corresponding to the land
        surface upgrades in ufs-weather-model for HR4.

        Resolves #2786

    commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb
    Author: David Huber <[email protected]>
    Date:   Fri Aug 2 15:41:29 2024 -0400

        Run METplus serially and correct the name of prod tasks (#2804)

        Adds 2 hot fixes:

        - METplus v9.1.3 has a bug in it that sometimes attempts to create
        multiple copies of the same directory when running in parallel, causing
        a Python error and downstream problems. This PR makes METplus run in
        serial mode, preventing such issues.
        - Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in
        workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod)

    commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri Aug 2 15:03:45 2024 -0400

        Update Java Agent launching script for Jenkins connections (#2762)

        Made updates to the Jenkins Launching Script for robustness and less
        ambiguous documentation:
        - Clearer distinction between required user token for the remote api and
        the systems token for launching
        - Added pre-checks: `gh` is authenticating, named compliant token and
        secret file exists
        - More robust Jason based parser of the remote api response for checking
        the state of the Node connection
        - For `cron` use a 5 minute pause and recheck was added before
        re-launching of the java agent
        - Added concise header documentation of requirements and purpose
        ---------

        Co-authored-by: David Huber <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

    commit b73b1fd203496db97f8067652659573a632bcc67
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri Aug 2 07:59:06 2024 -0400

        Fix erroneous cdump addition (#2803)

    commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3
    Author: Rahul Mahajan <[email protected]>
    Date:   Thu Aug 1 20:26:13 2024 -0400

        Update ocean post-processing triggers (#2784)

        This PR:
        - replaces `check_netcdf.sh` checker for ocean post-processing with with
        ocean output at the next forecast hour or finishing of the forecast job
        for ocean prod
        - removes no longer needed `ush/check_netcdf.sh`

    commit aa2af1ca8d59424a60a1730722bf528775d9e606
    Author: GeorgeGayno-NOAA <[email protected]>
    Date:   Thu Aug 1 16:46:10 2024 -0400

        Update the gfs_utils repository hash (#2801)

        # Description
        Point to the latest hash of the gfs-utils repository, which contains the
        bug fix to gaussian_sfcanl.

        Resolves #2669.
        Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73

    commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8
    Author: David Huber <[email protected]>
    Date:   Thu Aug 1 08:12:14 2024 -0400

        Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791)

        Changes how METplus jobs run so that they run on the last GFS cycle for
        a given `PDY`.

        This is a departure from operations where the METplus jobs run on the
        00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through
        `${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on
        `${PDY}18` for cycles 00-18. See
        https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details.

    commit 1cf8b448af562dbb7af198399c78c585977e81da
    Author: David Huber <[email protected]>
    Date:   Tue Jul 30 10:38:49 2024 -0400

        Simplify resource-related variables, remove CDUMP where unneeded (#2727)

        This overhauls resource-related variables to use a common set of
        variables for each job. In the process, this also removed the use of
        CDUMP in most cases.

        Resolves #1299 #2693

    commit 61875f25c9e971f82ae499b5b612d7f095deebd4
    Author: Eric Sinsky - NOAA <[email protected]>
    Date:   Mon Jul 29 14:40:03 2024 -0400

        Remove f000 from atmos rocoto tasks for replay cases (#2778)

        The main purpose of this PR is to remove the f000 from
        atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In
        cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater
        than `0`, it becomes necessary to have the first lead hour set to
        `OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For
        example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead
        time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and
        the minimum lead time for the ocean_prod rocoto task needs to be 6
        (assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up
        possible by removing 0 from fhrs for atmosphere-related tasks in
        `gefs_tasks.py` when replaying.

        This PR also moves where f000 is being removed for the ocean_prod and
        ice_prod tasks. The if-block that performs this f000 removal has been
        moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`.

        ---------

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

    commit f156a7894d639f177e3e2588f98eec1f6f59aa68
    Author: Jessica Meixner <[email protected]>
    Date:   Fri Jul 26 14:18:32 2024 -0500

        HR4 GWD update (#2732)

        This update is a combination of the gravity wave drag (GWD) versions
        from the NOAA/GSL and NOAA/PSL

    commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891
    Author: David Huber <[email protected]>
    Date:   Thu Jul 25 14:26:52 2024 -0400

        Temporarily disable METplus jobs (#2796)

    commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2
    Author: Guillaume Vernieres <[email protected]>
    Date:   Wed Jul 24 15:00:35 2024 -0400

        Refactoring of the marine B-matrix job (#2749)

        Refactor the functionality of B-matrix generation from the GDASApp

        Resolves #2743

    commit 65a7ab75dc0e4baba06a02e11ed0455787056a68
    Author: David Huber <[email protected]>
    Date:   Tue Jul 23 08:35:48 2024 -0400

        Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775)

        Removes the namespace-based construction of EnKF member COM directories
        in the enkf archive template.

    commit c45b9611f3e701b819bd33dc5af29033f060bb91
    Author: Eric Sinsky - NOAA <[email protected]>
    Date:   Tue Jul 23 00:33:16 2024 -0400

        Add task to process reforecast variables to save on WCOSS2 (#2680)

        # Description
        This PR adds an optional task to the global-workflow to process a subset
        of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for
        the GEFSv13 reforecast. This task is designed to process GEFS variables
        so that specific reforecast product requirements are met. A new variable
        in `config.base` called `DO_EXTRACTVARS` enables this task, which is
        currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by
        default and is specifically a task designed to be executed for the
        GEFSv13 reforecast.

        Refs #1878

        # Type of change
        - New feature (adds functionality)

        # Change characteristics
        - Is this a breaking change (a change in existing functionality)? NO
        - Does this change require a documentation update? NO

        # How has this been tested?
        This has been cloned and tested on WCOSS2. This will need to be tested
        on Hera and other platforms on which the reforecast may be running.

        # Checklist
        - [ ] Any dependent changes have been merged and published
        - [x] My code follows the style guidelines of this project
        - [x] I have performed a self-review of my own code
        - [ ] I have commented my code, particularly in hard-to-understand areas
        - [x] My changes generate no new warnings
        - [x] New and existing tests pass with my changes
        - [ ] I have made corresponding changes to the documentation if
        necessary

        ---------

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

    commit 71dc33c6ca991c16ce743760d99feaaf60f2218a
    Author: David Huber <[email protected]>
    Date:   Mon Jul 22 14:51:53 2024 -0400

        Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774)

        Fix metp* resources and check that they completed properly; add support for Orion Rocky 9

    commit 56df67a90fe090c425199f1285e5aac722c398b1
    Author: David Huber <[email protected]>
    Date:   Mon Jul 22 09:28:18 2024 -0400

        Hotfix: Update jcb to avoid git-lfs files (#2782)

        Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to
        be cloned on Hera.

        This hotfix points to a non-authoritative branch of the GDASApp
        (https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and
        should be updated ASAP back to the authoritative repository.

    commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jul 16 09:44:00 2024 -0400

        Address issues in creating XML for GFS forecast-only with app S2SWA (#2757)

        This bugfix PR:
        - fixes an issue where a user is unable to generate the XML for a GFS
        forecast-only experiment with APP=S2SWA

        Specifically, the changes are related to defining `aero_fcst_cdumps`.
        Following `setup_expt.py`, the user will have to set
        `AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in
        `config.base`.

    commit e0878dba0e53706a7f53429b61aee2936e2c21bf
    Author: Kate Friedman <[email protected]>
    Date:   Mon Jul 15 10:25:11 2024 -0400

        Updated prepobs and fit2obs versions for Orion Rocky9 (#2758)

        Update prepobs to v1.0.2 and fit2obs to v1.1.2

        These versions now support Orion Rocky9. Updates are included
        for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet.

    commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu Jul 11 17:48:47 2024 +0000

        CI maintenance updates and adding CI Unit Tests (#2740)

        This PR has a few maintenance updates to the CI pipeline and adds a test
        directory with Unit Tests
        **Major Maintenance updates:**
        - Added try blocks with appropriate messaging to GitHub PR of failure
        for:
        - - **scm** checkout
        - - build fail (with error logs sent as gists)
        - - create experiment fails with `stderr` sent to GitHub PR messaging
        - Pre-stage FAILS from the above are now captured these fails allow
        FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state
        labels in GitHub - see image below)
        **Minor Maintenance updates:**
        - Fix for STALLED cases reviled from PR 2700 (just needed a lambda
        specifier)
        - Fixed path to experiment directory in PR message (had dropped EXPDIR
        in path)
        - Needed `latin-1` decoder in reading log files for publishing
        **Added python Unit Tests for CI functionality:**
        - Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI
        utility codes
        - Cashed the install of Rocoto in the GitHub Runners to greatly reduce
        stetup time for running the unit tests
        - Unit Tests Python scripts added
        - `test_rocostat.py`: rocoto_statcount() rocoto_summary()
        rocoto_stalled()
          - `test_setup.py`: setup_expt() test_setup_xml()
          - `test_create_experment`: test_create_experiment()
          - - Runs all PR cases that do not have ICs in the GItHub Runner
        - Reporting mechanism in the Actions tab for Python Unit Testing results
        - Test case data for STALLED and RUNNING stored on S3 and pulled using
        wget during runtime of tests

    commit 5ef4db74649b8be03402c17aa29c024e71699a7b
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Thu Jul 11 08:59:24 2024 -0400

        Adds contents of constructor and initialize methods to marine LETKF class (#2635)

        Adds contents of constructor and initialize methods to marine LETKF class

        Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091
        ---------

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

    commit 8998ec7b74123e953b97a93fa14cc78d471a1aee
    Author: David Huber <[email protected]>
    Date:   Tue Jul 9 08:31:57 2024 -0400

        Fix GDAS group B restart archiving (#2735)

        Archives the GDAS restartb dataset at a 6-hour offset from restarta

        This allows cycled experiments to restart from the archives.
        The tabbing for the master archive templates was also added to
        improve readability.

        Resolves #2722

    commit 3ca74771255727033b9dc043c652ac585178629c
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Tue Jul 9 08:28:54 2024 -0400

        Add fcst dependency to ocnanalprep (#2728)

        Add previous cycle's `fcst` as a dependency to `ocnanalprep`

        This ensures that the availability of restart files to the latter. This addresses a
        seldomly-encountered race condition where `ocnanalprep` fails due to the
        lack of the files.

    commit 58fca1668aecd6fb1afd12a441256ad35900e075
    Author: Rahul Mahajan <[email protected]>
    Date:   Fri Jul 5 15:02:23 2024 -0400

        Update (partially) global-workflow for orion+rocky9 (#2741)

        This PR:
        - updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils,
        GFS-utils) to include recent update to their modulefiles for
        Orion+Rocky9 upgrade
        - updates the modulefiles in global-workflow to load modules from
        Orion+Rocky9 paths
        - updates modulefiles for `gwsetup` and `gwci` as well.
        - removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not
        installed.
        - adds `parm/config.gfs/config.resources.ORION` to address GSI
        performance degradation after Rocky 9 upgrade.

        This PR:
        - does not update the build for UPP. Standalone UPP is not available via
        ufs-weather-model as of #2729
        - will need a follow-up update for `prepobs` and `fit2obs` updated
        locations when they are installed in `glopara` space on Orion.

        # Type of change
        - Maintenance (code refactor, clean-up, new CI test, etc.)

        # Change characteristics
        - Is this a breaking change (a change in existing functionality)? NO
        - Does this change require a documentation update? NO

        # How has this been tested?
        This PR is not sufficient for Orion.
        This PR must be tested on other platforms (Hera, WCOSS2) as this PR
        updates submodules.

        # Checklist
        - [ ] Any dependent changes have been merged and published
        - [ ] My code follows the style guidelines of this project
        - [ ] I have performed a self-review of my own code
        - [ ] I have commented my code, particularly in hard-to-understand areas
        - [ ] My changes generate no new warnings
        - [ ] New and existing tests pass with my changes
        - [ ] I have made corresponding changes to the documentation if
        necessary

        ---------

        Co-authored-by: Kate Friedman <[email protected]>

    commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jul 3 21:07:49 2024 -0400

        Update ufs model hash to 20240625 (#2729)

        Updates UFS weather model hash to hash from 2024-06-24 which has orion
        porting updates + a few namelist updates.

    commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85
    Author: David Huber <[email protected]>
    Date:   Wed Jul 3 11:32:40 2024 -0400

        Hotfix for undefined CLUSTERS (#2748)

        Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses
        the native `dict` `get` method to prevent grabbing an unset entry.

    commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf
    Author: GwenChen-NOAA <[email protected]>
    Date:   Wed Jul 3 09:56:08 2024 -0400

        Update gempak job to run one fcst hour per task (#2671)

        This PR updates gempak jobs (gfs, gdas, and goes) from processing all
        forecast hours at once to one forecast hour at a time. This will reduce
        the job runtime to less than 5 min, so restart capability is not needed.

        Resolves #1250
        Ref #2666 #2667
        ---------

        Co-authored-by: Walter.Kolczynski <[email protected]>

    commit 8215ae654202186a4f753c3abe937b7b9b91a9c7
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jul 2 16:22:11 2024 -0400

        Hotfix for clusters from #2701 (#2747)

        Fixes an issue created from #2701 that added `CLUSTERS` to the
        `gaea.yaml`.

    commit 11943e36ba12b3df49c51942da780698fab02d38
    Author: DavidBurrows-NCO <[email protected]>
    Date:   Tue Jul 2 12:58:10 2024 -0400

        Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701)

        This PR sets up the ability on Gaea for auto generation of a clean xml
        file, i.e., an xml file that does not need any alterations before
        running rocoto.
        Refs #2572
        Refs #2664

    commit de8706702ead0630beb54d868f83aa2cb23f8f79
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Mon Jul 1 09:29:14 2024 -0400

        Update for JCB policies and stage DA job files with Jinja2-templates (#2700)

        This PR updates the `gdas.cd` hash to bring in new JCB conventions.
        Resolves #2699

        From #2654
        This PR will move much of the staging code that take place in the python
        initialization subroutines of the variational and ensemble DA jobs into
        Jinja2-templated YAML files to be passed into the wxflow file handler.
        Much of the staging has already been done this way, but this PR simply
        expands that strategy.

        The old Python routines that were doing this staging are now removed.
        This is part of a broader refactoring of the pygfs tasking.

        wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a
        companion to this PR.

        Co-authored-by: danholdaway <[email protected]>
        Co-authored-by: DavidNew-NOAA <[email protected]>
        Co-authored-by: DavidNew-NOAA <[email protected]>
        Co-authored-by: Dan Holdaway <[email protected]>

    commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b
    Author: Rahul Mahajan <[email protected]>
    Date:   Fri Jun 28 14:56:19 2024 -0400

        Revert PR 2681 (#2739)

        This PR:
        - reverts #2681 in part
        - keeps some changes for `RUN`.
        - is a hotfix
        - should be merged ASAP after consensus w/ @guillaumevernieres
        @CatherineThomas-NOAA @WalterKolczynski-NOAA

    commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed Jun 26 15:46:08 2024 -0400

        updated Finalize in Jenkinsfile and added try block around scm checkout (#2692)

        We are updating the Jenkins Pipeline with a try block around checkout to
        capture errors for the user.
        Also cleaned up Finalize and added section to clean out workspace on
        success.

    commit 968568f682bac7564095440bdb7813abefd76821
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 26 13:27:19 2024 -0400

        Activate snow DA test on WCOSS (#2720)

        Activate the snow DA test on WCOSS.

    commit 7706760bb8adbdf78cb640b02739023c886e7699
    Author: Rahul Mahajan <[email protected]>
    Date:   Wed Jun 26 10:02:22 2024 -0400

        Cleanup of stale RUNDIRS from an experiment (#2719)

        This PR:
        - removes stale temporary scratch run directories from `$DATAROOT/`
        every 3 days.
        - should help to scrub failed attempts.
        - removes an unused variable `RUNDIR` defined in `config.base`

    commit 8962991691b5f0857b813bddfd28aa1034d4bd2b
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jun 26 09:43:48 2024 -0400

        Update logic for MOM6 number of layers/exception values (#2681)

        Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine
        how many layers and sets the exception value for MOM6 to be 1e-34 for
        all scenarios. Note, we will no longer have zeros in the ocean grib
        output and the DA will also run without issues.

        Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615

    commit 12431f76bdce807067929415007592cffc8a2457
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Wed Jun 26 07:42:35 2024 -0600

        Update wave jobs to use COMIN/COMOUT (#2643)

        NCO has requested that each COM variable specify whether it is an input
        or an output.
        This completes that process for the global-workflow wave
        model and products tasks.
        Refs #2451

    commit b902c0bac126c323a07186ad8881384b032b6fda
    Author: David Huber <[email protected]>
    Date:   Tue Jun 25 07:48:46 2024 -0400

        Assign machine- and RUN-specific resources (#2672)

        Redefine resource variables based explicitly on RUN or CDUMP

        Additionally, machine-specific resources are moved out of
        config.resources and placed in respective config.resources.{machine}
        files.

        Resolves #177 #2672

    commit 5edbd123e2878a07f5cce8e3c7ea6147f286633a
    Merge: 09333c01d 4e1b937b6
    Author: Janet Derrico <[email protected]>
    Date:   Mon Jun 24 12:44:05 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit 4e1b937b67ed220120e81925c4507f03b9b8965f
    Author: David Huber <[email protected]>
    Date:   Mon Jun 24 10:50:52 2024 -0400

        Add minimum software requirements (#2712)

        Adds a table to HPC documentation stating the minimum support versions

    commit f43a86276aaef91efa28faadc71a3cf50e749efe
    Author: David Huber <[email protected]>
    Date:   Fri Jun 21 13:44:29 2024 -0400

        Fix and simplify online archiving and reenable METplus jobs (#2687)

        This fixes the online archiving portion of the `*arch` and `*earc00`
        jobs, a prerequisite for running METplus.  This also reenables
        METplus by default.

        The approach previously taken created `FileHandler` dictionaries at
        varying levels within the resulting yaml, which was not properly parsed
        by `exglobal_archive.py`. This approach creates a single `FileHandler`
        dictionary and is much less complicated overall.

        Resolves #2673 #2647

    commit 8993b42cb91144c0ab0501dc7841ea8d675c4701
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 19 21:51:22 2024 -0400

        Eliminate post groups (#2667)

        Eliminates the post groups used for upp and products jobs so that each
        task only processes one forecast hour. This is more efficient and
        greatly simplifies downstream dependencies that depend on a specific
        forecast hour.

        Resolves #2666
        Refs #2642

    commit 0b810c888239853fedd0e4584fe62536c6aaacdf
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 18 20:32:48 2024 -0600

        Removes misleading "No such file or directory" syntax errors from output files (#2688)

        This PR addresses issue #1252. The following is accomplished:

        - Prior to removing files, the existence of a file is checked prior to
        attempting to remove; this is performed as noted
        [here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369);
        this PR only addresses the the `chgrp` issue.

        Refs #1252

        ---------

        Co-authored-by: David Huber <[email protected]>

    commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 18 12:17:59 2024 -0600

        Hotfix for bug in template names. (#2697)

        This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/`
        template.
        Resolves #2696
        Refs #2451

    commit 35d4d99eaac669721add9ddcc793153e5ab3b30a
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 18 08:06:53 2024 -0600

        Update archive job to use COMIN/COMOUT (#2668)

        NCO has requested that each COM variable specify whether it is an input
        or an output. This completes that process for the global-workflow
        archive task.

        Refs #2451
        ---------

        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>
        Co-authored-by: David Huber <[email protected]>

    commit 47b3a581c8257fa24411fb400df8bb0e1e04972a
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jun 17 22:55:38 2024 -0400

        Turn on high-frequency output in extended test (#2679)

        Turns on high-frequency (hourly) output in the extended products test to
        exercise that aspect of the code. This test only runs on WCOSS.

        Also adds the hooks to optionally turn on the metplus jobs, but that is
        deferred as they are not currently working correctly.

    commit 38f2df9fb0c074b1f80d3c637080be79be693161
    Author: David Huber <[email protected]>
    Date:   Mon Jun 17 17:12:55 2024 +0000

        Optimize wavepostpnt (#2657)

        Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs

        This is done by
        1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by
        - performing operations on all files at once instead of looping over
        each file
            - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`)
            - combining `sed` and `grep` calls when possible
            - adding logic to `awk` calls instead of handling that logic in bash
        2) minimizing as much as possible the amount of data on disk that has to
        be read in (e.g. limiting sed to read only the line numbers it needs)
        ---------

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

    commit 5af325a6a4e0a14d180514a418603ca79fada487
    Author: Dan Holdaway <[email protected]>
    Date:   Fri Jun 14 18:05:23 2024 -0400

        Update GDASapp hash to move JCB into GDASapp (#2665)

        This PR moves JCB into GDASapp. The PR
        also bumps up the hash of GDASapp to what is in `feature/move_jcb`,
        which at time of writing is develop plus the absorption of JCB into
        GDASapp.
        Note that I also took the changes from
        https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the
        testing @RussTreadon-NOAA has done.

    commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b
    Author: Yaping Wang <[email protected]>
    Date:   Fri Jun 14 10:18:17 2024 -0500

        Add observation preparation job for aerosols DA to workflow (#2624)

        Add a prepaeroobs job to prepare aerosol obs files for DA.

        This job does quality control of the VIIRS aerosol raw observations and
        convert them to ioda format.

        Resolves #2623
        ---------

        Co-authored-by: ypwang19 <[email protected]>
        Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>
        Co-authored-by: Cory Martin <[email protected]>
        Co-authored-by: David Huber <[email protected]>

    commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4
    Author: Jessica Meixner <[email protected]>
    Date:   Fri Jun 14 11:04:41 2024 -0400

        Remove ocean daily files (#2689)

        This PR removes the ocn_daily files that are produced by the ocean
        component. These files can be recreated by averaging data that exists in
        the 6 hour aveaged files if needed.

        Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675
        Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by
        removing them and making this obsolete)

    commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu Jun 13 12:22:03 2024 -0400

        Update Jenkinsfile

        needed a comma

    commit dc21eac6c3941d7f30803891d91d82f4cc1f8183
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu Jun 13 11:41:14 2024 -0400

        Add Hercules-EMC to the Jenkins configurable parameter list (#2685)

        This quick-fix PR is to update the Jenkins Pipeline's configurable
        parameter list to include the **Hercules-EMC** node.
        This allows Jenkins users to restart Jobs in the controller when no
        updates have been made.

    commit ebacebfbe458634b8c80af6a735d6b6d01e4e406
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Thu Jun 13 11:20:24 2024 -0400

        Update gdas.cd and gsi_utils hashes (#2641)

        This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The
        updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea
        build for gsi_utils.

        Resolves #2640

    commit 34155fb4767769600a1ff95f0a65e37081addc2a
    Author: Neil Barton <[email protected]>
    Date:   Thu Jun 13 11:18:22 2024 -0400

        Add ability to use GEFS replay ICs (#2559)

        The PR allows the use of ICs from PSL's replay analysis. These replay
        ICs will be used for GEFS reforecasting and SFS. Two main changes are
        associated with these updates: (1) replay ICs being valid at 3Z, and (2)
        the use of warm starts.

        Resolves #1838

        ---------

        Co-authored-by: Jessica Meixner <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>

    commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Wed Jun 12 19:25:42 2024 -0600

        Replace `sleep` with `wait_for_file` (#2586)

        This PR addresses issue #2444. The following is accomplished:

        - All `sleep` statements are replaced with `wait_for_file` for the
        relevant scripts beneath `scripts` and `ush`;
        - Indentation and shell-norms are updated where applicable.

        Note: The WAFS scripts are not updated as per @aerorahul direction.

        Resolves #2444

        ---------

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

    commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 12 13:31:55 2024 -0400

        Add COM template for JEDI obs (#2678)

        Adds a COM template to define a path to store obs processed for JEDI.
        This will allow UFSDA to stop writing to COM_OBS, which should be
        read-only as it belongs to obsproc in operations.

        No functional change yet.

    commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed
    Author: Guoqing Ge <[email protected]>
    Date:   Wed Jun 12 09:06:23 2024 -0600

        Link both global-nest fix files and non-nest ones at the same time (#2632)

        This PR enables linking both global-nest fix files and non-nest ones at
        the same time and users can run both nesting and non-nesting experiments
        at the same time without worries about what fix files to be linked.

        Resolves #2631

    commit 61de004d4f9e9edf8a31bb173f2719b46451a36a
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jun 12 11:03:13 2024 -0400

        Update ufs-weather-model  (#2663)

        Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack
        allowing some temporary fixes to be reverted.
        * removes upp submodule
        * uses upp from the ufs-weather-model
        * restores the build and link that were hacked during the Hera Rocky 8
        transition to allow for UPP submodule
        * Removes forecast directories in clean-up

        Resolves #2617
        Resolves #2437

        ---------

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

    commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d
    Author: Eric Sinsky - NOAA <[email protected]>
    Date:   Wed Jun 12 01:15:37 2024 -0400

        Add ability to process ocean/ice products specific to GEFS (#2561)

        This PR begins to add the capability to produce GEFSv13 ocean and ice
        products in the global-workflow according to stakeholder requirements.
        The following features are added.

        - An oceanice prod yaml file has been added to address the ocean and ice
        products specific to GEFSv13.
        - The rocoto dependencies and config.base for GEFS have also been
        modified to allow for 24-hour averaged ocean and ice output.
        - Various scripts have been modified to allow for ocean and ice output
        frequencies of 24 hours.
        - `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN`
        and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`.

        Refs #1878

    commit 6691e7489650e0b738c176fbd096109288dc09b6
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 11 21:15:07 2024 -0600

        Update cleanup job to use COMIN/COMOUT (#2649)

        NCO has requested that each COM variable specify whether it is an input
        or an output. This completes that process for the global-workflow
        clean-up task.

        Refs #2451

        ---------

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

    commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Tue Jun 11 16:17:25 2024 -0400

        Add overwrite to creat experiment in BASH CI (#2676)

        This is a quick hotfix to the CI BASH driver script adding `--overwrite`
        to create experiment script to avoid errors from restarting an
        experiment.

    commit e7909af8d9e1f34140388a3f8556d8e582c58fe5
    Author: emilyhcliu <[email protected]>
    Date:   Mon Jun 10 15:11:27 2024 -0400

        Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py  (#2645)

        This PR proposes updates for the following two scripts:

        1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select
        CRTM cloud optical table based on cloud microphysical scheme indicated
        by `imp_physics'
        The default scheme in the GFS forecast model is Thompson scheme
        (imp_physics = 8).

        2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in
        the script due to increased variables to interplate increments and
        calculate analysis in the netcdf_io routines in GSI-utils.
        Here is the related [PR #46 for
        GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46).

        ---------

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

    commit 9caa51de8fb7be07d2e61775da01937d576964f6
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Thu Jun 6 22:15:23 2024 -0600

        Update RDHPCS Hera resource for `eupd` task (#2636)

        As per @wx20jjung, the resource for the `eupd` task have been updated
        for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job
        fails.

        Resolves #2454

        ---------

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

    commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b
    Author: DavidNew-NOAA <[email protected]>
    Date:   Thu Jun 6 11:49:03 2024 -0400

        Parameterize some things in config.atmanl and config.atmensanl (#2661)

        This PR adds some parameters in config.atmanl and config.atmensanl that
        can be altered with the defaults.yaml. The motivation is to make these
        files match those in the GDASApp JJOB tests (example:
        https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl),
        so we can just use the Global Workflow config.atmanl and
        config.atmensanl in the tests rather than custom ones in GDASApp that
        have to be separately updated every time the ones in the Global Workflow
        are updated.

    commit 54ea0b73a07921be5fbb07fe41e976888bd3e549
    Author: Guillaume Vernieres <[email protected]>
    Date:   Thu Jun 6 01:36:02 2024 -0400

        Add links to the ocean insitu obs processing tools (#2644)

        Add links to the marine bufr to ioda converters for the marine insitu
        observations.

        - fixes https://github.com/NOAA-EMC/GDASApp/issues/1106
        - waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135

    commit 205d0c2b13e2d7755cec75bf8c978ab20d453862
    Author: David Huber <[email protected]>
    Date:   Wed Jun 5 17:31:30 2024 +0000

        Update S4 point of contact in docs (#2660)

        Update the point of contact for global workflow issues on S4.

    commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Wed Jun 5 12:50:14 2024 -0400

        Enable wcoss2 ufsda build and module load (#2620)

        This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2.

        Resolves #2602
        Resolves #2579

    commit 67b833e0c7bc390865d453588b4609a1a7ede981
    Author: Jessica Meixner <[email protected]>
    Date:   Tue Jun 4 13:33:43 2024 -0400

        Update ufs-weather-model  (#2646)

        Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6
        This should resolve the issue and allow C768 runs on Hera and allow for CICE
        to run on WCOSS2 (due to library updates to allow linking).

        From what I can tell, all updates needed were done by
        @HenryWinterbottom-NOAA which were updates for CICE

        Fixes #2490

    commit c44d0ac86cfdf78eb87492431bf6d825e8bae637
    Author: GwenChen-NOAA <[email protected]>
    Date:   Tue Jun 4 10:29:49 2024 -0400

        Update wmo parm files to fix WMO header (#2652)

        This PR updates wmo parm files to switch WMO header of precipitation
        type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to
        instantaneous.

        Resolves #2566

    commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60
    Author: Cory Martin <[email protected]>
    Date:   Tue Jun 4 13:55:33 2024 +0000

        Add IAU to snow DA (and its test) (#2610)

        This PR enables IAU for the snow DA which is necessary for GFSv17.

        A snow analysis is created for the center of the window regardless, and
        an additional at the beginning of the window is added if IAU is on. The
        former is needed for UPP and the latter, to initialize the model.

        The increment is valid throughout the window for 3DVar, so the same
        increment is added to both forecasts.

        Additionally, the input file that goes into global_cycle has been
        updated to be the output of the JEDI snow analysis instead of the
        forecast (@jiaruidong2017 I recall discussing this, can you confirm this
        is right or am I mistaken)

        This PR also makes the CI test for snow DA (and aerosol DA) include IAU
        rather than without IAU,.

        ---------

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

    commit c92bf415060750127c9c05a62a1d2851c489551a
    Author: David Huber <[email protected]>
    Date:   Sat Jun 1 05:11:07 2024 +0000

        Archiving cleanup (#2621)

        1) Adds a lot of comments to the jinja templates for archiving
        2) Rearranges the gdas and enkf templates to a more logical order
        3) Fixes a couple of bugs in the enkf archiving of increments and
        analyses
        4) Disables archiving for the half cycle
        5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`,
        instead relying on `DO_FIT2OBS`
        6) Updates wxflow to add the option to not allow undefined variables
        when parsing jinja templates and invokes this feature when running
        archives

        Resolves #2612

    commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri May 31 04:57:08 2024 -0400

        Switch to Rocky 9 built external packages on Hercules (#2608)

        The workflow was updated to use modules built on Rocky 9, but the
        external packages (like prepobs) were still pointing to the versions
        built on CentOS (Orion). This transitions to packages built on Rocky 9.

        Updating of the tracker package has been deferred until later. As such,
        the tracker jobs have been disabled by returning immediately if they are
        on Hercules. Since these jobs are small, resource-wise, it should not
        meaningfully impact turnover time.

    commit 4422550c01c9214a2b3b8890bdcc898123ee216a
    Author: Guoqing Ge <[email protected]>
    Date:   Thu May 30 08:05:23 2024 -0600

        Add the capability to use slurm reservation nodes (#2627)

        Add the capability to use slurm reservation nodes
        Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE

        Resolves #2626

    commit a54153fd9d26126206bc07a1da4e80f50c0c5910
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed May 29 23:24:07 2024 -0400

        Update forecast job to use COMIN/COMOUT (#2622)

        NCO has requested that each COM variable specify whether it is an input
        or an output. This completes that process for the forecast job.

        Refs #2451

        ---------

        Co-authored-by: David Huber <[email protected]>

    commit d69a8af95d492982b918670322ed5c41ab074335
    Author: Jessica Meixner <[email protected]>
    Date:   Wed May 29 21:29:03 2024 -0400

        Update to add 1-deg global wave grid (#2619)

        This PR adds options to use a global 1 deg grid, intended for testing
        with the SFS application.

        Requires new fix file changes NOAA-EMC/global-workflow#2618

    commit 0b4670ecf83b99b72835c8380573b2bca7cf5324
    Author: Jessica Meixner <[email protected]>
    Date:   Wed May 29 17:17:21 2024 -0400

        Add C384mx025_3DVarAOWCDA yamls (#2625)

        Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder.

    commit 2e885d05c64b947f00a3cf055a1277fbfac195c9
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed May 29 13:00:51 2024 -0400

        Script to keep Jenkins Agent persistent from cron (#2634)

        This "persistent" Java Agent launch script can be ran from a cron job:

        - Uses Jenkins Remote API to check the status of the Node connection
        using curl for a given machine.
        - If it is not connected a new agent is launched for that node.

        Resolves #2633

    commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5
    Author: GwenChen-NOAA <[email protected]>
    Date:   Tue May 28 17:17:11 2024 -0400

        Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611)

        Based on users' feedback, this PR do the following:
        1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF
        2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD,
          and VOGRD) from "%g m below water surface" to "%g m below sea level"
        3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m)

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

    commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31
    Author: DavidNew-NOAA <[email protected]>
    Date:   Tue May 28 17:16:23 2024 -0400

        Add atmensanlfv3inc job (#2592)

        This PR creates the atmensanlfv3inc job, the ensemble version of
        atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is
        #[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS
        companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3).

    commit 50c2b8951b29a3c883a778becbf8582f9519eb48
    Author: Anil Kumar <[email protected]>
    Date:   Tue May 28 13:23:53 2024 -0400

        Global-workflow (AR) Generic updates for Gaea C5 (#2515)

        - Port global-workflow’s build and run capability to Gaea-C5
        - Building global-workflow on Gaea-C5
        - Setting up experiments with global-workflow on Gaea-C5

        ---------

        Co-authored-by: AnilKumar-NOAA <[email protected]>
        Co-authored-by: DavidBurrows-NCO <[email protected]>

    commit b6ca771a0c584cbfcbbf9be739765d5f3815df97
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri May 24 10:52:45 2024 -0400

        Update STMP and PTMP settings in host file for Orion and Hercules  (#2614)

        - Updating STMP and PTMP settings in host file for Orion and Hercules
        because they are cross mounted.
        - Also took the opportunity to finally update **SLURM_ACCOUNT** to
        **HPC_ACCOUT** in CI over rides.
        - Added a refactor of the `rocotostat.py` tool that is more pythonic and
        as a execute retry feature because the `rocotostat` utility on Orion has
        been failing sometimes.

    commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f
    Author: Guillaume Vernieres <[email protected]>
    Date:   Tue May 21 23:50:50 2024 -0400

        Sea-ice analysis insertion (#2584)

        Allows cycling and restarting CICE with the sea-ice analysis if the
        marine DA is switched on.

        Resolves #2568
        Resolves NOAA-EMC/GDASApp#1103

    commit 5369a1ff3a3969149fcf32810fad0e50216752b7
    Author: David Huber <[email protected]>
    Date:   Tue May 21 22:12:29 2024 +0000

        Refactored archiving (#2491)

        This provides a new pygfs task, archive.py, that provides all of the
        tools necessary to archive data to the local (`ARCDIR`) and backup
        (`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to
        define the file to be archived or tarred to replace the
        `hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts
        and make it easier to add new data and explicitly handle optional and
        required files.

        For `ATARDIR` archiving, a master jinja template is provided for each
        `RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2,
        master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both
        `enkfgdas` and `enkfgfs` `RUN`s. These templates then include the
        appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on
        experiment, cycle, and coupled parameters. Each of these templates
        corresponds to a single tarball to populate and are tabbed 4 spaces so
        they are defined within the master `datasets` dictionary.

        Future developers should not have to make modifications to archive.py
        unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then
        only a single `elif` needs to be added to the configure method to
        specify the master `ATARDIR` template to archive (e.g.
        `master_gefs.yaml.j2`). If a new component is coming online that needs
        to be archived to `ATARDIR` (e.g. SNOW), then create a new template for
        each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`)
        and reference the template in the appropriate master templates, e.g.

        `master_gdas.yaml:`
        ```jinja
        {% if DO_SNOW %}
        {% include "gdassnow.yaml.j2" %}
        {% endif %}
        ```

        A few other issues were addressed along the way:
        1. Aerosols have been reenabled. Aerosol forecasts should only be
        performed during gdas cycles, but analyses can be performed for both gfs
        and gdas cycles. This was accomplished by setting separate
        `AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs.
        2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`.
        This prevented restarts from being used for cice-enable experiments.
        This feature was not tested.
        3. Create a temporary fix for the `wgrib` utility. For spack-stack
        1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is
        open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in
        existing installations. Once complete, this temporary fix should be
        removed.
        4. The number of `earc` jobs has been reduced for lower resolution
        experiments. Both C48 and C96 experiments will now only have two earc
        jobs (one for the non-member files to archive and another for the member
        files). C192 will have up to 3 earc jobs (one non-member, one for
        members 1-40 and another for members 41-80, if needed).

        Resolves #2345
        Resolves #2318

        ---------

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

    commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri May 17 12:57:59 2024 -0400

         Add remove RUNDIRS step in CI before creating experements (#2607)

        As had been done in Bash CI we need to remove the RUNDIR in Jenkins
        before a creating an experiment in the event that case had beem
        previously ran.

    commit 09333c01dbafddb2d2fe7e181b479af3cc6d3621
    Merge: f7e9f4489 bb930050b
    Author: Janet Derrico <[email protected]>
    Date:   Thu May 16 14:33:19 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit bb930050b3cd51d28ecba6b231c8675f6d11856c
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Thu May 16 12:28:30 2024 -0400

        Adds jjob and other necessities for marine LETKF task (#2564)

        Adds jjob, rocoto script, config file, and other necessities for new
        marine LETKF task.

        Partially addresses NOAA-EMC/GDASApp#1091

    commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu May 16 12:12:06 2024 -0400

        Updating CI Machine configs with redundant PTMP (#2605)

        Quick fix adding PTMP as STMP in Machine configs for CI for completeness

    commit ef340ff33a6f89adf70838206ba3fd56a953fa7a
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu May 16 11:37:30 2024 -0400

        Fix race condition in CI between Orion and Hercules (#2604)

        Hotfix to solve race conditions in the CI system due to cross-mounted
        file systems between Orion and Hercules

    commit e8b17e27f719df280170dc3f5bd9f19917cefaf2
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed May 15 17:16:30 2024 -0400

        Remove existing EXPDIRs and COMROTs when CI is re-run (#2601)

        Quick hotfix for having default for re-runing jobs to start clean with
        new EXPDIRs and COMROTs

    commit b5d113efb1970ede5cd1d3d4dff8d96320519c41
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed May 15 16:52:49 2024 -0400

        Moving logic for skipping hosts in pr cases (#2573)

        This PR removes the logic of skipping hosts for pr cases from
        `create_experiment.py` and moves it to a test in the cron bash driver
        using a `parse_yaml.py` python tool.

        The Jenkins pipeline was not effected as it uses the
        `get_host_case_list.py` utility to form the cases on a per host bases.

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

    commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Wed May 15 13:13:30 2024 -0400

        Update gsi_utils.fd hash (#2598)

        This PR updates the `gsi_utils.fd` hash to bring in updates which add
        safeguards to
        -
        `src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90`
        - `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90`

        The safeguards are described in GSI-utils PR
        [#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated
        issue.

        Resolves #2597

    commit d5366c66bd67f89d118b18956fe230207cbf0aea
    Author: Kate Friedman <[email protected]>
    Date:   Wed May 15 13:12:56 2024 -0400

        Update CICE and MOM6 fix versions (#2600)

        This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions
        to the newer `20240416` timestamps, which includes updates and fixes to
        the `100` (1-deg) resolution files.

        Resolves #2480
        Resolves #2483
        Resolves #2595

    commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b
    Author: David Huber <[email protected]>
    Date:   Mon May 13 22:57:38 2024 +0000

        Limit gfswavepostpnt to 40 PEs/node (#2588)

        This fixes the slow runtime of the gfswavepostpnt job on Hercules. The
        job is very I/O intensive and does not scale well to large nodes, so
        limit the number of jobs/node to 40.

        Resolves #2587

    commit 4fb7c12c325702a47f27c802a5067efd33d0327c
    Author: Fanglin Yang <[email protected]>
    Date:   Mon May 13 16:37:51 2024 -0400

        Update damping and time-step (#2575)

        Updates the model to use explicit Rayleigh damping for u/v and implicit
        damping to w. This improves model stability and allows for longer
        timesteps. Also unifies the GDAS and GFS to use the same damping.

        Results from a test at the C1152 resolution (coupled model) can be found
        at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/

        Resolves #2574

        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
        Co-authored-by: Lisa Bengtsson <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>

    commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri May 10 14:17:13 2024 -0400

        Do not use BUILT_semphore to force rebuilds when re-run (#2593)

        Remove the placement of the `BUILT_semaphore` file after the build in
        the Jenkins Pipeline and force it to rebuild any changes after a PR is
        re-ran.

    commit 2346c6161f75ae02369cbf30f30c6150d3e12b66
    Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com>
    Date:   Thu May 9 21:17:06 2024 -0500

        Migration to Rocky8 spack-stack installations on Jet (#2458)

        # Description
        Migrates Global Workflow to Rocky8 spack-stack installations on Jet.
        Jet has moved from CentOS7 to Rocky8.

        Resolves #2377
        Refs NOAA-EMC/UPP#919
        Refs NOAA-EMC/gfs-utils#60
        Refs NOAA-EMC/GSI#732
        Refs NOAA-EMC/GSI-Monitor#130
        Refs NOAA-EMC/GSI-utils#33

    commit c7b3973014480a20dd8e24edaeb83a9e9e68159f
    Author: Jessica Meixner <[email protected]>
    Date:   Thu May 9 11:36:58 2024 -0400

        Updates for cold start half cycle, then continuing with IAU for WCDA (#2560)

        This PR allows us to run C384 S2S with IAU, but starting with the first
        half-cycle as a cold-start. This will be necessary for cycled testing as
        we build towards the full system for GFSv17. This updates the copying of
        the restarts for RUN=gdas for both ocean and ice copying what the atm
        model is doing. It also reduced the amount of restart files from 4 to 3.

        Other updates:
        * Add DOJEDI ocean triggers for archiving certain files update from:
        @CatherineThomas-NOAA
        * Adds COPY_FINAL_RESTARTS option to turn on/off copying the last
        restart file to COM. Defaults to off...
        * Defines model_start_date_current_cycle & model_start_date_next_cycle
        to help with knowing which IC to grab.

        Refs #2546

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

    commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2
    Author: Dan Holdaway <[email protected]>
    Date:   Wed May 8 20:52:48 2024 -0400

        Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477)

        Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI
        Configuration Builder (JCB) tool so that YAMLs can be made more portable
        and invoke the observation chronicle mechanism.

        Resolves #2476

        Co-authored-by: danholdaway <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

    commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed May 8 02:04:16 2024 -0400

        Add CI test for products (#2567)

        Adds a new version of the atm3DVar test that runs the full forecast
        length and produces most of the secondary products. For now, this test
        will only run on WCOSS due to gempak failures on other machines as well
        as computational needs. On other machines, the original version will run
        (the original version will not run on WCOSS). AWIPS remains off for now
        in this extended test due to a bug involving tocgrib2 and the convective
        precip fields (see #2566).

        The new test runs for 4½ cycles and the full 384-hr forecast length to
        ensure all gempak scripts are exercised. Since the cycle throttle is 3
        and the bulk of the time is in the free forecast, the cycles run mostly
        concurrently so it doesn't extend the total test time too much beyond
        that of a single 384-hr forecast.

        Fixes a bug in NPOESS that was introduced when the post filenames were
        reverted to the previous format for the GOES products until the final
        filenames are determined (#2499).

        Also removes the AWIPS g2 job from the rocoto mesh to complete the
        retirement of grib1 products.

        Resolves #2132
        Resolves #2445

    commit 9b6f8404ac4507d14adc404b77cfdf002b55e832
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue May 7 00:14:36 2024 -0400

        Add task to prepare emissions for GEFS (#2562)

        This PR:
        - introduces a task to prepare emissions for a forecast into the GEFS
        application.
        - adds configuration, j-job, rocoto job, ex-script and the python class
        for this job
        - updates GEFS workflow to be able to generate the XML to call this job.
        - updates the `fcst` and `efcs` job dependencies in the GEFS application
        to depend on `prep_emissions` if aerosols are turned ON.
        - provides a placeholder for @bbakernoaa to work on the details for
        preparing emissions.

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

    commit 233c18815d2e8e6b344f161fd0c102a4fbdfb66d
    Author: Dan Holdaway <[email protected]>
    Date:   Mon May 6 18:11:35 2024 -0400

        Single Executable for main GDAS JEDI applications (#2565)

        Changes that accompany GDAS PR (NOAA-EMC/GDASApp/pull/1075) that a…
kayeekayee added a commit to kayeekayee/global-workflow that referenced this issue Sep 26, 2024
@kayeekayee
Update develop branch, gsl_ufs_dev
d69c379 
Squashed commit of the following:

commit 4ad0d52a6fbb581a9804bd0bb627b7c52f338bad
Author: kayee.wong <[email protected]>
Date:   Thu Sep 19 19:20:06 2024 +0000

    For pygraf plotting.

commit 1bfba70ed6aaa3eb47974006ed0c5cae653b8ce8
Author: kayee.wong <[email protected]>
Date:   Thu Sep 19 04:27:55 2024 +0000

    Fixed gfsatmprod file name and gfsarch data type.

commit 4e0a81f7acf5ccba5de8d3bdf7ab19cae80812cb
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 18:37:50 2024 +0000

    Fix typos/links/dependancy.

commit d5fdcbf8d6e987dbdfcd6b4da34d0934c8d82c3b
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 07:37:52 2024 +0000

    Fixed missing config.base files.

commit c6239f925369b20fd8488e8537969e2f4f9e7725
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 06:53:47 2024 +0000

    Update submodule hashs.

commit 32bf790f67b818ff50a7f6b74388fb81ed175b3a
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 06:09:41 2024 +0000

    Update develop branch, gsl_ufs_dev
     - based on gsl_ufs_dev from KaYee's fork
       global-workflow: 07Aug24,37c53ac [develop_07Aug2024_37c53ac]
       UFS: 19Jul24, c127601
       FV3: 19Jul24, 2527c11
       UPP: 23Apr24, be0410e
       CCPP-PHYSICS: 19Jul24, 46df080
       UFS_UTILS: 26Jun24, 3ef2e6b

    Squashed commit of the following:

    commit 70b557836379bb7e545fcc6642e28d66cfc17735
    Merge: 5edbd123e 37c53ac69
    Author: Janet Derrico <[email protected]>
    Date:   Wed Aug 7 11:02:24 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04
    Author: Kate Friedman <[email protected]>
    Date:   Wed Aug 7 08:11:21 2024 -0400

        Revert MSU FIX_DIRs back to glopara (#2811)

    commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Tue Aug 6 14:47:36 2024 -0400

        Bugfix for updating label states in Jenkins (#2808)

        Quick bug fix for updating state labels in CI during finalize.
        (did not reference GitHub CLI executable correctly in the pipeline
        script)

    commit 8fee36f0307b0c08080e3a8fa8fa6703e7da5fce
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Aug 6 11:02:45 2024 -0400

        Clean-up temporary rundirs - take 2. (#2753)

        This PR:
        - is a follow-up to a previous PR that aggressively pruned run
        directories.
        - removes run directories for the current cycle in the clean-up if the
        cycle is successful. If the cycle is not successful, cleanup is not
        called and all run directories for the cycle are safe from being purged.
        - also updates the PR template to list/query for any updates to
        submodules.

        ---------

        Co-authored-by: David Huber <[email protected]>
        Co-authored-by: David Huber <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

    commit d599fff4aedd41ae587dbe02226acb12ff48efc1
    Author: HelinWei-NOAA <[email protected]>
    Date:   Mon Aug 5 05:31:31 2024 -0400

        Change land surface for HR4 (#2787)

        Resets the default value of opt_diag to 2 corresponding to the land
        surface upgrades in ufs-weather-model for HR4.

        Resolves #2786

    commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb
    Author: David Huber <[email protected]>
    Date:   Fri Aug 2 15:41:29 2024 -0400

        Run METplus serially and correct the name of prod tasks (#2804)

        Adds 2 hot fixes:

        - METplus v9.1.3 has a bug in it that sometimes attempts to create
        multiple copies of the same directory when running in parallel, causing
        a Python error and downstream problems. This PR makes METplus run in
        serial mode, preventing such issues.
        - Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in
        workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod)

    commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri Aug 2 15:03:45 2024 -0400

        Update Java Agent launching script for Jenkins connections (#2762)

        Made updates to the Jenkins Launching Script for robustness and less
        ambiguous documentation:
        - Clearer distinction between required user token for the remote api and
        the systems token for launching
        - Added pre-checks: `gh` is authenticating, named compliant token and
        secret file exists
        - More robust Jason based parser of the remote api response for checking
        the state of the Node connection
        - For `cron` use a 5 minute pause and recheck was added before
        re-launching of the java agent
        - Added concise header documentation of requirements and purpose
        ---------

        Co-authored-by: David Huber <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

    commit b73b1fd203496db97f8067652659573a632bcc67
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri Aug 2 07:59:06 2024 -0400

        Fix erroneous cdump addition (#2803)

    commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3
    Author: Rahul Mahajan <[email protected]>
    Date:   Thu Aug 1 20:26:13 2024 -0400

        Update ocean post-processing triggers (#2784)

        This PR:
        - replaces `check_netcdf.sh` checker for ocean post-processing with with
        ocean output at the next forecast hour or finishing of the forecast job
        for ocean prod
        - removes no longer needed `ush/check_netcdf.sh`

    commit aa2af1ca8d59424a60a1730722bf528775d9e606
    Author: GeorgeGayno-NOAA <[email protected]>
    Date:   Thu Aug 1 16:46:10 2024 -0400

        Update the gfs_utils repository hash (#2801)

        # Description
        Point to the latest hash of the gfs-utils repository, which contains the
        bug fix to gaussian_sfcanl.

        Resolves #2669.
        Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73

    commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8
    Author: David Huber <[email protected]>
    Date:   Thu Aug 1 08:12:14 2024 -0400

        Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791)

        Changes how METplus jobs run so that they run on the last GFS cycle for
        a given `PDY`.

        This is a departure from operations where the METplus jobs run on the
        00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through
        `${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on
        `${PDY}18` for cycles 00-18. See
        https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details.

    commit 1cf8b448af562dbb7af198399c78c585977e81da
    Author: David Huber <[email protected]>
    Date:   Tue Jul 30 10:38:49 2024 -0400

        Simplify resource-related variables, remove CDUMP where unneeded (#2727)

        This overhauls resource-related variables to use a common set of
        variables for each job. In the process, this also removed the use of
        CDUMP in most cases.

        Resolves #1299 #2693

    commit 61875f25c9e971f82ae499b5b612d7f095deebd4
    Author: Eric Sinsky - NOAA <[email protected]>
    Date:   Mon Jul 29 14:40:03 2024 -0400

        Remove f000 from atmos rocoto tasks for replay cases (#2778)

        The main purpose of this PR is to remove the f000 from
        atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In
        cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater
        than `0`, it becomes necessary to have the first lead hour set to
        `OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For
        example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead
        time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and
        the minimum lead time for the ocean_prod rocoto task needs to be 6
        (assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up
        possible by removing 0 from fhrs for atmosphere-related tasks in
        `gefs_tasks.py` when replaying.

        This PR also moves where f000 is being removed for the ocean_prod and
        ice_prod tasks. The if-block that performs this f000 removal has been
        moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`.

        ---------

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

    commit f156a7894d639f177e3e2588f98eec1f6f59aa68
    Author: Jessica Meixner <[email protected]>
    Date:   Fri Jul 26 14:18:32 2024 -0500

        HR4 GWD update (#2732)

        This update is a combination of the gravity wave drag (GWD) versions
        from the NOAA/GSL and NOAA/PSL

    commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891
    Author: David Huber <[email protected]>
    Date:   Thu Jul 25 14:26:52 2024 -0400

        Temporarily disable METplus jobs (#2796)

    commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2
    Author: Guillaume Vernieres <[email protected]>
    Date:   Wed Jul 24 15:00:35 2024 -0400

        Refactoring of the marine B-matrix job (#2749)

        Refactor the functionality of B-matrix generation from the GDASApp

        Resolves #2743

    commit 65a7ab75dc0e4baba06a02e11ed0455787056a68
    Author: David Huber <[email protected]>
    Date:   Tue Jul 23 08:35:48 2024 -0400

        Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775)

        Removes the namespace-based construction of EnKF member COM directories
        in the enkf archive template.

    commit c45b9611f3e701b819bd33dc5af29033f060bb91
    Author: Eric Sinsky - NOAA <[email protected]>
    Date:   Tue Jul 23 00:33:16 2024 -0400

        Add task to process reforecast variables to save on WCOSS2 (#2680)

        # Description
        This PR adds an optional task to the global-workflow to process a subset
        of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for
        the GEFSv13 reforecast. This task is designed to process GEFS variables
        so that specific reforecast product requirements are met. A new variable
        in `config.base` called `DO_EXTRACTVARS` enables this task, which is
        currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by
        default and is specifically a task designed to be executed for the
        GEFSv13 reforecast.

        Refs #1878

        # Type of change
        - New feature (adds functionality)

        # Change characteristics
        - Is this a breaking change (a change in existing functionality)? NO
        - Does this change require a documentation update? NO

        # How has this been tested?
        This has been cloned and tested on WCOSS2. This will need to be tested
        on Hera and other platforms on which the reforecast may be running.

        # Checklist
        - [ ] Any dependent changes have been merged and published
        - [x] My code follows the style guidelines of this project
        - [x] I have performed a self-review of my own code
        - [ ] I have commented my code, particularly in hard-to-understand areas
        - [x] My changes generate no new warnings
        - [x] New and existing tests pass with my changes
        - [ ] I have made corresponding changes to the documentation if
        necessary

        ---------

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

    commit 71dc33c6ca991c16ce743760d99feaaf60f2218a
    Author: David Huber <[email protected]>
    Date:   Mon Jul 22 14:51:53 2024 -0400

        Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774)

        Fix metp* resources and check that they completed properly; add support for Orion Rocky 9

    commit 56df67a90fe090c425199f1285e5aac722c398b1
    Author: David Huber <[email protected]>
    Date:   Mon Jul 22 09:28:18 2024 -0400

        Hotfix: Update jcb to avoid git-lfs files (#2782)

        Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to
        be cloned on Hera.

        This hotfix points to a non-authoritative branch of the GDASApp
        (https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and
        should be updated ASAP back to the authoritative repository.

    commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jul 16 09:44:00 2024 -0400

        Address issues in creating XML for GFS forecast-only with app S2SWA (#2757)

        This bugfix PR:
        - fixes an issue where a user is unable to generate the XML for a GFS
        forecast-only experiment with APP=S2SWA

        Specifically, the changes are related to defining `aero_fcst_cdumps`.
        Following `setup_expt.py`, the user will have to set
        `AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in
        `config.base`.

    commit e0878dba0e53706a7f53429b61aee2936e2c21bf
    Author: Kate Friedman <[email protected]>
    Date:   Mon Jul 15 10:25:11 2024 -0400

        Updated prepobs and fit2obs versions for Orion Rocky9 (#2758)

        Update prepobs to v1.0.2 and fit2obs to v1.1.2

        These versions now support Orion Rocky9. Updates are included
        for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet.

    commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu Jul 11 17:48:47 2024 +0000

        CI maintenance updates and adding CI Unit Tests (#2740)

        This PR has a few maintenance updates to the CI pipeline and adds a test
        directory with Unit Tests
        **Major Maintenance updates:**
        - Added try blocks with appropriate messaging to GitHub PR of failure
        for:
        - - **scm** checkout
        - - build fail (with error logs sent as gists)
        - - create experiment fails with `stderr` sent to GitHub PR messaging
        - Pre-stage FAILS from the above are now captured these fails allow
        FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state
        labels in GitHub - see image below)
        **Minor Maintenance updates:**
        - Fix for STALLED cases reviled from PR 2700 (just needed a lambda
        specifier)
        - Fixed path to experiment directory in PR message (had dropped EXPDIR
        in path)
        - Needed `latin-1` decoder in reading log files for publishing
        **Added python Unit Tests for CI functionality:**
        - Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI
        utility codes
        - Cashed the install of Rocoto in the GitHub Runners to greatly reduce
        stetup time for running the unit tests
        - Unit Tests Python scripts added
        - `test_rocostat.py`: rocoto_statcount() rocoto_summary()
        rocoto_stalled()
          - `test_setup.py`: setup_expt() test_setup_xml()
          - `test_create_experment`: test_create_experiment()
          - - Runs all PR cases that do not have ICs in the GItHub Runner
        - Reporting mechanism in the Actions tab for Python Unit Testing results
        - Test case data for STALLED and RUNNING stored on S3 and pulled using
        wget during runtime of tests

    commit 5ef4db74649b8be03402c17aa29c024e71699a7b
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Thu Jul 11 08:59:24 2024 -0400

        Adds contents of constructor and initialize methods to marine LETKF class (#2635)

        Adds contents of constructor and initialize methods to marine LETKF class

        Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091
        ---------

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

    commit 8998ec7b74123e953b97a93fa14cc78d471a1aee
    Author: David Huber <[email protected]>
    Date:   Tue Jul 9 08:31:57 2024 -0400

        Fix GDAS group B restart archiving (#2735)

        Archives the GDAS restartb dataset at a 6-hour offset from restarta

        This allows cycled experiments to restart from the archives.
        The tabbing for the master archive templates was also added to
        improve readability.

        Resolves #2722

    commit 3ca74771255727033b9dc043c652ac585178629c
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Tue Jul 9 08:28:54 2024 -0400

        Add fcst dependency to ocnanalprep (#2728)

        Add previous cycle's `fcst` as a dependency to `ocnanalprep`

        This ensures that the availability of restart files to the latter. This addresses a
        seldomly-encountered race condition where `ocnanalprep` fails due to the
        lack of the files.

    commit 58fca1668aecd6fb1afd12a441256ad35900e075
    Author: Rahul Mahajan <[email protected]>
    Date:   Fri Jul 5 15:02:23 2024 -0400

        Update (partially) global-workflow for orion+rocky9 (#2741)

        This PR:
        - updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils,
        GFS-utils) to include recent update to their modulefiles for
        Orion+Rocky9 upgrade
        - updates the modulefiles in global-workflow to load modules from
        Orion+Rocky9 paths
        - updates modulefiles for `gwsetup` and `gwci` as well.
        - removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not
        installed.
        - adds `parm/config.gfs/config.resources.ORION` to address GSI
        performance degradation after Rocky 9 upgrade.

        This PR:
        - does not update the build for UPP. Standalone UPP is not available via
        ufs-weather-model as of #2729
        - will need a follow-up update for `prepobs` and `fit2obs` updated
        locations when they are installed in `glopara` space on Orion.

        # Type of change
        - Maintenance (code refactor, clean-up, new CI test, etc.)

        # Change characteristics
        - Is this a breaking change (a change in existing functionality)? NO
        - Does this change require a documentation update? NO

        # How has this been tested?
        This PR is not sufficient for Orion.
        This PR must be tested on other platforms (Hera, WCOSS2) as this PR
        updates submodules.

        # Checklist
        - [ ] Any dependent changes have been merged and published
        - [ ] My code follows the style guidelines of this project
        - [ ] I have performed a self-review of my own code
        - [ ] I have commented my code, particularly in hard-to-understand areas
        - [ ] My changes generate no new warnings
        - [ ] New and existing tests pass with my changes
        - [ ] I have made corresponding changes to the documentation if
        necessary

        ---------

        Co-authored-by: Kate Friedman <[email protected]>

    commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jul 3 21:07:49 2024 -0400

        Update ufs model hash to 20240625 (#2729)

        Updates UFS weather model hash to hash from 2024-06-24 which has orion
        porting updates + a few namelist updates.

    commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85
    Author: David Huber <[email protected]>
    Date:   Wed Jul 3 11:32:40 2024 -0400

        Hotfix for undefined CLUSTERS (#2748)

        Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses
        the native `dict` `get` method to prevent grabbing an unset entry.

    commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf
    Author: GwenChen-NOAA <[email protected]>
    Date:   Wed Jul 3 09:56:08 2024 -0400

        Update gempak job to run one fcst hour per task (#2671)

        This PR updates gempak jobs (gfs, gdas, and goes) from processing all
        forecast hours at once to one forecast hour at a time. This will reduce
        the job runtime to less than 5 min, so restart capability is not needed.

        Resolves #1250
        Ref #2666 #2667
        ---------

        Co-authored-by: Walter.Kolczynski <[email protected]>

    commit 8215ae654202186a4f753c3abe937b7b9b91a9c7
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jul 2 16:22:11 2024 -0400

        Hotfix for clusters from #2701 (#2747)

        Fixes an issue created from #2701 that added `CLUSTERS` to the
        `gaea.yaml`.

    commit 11943e36ba12b3df49c51942da780698fab02d38
    Author: DavidBurrows-NCO <[email protected]>
    Date:   Tue Jul 2 12:58:10 2024 -0400

        Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701)

        This PR sets up the ability on Gaea for auto generation of a clean xml
        file, i.e., an xml file that does not need any alterations before
        running rocoto.
        Refs #2572
        Refs #2664

    commit de8706702ead0630beb54d868f83aa2cb23f8f79
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Mon Jul 1 09:29:14 2024 -0400

        Update for JCB policies and stage DA job files with Jinja2-templates (#2700)

        This PR updates the `gdas.cd` hash to bring in new JCB conventions.
        Resolves #2699

        From #2654
        This PR will move much of the staging code that take place in the python
        initialization subroutines of the variational and ensemble DA jobs into
        Jinja2-templated YAML files to be passed into the wxflow file handler.
        Much of the staging has already been done this way, but this PR simply
        expands that strategy.

        The old Python routines that were doing this staging are now removed.
        This is part of a broader refactoring of the pygfs tasking.

        wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a
        companion to this PR.

        Co-authored-by: danholdaway <[email protected]>
        Co-authored-by: DavidNew-NOAA <[email protected]>
        Co-authored-by: DavidNew-NOAA <[email protected]>
        Co-authored-by: Dan Holdaway <[email protected]>

    commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b
    Author: Rahul Mahajan <[email protected]>
    Date:   Fri Jun 28 14:56:19 2024 -0400

        Revert PR 2681 (#2739)

        This PR:
        - reverts #2681 in part
        - keeps some changes for `RUN`.
        - is a hotfix
        - should be merged ASAP after consensus w/ @guillaumevernieres
        @CatherineThomas-NOAA @WalterKolczynski-NOAA

    commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed Jun 26 15:46:08 2024 -0400

        updated Finalize in Jenkinsfile and added try block around scm checkout (#2692)

        We are updating the Jenkins Pipeline with a try block around checkout to
        capture errors for the user.
        Also cleaned up Finalize and added section to clean out workspace on
        success.

    commit 968568f682bac7564095440bdb7813abefd76821
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 26 13:27:19 2024 -0400

        Activate snow DA test on WCOSS (#2720)

        Activate the snow DA test on WCOSS.

    commit 7706760bb8adbdf78cb640b02739023c886e7699
    Author: Rahul Mahajan <[email protected]>
    Date:   Wed Jun 26 10:02:22 2024 -0400

        Cleanup of stale RUNDIRS from an experiment (#2719)

        This PR:
        - removes stale temporary scratch run directories from `$DATAROOT/`
        every 3 days.
        - should help to scrub failed attempts.
        - removes an unused variable `RUNDIR` defined in `config.base`

    commit 8962991691b5f0857b813bddfd28aa1034d4bd2b
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jun 26 09:43:48 2024 -0400

        Update logic for MOM6 number of layers/exception values (#2681)

        Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine
        how many layers and sets the exception value for MOM6 to be 1e-34 for
        all scenarios. Note, we will no longer have zeros in the ocean grib
        output and the DA will also run without issues.

        Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615

    commit 12431f76bdce807067929415007592cffc8a2457
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Wed Jun 26 07:42:35 2024 -0600

        Update wave jobs to use COMIN/COMOUT (#2643)

        NCO has requested that each COM variable specify whether it is an input
        or an output.
        This completes that process for the global-workflow wave
        model and products tasks.
        Refs #2451

    commit b902c0bac126c323a07186ad8881384b032b6fda
    Author: David Huber <[email protected]>
    Date:   Tue Jun 25 07:48:46 2024 -0400

        Assign machine- and RUN-specific resources (#2672)

        Redefine resource variables based explicitly on RUN or CDUMP

        Additionally, machine-specific resources are moved out of
        config.resources and placed in respective config.resources.{machine}
        files.

        Resolves #177 #2672

    commit 5edbd123e2878a07f5cce8e3c7ea6147f286633a
    Merge: 09333c01d 4e1b937b6
    Author: Janet Derrico <[email protected]>
    Date:   Mon Jun 24 12:44:05 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit 4e1b937b67ed220120e81925c4507f03b9b8965f
    Author: David Huber <[email protected]>
    Date:   Mon Jun 24 10:50:52 2024 -0400

        Add minimum software requirements (#2712)

        Adds a table to HPC documentation stating the minimum support versions

    commit f43a86276aaef91efa28faadc71a3cf50e749efe
    Author: David Huber <[email protected]>
    Date:   Fri Jun 21 13:44:29 2024 -0400

        Fix and simplify online archiving and reenable METplus jobs (#2687)

        This fixes the online archiving portion of the `*arch` and `*earc00`
        jobs, a prerequisite for running METplus.  This also reenables
        METplus by default.

        The approach previously taken created `FileHandler` dictionaries at
        varying levels within the resulting yaml, which was not properly parsed
        by `exglobal_archive.py`. This approach creates a single `FileHandler`
        dictionary and is much less complicated overall.

        Resolves #2673 #2647

    commit 8993b42cb91144c0ab0501dc7841ea8d675c4701
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 19 21:51:22 2024 -0400

        Eliminate post groups (#2667)

        Eliminates the post groups used for upp and products jobs so that each
        task only processes one forecast hour. This is more efficient and
        greatly simplifies downstream dependencies that depend on a specific
        forecast hour.

        Resolves #2666
        Refs #2642

    commit 0b810c888239853fedd0e4584fe62536c6aaacdf
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 18 20:32:48 2024 -0600

        Removes misleading "No such file or directory" syntax errors from output files (#2688)

        This PR addresses issue #1252. The following is accomplished:

        - Prior to removing files, the existence of a file is checked prior to
        attempting to remove; this is performed as noted
        [here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369);
        this PR only addresses the the `chgrp` issue.

        Refs #1252

        ---------

        Co-authored-by: David Huber <[email protected]>

    commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 18 12:17:59 2024 -0600

        Hotfix for bug in template names. (#2697)

        This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/`
        template.
        Resolves #2696
        Refs #2451

    commit 35d4d99eaac669721add9ddcc793153e5ab3b30a
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 18 08:06:53 2024 -0600

        Update archive job to use COMIN/COMOUT (#2668)

        NCO has requested that each COM variable specify whether it is an input
        or an output. This completes that process for the global-workflow
        archive task.

        Refs #2451
        ---------

        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>
        Co-authored-by: David Huber <[email protected]>

    commit 47b3a581c8257fa24411fb400df8bb0e1e04972a
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jun 17 22:55:38 2024 -0400

        Turn on high-frequency output in extended test (#2679)

        Turns on high-frequency (hourly) output in the extended products test to
        exercise that aspect of the code. This test only runs on WCOSS.

        Also adds the hooks to optionally turn on the metplus jobs, but that is
        deferred as they are not currently working correctly.

    commit 38f2df9fb0c074b1f80d3c637080be79be693161
    Author: David Huber <[email protected]>
    Date:   Mon Jun 17 17:12:55 2024 +0000

        Optimize wavepostpnt (#2657)

        Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs

        This is done by
        1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by
        - performing operations on all files at once instead of looping over
        each file
            - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`)
            - combining `sed` and `grep` calls when possible
            - adding logic to `awk` calls instead of handling that logic in bash
        2) minimizing as much as possible the amount of data on disk that has to
        be read in (e.g. limiting sed to read only the line numbers it needs)
        ---------

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

    commit 5af325a6a4e0a14d180514a418603ca79fada487
    Author: Dan Holdaway <[email protected]>
    Date:   Fri Jun 14 18:05:23 2024 -0400

        Update GDASapp hash to move JCB into GDASapp (#2665)

        This PR moves JCB into GDASapp. The PR
        also bumps up the hash of GDASapp to what is in `feature/move_jcb`,
        which at time of writing is develop plus the absorption of JCB into
        GDASapp.
        Note that I also took the changes from
        https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the
        testing @RussTreadon-NOAA has done.

    commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b
    Author: Yaping Wang <[email protected]>
    Date:   Fri Jun 14 10:18:17 2024 -0500

        Add observation preparation job for aerosols DA to workflow (#2624)

        Add a prepaeroobs job to prepare aerosol obs files for DA.

        This job does quality control of the VIIRS aerosol raw observations and
        convert them to ioda format.

        Resolves #2623
        ---------

        Co-authored-by: ypwang19 <[email protected]>
        Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>
        Co-authored-by: Cory Martin <[email protected]>
        Co-authored-by: David Huber <[email protected]>

    commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4
    Author: Jessica Meixner <[email protected]>
    Date:   Fri Jun 14 11:04:41 2024 -0400

        Remove ocean daily files (#2689)

        This PR removes the ocn_daily files that are produced by the ocean
        component. These files can be recreated by averaging data that exists in
        the 6 hour aveaged files if needed.

        Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675
        Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by
        removing them and making this obsolete)

    commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu Jun 13 12:22:03 2024 -0400

        Update Jenkinsfile

        needed a comma

    commit dc21eac6c3941d7f30803891d91d82f4cc1f8183
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu Jun 13 11:41:14 2024 -0400

        Add Hercules-EMC to the Jenkins configurable parameter list (#2685)

        This quick-fix PR is to update the Jenkins Pipeline's configurable
        parameter list to include the **Hercules-EMC** node.
        This allows Jenkins users to restart Jobs in the controller when no
        updates have been made.

    commit ebacebfbe458634b8c80af6a735d6b6d01e4e406
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Thu Jun 13 11:20:24 2024 -0400

        Update gdas.cd and gsi_utils hashes (#2641)

        This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The
        updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea
        build for gsi_utils.

        Resolves #2640

    commit 34155fb4767769600a1ff95f0a65e37081addc2a
    Author: Neil Barton <[email protected]>
    Date:   Thu Jun 13 11:18:22 2024 -0400

        Add ability to use GEFS replay ICs (#2559)

        The PR allows the use of ICs from PSL's replay analysis. These replay
        ICs will be used for GEFS reforecasting and SFS. Two main changes are
        associated with these updates: (1) replay ICs being valid at 3Z, and (2)
        the use of warm starts.

        Resolves #1838

        ---------

        Co-authored-by: Jessica Meixner <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>

    commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Wed Jun 12 19:25:42 2024 -0600

        Replace `sleep` with `wait_for_file` (#2586)

        This PR addresses issue #2444. The following is accomplished:

        - All `sleep` statements are replaced with `wait_for_file` for the
        relevant scripts beneath `scripts` and `ush`;
        - Indentation and shell-norms are updated where applicable.

        Note: The WAFS scripts are not updated as per @aerorahul direction.

        Resolves #2444

        ---------

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

    commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 12 13:31:55 2024 -0400

        Add COM template for JEDI obs (#2678)

        Adds a COM template to define a path to store obs processed for JEDI.
        This will allow UFSDA to stop writing to COM_OBS, which should be
        read-only as it belongs to obsproc in operations.

        No functional change yet.

    commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed
    Author: Guoqing Ge <[email protected]>
    Date:   Wed Jun 12 09:06:23 2024 -0600

        Link both global-nest fix files and non-nest ones at the same time (#2632)

        This PR enables linking both global-nest fix files and non-nest ones at
        the same time and users can run both nesting and non-nesting experiments
        at the same time without worries about what fix files to be linked.

        Resolves #2631

    commit 61de004d4f9e9edf8a31bb173f2719b46451a36a
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jun 12 11:03:13 2024 -0400

        Update ufs-weather-model  (#2663)

        Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack
        allowing some temporary fixes to be reverted.
        * removes upp submodule
        * uses upp from the ufs-weather-model
        * restores the build and link that were hacked during the Hera Rocky 8
        transition to allow for UPP submodule
        * Removes forecast directories in clean-up

        Resolves #2617
        Resolves #2437

        ---------

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

    commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d
    Author: Eric Sinsky - NOAA <[email protected]>
    Date:   Wed Jun 12 01:15:37 2024 -0400

        Add ability to process ocean/ice products specific to GEFS (#2561)

        This PR begins to add the capability to produce GEFSv13 ocean and ice
        products in the global-workflow according to stakeholder requirements.
        The following features are added.

        - An oceanice prod yaml file has been added to address the ocean and ice
        products specific to GEFSv13.
        - The rocoto dependencies and config.base for GEFS have also been
        modified to allow for 24-hour averaged ocean and ice output.
        - Various scripts have been modified to allow for ocean and ice output
        frequencies of 24 hours.
        - `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN`
        and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`.

        Refs #1878

    commit 6691e7489650e0b738c176fbd096109288dc09b6
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 11 21:15:07 2024 -0600

        Update cleanup job to use COMIN/COMOUT (#2649)

        NCO has requested that each COM variable specify whether it is an input
        or an output. This completes that process for the global-workflow
        clean-up task.

        Refs #2451

        ---------

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

    commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Tue Jun 11 16:17:25 2024 -0400

        Add overwrite to creat experiment in BASH CI (#2676)

        This is a quick hotfix to the CI BASH driver script adding `--overwrite`
        to create experiment script to avoid errors from restarting an
        experiment.

    commit e7909af8d9e1f34140388a3f8556d8e582c58fe5
    Author: emilyhcliu <[email protected]>
    Date:   Mon Jun 10 15:11:27 2024 -0400

        Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py  (#2645)

        This PR proposes updates for the following two scripts:

        1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select
        CRTM cloud optical table based on cloud microphysical scheme indicated
        by `imp_physics'
        The default scheme in the GFS forecast model is Thompson scheme
        (imp_physics = 8).

        2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in
        the script due to increased variables to interplate increments and
        calculate analysis in the netcdf_io routines in GSI-utils.
        Here is the related [PR #46 for
        GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46).

        ---------

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

    commit 9caa51de8fb7be07d2e61775da01937d576964f6
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Thu Jun 6 22:15:23 2024 -0600

        Update RDHPCS Hera resource for `eupd` task (#2636)

        As per @wx20jjung, the resource for the `eupd` task have been updated
        for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job
        fails.

        Resolves #2454

        ---------

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

    commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b
    Author: DavidNew-NOAA <[email protected]>
    Date:   Thu Jun 6 11:49:03 2024 -0400

        Parameterize some things in config.atmanl and config.atmensanl (#2661)

        This PR adds some parameters in config.atmanl and config.atmensanl that
        can be altered with the defaults.yaml. The motivation is to make these
        files match those in the GDASApp JJOB tests (example:
        https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl),
        so we can just use the Global Workflow config.atmanl and
        config.atmensanl in the tests rather than custom ones in GDASApp that
        have to be separately updated every time the ones in the Global Workflow
        are updated.

    commit 54ea0b73a07921be5fbb07fe41e976888bd3e549
    Author: Guillaume Vernieres <[email protected]>
    Date:   Thu Jun 6 01:36:02 2024 -0400

        Add links to the ocean insitu obs processing tools (#2644)

        Add links to the marine bufr to ioda converters for the marine insitu
        observations.

        - fixes https://github.com/NOAA-EMC/GDASApp/issues/1106
        - waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135

    commit 205d0c2b13e2d7755cec75bf8c978ab20d453862
    Author: David Huber <[email protected]>
    Date:   Wed Jun 5 17:31:30 2024 +0000

        Update S4 point of contact in docs (#2660)

        Update the point of contact for global workflow issues on S4.

    commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Wed Jun 5 12:50:14 2024 -0400

        Enable wcoss2 ufsda build and module load (#2620)

        This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2.

        Resolves #2602
        Resolves #2579

    commit 67b833e0c7bc390865d453588b4609a1a7ede981
    Author: Jessica Meixner <[email protected]>
    Date:   Tue Jun 4 13:33:43 2024 -0400

        Update ufs-weather-model  (#2646)

        Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6
        This should resolve the issue and allow C768 runs on Hera and allow for CICE
        to run on WCOSS2 (due to library updates to allow linking).

        From what I can tell, all updates needed were done by
        @HenryWinterbottom-NOAA which were updates for CICE

        Fixes #2490

    commit c44d0ac86cfdf78eb87492431bf6d825e8bae637
    Author: GwenChen-NOAA <[email protected]>
    Date:   Tue Jun 4 10:29:49 2024 -0400

        Update wmo parm files to fix WMO header (#2652)

        This PR updates wmo parm files to switch WMO header of precipitation
        type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to
        instantaneous.

        Resolves #2566

    commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60
    Author: Cory Martin <[email protected]>
    Date:   Tue Jun 4 13:55:33 2024 +0000

        Add IAU to snow DA (and its test) (#2610)

        This PR enables IAU for the snow DA which is necessary for GFSv17.

        A snow analysis is created for the center of the window regardless, and
        an additional at the beginning of the window is added if IAU is on. The
        former is needed for UPP and the latter, to initialize the model.

        The increment is valid throughout the window for 3DVar, so the same
        increment is added to both forecasts.

        Additionally, the input file that goes into global_cycle has been
        updated to be the output of the JEDI snow analysis instead of the
        forecast (@jiaruidong2017 I recall discussing this, can you confirm this
        is right or am I mistaken)

        This PR also makes the CI test for snow DA (and aerosol DA) include IAU
        rather than without IAU,.

        ---------

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

    commit c92bf415060750127c9c05a62a1d2851c489551a
    Author: David Huber <[email protected]>
    Date:   Sat Jun 1 05:11:07 2024 +0000

        Archiving cleanup (#2621)

        1) Adds a lot of comments to the jinja templates for archiving
        2) Rearranges the gdas and enkf templates to a more logical order
        3) Fixes a couple of bugs in the enkf archiving of increments and
        analyses
        4) Disables archiving for the half cycle
        5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`,
        instead relying on `DO_FIT2OBS`
        6) Updates wxflow to add the option to not allow undefined variables
        when parsing jinja templates and invokes this feature when running
        archives

        Resolves #2612

    commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri May 31 04:57:08 2024 -0400

        Switch to Rocky 9 built external packages on Hercules (#2608)

        The workflow was updated to use modules built on Rocky 9, but the
        external packages (like prepobs) were still pointing to the versions
        built on CentOS (Orion). This transitions to packages built on Rocky 9.

        Updating of the tracker package has been deferred until later. As such,
        the tracker jobs have been disabled by returning immediately if they are
        on Hercules. Since these jobs are small, resource-wise, it should not
        meaningfully impact turnover time.

    commit 4422550c01c9214a2b3b8890bdcc898123ee216a
    Author: Guoqing Ge <[email protected]>
    Date:   Thu May 30 08:05:23 2024 -0600

        Add the capability to use slurm reservation nodes (#2627)

        Add the capability to use slurm reservation nodes
        Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE

        Resolves #2626

    commit a54153fd9d26126206bc07a1da4e80f50c0c5910
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed May 29 23:24:07 2024 -0400

        Update forecast job to use COMIN/COMOUT (#2622)

        NCO has requested that each COM variable specify whether it is an input
        or an output. This completes that process for the forecast job.

        Refs #2451

        ---------

        Co-authored-by: David Huber <[email protected]>

    commit d69a8af95d492982b918670322ed5c41ab074335
    Author: Jessica Meixner <[email protected]>
    Date:   Wed May 29 21:29:03 2024 -0400

        Update to add 1-deg global wave grid (#2619)

        This PR adds options to use a global 1 deg grid, intended for testing
        with the SFS application.

        Requires new fix file changes NOAA-EMC/global-workflow#2618

    commit 0b4670ecf83b99b72835c8380573b2bca7cf5324
    Author: Jessica Meixner <[email protected]>
    Date:   Wed May 29 17:17:21 2024 -0400

        Add C384mx025_3DVarAOWCDA yamls (#2625)

        Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder.

    commit 2e885d05c64b947f00a3cf055a1277fbfac195c9
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed May 29 13:00:51 2024 -0400

        Script to keep Jenkins Agent persistent from cron (#2634)

        This "persistent" Java Agent launch script can be ran from a cron job:

        - Uses Jenkins Remote API to check the status of the Node connection
        using curl for a given machine.
        - If it is not connected a new agent is launched for that node.

        Resolves #2633

    commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5
    Author: GwenChen-NOAA <[email protected]>
    Date:   Tue May 28 17:17:11 2024 -0400

        Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611)

        Based on users' feedback, this PR do the following:
        1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF
        2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD,
          and VOGRD) from "%g m below water surface" to "%g m below sea level"
        3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m)

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

    commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31
    Author: DavidNew-NOAA <[email protected]>
    Date:   Tue May 28 17:16:23 2024 -0400

        Add atmensanlfv3inc job (#2592)

        This PR creates the atmensanlfv3inc job, the ensemble version of
        atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is
        #[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS
        companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3).

    commit 50c2b8951b29a3c883a778becbf8582f9519eb48
    Author: Anil Kumar <[email protected]>
    Date:   Tue May 28 13:23:53 2024 -0400

        Global-workflow (AR) Generic updates for Gaea C5 (#2515)

        - Port global-workflow’s build and run capability to Gaea-C5
        - Building global-workflow on Gaea-C5
        - Setting up experiments with global-workflow on Gaea-C5

        ---------

        Co-authored-by: AnilKumar-NOAA <[email protected]>
        Co-authored-by: DavidBurrows-NCO <[email protected]>

    commit b6ca771a0c584cbfcbbf9be739765d5f3815df97
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri May 24 10:52:45 2024 -0400

        Update STMP and PTMP settings in host file for Orion and Hercules  (#2614)

        - Updating STMP and PTMP settings in host file for Orion and Hercules
        because they are cross mounted.
        - Also took the opportunity to finally update **SLURM_ACCOUNT** to
        **HPC_ACCOUT** in CI over rides.
        - Added a refactor of the `rocotostat.py` tool that is more pythonic and
        as a execute retry feature because the `rocotostat` utility on Orion has
        been failing sometimes.

    commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f
    Author: Guillaume Vernieres <[email protected]>
    Date:   Tue May 21 23:50:50 2024 -0400

        Sea-ice analysis insertion (#2584)

        Allows cycling and restarting CICE with the sea-ice analysis if the
        marine DA is switched on.

        Resolves #2568
        Resolves NOAA-EMC/GDASApp#1103

    commit 5369a1ff3a3969149fcf32810fad0e50216752b7
    Author: David Huber <[email protected]>
    Date:   Tue May 21 22:12:29 2024 +0000

        Refactored archiving (#2491)

        This provides a new pygfs task, archive.py, that provides all of the
        tools necessary to archive data to the local (`ARCDIR`) and backup
        (`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to
        define the file to be archived or tarred to replace the
        `hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts
        and make it easier to add new data and explicitly handle optional and
        required files.

        For `ATARDIR` archiving, a master jinja template is provided for each
        `RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2,
        master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both
        `enkfgdas` and `enkfgfs` `RUN`s. These templates then include the
        appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on
        experiment, cycle, and coupled parameters. Each of these templates
        corresponds to a single tarball to populate and are tabbed 4 spaces so
        they are defined within the master `datasets` dictionary.

        Future developers should not have to make modifications to archive.py
        unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then
        only a single `elif` needs to be added to the configure method to
        specify the master `ATARDIR` template to archive (e.g.
        `master_gefs.yaml.j2`). If a new component is coming online that needs
        to be archived to `ATARDIR` (e.g. SNOW), then create a new template for
        each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`)
        and reference the template in the appropriate master templates, e.g.

        `master_gdas.yaml:`
        ```jinja
        {% if DO_SNOW %}
        {% include "gdassnow.yaml.j2" %}
        {% endif %}
        ```

        A few other issues were addressed along the way:
        1. Aerosols have been reenabled. Aerosol forecasts should only be
        performed during gdas cycles, but analyses can be performed for both gfs
        and gdas cycles. This was accomplished by setting separate
        `AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs.
        2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`.
        This prevented restarts from being used for cice-enable experiments.
        This feature was not tested.
        3. Create a temporary fix for the `wgrib` utility. For spack-stack
        1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is
        open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in
        existing installations. Once complete, this temporary fix should be
        removed.
        4. The number of `earc` jobs has been reduced for lower resolution
        experiments. Both C48 and C96 experiments will now only have two earc
        jobs (one for the non-member files to archive and another for the member
        files). C192 will have up to 3 earc jobs (one non-member, one for
        members 1-40 and another for members 41-80, if needed).

        Resolves #2345
        Resolves #2318

        ---------

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

    commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri May 17 12:57:59 2024 -0400

         Add remove RUNDIRS step in CI before creating experements (#2607)

        As had been done in Bash CI we need to remove the RUNDIR in Jenkins
        before a creating an experiment in the event that case had beem
        previously ran.

    commit 09333c01dbafddb2d2fe7e181b479af3cc6d3621
    Merge: f7e9f4489 bb930050b
    Author: Janet Derrico <[email protected]>
    Date:   Thu May 16 14:33:19 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit bb930050b3cd51d28ecba6b231c8675f6d11856c
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Thu May 16 12:28:30 2024 -0400

        Adds jjob and other necessities for marine LETKF task (#2564)

        Adds jjob, rocoto script, config file, and other necessities for new
        marine LETKF task.

        Partially addresses NOAA-EMC/GDASApp#1091

    commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu May 16 12:12:06 2024 -0400

        Updating CI Machine configs with redundant PTMP (#2605)

        Quick fix adding PTMP as STMP in Machine configs for CI for completeness

    commit ef340ff33a6f89adf70838206ba3fd56a953fa7a
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu May 16 11:37:30 2024 -0400

        Fix race condition in CI between Orion and Hercules (#2604)

        Hotfix to solve race conditions in the CI system due to cross-mounted
        file systems between Orion and Hercules

    commit e8b17e27f719df280170dc3f5bd9f19917cefaf2
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed May 15 17:16:30 2024 -0400

        Remove existing EXPDIRs and COMROTs when CI is re-run (#2601)

        Quick hotfix for having default for re-runing jobs to start clean with
        new EXPDIRs and COMROTs

    commit b5d113efb1970ede5cd1d3d4dff8d96320519c41
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed May 15 16:52:49 2024 -0400

        Moving logic for skipping hosts in pr cases (#2573)

        This PR removes the logic of skipping hosts for pr cases from
        `create_experiment.py` and moves it to a test in the cron bash driver
        using a `parse_yaml.py` python tool.

        The Jenkins pipeline was not effected as it uses the
        `get_host_case_list.py` utility to form the cases on a per host bases.

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

    commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Wed May 15 13:13:30 2024 -0400

        Update gsi_utils.fd hash (#2598)

        This PR updates the `gsi_utils.fd` hash to bring in updates which add
        safeguards to
        -
        `src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90`
        - `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90`

        The safeguards are described in GSI-utils PR
        [#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated
        issue.

        Resolves #2597

    commit d5366c66bd67f89d118b18956fe230207cbf0aea
    Author: Kate Friedman <[email protected]>
    Date:   Wed May 15 13:12:56 2024 -0400

        Update CICE and MOM6 fix versions (#2600)

        This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions
        to the newer `20240416` timestamps, which includes updates and fixes to
        the `100` (1-deg) resolution files.

        Resolves #2480
        Resolves #2483
        Resolves #2595

    commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b
    Author: David Huber <[email protected]>
    Date:   Mon May 13 22:57:38 2024 +0000

        Limit gfswavepostpnt to 40 PEs/node (#2588)

        This fixes the slow runtime of the gfswavepostpnt job on Hercules. The
        job is very I/O intensive and does not scale well to large nodes, so
        limit the number of jobs/node to 40.

        Resolves #2587

    commit 4fb7c12c325702a47f27c802a5067efd33d0327c
    Author: Fanglin Yang <[email protected]>
    Date:   Mon May 13 16:37:51 2024 -0400

        Update damping and time-step (#2575)

        Updates the model to use explicit Rayleigh damping for u/v and implicit
        damping to w. This improves model stability and allows for longer
        timesteps. Also unifies the GDAS and GFS to use the same damping.

        Results from a test at the C1152 resolution (coupled model) can be found
        at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/

        Resolves #2574

        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
        Co-authored-by: Lisa Bengtsson <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>

    commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri May 10 14:17:13 2024 -0400

        Do not use BUILT_semphore to force rebuilds when re-run (#2593)

        Remove the placement of the `BUILT_semaphore` file after the build in
        the Jenkins Pipeline and force it to rebuild any changes after a PR is
        re-ran.

    commit 2346c6161f75ae02369cbf30f30c6150d3e12b66
    Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com>
    Date:   Thu May 9 21:17:06 2024 -0500

        Migration to Rocky8 spack-stack installations on Jet (#2458)

        # Description
        Migrates Global Workflow to Rocky8 spack-stack installations on Jet.
        Jet has moved from CentOS7 to Rocky8.

        Resolves #2377
        Refs NOAA-EMC/UPP#919
        Refs NOAA-EMC/gfs-utils#60
        Refs NOAA-EMC/GSI#732
        Refs NOAA-EMC/GSI-Monitor#130
        Refs NOAA-EMC/GSI-utils#33

    commit c7b3973014480a20dd8e24edaeb83a9e9e68159f
    Author: Jessica Meixner <[email protected]>
    Date:   Thu May 9 11:36:58 2024 -0400

        Updates for cold start half cycle, then continuing with IAU for WCDA (#2560)

        This PR allows us to run C384 S2S with IAU, but starting with the first
        half-cycle as a cold-start. This will be necessary for cycled testing as
        we build towards the full system for GFSv17. This updates the copying of
        the restarts for RUN=gdas for both ocean and ice copying what the atm
        model is doing. It also reduced the amount of restart files from 4 to 3.

        Other updates:
        * Add DOJEDI ocean triggers for archiving certain files update from:
        @CatherineThomas-NOAA
        * Adds COPY_FINAL_RESTARTS option to turn on/off copying the last
        restart file to COM. Defaults to off...
        * Defines model_start_date_current_cycle & model_start_date_next_cycle
        to help with knowing which IC to grab.

        Refs #2546

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

    commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2
    Author: Dan Holdaway <[email protected]>
    Date:   Wed May 8 20:52:48 2024 -0400

        Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477)

        Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI
        Configuration Builder (JCB) tool so that YAMLs can be made more portable
        and invoke the observation chronicle mechanism.

        Resolves #2476

        Co-authored-by: danholdaway <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

    commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed May 8 02:04:16 2024 -0400

        Add CI test for products (#2567)

        Adds a new version of the atm3DVar test that runs the full forecast
        length and produces most of the secondary products. For now, this test
        will only run on WCOSS due to gempak failures on other machines as well
        as computational needs. On other machines, the original version will run
        (the original version will not run on WCOSS). AWIPS remains off for now
        in this extended test due to a bug involving tocgrib2 and the convective
        precip fields (see #2566).

        The new test runs for 4½ cycles and the full 384-hr forecast length to
        ensure all gempak scripts are exercised. Since the cycle throttle is 3
        and the bulk of the time is in the free forecast, the cycles run mostly
        concurrently so it doesn't extend the total test time too much beyond
        that of a single 384-hr forecast.

        Fixes a bug in NPOESS that was introduced when the post filenames were
        reverted to the previous format for the GOES products until the final
        filenames are determined (#2499).

        Also removes the AWIPS g2 job from the rocoto mesh to complete the
        retirement of grib1 products.

        Resolves #2132
        Resolves #2445

    commit 9b6f8404ac4507d14adc404b77cfdf002b55e832
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue May 7 00:14:36 2024 -0400

        Add task to prepare emissions for GEFS (#2562)

        This PR:
        - introduces a task to prepare emissions for a forecast into the GEFS
        application.
        - adds configuration, j-job, rocoto job, ex-script and the python class
        for this job
        - updates GEFS workflow to be able to generate the XML to call this job.
        - updates the `fcst` and `efcs` job dependencies in the GEFS application
        to depend on `prep_emissions` if aerosols are turned ON.
        - provides a placeholder for @bbakernoaa to work on the details for
        preparing emissions.

        Co-authored-by: Walter Kolczynski - NOAA <Walt…
jderrico-noaa pushed a commit to NOAA-GSL/global-workflow that referenced this issue Sep 27, 2024
@kayeekayee
Update develop branch, gsl_ufs_dev (#66)
411e6d4 
* Added alpha_fd coefficient for Beljaars TOFD in GSL drag
bug fix
Update INFO

* Update develop branch, gsl_ufs_dev

Squashed commit of the following:

commit 4ad0d52a6fbb581a9804bd0bb627b7c52f338bad
Author: kayee.wong <[email protected]>
Date:   Thu Sep 19 19:20:06 2024 +0000

    For pygraf plotting.

commit 1bfba70ed6aaa3eb47974006ed0c5cae653b8ce8
Author: kayee.wong <[email protected]>
Date:   Thu Sep 19 04:27:55 2024 +0000

    Fixed gfsatmprod file name and gfsarch data type.

commit 4e0a81f7acf5ccba5de8d3bdf7ab19cae80812cb
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 18:37:50 2024 +0000

    Fix typos/links/dependancy.

commit d5fdcbf8d6e987dbdfcd6b4da34d0934c8d82c3b
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 07:37:52 2024 +0000

    Fixed missing config.base files.

commit c6239f925369b20fd8488e8537969e2f4f9e7725
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 06:53:47 2024 +0000

    Update submodule hashs.

commit 32bf790f67b818ff50a7f6b74388fb81ed175b3a
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 06:09:41 2024 +0000

    Update develop branch, gsl_ufs_dev
     - based on gsl_ufs_dev from KaYee's fork
       global-workflow: 07Aug24,37c53ac [develop_07Aug2024_37c53ac]
       UFS: 19Jul24, c127601
       FV3: 19Jul24, 2527c11
       UPP: 23Apr24, be0410e
       CCPP-PHYSICS: 19Jul24, 46df080
       UFS_UTILS: 26Jun24, 3ef2e6b

    Squashed commit of the following:

    commit 70b557836379bb7e545fcc6642e28d66cfc17735
    Merge: 5edbd123e 37c53ac69
    Author: Janet Derrico <[email protected]>
    Date:   Wed Aug 7 11:02:24 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04
    Author: Kate Friedman <[email protected]>
    Date:   Wed Aug 7 08:11:21 2024 -0400

        Revert MSU FIX_DIRs back to glopara (#2811)

    commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Tue Aug 6 14:47:36 2024 -0400

        Bugfix for updating label states in Jenkins (#2808)

        Quick bug fix for updating state labels in CI during finalize.
        (did not reference GitHub CLI executable correctly in the pipeline
        script)

    commit 8fee36f0307b0c08080e3a8fa8fa6703e7da5fce
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Aug 6 11:02:45 2024 -0400

        Clean-up temporary rundirs - take 2. (#2753)

        This PR:
        - is a follow-up to a previous PR that aggressively pruned run
        directories.
        - removes run directories for the current cycle in the clean-up if the
        cycle is successful. If the cycle is not successful, cleanup is not
        called and all run directories for the cycle are safe from being purged.
        - also updates the PR template to list/query for any updates to
        submodules.

        ---------

        Co-authored-by: David Huber <[email protected]>
        Co-authored-by: David Huber <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

    commit d599fff4aedd41ae587dbe02226acb12ff48efc1
    Author: HelinWei-NOAA <[email protected]>
    Date:   Mon Aug 5 05:31:31 2024 -0400

        Change land surface for HR4 (#2787)

        Resets the default value of opt_diag to 2 corresponding to the land
        surface upgrades in ufs-weather-model for HR4.

        Resolves #2786

    commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb
    Author: David Huber <[email protected]>
    Date:   Fri Aug 2 15:41:29 2024 -0400

        Run METplus serially and correct the name of prod tasks (#2804)

        Adds 2 hot fixes:

        - METplus v9.1.3 has a bug in it that sometimes attempts to create
        multiple copies of the same directory when running in parallel, causing
        a Python error and downstream problems. This PR makes METplus run in
        serial mode, preventing such issues.
        - Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in
        workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod)

    commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri Aug 2 15:03:45 2024 -0400

        Update Java Agent launching script for Jenkins connections (#2762)

        Made updates to the Jenkins Launching Script for robustness and less
        ambiguous documentation:
        - Clearer distinction between required user token for the remote api and
        the systems token for launching
        - Added pre-checks: `gh` is authenticating, named compliant token and
        secret file exists
        - More robust Jason based parser of the remote api response for checking
        the state of the Node connection
        - For `cron` use a 5 minute pause and recheck was added before
        re-launching of the java agent
        - Added concise header documentation of requirements and purpose
        ---------

        Co-authored-by: David Huber <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

    commit b73b1fd203496db97f8067652659573a632bcc67
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri Aug 2 07:59:06 2024 -0400

        Fix erroneous cdump addition (#2803)

    commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3
    Author: Rahul Mahajan <[email protected]>
    Date:   Thu Aug 1 20:26:13 2024 -0400

        Update ocean post-processing triggers (#2784)

        This PR:
        - replaces `check_netcdf.sh` checker for ocean post-processing with with
        ocean output at the next forecast hour or finishing of the forecast job
        for ocean prod
        - removes no longer needed `ush/check_netcdf.sh`

    commit aa2af1ca8d59424a60a1730722bf528775d9e606
    Author: GeorgeGayno-NOAA <[email protected]>
    Date:   Thu Aug 1 16:46:10 2024 -0400

        Update the gfs_utils repository hash (#2801)

        # Description
        Point to the latest hash of the gfs-utils repository, which contains the
        bug fix to gaussian_sfcanl.

        Resolves #2669.
        Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73

    commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8
    Author: David Huber <[email protected]>
    Date:   Thu Aug 1 08:12:14 2024 -0400

        Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791)

        Changes how METplus jobs run so that they run on the last GFS cycle for
        a given `PDY`.

        This is a departure from operations where the METplus jobs run on the
        00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through
        `${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on
        `${PDY}18` for cycles 00-18. See
        https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details.

    commit 1cf8b448af562dbb7af198399c78c585977e81da
    Author: David Huber <[email protected]>
    Date:   Tue Jul 30 10:38:49 2024 -0400

        Simplify resource-related variables, remove CDUMP where unneeded (#2727)

        This overhauls resource-related variables to use a common set of
        variables for each job. In the process, this also removed the use of
        CDUMP in most cases.

        Resolves #1299 #2693

    commit 61875f25c9e971f82ae499b5b612d7f095deebd4
    Author: Eric Sinsky - NOAA <[email protected]>
    Date:   Mon Jul 29 14:40:03 2024 -0400

        Remove f000 from atmos rocoto tasks for replay cases (#2778)

        The main purpose of this PR is to remove the f000 from
        atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In
        cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater
        than `0`, it becomes necessary to have the first lead hour set to
        `OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For
        example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead
        time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and
        the minimum lead time for the ocean_prod rocoto task needs to be 6
        (assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up
        possible by removing 0 from fhrs for atmosphere-related tasks in
        `gefs_tasks.py` when replaying.

        This PR also moves where f000 is being removed for the ocean_prod and
        ice_prod tasks. The if-block that performs this f000 removal has been
        moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`.

        ---------

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

    commit f156a7894d639f177e3e2588f98eec1f6f59aa68
    Author: Jessica Meixner <[email protected]>
    Date:   Fri Jul 26 14:18:32 2024 -0500

        HR4 GWD update (#2732)

        This update is a combination of the gravity wave drag (GWD) versions
        from the NOAA/GSL and NOAA/PSL

    commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891
    Author: David Huber <[email protected]>
    Date:   Thu Jul 25 14:26:52 2024 -0400

        Temporarily disable METplus jobs (#2796)

    commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2
    Author: Guillaume Vernieres <[email protected]>
    Date:   Wed Jul 24 15:00:35 2024 -0400

        Refactoring of the marine B-matrix job (#2749)

        Refactor the functionality of B-matrix generation from the GDASApp

        Resolves #2743

    commit 65a7ab75dc0e4baba06a02e11ed0455787056a68
    Author: David Huber <[email protected]>
    Date:   Tue Jul 23 08:35:48 2024 -0400

        Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775)

        Removes the namespace-based construction of EnKF member COM directories
        in the enkf archive template.

    commit c45b9611f3e701b819bd33dc5af29033f060bb91
    Author: Eric Sinsky - NOAA <[email protected]>
    Date:   Tue Jul 23 00:33:16 2024 -0400

        Add task to process reforecast variables to save on WCOSS2 (#2680)

        # Description
        This PR adds an optional task to the global-workflow to process a subset
        of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for
        the GEFSv13 reforecast. This task is designed to process GEFS variables
        so that specific reforecast product requirements are met. A new variable
        in `config.base` called `DO_EXTRACTVARS` enables this task, which is
        currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by
        default and is specifically a task designed to be executed for the
        GEFSv13 reforecast.

        Refs #1878

        # Type of change
        - New feature (adds functionality)

        # Change characteristics
        - Is this a breaking change (a change in existing functionality)? NO
        - Does this change require a documentation update? NO

        # How has this been tested?
        This has been cloned and tested on WCOSS2. This will need to be tested
        on Hera and other platforms on which the reforecast may be running.

        # Checklist
        - [ ] Any dependent changes have been merged and published
        - [x] My code follows the style guidelines of this project
        - [x] I have performed a self-review of my own code
        - [ ] I have commented my code, particularly in hard-to-understand areas
        - [x] My changes generate no new warnings
        - [x] New and existing tests pass with my changes
        - [ ] I have made corresponding changes to the documentation if
        necessary

        ---------

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

    commit 71dc33c6ca991c16ce743760d99feaaf60f2218a
    Author: David Huber <[email protected]>
    Date:   Mon Jul 22 14:51:53 2024 -0400

        Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774)

        Fix metp* resources and check that they completed properly; add support for Orion Rocky 9

    commit 56df67a90fe090c425199f1285e5aac722c398b1
    Author: David Huber <[email protected]>
    Date:   Mon Jul 22 09:28:18 2024 -0400

        Hotfix: Update jcb to avoid git-lfs files (#2782)

        Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to
        be cloned on Hera.

        This hotfix points to a non-authoritative branch of the GDASApp
        (https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and
        should be updated ASAP back to the authoritative repository.

    commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jul 16 09:44:00 2024 -0400

        Address issues in creating XML for GFS forecast-only with app S2SWA (#2757)

        This bugfix PR:
        - fixes an issue where a user is unable to generate the XML for a GFS
        forecast-only experiment with APP=S2SWA

        Specifically, the changes are related to defining `aero_fcst_cdumps`.
        Following `setup_expt.py`, the user will have to set
        `AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in
        `config.base`.

    commit e0878dba0e53706a7f53429b61aee2936e2c21bf
    Author: Kate Friedman <[email protected]>
    Date:   Mon Jul 15 10:25:11 2024 -0400

        Updated prepobs and fit2obs versions for Orion Rocky9 (#2758)

        Update prepobs to v1.0.2 and fit2obs to v1.1.2

        These versions now support Orion Rocky9. Updates are included
        for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet.

    commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu Jul 11 17:48:47 2024 +0000

        CI maintenance updates and adding CI Unit Tests (#2740)

        This PR has a few maintenance updates to the CI pipeline and adds a test
        directory with Unit Tests
        **Major Maintenance updates:**
        - Added try blocks with appropriate messaging to GitHub PR of failure
        for:
        - - **scm** checkout
        - - build fail (with error logs sent as gists)
        - - create experiment fails with `stderr` sent to GitHub PR messaging
        - Pre-stage FAILS from the above are now captured these fails allow
        FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state
        labels in GitHub - see image below)
        **Minor Maintenance updates:**
        - Fix for STALLED cases reviled from PR 2700 (just needed a lambda
        specifier)
        - Fixed path to experiment directory in PR message (had dropped EXPDIR
        in path)
        - Needed `latin-1` decoder in reading log files for publishing
        **Added python Unit Tests for CI functionality:**
        - Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI
        utility codes
        - Cashed the install of Rocoto in the GitHub Runners to greatly reduce
        stetup time for running the unit tests
        - Unit Tests Python scripts added
        - `test_rocostat.py`: rocoto_statcount() rocoto_summary()
        rocoto_stalled()
          - `test_setup.py`: setup_expt() test_setup_xml()
          - `test_create_experment`: test_create_experiment()
          - - Runs all PR cases that do not have ICs in the GItHub Runner
        - Reporting mechanism in the Actions tab for Python Unit Testing results
        - Test case data for STALLED and RUNNING stored on S3 and pulled using
        wget during runtime of tests

    commit 5ef4db74649b8be03402c17aa29c024e71699a7b
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Thu Jul 11 08:59:24 2024 -0400

        Adds contents of constructor and initialize methods to marine LETKF class (#2635)

        Adds contents of constructor and initialize methods to marine LETKF class

        Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091
        ---------

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

    commit 8998ec7b74123e953b97a93fa14cc78d471a1aee
    Author: David Huber <[email protected]>
    Date:   Tue Jul 9 08:31:57 2024 -0400

        Fix GDAS group B restart archiving (#2735)

        Archives the GDAS restartb dataset at a 6-hour offset from restarta

        This allows cycled experiments to restart from the archives.
        The tabbing for the master archive templates was also added to
        improve readability.

        Resolves #2722

    commit 3ca74771255727033b9dc043c652ac585178629c
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Tue Jul 9 08:28:54 2024 -0400

        Add fcst dependency to ocnanalprep (#2728)

        Add previous cycle's `fcst` as a dependency to `ocnanalprep`

        This ensures that the availability of restart files to the latter. This addresses a
        seldomly-encountered race condition where `ocnanalprep` fails due to the
        lack of the files.

    commit 58fca1668aecd6fb1afd12a441256ad35900e075
    Author: Rahul Mahajan <[email protected]>
    Date:   Fri Jul 5 15:02:23 2024 -0400

        Update (partially) global-workflow for orion+rocky9 (#2741)

        This PR:
        - updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils,
        GFS-utils) to include recent update to their modulefiles for
        Orion+Rocky9 upgrade
        - updates the modulefiles in global-workflow to load modules from
        Orion+Rocky9 paths
        - updates modulefiles for `gwsetup` and `gwci` as well.
        - removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not
        installed.
        - adds `parm/config.gfs/config.resources.ORION` to address GSI
        performance degradation after Rocky 9 upgrade.

        This PR:
        - does not update the build for UPP. Standalone UPP is not available via
        ufs-weather-model as of #2729
        - will need a follow-up update for `prepobs` and `fit2obs` updated
        locations when they are installed in `glopara` space on Orion.

        # Type of change
        - Maintenance (code refactor, clean-up, new CI test, etc.)

        # Change characteristics
        - Is this a breaking change (a change in existing functionality)? NO
        - Does this change require a documentation update? NO

        # How has this been tested?
        This PR is not sufficient for Orion.
        This PR must be tested on other platforms (Hera, WCOSS2) as this PR
        updates submodules.

        # Checklist
        - [ ] Any dependent changes have been merged and published
        - [ ] My code follows the style guidelines of this project
        - [ ] I have performed a self-review of my own code
        - [ ] I have commented my code, particularly in hard-to-understand areas
        - [ ] My changes generate no new warnings
        - [ ] New and existing tests pass with my changes
        - [ ] I have made corresponding changes to the documentation if
        necessary

        ---------

        Co-authored-by: Kate Friedman <[email protected]>

    commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jul 3 21:07:49 2024 -0400

        Update ufs model hash to 20240625 (#2729)

        Updates UFS weather model hash to hash from 2024-06-24 which has orion
        porting updates + a few namelist updates.

    commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85
    Author: David Huber <[email protected]>
    Date:   Wed Jul 3 11:32:40 2024 -0400

        Hotfix for undefined CLUSTERS (#2748)

        Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses
        the native `dict` `get` method to prevent grabbing an unset entry.

    commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf
    Author: GwenChen-NOAA <[email protected]>
    Date:   Wed Jul 3 09:56:08 2024 -0400

        Update gempak job to run one fcst hour per task (#2671)

        This PR updates gempak jobs (gfs, gdas, and goes) from processing all
        forecast hours at once to one forecast hour at a time. This will reduce
        the job runtime to less than 5 min, so restart capability is not needed.

        Resolves #1250
        Ref #2666 #2667
        ---------

        Co-authored-by: Walter.Kolczynski <[email protected]>

    commit 8215ae654202186a4f753c3abe937b7b9b91a9c7
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jul 2 16:22:11 2024 -0400

        Hotfix for clusters from #2701 (#2747)

        Fixes an issue created from #2701 that added `CLUSTERS` to the
        `gaea.yaml`.

    commit 11943e36ba12b3df49c51942da780698fab02d38
    Author: DavidBurrows-NCO <[email protected]>
    Date:   Tue Jul 2 12:58:10 2024 -0400

        Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701)

        This PR sets up the ability on Gaea for auto generation of a clean xml
        file, i.e., an xml file that does not need any alterations before
        running rocoto.
        Refs #2572
        Refs #2664

    commit de8706702ead0630beb54d868f83aa2cb23f8f79
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Mon Jul 1 09:29:14 2024 -0400

        Update for JCB policies and stage DA job files with Jinja2-templates (#2700)

        This PR updates the `gdas.cd` hash to bring in new JCB conventions.
        Resolves #2699

        From #2654
        This PR will move much of the staging code that take place in the python
        initialization subroutines of the variational and ensemble DA jobs into
        Jinja2-templated YAML files to be passed into the wxflow file handler.
        Much of the staging has already been done this way, but this PR simply
        expands that strategy.

        The old Python routines that were doing this staging are now removed.
        This is part of a broader refactoring of the pygfs tasking.

        wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a
        companion to this PR.

        Co-authored-by: danholdaway <[email protected]>
        Co-authored-by: DavidNew-NOAA <[email protected]>
        Co-authored-by: DavidNew-NOAA <[email protected]>
        Co-authored-by: Dan Holdaway <[email protected]>

    commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b
    Author: Rahul Mahajan <[email protected]>
    Date:   Fri Jun 28 14:56:19 2024 -0400

        Revert PR 2681 (#2739)

        This PR:
        - reverts #2681 in part
        - keeps some changes for `RUN`.
        - is a hotfix
        - should be merged ASAP after consensus w/ @guillaumevernieres
        @CatherineThomas-NOAA @WalterKolczynski-NOAA

    commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed Jun 26 15:46:08 2024 -0400

        updated Finalize in Jenkinsfile and added try block around scm checkout (#2692)

        We are updating the Jenkins Pipeline with a try block around checkout to
        capture errors for the user.
        Also cleaned up Finalize and added section to clean out workspace on
        success.

    commit 968568f682bac7564095440bdb7813abefd76821
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 26 13:27:19 2024 -0400

        Activate snow DA test on WCOSS (#2720)

        Activate the snow DA test on WCOSS.

    commit 7706760bb8adbdf78cb640b02739023c886e7699
    Author: Rahul Mahajan <[email protected]>
    Date:   Wed Jun 26 10:02:22 2024 -0400

        Cleanup of stale RUNDIRS from an experiment (#2719)

        This PR:
        - removes stale temporary scratch run directories from `$DATAROOT/`
        every 3 days.
        - should help to scrub failed attempts.
        - removes an unused variable `RUNDIR` defined in `config.base`

    commit 8962991691b5f0857b813bddfd28aa1034d4bd2b
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jun 26 09:43:48 2024 -0400

        Update logic for MOM6 number of layers/exception values (#2681)

        Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine
        how many layers and sets the exception value for MOM6 to be 1e-34 for
        all scenarios. Note, we will no longer have zeros in the ocean grib
        output and the DA will also run without issues.

        Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615

    commit 12431f76bdce807067929415007592cffc8a2457
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Wed Jun 26 07:42:35 2024 -0600

        Update wave jobs to use COMIN/COMOUT (#2643)

        NCO has requested that each COM variable specify whether it is an input
        or an output.
        This completes that process for the global-workflow wave
        model and products tasks.
        Refs #2451

    commit b902c0bac126c323a07186ad8881384b032b6fda
    Author: David Huber <[email protected]>
    Date:   Tue Jun 25 07:48:46 2024 -0400

        Assign machine- and RUN-specific resources (#2672)

        Redefine resource variables based explicitly on RUN or CDUMP

        Additionally, machine-specific resources are moved out of
        config.resources and placed in respective config.resources.{machine}
        files.

        Resolves #177 #2672

    commit 5edbd123e2878a07f5cce8e3c7ea6147f286633a
    Merge: 09333c01d 4e1b937b6
    Author: Janet Derrico <[email protected]>
    Date:   Mon Jun 24 12:44:05 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit 4e1b937b67ed220120e81925c4507f03b9b8965f
    Author: David Huber <[email protected]>
    Date:   Mon Jun 24 10:50:52 2024 -0400

        Add minimum software requirements (#2712)

        Adds a table to HPC documentation stating the minimum support versions

    commit f43a86276aaef91efa28faadc71a3cf50e749efe
    Author: David Huber <[email protected]>
    Date:   Fri Jun 21 13:44:29 2024 -0400

        Fix and simplify online archiving and reenable METplus jobs (#2687)

        This fixes the online archiving portion of the `*arch` and `*earc00`
        jobs, a prerequisite for running METplus.  This also reenables
        METplus by default.

        The approach previously taken created `FileHandler` dictionaries at
        varying levels within the resulting yaml, which was not properly parsed
        by `exglobal_archive.py`. This approach creates a single `FileHandler`
        dictionary and is much less complicated overall.

        Resolves #2673 #2647

    commit 8993b42cb91144c0ab0501dc7841ea8d675c4701
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 19 21:51:22 2024 -0400

        Eliminate post groups (#2667)

        Eliminates the post groups used for upp and products jobs so that each
        task only processes one forecast hour. This is more efficient and
        greatly simplifies downstream dependencies that depend on a specific
        forecast hour.

        Resolves #2666
        Refs #2642

    commit 0b810c888239853fedd0e4584fe62536c6aaacdf
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 18 20:32:48 2024 -0600

        Removes misleading "No such file or directory" syntax errors from output files (#2688)

        This PR addresses issue #1252. The following is accomplished:

        - Prior to removing files, the existence of a file is checked prior to
        attempting to remove; this is performed as noted
        [here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369);
        this PR only addresses the the `chgrp` issue.

        Refs #1252

        ---------

        Co-authored-by: David Huber <[email protected]>

    commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 18 12:17:59 2024 -0600

        Hotfix for bug in template names. (#2697)

        This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/`
        template.
        Resolves #2696
        Refs #2451

    commit 35d4d99eaac669721add9ddcc793153e5ab3b30a
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 18 08:06:53 2024 -0600

        Update archive job to use COMIN/COMOUT (#2668)

        NCO has requested that each COM variable specify whether it is an input
        or an output. This completes that process for the global-workflow
        archive task.

        Refs #2451
        ---------

        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>
        Co-authored-by: David Huber <[email protected]>

    commit 47b3a581c8257fa24411fb400df8bb0e1e04972a
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jun 17 22:55:38 2024 -0400

        Turn on high-frequency output in extended test (#2679)

        Turns on high-frequency (hourly) output in the extended products test to
        exercise that aspect of the code. This test only runs on WCOSS.

        Also adds the hooks to optionally turn on the metplus jobs, but that is
        deferred as they are not currently working correctly.

    commit 38f2df9fb0c074b1f80d3c637080be79be693161
    Author: David Huber <[email protected]>
    Date:   Mon Jun 17 17:12:55 2024 +0000

        Optimize wavepostpnt (#2657)

        Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs

        This is done by
        1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by
        - performing operations on all files at once instead of looping over
        each file
            - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`)
            - combining `sed` and `grep` calls when possible
            - adding logic to `awk` calls instead of handling that logic in bash
        2) minimizing as much as possible the amount of data on disk that has to
        be read in (e.g. limiting sed to read only the line numbers it needs)
        ---------

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

    commit 5af325a6a4e0a14d180514a418603ca79fada487
    Author: Dan Holdaway <[email protected]>
    Date:   Fri Jun 14 18:05:23 2024 -0400

        Update GDASapp hash to move JCB into GDASapp (#2665)

        This PR moves JCB into GDASapp. The PR
        also bumps up the hash of GDASapp to what is in `feature/move_jcb`,
        which at time of writing is develop plus the absorption of JCB into
        GDASapp.
        Note that I also took the changes from
        https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the
        testing @RussTreadon-NOAA has done.

    commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b
    Author: Yaping Wang <[email protected]>
    Date:   Fri Jun 14 10:18:17 2024 -0500

        Add observation preparation job for aerosols DA to workflow (#2624)

        Add a prepaeroobs job to prepare aerosol obs files for DA.

        This job does quality control of the VIIRS aerosol raw observations and
        convert them to ioda format.

        Resolves #2623
        ---------

        Co-authored-by: ypwang19 <[email protected]>
        Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>
        Co-authored-by: Cory Martin <[email protected]>
        Co-authored-by: David Huber <[email protected]>

    commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4
    Author: Jessica Meixner <[email protected]>
    Date:   Fri Jun 14 11:04:41 2024 -0400

        Remove ocean daily files (#2689)

        This PR removes the ocn_daily files that are produced by the ocean
        component. These files can be recreated by averaging data that exists in
        the 6 hour aveaged files if needed.

        Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675
        Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by
        removing them and making this obsolete)

    commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu Jun 13 12:22:03 2024 -0400

        Update Jenkinsfile

        needed a comma

    commit dc21eac6c3941d7f30803891d91d82f4cc1f8183
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu Jun 13 11:41:14 2024 -0400

        Add Hercules-EMC to the Jenkins configurable parameter list (#2685)

        This quick-fix PR is to update the Jenkins Pipeline's configurable
        parameter list to include the **Hercules-EMC** node.
        This allows Jenkins users to restart Jobs in the controller when no
        updates have been made.

    commit ebacebfbe458634b8c80af6a735d6b6d01e4e406
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Thu Jun 13 11:20:24 2024 -0400

        Update gdas.cd and gsi_utils hashes (#2641)

        This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The
        updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea
        build for gsi_utils.

        Resolves #2640

    commit 34155fb4767769600a1ff95f0a65e37081addc2a
    Author: Neil Barton <[email protected]>
    Date:   Thu Jun 13 11:18:22 2024 -0400

        Add ability to use GEFS replay ICs (#2559)

        The PR allows the use of ICs from PSL's replay analysis. These replay
        ICs will be used for GEFS reforecasting and SFS. Two main changes are
        associated with these updates: (1) replay ICs being valid at 3Z, and (2)
        the use of warm starts.

        Resolves #1838

        ---------

        Co-authored-by: Jessica Meixner <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>

    commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Wed Jun 12 19:25:42 2024 -0600

        Replace `sleep` with `wait_for_file` (#2586)

        This PR addresses issue #2444. The following is accomplished:

        - All `sleep` statements are replaced with `wait_for_file` for the
        relevant scripts beneath `scripts` and `ush`;
        - Indentation and shell-norms are updated where applicable.

        Note: The WAFS scripts are not updated as per @aerorahul direction.

        Resolves #2444

        ---------

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

    commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 12 13:31:55 2024 -0400

        Add COM template for JEDI obs (#2678)

        Adds a COM template to define a path to store obs processed for JEDI.
        This will allow UFSDA to stop writing to COM_OBS, which should be
        read-only as it belongs to obsproc in operations.

        No functional change yet.

    commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed
    Author: Guoqing Ge <[email protected]>
    Date:   Wed Jun 12 09:06:23 2024 -0600

        Link both global-nest fix files and non-nest ones at the same time (#2632)

        This PR enables linking both global-nest fix files and non-nest ones at
        the same time and users can run both nesting and non-nesting experiments
        at the same time without worries about what fix files to be linked.

        Resolves #2631

    commit 61de004d4f9e9edf8a31bb173f2719b46451a36a
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jun 12 11:03:13 2024 -0400

        Update ufs-weather-model  (#2663)

        Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack
        allowing some temporary fixes to be reverted.
        * removes upp submodule
        * uses upp from the ufs-weather-model
        * restores the build and link that were hacked during the Hera Rocky 8
        transition to allow for UPP submodule
        * Removes forecast directories in clean-up

        Resolves #2617
        Resolves #2437

        ---------

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

    commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d
    Author: Eric Sinsky - NOAA <[email protected]>
    Date:   Wed Jun 12 01:15:37 2024 -0400

        Add ability to process ocean/ice products specific to GEFS (#2561)

        This PR begins to add the capability to produce GEFSv13 ocean and ice
        products in the global-workflow according to stakeholder requirements.
        The following features are added.

        - An oceanice prod yaml file has been added to address the ocean and ice
        products specific to GEFSv13.
        - The rocoto dependencies and config.base for GEFS have also been
        modified to allow for 24-hour averaged ocean and ice output.
        - Various scripts have been modified to allow for ocean and ice output
        frequencies of 24 hours.
        - `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN`
        and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`.

        Refs #1878

    commit 6691e7489650e0b738c176fbd096109288dc09b6
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 11 21:15:07 2024 -0600

        Update cleanup job to use COMIN/COMOUT (#2649)

        NCO has requested that each COM variable specify whether it is an input
        or an output. This completes that process for the global-workflow
        clean-up task.

        Refs #2451

        ---------

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

    commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Tue Jun 11 16:17:25 2024 -0400

        Add overwrite to creat experiment in BASH CI (#2676)

        This is a quick hotfix to the CI BASH driver script adding `--overwrite`
        to create experiment script to avoid errors from restarting an
        experiment.

    commit e7909af8d9e1f34140388a3f8556d8e582c58fe5
    Author: emilyhcliu <[email protected]>
    Date:   Mon Jun 10 15:11:27 2024 -0400

        Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py  (#2645)

        This PR proposes updates for the following two scripts:

        1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select
        CRTM cloud optical table based on cloud microphysical scheme indicated
        by `imp_physics'
        The default scheme in the GFS forecast model is Thompson scheme
        (imp_physics = 8).

        2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in
        the script due to increased variables to interplate increments and
        calculate analysis in the netcdf_io routines in GSI-utils.
        Here is the related [PR #46 for
        GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46).

        ---------

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

    commit 9caa51de8fb7be07d2e61775da01937d576964f6
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Thu Jun 6 22:15:23 2024 -0600

        Update RDHPCS Hera resource for `eupd` task (#2636)

        As per @wx20jjung, the resource for the `eupd` task have been updated
        for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job
        fails.

        Resolves #2454

        ---------

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

    commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b
    Author: DavidNew-NOAA <[email protected]>
    Date:   Thu Jun 6 11:49:03 2024 -0400

        Parameterize some things in config.atmanl and config.atmensanl (#2661)

        This PR adds some parameters in config.atmanl and config.atmensanl that
        can be altered with the defaults.yaml. The motivation is to make these
        files match those in the GDASApp JJOB tests (example:
        https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl),
        so we can just use the Global Workflow config.atmanl and
        config.atmensanl in the tests rather than custom ones in GDASApp that
        have to be separately updated every time the ones in the Global Workflow
        are updated.

    commit 54ea0b73a07921be5fbb07fe41e976888bd3e549
    Author: Guillaume Vernieres <[email protected]>
    Date:   Thu Jun 6 01:36:02 2024 -0400

        Add links to the ocean insitu obs processing tools (#2644)

        Add links to the marine bufr to ioda converters for the marine insitu
        observations.

        - fixes https://github.com/NOAA-EMC/GDASApp/issues/1106
        - waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135

    commit 205d0c2b13e2d7755cec75bf8c978ab20d453862
    Author: David Huber <[email protected]>
    Date:   Wed Jun 5 17:31:30 2024 +0000

        Update S4 point of contact in docs (#2660)

        Update the point of contact for global workflow issues on S4.

    commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Wed Jun 5 12:50:14 2024 -0400

        Enable wcoss2 ufsda build and module load (#2620)

        This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2.

        Resolves #2602
        Resolves #2579

    commit 67b833e0c7bc390865d453588b4609a1a7ede981
    Author: Jessica Meixner <[email protected]>
    Date:   Tue Jun 4 13:33:43 2024 -0400

        Update ufs-weather-model  (#2646)

        Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6
        This should resolve the issue and allow C768 runs on Hera and allow for CICE
        to run on WCOSS2 (due to library updates to allow linking).

        From what I can tell, all updates needed were done by
        @HenryWinterbottom-NOAA which were updates for CICE

        Fixes #2490

    commit c44d0ac86cfdf78eb87492431bf6d825e8bae637
    Author: GwenChen-NOAA <[email protected]>
    Date:   Tue Jun 4 10:29:49 2024 -0400

        Update wmo parm files to fix WMO header (#2652)

        This PR updates wmo parm files to switch WMO header of precipitation
        type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to
        instantaneous.

        Resolves #2566

    commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60
    Author: Cory Martin <[email protected]>
    Date:   Tue Jun 4 13:55:33 2024 +0000

        Add IAU to snow DA (and its test) (#2610)

        This PR enables IAU for the snow DA which is necessary for GFSv17.

        A snow analysis is created for the center of the window regardless, and
        an additional at the beginning of the window is added if IAU is on. The
        former is needed for UPP and the latter, to initialize the model.

        The increment is valid throughout the window for 3DVar, so the same
        increment is added to both forecasts.

        Additionally, the input file that goes into global_cycle has been
        updated to be the output of the JEDI snow analysis instead of the
        forecast (@jiaruidong2017 I recall discussing this, can you confirm this
        is right or am I mistaken)

        This PR also makes the CI test for snow DA (and aerosol DA) include IAU
        rather than without IAU,.

        ---------

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

    commit c92bf415060750127c9c05a62a1d2851c489551a
    Author: David Huber <[email protected]>
    Date:   Sat Jun 1 05:11:07 2024 +0000

        Archiving cleanup (#2621)

        1) Adds a lot of comments to the jinja templates for archiving
        2) Rearranges the gdas and enkf templates to a more logical order
        3) Fixes a couple of bugs in the enkf archiving of increments and
        analyses
        4) Disables archiving for the half cycle
        5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`,
        instead relying on `DO_FIT2OBS`
        6) Updates wxflow to add the option to not allow undefined variables
        when parsing jinja templates and invokes this feature when running
        archives

        Resolves #2612

    commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri May 31 04:57:08 2024 -0400

        Switch to Rocky 9 built external packages on Hercules (#2608)

        The workflow was updated to use modules built on Rocky 9, but the
        external packages (like prepobs) were still pointing to the versions
        built on CentOS (Orion). This transitions to packages built on Rocky 9.

        Updating of the tracker package has been deferred until later. As such,
        the tracker jobs have been disabled by returning immediately if they are
        on Hercules. Since these jobs are small, resource-wise, it should not
        meaningfully impact turnover time.

    commit 4422550c01c9214a2b3b8890bdcc898123ee216a
    Author: Guoqing Ge <[email protected]>
    Date:   Thu May 30 08:05:23 2024 -0600

        Add the capability to use slurm reservation nodes (#2627)

        Add the capability to use slurm reservation nodes
        Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE

        Resolves #2626

    commit a54153fd9d26126206bc07a1da4e80f50c0c5910
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed May 29 23:24:07 2024 -0400

        Update forecast job to use COMIN/COMOUT (#2622)

        NCO has requested that each COM variable specify whether it is an input
        or an output. This completes that process for the forecast job.

        Refs #2451

        ---------

        Co-authored-by: David Huber <[email protected]>

    commit d69a8af95d492982b918670322ed5c41ab074335
    Author: Jessica Meixner <[email protected]>
    Date:   Wed May 29 21:29:03 2024 -0400

        Update to add 1-deg global wave grid (#2619)

        This PR adds options to use a global 1 deg grid, intended for testing
        with the SFS application.

        Requires new fix file changes NOAA-EMC/global-workflow#2618

    commit 0b4670ecf83b99b72835c8380573b2bca7cf5324
    Author: Jessica Meixner <[email protected]>
    Date:   Wed May 29 17:17:21 2024 -0400

        Add C384mx025_3DVarAOWCDA yamls (#2625)

        Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder.

    commit 2e885d05c64b947f00a3cf055a1277fbfac195c9
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed May 29 13:00:51 2024 -0400

        Script to keep Jenkins Agent persistent from cron (#2634)

        This "persistent" Java Agent launch script can be ran from a cron job:

        - Uses Jenkins Remote API to check the status of the Node connection
        using curl for a given machine.
        - If it is not connected a new agent is launched for that node.

        Resolves #2633

    commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5
    Author: GwenChen-NOAA <[email protected]>
    Date:   Tue May 28 17:17:11 2024 -0400

        Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611)

        Based on users' feedback, this PR do the following:
        1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF
        2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD,
          and VOGRD) from "%g m below water surface" to "%g m below sea level"
        3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m)

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

    commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31
    Author: DavidNew-NOAA <[email protected]>
    Date:   Tue May 28 17:16:23 2024 -0400

        Add atmensanlfv3inc job (#2592)

        This PR creates the atmensanlfv3inc job, the ensemble version of
        atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is
        #[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS
        companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3).

    commit 50c2b8951b29a3c883a778becbf8582f9519eb48
    Author: Anil Kumar <[email protected]>
    Date:   Tue May 28 13:23:53 2024 -0400

        Global-workflow (AR) Generic updates for Gaea C5 (#2515)

        - Port global-workflow’s build and run capability to Gaea-C5
        - Building global-workflow on Gaea-C5
        - Setting up experiments with global-workflow on Gaea-C5

        ---------

        Co-authored-by: AnilKumar-NOAA <[email protected]>
        Co-authored-by: DavidBurrows-NCO <[email protected]>

    commit b6ca771a0c584cbfcbbf9be739765d5f3815df97
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri May 24 10:52:45 2024 -0400

        Update STMP and PTMP settings in host file for Orion and Hercules  (#2614)

        - Updating STMP and PTMP settings in host file for Orion and Hercules
        because they are cross mounted.
        - Also took the opportunity to finally update **SLURM_ACCOUNT** to
        **HPC_ACCOUT** in CI over rides.
        - Added a refactor of the `rocotostat.py` tool that is more pythonic and
        as a execute retry feature because the `rocotostat` utility on Orion has
        been failing sometimes.

    commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f
    Author: Guillaume Vernieres <[email protected]>
    Date:   Tue May 21 23:50:50 2024 -0400

        Sea-ice analysis insertion (#2584)

        Allows cycling and restarting CICE with the sea-ice analysis if the
        marine DA is switched on.

        Resolves #2568
        Resolves NOAA-EMC/GDASApp#1103

    commit 5369a1ff3a3969149fcf32810fad0e50216752b7
    Author: David Huber <[email protected]>
    Date:   Tue May 21 22:12:29 2024 +0000

        Refactored archiving (#2491)

        This provides a new pygfs task, archive.py, that provides all of the
        tools necessary to archive data to the local (`ARCDIR`) and backup
        (`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to
        define the file to be archived or tarred to replace the
        `hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts
        and make it easier to add new data and explicitly handle optional and
        required files.

        For `ATARDIR` archiving, a master jinja template is provided for each
        `RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2,
        master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both
        `enkfgdas` and `enkfgfs` `RUN`s. These templates then include the
        appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on
        experiment, cycle, and coupled parameters. Each of these templates
        corresponds to a single tarball to populate and are tabbed 4 spaces so
        they are defined within the master `datasets` dictionary.

        Future developers should not have to make modifications to archive.py
        unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then
        only a single `elif` needs to be added to the configure method to
        specify the master `ATARDIR` template to archive (e.g.
        `master_gefs.yaml.j2`). If a new component is coming online that needs
        to be archived to `ATARDIR` (e.g. SNOW), then create a new template for
        each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`)
        and reference the template in the appropriate master templates, e.g.

        `master_gdas.yaml:`
        ```jinja
        {% if DO_SNOW %}
        {% include "gdassnow.yaml.j2" %}
        {% endif %}
        ```

        A few other issues were addressed along the way:
        1. Aerosols have been reenabled. Aerosol forecasts should only be
        performed during gdas cycles, but analyses can be performed for both gfs
        and gdas cycles. This was accomplished by setting separate
        `AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs.
        2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`.
        This prevented restarts from being used for cice-enable experiments.
        This feature was not tested.
        3. Create a temporary fix for the `wgrib` utility. For spack-stack
        1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is
        open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in
        existing installations. Once complete, this temporary fix should be
        removed.
        4. The number of `earc` jobs has been reduced for lower resolution
        experiments. Both C48 and C96 experiments will now only have two earc
        jobs (one for the non-member files to archive and another for the member
        files). C192 will have up to 3 earc jobs (one non-member, one for
        members 1-40 and another for members 41-80, if needed).

        Resolves #2345
        Resolves #2318

        ---------

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

    commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri May 17 12:57:59 2024 -0400

         Add remove RUNDIRS step in CI before creating experements (#2607)

        As had been done in Bash CI we need to remove the RUNDIR in Jenkins
        before a creating an experiment in the event that case had beem
        previously ran.

    commit 09333c01dbafddb2d2fe7e181b479af3cc6d3621
    Merge: f7e9f4489 bb930050b
    Author: Janet Derrico <[email protected]>
    Date:   Thu May 16 14:33:19 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit bb930050b3cd51d28ecba6b231c8675f6d11856c
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Thu May 16 12:28:30 2024 -0400

        Adds jjob and other necessities for marine LETKF task (#2564)

        Adds jjob, rocoto script, config file, and other necessities for new
        marine LETKF task.

        Partially addresses NOAA-EMC/GDASApp#1091

    commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu May 16 12:12:06 2024 -0400

        Updating CI Machine configs with redundant PTMP (#2605)

        Quick fix adding PTMP as STMP in Machine configs for CI for completeness

    commit ef340ff33a6f89adf70838206ba3fd56a953fa7a
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu May 16 11:37:30 2024 -0400

        Fix race condition in CI between Orion and Hercules (#2604)

        Hotfix to solve race conditions in the CI system due to cross-mounted
        file systems between Orion and Hercules

    commit e8b17e27f719df280170dc3f5bd9f19917cefaf2
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed May 15 17:16:30 2024 -0400

        Remove existing EXPDIRs and COMROTs when CI is re-run (#2601)

        Quick hotfix for having default for re-runing jobs to start clean with
        new EXPDIRs and COMROTs

    commit b5d113efb1970ede5cd1d3d4dff8d96320519c41
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed May 15 16:52:49 2024 -0400

        Moving logic for skipping hosts in pr cases (#2573)

        This PR removes the logic of skipping hosts for pr cases from
        `create_experiment.py` and moves it to a test in the cron bash driver
        using a `parse_yaml.py` python tool.

        The Jenkins pipeline was not effected as it uses the
        `get_host_case_list.py` utility to form the cases on a per host bases.

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

    commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Wed May 15 13:13:30 2024 -0400

        Update gsi_utils.fd hash (#2598)

        This PR updates the `gsi_utils.fd` hash to bring in updates which add
        safeguards to
        -
        `src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90`
        - `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90`

        The safeguards are described in GSI-utils PR
        [#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated
        issue.

        Resolves #2597

    commit d5366c66bd67f89d118b18956fe230207cbf0aea
    Author: Kate Friedman <[email protected]>
    Date:   Wed May 15 13:12:56 2024 -0400

        Update CICE and MOM6 fix versions (#2600)

        This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions
        to the newer `20240416` timestamps, which includes updates and fixes to
        the `100` (1-deg) resolution files.

        Resolves #2480
        Resolves #2483
        Resolves #2595

    commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b
    Author: David Huber <[email protected]>
    Date:   Mon May 13 22:57:38 2024 +0000

        Limit gfswavepostpnt to 40 PEs/node (#2588)

        This fixes the slow runtime of the gfswavepostpnt job on Hercules. The
        job is very I/O intensive and does not scale well to large nodes, so
        limit the number of jobs/node to 40.

        Resolves #2587

    commit 4fb7c12c325702a47f27c802a5067efd33d0327c
    Author: Fanglin Yang <[email protected]>
    Date:   Mon May 13 16:37:51 2024 -0400

        Update damping and time-step (#2575)

        Updates the model to use explicit Rayleigh damping for u/v and implicit
        damping to w. This improves model stability and allows for longer
        timesteps. Also unifies the GDAS and GFS to use the same damping.

        Results from a test at the C1152 resolution (coupled model) can be found
        at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/

        Resolves #2574

        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
        Co-authored-by: Lisa Bengtsson <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>

    commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri May 10 14:17:13 2024 -0400

        Do not use BUILT_semphore to force rebuilds when re-run (#2593)

        Remove the placement of the `BUILT_semaphore` file after the build in
        the Jenkins Pipeline and force it to rebuild any changes after a PR is
        re-ran.

    commit 2346c6161f75ae02369cbf30f30c6150d3e12b66
    Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com>
    Date:   Thu May 9 21:17:06 2024 -0500

        Migration to Rocky8 spack-stack installations on Jet (#2458)

        # Description
        Migrates Global Workflow to Rocky8 spack-stack installations on Jet.
        Jet has moved from CentOS7 to Rocky8.

        Resolves #2377
        Refs NOAA-EMC/UPP#919
        Refs NOAA-EMC/gfs-utils#60
        Refs NOAA-EMC/GSI#732
        Refs NOAA-EMC/GSI-Monitor#130
        Refs NOAA-EMC/GSI-utils#33

    commit c7b3973014480a20dd8e24edaeb83a9e9e68159f
    Author: Jessica Meixner <[email protected]>
    Date:   Thu May 9 11:36:58 2024 -0400

        Updates for cold start half cycle, then continuing with IAU for WCDA (#2560)

        This PR allows us to run C384 S2S with IAU, but starting with the first
        half-cycle as a cold-start. This will be necessary for cycled testing as
        we build towards the full system for GFSv17. This updates the copying of
        the restarts for RUN=gdas for both ocean and ice copying what the atm
        model is doing. It also reduced the amount of restart files from 4 to 3.

        Other updates:
        * Add DOJEDI ocean triggers for archiving certain files update from:
        @CatherineThomas-NOAA
        * Adds COPY_FINAL_RESTARTS option to turn on/off copying the last
        restart file to COM. Defaults to off...
        * Defines model_start_date_current_cycle & model_start_date_next_cycle
        to help with knowing which IC to grab.

        Refs #2546

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

    commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2
    Author: Dan Holdaway <[email protected]>
    Date:   Wed May 8 20:52:48 2024 -0400

        Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477)

        Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI
        Configuration Builder (JCB) tool so that YAMLs can be made more portable
        and invoke the observation chronicle mechanism.

        Resolves #2476

        Co-authored-by: danholdaway <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

    commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed May 8 02:04:16 2024 -0400

        Add CI test for products (#2567)

        Adds a new version of the atm3DVar test that runs the full forecast
        length and produces most of the secondary products. For now, this test
        will only run on WCOSS due to gempak failures on other machines as well
        as computational needs. On other machines, the original version will run
        (the original version will not run on WCOSS). A…
jderrico-noaa pushed a commit to NOAA-GSL/global-workflow that referenced this issue Sep 27, 2024
@kayeekayee
Update realtime branch, gsl_ufs_rt (#64)
b997e7d 
* Update realtime branch, gsl_ufs_rt.

Squashed commit of the following:

commit 4e0a81f7acf5ccba5de8d3bdf7ab19cae80812cb
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 18:37:50 2024 +0000

    Fix typos/links/dependancy.

commit d5fdcbf8d6e987dbdfcd6b4da34d0934c8d82c3b
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 07:37:52 2024 +0000

    Fixed missing config.base files.

commit c6239f925369b20fd8488e8537969e2f4f9e7725
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 06:53:47 2024 +0000

    Update submodule hashs.

commit 32bf790f67b818ff50a7f6b74388fb81ed175b3a
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 06:09:41 2024 +0000

    Update develop branch, gsl_ufs_dev
     - based on gsl_ufs_dev from KaYee's fork
       global-workflow: 07Aug24,37c53ac [develop_07Aug2024_37c53ac]
       UFS: 19Jul24, c127601
       FV3: 19Jul24, 2527c11
       UPP: 23Apr24, be0410e
       CCPP-PHYSICS: 19Jul24, 46df080
       UFS_UTILS: 26Jun24, 3ef2e6b

    Squashed commit of the following:

    commit 70b557836379bb7e545fcc6642e28d66cfc17735
    Merge: 5edbd123e 37c53ac69
    Author: Janet Derrico <[email protected]>
    Date:   Wed Aug 7 11:02:24 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04
    Author: Kate Friedman <[email protected]>
    Date:   Wed Aug 7 08:11:21 2024 -0400

        Revert MSU FIX_DIRs back to glopara (#2811)

    commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Tue Aug 6 14:47:36 2024 -0400

        Bugfix for updating label states in Jenkins (#2808)

        Quick bug fix for updating state labels in CI during finalize.
        (did not reference GitHub CLI executable correctly in the pipeline
        script)

    commit 8fee36f0307b0c08080e3a8fa8fa6703e7da5fce
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Aug 6 11:02:45 2024 -0400

        Clean-up temporary rundirs - take 2. (#2753)

        This PR:
        - is a follow-up to a previous PR that aggressively pruned run
        directories.
        - removes run directories for the current cycle in the clean-up if the
        cycle is successful. If the cycle is not successful, cleanup is not
        called and all run directories for the cycle are safe from being purged.
        - also updates the PR template to list/query for any updates to
        submodules.

        ---------

        Co-authored-by: David Huber <[email protected]>
        Co-authored-by: David Huber <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

    commit d599fff4aedd41ae587dbe02226acb12ff48efc1
    Author: HelinWei-NOAA <[email protected]>
    Date:   Mon Aug 5 05:31:31 2024 -0400

        Change land surface for HR4 (#2787)

        Resets the default value of opt_diag to 2 corresponding to the land
        surface upgrades in ufs-weather-model for HR4.

        Resolves #2786

    commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb
    Author: David Huber <[email protected]>
    Date:   Fri Aug 2 15:41:29 2024 -0400

        Run METplus serially and correct the name of prod tasks (#2804)

        Adds 2 hot fixes:

        - METplus v9.1.3 has a bug in it that sometimes attempts to create
        multiple copies of the same directory when running in parallel, causing
        a Python error and downstream problems. This PR makes METplus run in
        serial mode, preventing such issues.
        - Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in
        workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod)

    commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri Aug 2 15:03:45 2024 -0400

        Update Java Agent launching script for Jenkins connections (#2762)

        Made updates to the Jenkins Launching Script for robustness and less
        ambiguous documentation:
        - Clearer distinction between required user token for the remote api and
        the systems token for launching
        - Added pre-checks: `gh` is authenticating, named compliant token and
        secret file exists
        - More robust Jason based parser of the remote api response for checking
        the state of the Node connection
        - For `cron` use a 5 minute pause and recheck was added before
        re-launching of the java agent
        - Added concise header documentation of requirements and purpose
        ---------

        Co-authored-by: David Huber <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

    commit b73b1fd203496db97f8067652659573a632bcc67
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri Aug 2 07:59:06 2024 -0400

        Fix erroneous cdump addition (#2803)

    commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3
    Author: Rahul Mahajan <[email protected]>
    Date:   Thu Aug 1 20:26:13 2024 -0400

        Update ocean post-processing triggers (#2784)

        This PR:
        - replaces `check_netcdf.sh` checker for ocean post-processing with with
        ocean output at the next forecast hour or finishing of the forecast job
        for ocean prod
        - removes no longer needed `ush/check_netcdf.sh`

    commit aa2af1ca8d59424a60a1730722bf528775d9e606
    Author: GeorgeGayno-NOAA <[email protected]>
    Date:   Thu Aug 1 16:46:10 2024 -0400

        Update the gfs_utils repository hash (#2801)

        # Description
        Point to the latest hash of the gfs-utils repository, which contains the
        bug fix to gaussian_sfcanl.

        Resolves #2669.
        Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73

    commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8
    Author: David Huber <[email protected]>
    Date:   Thu Aug 1 08:12:14 2024 -0400

        Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791)

        Changes how METplus jobs run so that they run on the last GFS cycle for
        a given `PDY`.

        This is a departure from operations where the METplus jobs run on the
        00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through
        `${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on
        `${PDY}18` for cycles 00-18. See
        https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details.

    commit 1cf8b448af562dbb7af198399c78c585977e81da
    Author: David Huber <[email protected]>
    Date:   Tue Jul 30 10:38:49 2024 -0400

        Simplify resource-related variables, remove CDUMP where unneeded (#2727)

        This overhauls resource-related variables to use a common set of
        variables for each job. In the process, this also removed the use of
        CDUMP in most cases.

        Resolves #1299 #2693

    commit 61875f25c9e971f82ae499b5b612d7f095deebd4
    Author: Eric Sinsky - NOAA <[email protected]>
    Date:   Mon Jul 29 14:40:03 2024 -0400

        Remove f000 from atmos rocoto tasks for replay cases (#2778)

        The main purpose of this PR is to remove the f000 from
        atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In
        cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater
        than `0`, it becomes necessary to have the first lead hour set to
        `OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For
        example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead
        time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and
        the minimum lead time for the ocean_prod rocoto task needs to be 6
        (assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up
        possible by removing 0 from fhrs for atmosphere-related tasks in
        `gefs_tasks.py` when replaying.

        This PR also moves where f000 is being removed for the ocean_prod and
        ice_prod tasks. The if-block that performs this f000 removal has been
        moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`.

        ---------

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

    commit f156a7894d639f177e3e2588f98eec1f6f59aa68
    Author: Jessica Meixner <[email protected]>
    Date:   Fri Jul 26 14:18:32 2024 -0500

        HR4 GWD update (#2732)

        This update is a combination of the gravity wave drag (GWD) versions
        from the NOAA/GSL and NOAA/PSL

    commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891
    Author: David Huber <[email protected]>
    Date:   Thu Jul 25 14:26:52 2024 -0400

        Temporarily disable METplus jobs (#2796)

    commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2
    Author: Guillaume Vernieres <[email protected]>
    Date:   Wed Jul 24 15:00:35 2024 -0400

        Refactoring of the marine B-matrix job (#2749)

        Refactor the functionality of B-matrix generation from the GDASApp

        Resolves #2743

    commit 65a7ab75dc0e4baba06a02e11ed0455787056a68
    Author: David Huber <[email protected]>
    Date:   Tue Jul 23 08:35:48 2024 -0400

        Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775)

        Removes the namespace-based construction of EnKF member COM directories
        in the enkf archive template.

    commit c45b9611f3e701b819bd33dc5af29033f060bb91
    Author: Eric Sinsky - NOAA <[email protected]>
    Date:   Tue Jul 23 00:33:16 2024 -0400

        Add task to process reforecast variables to save on WCOSS2 (#2680)

        # Description
        This PR adds an optional task to the global-workflow to process a subset
        of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for
        the GEFSv13 reforecast. This task is designed to process GEFS variables
        so that specific reforecast product requirements are met. A new variable
        in `config.base` called `DO_EXTRACTVARS` enables this task, which is
        currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by
        default and is specifically a task designed to be executed for the
        GEFSv13 reforecast.

        Refs #1878

        # Type of change
        - New feature (adds functionality)

        # Change characteristics
        - Is this a breaking change (a change in existing functionality)? NO
        - Does this change require a documentation update? NO

        # How has this been tested?
        This has been cloned and tested on WCOSS2. This will need to be tested
        on Hera and other platforms on which the reforecast may be running.

        # Checklist
        - [ ] Any dependent changes have been merged and published
        - [x] My code follows the style guidelines of this project
        - [x] I have performed a self-review of my own code
        - [ ] I have commented my code, particularly in hard-to-understand areas
        - [x] My changes generate no new warnings
        - [x] New and existing tests pass with my changes
        - [ ] I have made corresponding changes to the documentation if
        necessary

        ---------

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

    commit 71dc33c6ca991c16ce743760d99feaaf60f2218a
    Author: David Huber <[email protected]>
    Date:   Mon Jul 22 14:51:53 2024 -0400

        Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774)

        Fix metp* resources and check that they completed properly; add support for Orion Rocky 9

    commit 56df67a90fe090c425199f1285e5aac722c398b1
    Author: David Huber <[email protected]>
    Date:   Mon Jul 22 09:28:18 2024 -0400

        Hotfix: Update jcb to avoid git-lfs files (#2782)

        Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to
        be cloned on Hera.

        This hotfix points to a non-authoritative branch of the GDASApp
        (https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and
        should be updated ASAP back to the authoritative repository.

    commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jul 16 09:44:00 2024 -0400

        Address issues in creating XML for GFS forecast-only with app S2SWA (#2757)

        This bugfix PR:
        - fixes an issue where a user is unable to generate the XML for a GFS
        forecast-only experiment with APP=S2SWA

        Specifically, the changes are related to defining `aero_fcst_cdumps`.
        Following `setup_expt.py`, the user will have to set
        `AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in
        `config.base`.

    commit e0878dba0e53706a7f53429b61aee2936e2c21bf
    Author: Kate Friedman <[email protected]>
    Date:   Mon Jul 15 10:25:11 2024 -0400

        Updated prepobs and fit2obs versions for Orion Rocky9 (#2758)

        Update prepobs to v1.0.2 and fit2obs to v1.1.2

        These versions now support Orion Rocky9. Updates are included
        for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet.

    commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu Jul 11 17:48:47 2024 +0000

        CI maintenance updates and adding CI Unit Tests (#2740)

        This PR has a few maintenance updates to the CI pipeline and adds a test
        directory with Unit Tests
        **Major Maintenance updates:**
        - Added try blocks with appropriate messaging to GitHub PR of failure
        for:
        - - **scm** checkout
        - - build fail (with error logs sent as gists)
        - - create experiment fails with `stderr` sent to GitHub PR messaging
        - Pre-stage FAILS from the above are now captured these fails allow
        FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state
        labels in GitHub - see image below)
        **Minor Maintenance updates:**
        - Fix for STALLED cases reviled from PR 2700 (just needed a lambda
        specifier)
        - Fixed path to experiment directory in PR message (had dropped EXPDIR
        in path)
        - Needed `latin-1` decoder in reading log files for publishing
        **Added python Unit Tests for CI functionality:**
        - Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI
        utility codes
        - Cashed the install of Rocoto in the GitHub Runners to greatly reduce
        stetup time for running the unit tests
        - Unit Tests Python scripts added
        - `test_rocostat.py`: rocoto_statcount() rocoto_summary()
        rocoto_stalled()
          - `test_setup.py`: setup_expt() test_setup_xml()
          - `test_create_experment`: test_create_experiment()
          - - Runs all PR cases that do not have ICs in the GItHub Runner
        - Reporting mechanism in the Actions tab for Python Unit Testing results
        - Test case data for STALLED and RUNNING stored on S3 and pulled using
        wget during runtime of tests

    commit 5ef4db74649b8be03402c17aa29c024e71699a7b
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Thu Jul 11 08:59:24 2024 -0400

        Adds contents of constructor and initialize methods to marine LETKF class (#2635)

        Adds contents of constructor and initialize methods to marine LETKF class

        Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091
        ---------

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

    commit 8998ec7b74123e953b97a93fa14cc78d471a1aee
    Author: David Huber <[email protected]>
    Date:   Tue Jul 9 08:31:57 2024 -0400

        Fix GDAS group B restart archiving (#2735)

        Archives the GDAS restartb dataset at a 6-hour offset from restarta

        This allows cycled experiments to restart from the archives.
        The tabbing for the master archive templates was also added to
        improve readability.

        Resolves #2722

    commit 3ca74771255727033b9dc043c652ac585178629c
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Tue Jul 9 08:28:54 2024 -0400

        Add fcst dependency to ocnanalprep (#2728)

        Add previous cycle's `fcst` as a dependency to `ocnanalprep`

        This ensures that the availability of restart files to the latter. This addresses a
        seldomly-encountered race condition where `ocnanalprep` fails due to the
        lack of the files.

    commit 58fca1668aecd6fb1afd12a441256ad35900e075
    Author: Rahul Mahajan <[email protected]>
    Date:   Fri Jul 5 15:02:23 2024 -0400

        Update (partially) global-workflow for orion+rocky9 (#2741)

        This PR:
        - updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils,
        GFS-utils) to include recent update to their modulefiles for
        Orion+Rocky9 upgrade
        - updates the modulefiles in global-workflow to load modules from
        Orion+Rocky9 paths
        - updates modulefiles for `gwsetup` and `gwci` as well.
        - removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not
        installed.
        - adds `parm/config.gfs/config.resources.ORION` to address GSI
        performance degradation after Rocky 9 upgrade.

        This PR:
        - does not update the build for UPP. Standalone UPP is not available via
        ufs-weather-model as of #2729
        - will need a follow-up update for `prepobs` and `fit2obs` updated
        locations when they are installed in `glopara` space on Orion.

        # Type of change
        - Maintenance (code refactor, clean-up, new CI test, etc.)

        # Change characteristics
        - Is this a breaking change (a change in existing functionality)? NO
        - Does this change require a documentation update? NO

        # How has this been tested?
        This PR is not sufficient for Orion.
        This PR must be tested on other platforms (Hera, WCOSS2) as this PR
        updates submodules.

        # Checklist
        - [ ] Any dependent changes have been merged and published
        - [ ] My code follows the style guidelines of this project
        - [ ] I have performed a self-review of my own code
        - [ ] I have commented my code, particularly in hard-to-understand areas
        - [ ] My changes generate no new warnings
        - [ ] New and existing tests pass with my changes
        - [ ] I have made corresponding changes to the documentation if
        necessary

        ---------

        Co-authored-by: Kate Friedman <[email protected]>

    commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jul 3 21:07:49 2024 -0400

        Update ufs model hash to 20240625 (#2729)

        Updates UFS weather model hash to hash from 2024-06-24 which has orion
        porting updates + a few namelist updates.

    commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85
    Author: David Huber <[email protected]>
    Date:   Wed Jul 3 11:32:40 2024 -0400

        Hotfix for undefined CLUSTERS (#2748)

        Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses
        the native `dict` `get` method to prevent grabbing an unset entry.

    commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf
    Author: GwenChen-NOAA <[email protected]>
    Date:   Wed Jul 3 09:56:08 2024 -0400

        Update gempak job to run one fcst hour per task (#2671)

        This PR updates gempak jobs (gfs, gdas, and goes) from processing all
        forecast hours at once to one forecast hour at a time. This will reduce
        the job runtime to less than 5 min, so restart capability is not needed.

        Resolves #1250
        Ref #2666 #2667
        ---------

        Co-authored-by: Walter.Kolczynski <[email protected]>

    commit 8215ae654202186a4f753c3abe937b7b9b91a9c7
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jul 2 16:22:11 2024 -0400

        Hotfix for clusters from #2701 (#2747)

        Fixes an issue created from #2701 that added `CLUSTERS` to the
        `gaea.yaml`.

    commit 11943e36ba12b3df49c51942da780698fab02d38
    Author: DavidBurrows-NCO <[email protected]>
    Date:   Tue Jul 2 12:58:10 2024 -0400

        Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701)

        This PR sets up the ability on Gaea for auto generation of a clean xml
        file, i.e., an xml file that does not need any alterations before
        running rocoto.
        Refs #2572
        Refs #2664

    commit de8706702ead0630beb54d868f83aa2cb23f8f79
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Mon Jul 1 09:29:14 2024 -0400

        Update for JCB policies and stage DA job files with Jinja2-templates (#2700)

        This PR updates the `gdas.cd` hash to bring in new JCB conventions.
        Resolves #2699

        From #2654
        This PR will move much of the staging code that take place in the python
        initialization subroutines of the variational and ensemble DA jobs into
        Jinja2-templated YAML files to be passed into the wxflow file handler.
        Much of the staging has already been done this way, but this PR simply
        expands that strategy.

        The old Python routines that were doing this staging are now removed.
        This is part of a broader refactoring of the pygfs tasking.

        wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a
        companion to this PR.

        Co-authored-by: danholdaway <[email protected]>
        Co-authored-by: DavidNew-NOAA <[email protected]>
        Co-authored-by: DavidNew-NOAA <[email protected]>
        Co-authored-by: Dan Holdaway <[email protected]>

    commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b
    Author: Rahul Mahajan <[email protected]>
    Date:   Fri Jun 28 14:56:19 2024 -0400

        Revert PR 2681 (#2739)

        This PR:
        - reverts #2681 in part
        - keeps some changes for `RUN`.
        - is a hotfix
        - should be merged ASAP after consensus w/ @guillaumevernieres
        @CatherineThomas-NOAA @WalterKolczynski-NOAA

    commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed Jun 26 15:46:08 2024 -0400

        updated Finalize in Jenkinsfile and added try block around scm checkout (#2692)

        We are updating the Jenkins Pipeline with a try block around checkout to
        capture errors for the user.
        Also cleaned up Finalize and added section to clean out workspace on
        success.

    commit 968568f682bac7564095440bdb7813abefd76821
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 26 13:27:19 2024 -0400

        Activate snow DA test on WCOSS (#2720)

        Activate the snow DA test on WCOSS.

    commit 7706760bb8adbdf78cb640b02739023c886e7699
    Author: Rahul Mahajan <[email protected]>
    Date:   Wed Jun 26 10:02:22 2024 -0400

        Cleanup of stale RUNDIRS from an experiment (#2719)

        This PR:
        - removes stale temporary scratch run directories from `$DATAROOT/`
        every 3 days.
        - should help to scrub failed attempts.
        - removes an unused variable `RUNDIR` defined in `config.base`

    commit 8962991691b5f0857b813bddfd28aa1034d4bd2b
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jun 26 09:43:48 2024 -0400

        Update logic for MOM6 number of layers/exception values (#2681)

        Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine
        how many layers and sets the exception value for MOM6 to be 1e-34 for
        all scenarios. Note, we will no longer have zeros in the ocean grib
        output and the DA will also run without issues.

        Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615

    commit 12431f76bdce807067929415007592cffc8a2457
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Wed Jun 26 07:42:35 2024 -0600

        Update wave jobs to use COMIN/COMOUT (#2643)

        NCO has requested that each COM variable specify whether it is an input
        or an output.
        This completes that process for the global-workflow wave
        model and products tasks.
        Refs #2451

    commit b902c0bac126c323a07186ad8881384b032b6fda
    Author: David Huber <[email protected]>
    Date:   Tue Jun 25 07:48:46 2024 -0400

        Assign machine- and RUN-specific resources (#2672)

        Redefine resource variables based explicitly on RUN or CDUMP

        Additionally, machine-specific resources are moved out of
        config.resources and placed in respective config.resources.{machine}
        files.

        Resolves #177 #2672

    commit 5edbd123e2878a07f5cce8e3c7ea6147f286633a
    Merge: 09333c01d 4e1b937b6
    Author: Janet Derrico <[email protected]>
    Date:   Mon Jun 24 12:44:05 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit 4e1b937b67ed220120e81925c4507f03b9b8965f
    Author: David Huber <[email protected]>
    Date:   Mon Jun 24 10:50:52 2024 -0400

        Add minimum software requirements (#2712)

        Adds a table to HPC documentation stating the minimum support versions

    commit f43a86276aaef91efa28faadc71a3cf50e749efe
    Author: David Huber <[email protected]>
    Date:   Fri Jun 21 13:44:29 2024 -0400

        Fix and simplify online archiving and reenable METplus jobs (#2687)

        This fixes the online archiving portion of the `*arch` and `*earc00`
        jobs, a prerequisite for running METplus.  This also reenables
        METplus by default.

        The approach previously taken created `FileHandler` dictionaries at
        varying levels within the resulting yaml, which was not properly parsed
        by `exglobal_archive.py`. This approach creates a single `FileHandler`
        dictionary and is much less complicated overall.

        Resolves #2673 #2647

    commit 8993b42cb91144c0ab0501dc7841ea8d675c4701
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 19 21:51:22 2024 -0400

        Eliminate post groups (#2667)

        Eliminates the post groups used for upp and products jobs so that each
        task only processes one forecast hour. This is more efficient and
        greatly simplifies downstream dependencies that depend on a specific
        forecast hour.

        Resolves #2666
        Refs #2642

    commit 0b810c888239853fedd0e4584fe62536c6aaacdf
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 18 20:32:48 2024 -0600

        Removes misleading "No such file or directory" syntax errors from output files (#2688)

        This PR addresses issue #1252. The following is accomplished:

        - Prior to removing files, the existence of a file is checked prior to
        attempting to remove; this is performed as noted
        [here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369);
        this PR only addresses the the `chgrp` issue.

        Refs #1252

        ---------

        Co-authored-by: David Huber <[email protected]>

    commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 18 12:17:59 2024 -0600

        Hotfix for bug in template names. (#2697)

        This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/`
        template.
        Resolves #2696
        Refs #2451

    commit 35d4d99eaac669721add9ddcc793153e5ab3b30a
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 18 08:06:53 2024 -0600

        Update archive job to use COMIN/COMOUT (#2668)

        NCO has requested that each COM variable specify whether it is an input
        or an output. This completes that process for the global-workflow
        archive task.

        Refs #2451
        ---------

        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>
        Co-authored-by: David Huber <[email protected]>

    commit 47b3a581c8257fa24411fb400df8bb0e1e04972a
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jun 17 22:55:38 2024 -0400

        Turn on high-frequency output in extended test (#2679)

        Turns on high-frequency (hourly) output in the extended products test to
        exercise that aspect of the code. This test only runs on WCOSS.

        Also adds the hooks to optionally turn on the metplus jobs, but that is
        deferred as they are not currently working correctly.

    commit 38f2df9fb0c074b1f80d3c637080be79be693161
    Author: David Huber <[email protected]>
    Date:   Mon Jun 17 17:12:55 2024 +0000

        Optimize wavepostpnt (#2657)

        Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs

        This is done by
        1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by
        - performing operations on all files at once instead of looping over
        each file
            - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`)
            - combining `sed` and `grep` calls when possible
            - adding logic to `awk` calls instead of handling that logic in bash
        2) minimizing as much as possible the amount of data on disk that has to
        be read in (e.g. limiting sed to read only the line numbers it needs)
        ---------

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

    commit 5af325a6a4e0a14d180514a418603ca79fada487
    Author: Dan Holdaway <[email protected]>
    Date:   Fri Jun 14 18:05:23 2024 -0400

        Update GDASapp hash to move JCB into GDASapp (#2665)

        This PR moves JCB into GDASapp. The PR
        also bumps up the hash of GDASapp to what is in `feature/move_jcb`,
        which at time of writing is develop plus the absorption of JCB into
        GDASapp.
        Note that I also took the changes from
        https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the
        testing @RussTreadon-NOAA has done.

    commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b
    Author: Yaping Wang <[email protected]>
    Date:   Fri Jun 14 10:18:17 2024 -0500

        Add observation preparation job for aerosols DA to workflow (#2624)

        Add a prepaeroobs job to prepare aerosol obs files for DA.

        This job does quality control of the VIIRS aerosol raw observations and
        convert them to ioda format.

        Resolves #2623
        ---------

        Co-authored-by: ypwang19 <[email protected]>
        Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>
        Co-authored-by: Cory Martin <[email protected]>
        Co-authored-by: David Huber <[email protected]>

    commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4
    Author: Jessica Meixner <[email protected]>
    Date:   Fri Jun 14 11:04:41 2024 -0400

        Remove ocean daily files (#2689)

        This PR removes the ocn_daily files that are produced by the ocean
        component. These files can be recreated by averaging data that exists in
        the 6 hour aveaged files if needed.

        Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675
        Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by
        removing them and making this obsolete)

    commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu Jun 13 12:22:03 2024 -0400

        Update Jenkinsfile

        needed a comma

    commit dc21eac6c3941d7f30803891d91d82f4cc1f8183
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu Jun 13 11:41:14 2024 -0400

        Add Hercules-EMC to the Jenkins configurable parameter list (#2685)

        This quick-fix PR is to update the Jenkins Pipeline's configurable
        parameter list to include the **Hercules-EMC** node.
        This allows Jenkins users to restart Jobs in the controller when no
        updates have been made.

    commit ebacebfbe458634b8c80af6a735d6b6d01e4e406
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Thu Jun 13 11:20:24 2024 -0400

        Update gdas.cd and gsi_utils hashes (#2641)

        This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The
        updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea
        build for gsi_utils.

        Resolves #2640

    commit 34155fb4767769600a1ff95f0a65e37081addc2a
    Author: Neil Barton <[email protected]>
    Date:   Thu Jun 13 11:18:22 2024 -0400

        Add ability to use GEFS replay ICs (#2559)

        The PR allows the use of ICs from PSL's replay analysis. These replay
        ICs will be used for GEFS reforecasting and SFS. Two main changes are
        associated with these updates: (1) replay ICs being valid at 3Z, and (2)
        the use of warm starts.

        Resolves #1838

        ---------

        Co-authored-by: Jessica Meixner <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>

    commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Wed Jun 12 19:25:42 2024 -0600

        Replace `sleep` with `wait_for_file` (#2586)

        This PR addresses issue #2444. The following is accomplished:

        - All `sleep` statements are replaced with `wait_for_file` for the
        relevant scripts beneath `scripts` and `ush`;
        - Indentation and shell-norms are updated where applicable.

        Note: The WAFS scripts are not updated as per @aerorahul direction.

        Resolves #2444

        ---------

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

    commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 12 13:31:55 2024 -0400

        Add COM template for JEDI obs (#2678)

        Adds a COM template to define a path to store obs processed for JEDI.
        This will allow UFSDA to stop writing to COM_OBS, which should be
        read-only as it belongs to obsproc in operations.

        No functional change yet.

    commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed
    Author: Guoqing Ge <[email protected]>
    Date:   Wed Jun 12 09:06:23 2024 -0600

        Link both global-nest fix files and non-nest ones at the same time (#2632)

        This PR enables linking both global-nest fix files and non-nest ones at
        the same time and users can run both nesting and non-nesting experiments
        at the same time without worries about what fix files to be linked.

        Resolves #2631

    commit 61de004d4f9e9edf8a31bb173f2719b46451a36a
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jun 12 11:03:13 2024 -0400

        Update ufs-weather-model  (#2663)

        Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack
        allowing some temporary fixes to be reverted.
        * removes upp submodule
        * uses upp from the ufs-weather-model
        * restores the build and link that were hacked during the Hera Rocky 8
        transition to allow for UPP submodule
        * Removes forecast directories in clean-up

        Resolves #2617
        Resolves #2437

        ---------

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

    commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d
    Author: Eric Sinsky - NOAA <[email protected]>
    Date:   Wed Jun 12 01:15:37 2024 -0400

        Add ability to process ocean/ice products specific to GEFS (#2561)

        This PR begins to add the capability to produce GEFSv13 ocean and ice
        products in the global-workflow according to stakeholder requirements.
        The following features are added.

        - An oceanice prod yaml file has been added to address the ocean and ice
        products specific to GEFSv13.
        - The rocoto dependencies and config.base for GEFS have also been
        modified to allow for 24-hour averaged ocean and ice output.
        - Various scripts have been modified to allow for ocean and ice output
        frequencies of 24 hours.
        - `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN`
        and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`.

        Refs #1878

    commit 6691e7489650e0b738c176fbd096109288dc09b6
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 11 21:15:07 2024 -0600

        Update cleanup job to use COMIN/COMOUT (#2649)

        NCO has requested that each COM variable specify whether it is an input
        or an output. This completes that process for the global-workflow
        clean-up task.

        Refs #2451

        ---------

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

    commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Tue Jun 11 16:17:25 2024 -0400

        Add overwrite to creat experiment in BASH CI (#2676)

        This is a quick hotfix to the CI BASH driver script adding `--overwrite`
        to create experiment script to avoid errors from restarting an
        experiment.

    commit e7909af8d9e1f34140388a3f8556d8e582c58fe5
    Author: emilyhcliu <[email protected]>
    Date:   Mon Jun 10 15:11:27 2024 -0400

        Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py  (#2645)

        This PR proposes updates for the following two scripts:

        1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select
        CRTM cloud optical table based on cloud microphysical scheme indicated
        by `imp_physics'
        The default scheme in the GFS forecast model is Thompson scheme
        (imp_physics = 8).

        2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in
        the script due to increased variables to interplate increments and
        calculate analysis in the netcdf_io routines in GSI-utils.
        Here is the related [PR #46 for
        GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46).

        ---------

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

    commit 9caa51de8fb7be07d2e61775da01937d576964f6
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Thu Jun 6 22:15:23 2024 -0600

        Update RDHPCS Hera resource for `eupd` task (#2636)

        As per @wx20jjung, the resource for the `eupd` task have been updated
        for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job
        fails.

        Resolves #2454

        ---------

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

    commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b
    Author: DavidNew-NOAA <[email protected]>
    Date:   Thu Jun 6 11:49:03 2024 -0400

        Parameterize some things in config.atmanl and config.atmensanl (#2661)

        This PR adds some parameters in config.atmanl and config.atmensanl that
        can be altered with the defaults.yaml. The motivation is to make these
        files match those in the GDASApp JJOB tests (example:
        https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl),
        so we can just use the Global Workflow config.atmanl and
        config.atmensanl in the tests rather than custom ones in GDASApp that
        have to be separately updated every time the ones in the Global Workflow
        are updated.

    commit 54ea0b73a07921be5fbb07fe41e976888bd3e549
    Author: Guillaume Vernieres <[email protected]>
    Date:   Thu Jun 6 01:36:02 2024 -0400

        Add links to the ocean insitu obs processing tools (#2644)

        Add links to the marine bufr to ioda converters for the marine insitu
        observations.

        - fixes https://github.com/NOAA-EMC/GDASApp/issues/1106
        - waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135

    commit 205d0c2b13e2d7755cec75bf8c978ab20d453862
    Author: David Huber <[email protected]>
    Date:   Wed Jun 5 17:31:30 2024 +0000

        Update S4 point of contact in docs (#2660)

        Update the point of contact for global workflow issues on S4.

    commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Wed Jun 5 12:50:14 2024 -0400

        Enable wcoss2 ufsda build and module load (#2620)

        This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2.

        Resolves #2602
        Resolves #2579

    commit 67b833e0c7bc390865d453588b4609a1a7ede981
    Author: Jessica Meixner <[email protected]>
    Date:   Tue Jun 4 13:33:43 2024 -0400

        Update ufs-weather-model  (#2646)

        Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6
        This should resolve the issue and allow C768 runs on Hera and allow for CICE
        to run on WCOSS2 (due to library updates to allow linking).

        From what I can tell, all updates needed were done by
        @HenryWinterbottom-NOAA which were updates for CICE

        Fixes #2490

    commit c44d0ac86cfdf78eb87492431bf6d825e8bae637
    Author: GwenChen-NOAA <[email protected]>
    Date:   Tue Jun 4 10:29:49 2024 -0400

        Update wmo parm files to fix WMO header (#2652)

        This PR updates wmo parm files to switch WMO header of precipitation
        type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to
        instantaneous.

        Resolves #2566

    commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60
    Author: Cory Martin <[email protected]>
    Date:   Tue Jun 4 13:55:33 2024 +0000

        Add IAU to snow DA (and its test) (#2610)

        This PR enables IAU for the snow DA which is necessary for GFSv17.

        A snow analysis is created for the center of the window regardless, and
        an additional at the beginning of the window is added if IAU is on. The
        former is needed for UPP and the latter, to initialize the model.

        The increment is valid throughout the window for 3DVar, so the same
        increment is added to both forecasts.

        Additionally, the input file that goes into global_cycle has been
        updated to be the output of the JEDI snow analysis instead of the
        forecast (@jiaruidong2017 I recall discussing this, can you confirm this
        is right or am I mistaken)

        This PR also makes the CI test for snow DA (and aerosol DA) include IAU
        rather than without IAU,.

        ---------

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

    commit c92bf415060750127c9c05a62a1d2851c489551a
    Author: David Huber <[email protected]>
    Date:   Sat Jun 1 05:11:07 2024 +0000

        Archiving cleanup (#2621)

        1) Adds a lot of comments to the jinja templates for archiving
        2) Rearranges the gdas and enkf templates to a more logical order
        3) Fixes a couple of bugs in the enkf archiving of increments and
        analyses
        4) Disables archiving for the half cycle
        5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`,
        instead relying on `DO_FIT2OBS`
        6) Updates wxflow to add the option to not allow undefined variables
        when parsing jinja templates and invokes this feature when running
        archives

        Resolves #2612

    commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri May 31 04:57:08 2024 -0400

        Switch to Rocky 9 built external packages on Hercules (#2608)

        The workflow was updated to use modules built on Rocky 9, but the
        external packages (like prepobs) were still pointing to the versions
        built on CentOS (Orion). This transitions to packages built on Rocky 9.

        Updating of the tracker package has been deferred until later. As such,
        the tracker jobs have been disabled by returning immediately if they are
        on Hercules. Since these jobs are small, resource-wise, it should not
        meaningfully impact turnover time.

    commit 4422550c01c9214a2b3b8890bdcc898123ee216a
    Author: Guoqing Ge <[email protected]>
    Date:   Thu May 30 08:05:23 2024 -0600

        Add the capability to use slurm reservation nodes (#2627)

        Add the capability to use slurm reservation nodes
        Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE

        Resolves #2626

    commit a54153fd9d26126206bc07a1da4e80f50c0c5910
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed May 29 23:24:07 2024 -0400

        Update forecast job to use COMIN/COMOUT (#2622)

        NCO has requested that each COM variable specify whether it is an input
        or an output. This completes that process for the forecast job.

        Refs #2451

        ---------

        Co-authored-by: David Huber <[email protected]>

    commit d69a8af95d492982b918670322ed5c41ab074335
    Author: Jessica Meixner <[email protected]>
    Date:   Wed May 29 21:29:03 2024 -0400

        Update to add 1-deg global wave grid (#2619)

        This PR adds options to use a global 1 deg grid, intended for testing
        with the SFS application.

        Requires new fix file changes NOAA-EMC/global-workflow#2618

    commit 0b4670ecf83b99b72835c8380573b2bca7cf5324
    Author: Jessica Meixner <[email protected]>
    Date:   Wed May 29 17:17:21 2024 -0400

        Add C384mx025_3DVarAOWCDA yamls (#2625)

        Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder.

    commit 2e885d05c64b947f00a3cf055a1277fbfac195c9
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed May 29 13:00:51 2024 -0400

        Script to keep Jenkins Agent persistent from cron (#2634)

        This "persistent" Java Agent launch script can be ran from a cron job:

        - Uses Jenkins Remote API to check the status of the Node connection
        using curl for a given machine.
        - If it is not connected a new agent is launched for that node.

        Resolves #2633

    commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5
    Author: GwenChen-NOAA <[email protected]>
    Date:   Tue May 28 17:17:11 2024 -0400

        Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611)

        Based on users' feedback, this PR do the following:
        1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF
        2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD,
          and VOGRD) from "%g m below water surface" to "%g m below sea level"
        3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m)

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

    commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31
    Author: DavidNew-NOAA <[email protected]>
    Date:   Tue May 28 17:16:23 2024 -0400

        Add atmensanlfv3inc job (#2592)

        This PR creates the atmensanlfv3inc job, the ensemble version of
        atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is
        #[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS
        companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3).

    commit 50c2b8951b29a3c883a778becbf8582f9519eb48
    Author: Anil Kumar <[email protected]>
    Date:   Tue May 28 13:23:53 2024 -0400

        Global-workflow (AR) Generic updates for Gaea C5 (#2515)

        - Port global-workflow’s build and run capability to Gaea-C5
        - Building global-workflow on Gaea-C5
        - Setting up experiments with global-workflow on Gaea-C5

        ---------

        Co-authored-by: AnilKumar-NOAA <[email protected]>
        Co-authored-by: DavidBurrows-NCO <[email protected]>

    commit b6ca771a0c584cbfcbbf9be739765d5f3815df97
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri May 24 10:52:45 2024 -0400

        Update STMP and PTMP settings in host file for Orion and Hercules  (#2614)

        - Updating STMP and PTMP settings in host file for Orion and Hercules
        because they are cross mounted.
        - Also took the opportunity to finally update **SLURM_ACCOUNT** to
        **HPC_ACCOUT** in CI over rides.
        - Added a refactor of the `rocotostat.py` tool that is more pythonic and
        as a execute retry feature because the `rocotostat` utility on Orion has
        been failing sometimes.

    commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f
    Author: Guillaume Vernieres <[email protected]>
    Date:   Tue May 21 23:50:50 2024 -0400

        Sea-ice analysis insertion (#2584)

        Allows cycling and restarting CICE with the sea-ice analysis if the
        marine DA is switched on.

        Resolves #2568
        Resolves NOAA-EMC/GDASApp#1103

    commit 5369a1ff3a3969149fcf32810fad0e50216752b7
    Author: David Huber <[email protected]>
    Date:   Tue May 21 22:12:29 2024 +0000

        Refactored archiving (#2491)

        This provides a new pygfs task, archive.py, that provides all of the
        tools necessary to archive data to the local (`ARCDIR`) and backup
        (`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to
        define the file to be archived or tarred to replace the
        `hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts
        and make it easier to add new data and explicitly handle optional and
        required files.

        For `ATARDIR` archiving, a master jinja template is provided for each
        `RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2,
        master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both
        `enkfgdas` and `enkfgfs` `RUN`s. These templates then include the
        appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on
        experiment, cycle, and coupled parameters. Each of these templates
        corresponds to a single tarball to populate and are tabbed 4 spaces so
        they are defined within the master `datasets` dictionary.

        Future developers should not have to make modifications to archive.py
        unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then
        only a single `elif` needs to be added to the configure method to
        specify the master `ATARDIR` template to archive (e.g.
        `master_gefs.yaml.j2`). If a new component is coming online that needs
        to be archived to `ATARDIR` (e.g. SNOW), then create a new template for
        each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`)
        and reference the template in the appropriate master templates, e.g.

        `master_gdas.yaml:`
        ```jinja
        {% if DO_SNOW %}
        {% include "gdassnow.yaml.j2" %}
        {% endif %}
        ```

        A few other issues were addressed along the way:
        1. Aerosols have been reenabled. Aerosol forecasts should only be
        performed during gdas cycles, but analyses can be performed for both gfs
        and gdas cycles. This was accomplished by setting separate
        `AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs.
        2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`.
        This prevented restarts from being used for cice-enable experiments.
        This feature was not tested.
        3. Create a temporary fix for the `wgrib` utility. For spack-stack
        1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is
        open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in
        existing installations. Once complete, this temporary fix should be
        removed.
        4. The number of `earc` jobs has been reduced for lower resolution
        experiments. Both C48 and C96 experiments will now only have two earc
        jobs (one for the non-member files to archive and another for the member
        files). C192 will have up to 3 earc jobs (one non-member, one for
        members 1-40 and another for members 41-80, if needed).

        Resolves #2345
        Resolves #2318

        ---------

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

    commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri May 17 12:57:59 2024 -0400

         Add remove RUNDIRS step in CI before creating experements (#2607)

        As had been done in Bash CI we need to remove the RUNDIR in Jenkins
        before a creating an experiment in the event that case had beem
        previously ran.

    commit 09333c01dbafddb2d2fe7e181b479af3cc6d3621
    Merge: f7e9f4489 bb930050b
    Author: Janet Derrico <[email protected]>
    Date:   Thu May 16 14:33:19 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit bb930050b3cd51d28ecba6b231c8675f6d11856c
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Thu May 16 12:28:30 2024 -0400

        Adds jjob and other necessities for marine LETKF task (#2564)

        Adds jjob, rocoto script, config file, and other necessities for new
        marine LETKF task.

        Partially addresses NOAA-EMC/GDASApp#1091

    commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu May 16 12:12:06 2024 -0400

        Updating CI Machine configs with redundant PTMP (#2605)

        Quick fix adding PTMP as STMP in Machine configs for CI for completeness

    commit ef340ff33a6f89adf70838206ba3fd56a953fa7a
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu May 16 11:37:30 2024 -0400

        Fix race condition in CI between Orion and Hercules (#2604)

        Hotfix to solve race conditions in the CI system due to cross-mounted
        file systems between Orion and Hercules

    commit e8b17e27f719df280170dc3f5bd9f19917cefaf2
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed May 15 17:16:30 2024 -0400

        Remove existing EXPDIRs and COMROTs when CI is re-run (#2601)

        Quick hotfix for having default for re-runing jobs to start clean with
        new EXPDIRs and COMROTs

    commit b5d113efb1970ede5cd1d3d4dff8d96320519c41
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed May 15 16:52:49 2024 -0400

        Moving logic for skipping hosts in pr cases (#2573)

        This PR removes the logic of skipping hosts for pr cases from
        `create_experiment.py` and moves it to a test in the cron bash driver
        using a `parse_yaml.py` python tool.

        The Jenkins pipeline was not effected as it uses the
        `get_host_case_list.py` utility to form the cases on a per host bases.

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

    commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Wed May 15 13:13:30 2024 -0400

        Update gsi_utils.fd hash (#2598)

        This PR updates the `gsi_utils.fd` hash to bring in updates which add
        safeguards to
        -
        `src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90`
        - `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90`

        The safeguards are described in GSI-utils PR
        [#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated
        issue.

        Resolves #2597

    commit d5366c66bd67f89d118b18956fe230207cbf0aea
    Author: Kate Friedman <[email protected]>
    Date:   Wed May 15 13:12:56 2024 -0400

        Update CICE and MOM6 fix versions (#2600)

        This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions
        to the newer `20240416` timestamps, which includes updates and fixes to
        the `100` (1-deg) resolution files.

        Resolves #2480
        Resolves #2483
        Resolves #2595

    commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b
    Author: David Huber <[email protected]>
    Date:   Mon May 13 22:57:38 2024 +0000

        Limit gfswavepostpnt to 40 PEs/node (#2588)

        This fixes the slow runtime of the gfswavepostpnt job on Hercules. The
        job is very I/O intensive and does not scale well to large nodes, so
        limit the number of jobs/node to 40.

        Resolves #2587

    commit 4fb7c12c325702a47f27c802a5067efd33d0327c
    Author: Fanglin Yang <[email protected]>
    Date:   Mon May 13 16:37:51 2024 -0400

        Update damping and time-step (#2575)

        Updates the model to use explicit Rayleigh damping for u/v and implicit
        damping to w. This improves model stability and allows for longer
        timesteps. Also unifies the GDAS and GFS to use the same damping.

        Results from a test at the C1152 resolution (coupled model) can be found
        at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/

        Resolves #2574

        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
        Co-authored-by: Lisa Bengtsson <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>

    commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri May 10 14:17:13 2024 -0400

        Do not use BUILT_semphore to force rebuilds when re-run (#2593)

        Remove the placement of the `BUILT_semaphore` file after the build in
        the Jenkins Pipeline and force it to rebuild any changes after a PR is
        re-ran.

    commit 2346c6161f75ae02369cbf30f30c6150d3e12b66
    Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com>
    Date:   Thu May 9 21:17:06 2024 -0500

        Migration to Rocky8 spack-stack installations on Jet (#2458)

        # Description
        Migrates Global Workflow to Rocky8 spack-stack installations on Jet.
        Jet has moved from CentOS7 to Rocky8.

        Resolves #2377
        Refs NOAA-EMC/UPP#919
        Refs NOAA-EMC/gfs-utils#60
        Refs NOAA-EMC/GSI#732
        Refs NOAA-EMC/GSI-Monitor#130
        Refs NOAA-EMC/GSI-utils#33

    commit c7b3973014480a20dd8e24edaeb83a9e9e68159f
    Author: Jessica Meixner <[email protected]>
    Date:   Thu May 9 11:36:58 2024 -0400

        Updates for cold start half cycle, then continuing with IAU for WCDA (#2560)

        This PR allows us to run C384 S2S with IAU, but starting with the first
        half-cycle as a cold-start. This will be necessary for cycled testing as
        we build towards the full system for GFSv17. This updates the copying of
        the restarts for RUN=gdas for both ocean and ice copying what the atm
        model is doing. It also reduced the amount of restart files from 4 to 3.

        Other updates:
        * Add DOJEDI ocean triggers for archiving certain files update from:
        @CatherineThomas-NOAA
        * Adds COPY_FINAL_RESTARTS option to turn on/off copying the last
        restart file to COM. Defaults to off...
        * Defines model_start_date_current_cycle & model_start_date_next_cycle
        to help with knowing which IC to grab.

        Refs #2546

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

    commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2
    Author: Dan Holdaway <[email protected]>
    Date:   Wed May 8 20:52:48 2024 -0400

        Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477)

        Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI
        Configuration Builder (JCB) tool so that YAMLs can be made more portable
        and invoke the observation chronicle mechanism.

        Resolves #2476

        Co-authored-by: danholdaway <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

    commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed May 8 02:04:16 2024 -0400

        Add CI test for products (#2567)

        Adds a new version of the atm3DVar test that runs the full forecast
        length and produces most of the secondary products. For now, this test
        will only run on WCOSS due to gempak failures on other machines as well
        as computational needs. On other machines, the original version will run
        (the original version will not run on WCOSS). AWIPS remains off for now
        in this extended test due to a bug involving tocgrib2 and the convective
        precip fields (see #2566).

        The new test runs for 4½ cycles and the full 384-hr forecast length to
        ensure all gempak scripts are exercised. Since the cycle throttle is 3
        and the bulk of the time is in the free forecast, the cycles run mostly
        concurrently so it doesn't extend the t…
jderrico-noaa pushed a commit to NOAA-GSL/global-workflow that referenced this issue Sep 27, 2024
@kayeekayee
Update realtime branch, gsl_ufs_rtdev1 (#65)
25b870d 
* Update realtime branch, gsl_ufs_rtdev1.

Squashed commit of the following:

commit 4e0a81f7acf5ccba5de8d3bdf7ab19cae80812cb
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 18:37:50 2024 +0000

    Fix typos/links/dependancy.

commit d5fdcbf8d6e987dbdfcd6b4da34d0934c8d82c3b
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 07:37:52 2024 +0000

    Fixed missing config.base files.

commit c6239f925369b20fd8488e8537969e2f4f9e7725
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 06:53:47 2024 +0000

    Update submodule hashs.

commit 32bf790f67b818ff50a7f6b74388fb81ed175b3a
Author: kayee.wong <[email protected]>
Date:   Wed Sep 18 06:09:41 2024 +0000

    Update develop branch, gsl_ufs_dev
     - based on gsl_ufs_dev from KaYee's fork
       global-workflow: 07Aug24,37c53ac [develop_07Aug2024_37c53ac]
       UFS: 19Jul24, c127601
       FV3: 19Jul24, 2527c11
       UPP: 23Apr24, be0410e
       CCPP-PHYSICS: 19Jul24, 46df080
       UFS_UTILS: 26Jun24, 3ef2e6b

    Squashed commit of the following:

    commit 70b557836379bb7e545fcc6642e28d66cfc17735
    Merge: 5edbd123e 37c53ac69
    Author: Janet Derrico <[email protected]>
    Date:   Wed Aug 7 11:02:24 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04
    Author: Kate Friedman <[email protected]>
    Date:   Wed Aug 7 08:11:21 2024 -0400

        Revert MSU FIX_DIRs back to glopara (#2811)

    commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Tue Aug 6 14:47:36 2024 -0400

        Bugfix for updating label states in Jenkins (#2808)

        Quick bug fix for updating state labels in CI during finalize.
        (did not reference GitHub CLI executable correctly in the pipeline
        script)

    commit 8fee36f0307b0c08080e3a8fa8fa6703e7da5fce
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Aug 6 11:02:45 2024 -0400

        Clean-up temporary rundirs - take 2. (#2753)

        This PR:
        - is a follow-up to a previous PR that aggressively pruned run
        directories.
        - removes run directories for the current cycle in the clean-up if the
        cycle is successful. If the cycle is not successful, cleanup is not
        called and all run directories for the cycle are safe from being purged.
        - also updates the PR template to list/query for any updates to
        submodules.

        ---------

        Co-authored-by: David Huber <[email protected]>
        Co-authored-by: David Huber <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

    commit d599fff4aedd41ae587dbe02226acb12ff48efc1
    Author: HelinWei-NOAA <[email protected]>
    Date:   Mon Aug 5 05:31:31 2024 -0400

        Change land surface for HR4 (#2787)

        Resets the default value of opt_diag to 2 corresponding to the land
        surface upgrades in ufs-weather-model for HR4.

        Resolves #2786

    commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb
    Author: David Huber <[email protected]>
    Date:   Fri Aug 2 15:41:29 2024 -0400

        Run METplus serially and correct the name of prod tasks (#2804)

        Adds 2 hot fixes:

        - METplus v9.1.3 has a bug in it that sometimes attempts to create
        multiple copies of the same directory when running in parallel, causing
        a Python error and downstream problems. This PR makes METplus run in
        serial mode, preventing such issues.
        - Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in
        workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod)

    commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri Aug 2 15:03:45 2024 -0400

        Update Java Agent launching script for Jenkins connections (#2762)

        Made updates to the Jenkins Launching Script for robustness and less
        ambiguous documentation:
        - Clearer distinction between required user token for the remote api and
        the systems token for launching
        - Added pre-checks: `gh` is authenticating, named compliant token and
        secret file exists
        - More robust Jason based parser of the remote api response for checking
        the state of the Node connection
        - For `cron` use a 5 minute pause and recheck was added before
        re-launching of the java agent
        - Added concise header documentation of requirements and purpose
        ---------

        Co-authored-by: David Huber <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

    commit b73b1fd203496db97f8067652659573a632bcc67
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri Aug 2 07:59:06 2024 -0400

        Fix erroneous cdump addition (#2803)

    commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3
    Author: Rahul Mahajan <[email protected]>
    Date:   Thu Aug 1 20:26:13 2024 -0400

        Update ocean post-processing triggers (#2784)

        This PR:
        - replaces `check_netcdf.sh` checker for ocean post-processing with with
        ocean output at the next forecast hour or finishing of the forecast job
        for ocean prod
        - removes no longer needed `ush/check_netcdf.sh`

    commit aa2af1ca8d59424a60a1730722bf528775d9e606
    Author: GeorgeGayno-NOAA <[email protected]>
    Date:   Thu Aug 1 16:46:10 2024 -0400

        Update the gfs_utils repository hash (#2801)

        # Description
        Point to the latest hash of the gfs-utils repository, which contains the
        bug fix to gaussian_sfcanl.

        Resolves #2669.
        Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73

    commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8
    Author: David Huber <[email protected]>
    Date:   Thu Aug 1 08:12:14 2024 -0400

        Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791)

        Changes how METplus jobs run so that they run on the last GFS cycle for
        a given `PDY`.

        This is a departure from operations where the METplus jobs run on the
        00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through
        `${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on
        `${PDY}18` for cycles 00-18. See
        https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details.

    commit 1cf8b448af562dbb7af198399c78c585977e81da
    Author: David Huber <[email protected]>
    Date:   Tue Jul 30 10:38:49 2024 -0400

        Simplify resource-related variables, remove CDUMP where unneeded (#2727)

        This overhauls resource-related variables to use a common set of
        variables for each job. In the process, this also removed the use of
        CDUMP in most cases.

        Resolves #1299 #2693

    commit 61875f25c9e971f82ae499b5b612d7f095deebd4
    Author: Eric Sinsky - NOAA <[email protected]>
    Date:   Mon Jul 29 14:40:03 2024 -0400

        Remove f000 from atmos rocoto tasks for replay cases (#2778)

        The main purpose of this PR is to remove the f000 from
        atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In
        cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater
        than `0`, it becomes necessary to have the first lead hour set to
        `OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For
        example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead
        time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and
        the minimum lead time for the ocean_prod rocoto task needs to be 6
        (assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up
        possible by removing 0 from fhrs for atmosphere-related tasks in
        `gefs_tasks.py` when replaying.

        This PR also moves where f000 is being removed for the ocean_prod and
        ice_prod tasks. The if-block that performs this f000 removal has been
        moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`.

        ---------

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

    commit f156a7894d639f177e3e2588f98eec1f6f59aa68
    Author: Jessica Meixner <[email protected]>
    Date:   Fri Jul 26 14:18:32 2024 -0500

        HR4 GWD update (#2732)

        This update is a combination of the gravity wave drag (GWD) versions
        from the NOAA/GSL and NOAA/PSL

    commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891
    Author: David Huber <[email protected]>
    Date:   Thu Jul 25 14:26:52 2024 -0400

        Temporarily disable METplus jobs (#2796)

    commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2
    Author: Guillaume Vernieres <[email protected]>
    Date:   Wed Jul 24 15:00:35 2024 -0400

        Refactoring of the marine B-matrix job (#2749)

        Refactor the functionality of B-matrix generation from the GDASApp

        Resolves #2743

    commit 65a7ab75dc0e4baba06a02e11ed0455787056a68
    Author: David Huber <[email protected]>
    Date:   Tue Jul 23 08:35:48 2024 -0400

        Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775)

        Removes the namespace-based construction of EnKF member COM directories
        in the enkf archive template.

    commit c45b9611f3e701b819bd33dc5af29033f060bb91
    Author: Eric Sinsky - NOAA <[email protected]>
    Date:   Tue Jul 23 00:33:16 2024 -0400

        Add task to process reforecast variables to save on WCOSS2 (#2680)

        # Description
        This PR adds an optional task to the global-workflow to process a subset
        of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for
        the GEFSv13 reforecast. This task is designed to process GEFS variables
        so that specific reforecast product requirements are met. A new variable
        in `config.base` called `DO_EXTRACTVARS` enables this task, which is
        currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by
        default and is specifically a task designed to be executed for the
        GEFSv13 reforecast.

        Refs #1878

        # Type of change
        - New feature (adds functionality)

        # Change characteristics
        - Is this a breaking change (a change in existing functionality)? NO
        - Does this change require a documentation update? NO

        # How has this been tested?
        This has been cloned and tested on WCOSS2. This will need to be tested
        on Hera and other platforms on which the reforecast may be running.

        # Checklist
        - [ ] Any dependent changes have been merged and published
        - [x] My code follows the style guidelines of this project
        - [x] I have performed a self-review of my own code
        - [ ] I have commented my code, particularly in hard-to-understand areas
        - [x] My changes generate no new warnings
        - [x] New and existing tests pass with my changes
        - [ ] I have made corresponding changes to the documentation if
        necessary

        ---------

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

    commit 71dc33c6ca991c16ce743760d99feaaf60f2218a
    Author: David Huber <[email protected]>
    Date:   Mon Jul 22 14:51:53 2024 -0400

        Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774)

        Fix metp* resources and check that they completed properly; add support for Orion Rocky 9

    commit 56df67a90fe090c425199f1285e5aac722c398b1
    Author: David Huber <[email protected]>
    Date:   Mon Jul 22 09:28:18 2024 -0400

        Hotfix: Update jcb to avoid git-lfs files (#2782)

        Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to
        be cloned on Hera.

        This hotfix points to a non-authoritative branch of the GDASApp
        (https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and
        should be updated ASAP back to the authoritative repository.

    commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jul 16 09:44:00 2024 -0400

        Address issues in creating XML for GFS forecast-only with app S2SWA (#2757)

        This bugfix PR:
        - fixes an issue where a user is unable to generate the XML for a GFS
        forecast-only experiment with APP=S2SWA

        Specifically, the changes are related to defining `aero_fcst_cdumps`.
        Following `setup_expt.py`, the user will have to set
        `AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in
        `config.base`.

    commit e0878dba0e53706a7f53429b61aee2936e2c21bf
    Author: Kate Friedman <[email protected]>
    Date:   Mon Jul 15 10:25:11 2024 -0400

        Updated prepobs and fit2obs versions for Orion Rocky9 (#2758)

        Update prepobs to v1.0.2 and fit2obs to v1.1.2

        These versions now support Orion Rocky9. Updates are included
        for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet.

    commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu Jul 11 17:48:47 2024 +0000

        CI maintenance updates and adding CI Unit Tests (#2740)

        This PR has a few maintenance updates to the CI pipeline and adds a test
        directory with Unit Tests
        **Major Maintenance updates:**
        - Added try blocks with appropriate messaging to GitHub PR of failure
        for:
        - - **scm** checkout
        - - build fail (with error logs sent as gists)
        - - create experiment fails with `stderr` sent to GitHub PR messaging
        - Pre-stage FAILS from the above are now captured these fails allow
        FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state
        labels in GitHub - see image below)
        **Minor Maintenance updates:**
        - Fix for STALLED cases reviled from PR 2700 (just needed a lambda
        specifier)
        - Fixed path to experiment directory in PR message (had dropped EXPDIR
        in path)
        - Needed `latin-1` decoder in reading log files for publishing
        **Added python Unit Tests for CI functionality:**
        - Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI
        utility codes
        - Cashed the install of Rocoto in the GitHub Runners to greatly reduce
        stetup time for running the unit tests
        - Unit Tests Python scripts added
        - `test_rocostat.py`: rocoto_statcount() rocoto_summary()
        rocoto_stalled()
          - `test_setup.py`: setup_expt() test_setup_xml()
          - `test_create_experment`: test_create_experiment()
          - - Runs all PR cases that do not have ICs in the GItHub Runner
        - Reporting mechanism in the Actions tab for Python Unit Testing results
        - Test case data for STALLED and RUNNING stored on S3 and pulled using
        wget during runtime of tests

    commit 5ef4db74649b8be03402c17aa29c024e71699a7b
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Thu Jul 11 08:59:24 2024 -0400

        Adds contents of constructor and initialize methods to marine LETKF class (#2635)

        Adds contents of constructor and initialize methods to marine LETKF class

        Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091
        ---------

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

    commit 8998ec7b74123e953b97a93fa14cc78d471a1aee
    Author: David Huber <[email protected]>
    Date:   Tue Jul 9 08:31:57 2024 -0400

        Fix GDAS group B restart archiving (#2735)

        Archives the GDAS restartb dataset at a 6-hour offset from restarta

        This allows cycled experiments to restart from the archives.
        The tabbing for the master archive templates was also added to
        improve readability.

        Resolves #2722

    commit 3ca74771255727033b9dc043c652ac585178629c
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Tue Jul 9 08:28:54 2024 -0400

        Add fcst dependency to ocnanalprep (#2728)

        Add previous cycle's `fcst` as a dependency to `ocnanalprep`

        This ensures that the availability of restart files to the latter. This addresses a
        seldomly-encountered race condition where `ocnanalprep` fails due to the
        lack of the files.

    commit 58fca1668aecd6fb1afd12a441256ad35900e075
    Author: Rahul Mahajan <[email protected]>
    Date:   Fri Jul 5 15:02:23 2024 -0400

        Update (partially) global-workflow for orion+rocky9 (#2741)

        This PR:
        - updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils,
        GFS-utils) to include recent update to their modulefiles for
        Orion+Rocky9 upgrade
        - updates the modulefiles in global-workflow to load modules from
        Orion+Rocky9 paths
        - updates modulefiles for `gwsetup` and `gwci` as well.
        - removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not
        installed.
        - adds `parm/config.gfs/config.resources.ORION` to address GSI
        performance degradation after Rocky 9 upgrade.

        This PR:
        - does not update the build for UPP. Standalone UPP is not available via
        ufs-weather-model as of #2729
        - will need a follow-up update for `prepobs` and `fit2obs` updated
        locations when they are installed in `glopara` space on Orion.

        # Type of change
        - Maintenance (code refactor, clean-up, new CI test, etc.)

        # Change characteristics
        - Is this a breaking change (a change in existing functionality)? NO
        - Does this change require a documentation update? NO

        # How has this been tested?
        This PR is not sufficient for Orion.
        This PR must be tested on other platforms (Hera, WCOSS2) as this PR
        updates submodules.

        # Checklist
        - [ ] Any dependent changes have been merged and published
        - [ ] My code follows the style guidelines of this project
        - [ ] I have performed a self-review of my own code
        - [ ] I have commented my code, particularly in hard-to-understand areas
        - [ ] My changes generate no new warnings
        - [ ] New and existing tests pass with my changes
        - [ ] I have made corresponding changes to the documentation if
        necessary

        ---------

        Co-authored-by: Kate Friedman <[email protected]>

    commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jul 3 21:07:49 2024 -0400

        Update ufs model hash to 20240625 (#2729)

        Updates UFS weather model hash to hash from 2024-06-24 which has orion
        porting updates + a few namelist updates.

    commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85
    Author: David Huber <[email protected]>
    Date:   Wed Jul 3 11:32:40 2024 -0400

        Hotfix for undefined CLUSTERS (#2748)

        Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses
        the native `dict` `get` method to prevent grabbing an unset entry.

    commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf
    Author: GwenChen-NOAA <[email protected]>
    Date:   Wed Jul 3 09:56:08 2024 -0400

        Update gempak job to run one fcst hour per task (#2671)

        This PR updates gempak jobs (gfs, gdas, and goes) from processing all
        forecast hours at once to one forecast hour at a time. This will reduce
        the job runtime to less than 5 min, so restart capability is not needed.

        Resolves #1250
        Ref #2666 #2667
        ---------

        Co-authored-by: Walter.Kolczynski <[email protected]>

    commit 8215ae654202186a4f753c3abe937b7b9b91a9c7
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jul 2 16:22:11 2024 -0400

        Hotfix for clusters from #2701 (#2747)

        Fixes an issue created from #2701 that added `CLUSTERS` to the
        `gaea.yaml`.

    commit 11943e36ba12b3df49c51942da780698fab02d38
    Author: DavidBurrows-NCO <[email protected]>
    Date:   Tue Jul 2 12:58:10 2024 -0400

        Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701)

        This PR sets up the ability on Gaea for auto generation of a clean xml
        file, i.e., an xml file that does not need any alterations before
        running rocoto.
        Refs #2572
        Refs #2664

    commit de8706702ead0630beb54d868f83aa2cb23f8f79
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Mon Jul 1 09:29:14 2024 -0400

        Update for JCB policies and stage DA job files with Jinja2-templates (#2700)

        This PR updates the `gdas.cd` hash to bring in new JCB conventions.
        Resolves #2699

        From #2654
        This PR will move much of the staging code that take place in the python
        initialization subroutines of the variational and ensemble DA jobs into
        Jinja2-templated YAML files to be passed into the wxflow file handler.
        Much of the staging has already been done this way, but this PR simply
        expands that strategy.

        The old Python routines that were doing this staging are now removed.
        This is part of a broader refactoring of the pygfs tasking.

        wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a
        companion to this PR.

        Co-authored-by: danholdaway <[email protected]>
        Co-authored-by: DavidNew-NOAA <[email protected]>
        Co-authored-by: DavidNew-NOAA <[email protected]>
        Co-authored-by: Dan Holdaway <[email protected]>

    commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b
    Author: Rahul Mahajan <[email protected]>
    Date:   Fri Jun 28 14:56:19 2024 -0400

        Revert PR 2681 (#2739)

        This PR:
        - reverts #2681 in part
        - keeps some changes for `RUN`.
        - is a hotfix
        - should be merged ASAP after consensus w/ @guillaumevernieres
        @CatherineThomas-NOAA @WalterKolczynski-NOAA

    commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed Jun 26 15:46:08 2024 -0400

        updated Finalize in Jenkinsfile and added try block around scm checkout (#2692)

        We are updating the Jenkins Pipeline with a try block around checkout to
        capture errors for the user.
        Also cleaned up Finalize and added section to clean out workspace on
        success.

    commit 968568f682bac7564095440bdb7813abefd76821
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 26 13:27:19 2024 -0400

        Activate snow DA test on WCOSS (#2720)

        Activate the snow DA test on WCOSS.

    commit 7706760bb8adbdf78cb640b02739023c886e7699
    Author: Rahul Mahajan <[email protected]>
    Date:   Wed Jun 26 10:02:22 2024 -0400

        Cleanup of stale RUNDIRS from an experiment (#2719)

        This PR:
        - removes stale temporary scratch run directories from `$DATAROOT/`
        every 3 days.
        - should help to scrub failed attempts.
        - removes an unused variable `RUNDIR` defined in `config.base`

    commit 8962991691b5f0857b813bddfd28aa1034d4bd2b
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jun 26 09:43:48 2024 -0400

        Update logic for MOM6 number of layers/exception values (#2681)

        Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine
        how many layers and sets the exception value for MOM6 to be 1e-34 for
        all scenarios. Note, we will no longer have zeros in the ocean grib
        output and the DA will also run without issues.

        Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615

    commit 12431f76bdce807067929415007592cffc8a2457
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Wed Jun 26 07:42:35 2024 -0600

        Update wave jobs to use COMIN/COMOUT (#2643)

        NCO has requested that each COM variable specify whether it is an input
        or an output.
        This completes that process for the global-workflow wave
        model and products tasks.
        Refs #2451

    commit b902c0bac126c323a07186ad8881384b032b6fda
    Author: David Huber <[email protected]>
    Date:   Tue Jun 25 07:48:46 2024 -0400

        Assign machine- and RUN-specific resources (#2672)

        Redefine resource variables based explicitly on RUN or CDUMP

        Additionally, machine-specific resources are moved out of
        config.resources and placed in respective config.resources.{machine}
        files.

        Resolves #177 #2672

    commit 5edbd123e2878a07f5cce8e3c7ea6147f286633a
    Merge: 09333c01d 4e1b937b6
    Author: Janet Derrico <[email protected]>
    Date:   Mon Jun 24 12:44:05 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit 4e1b937b67ed220120e81925c4507f03b9b8965f
    Author: David Huber <[email protected]>
    Date:   Mon Jun 24 10:50:52 2024 -0400

        Add minimum software requirements (#2712)

        Adds a table to HPC documentation stating the minimum support versions

    commit f43a86276aaef91efa28faadc71a3cf50e749efe
    Author: David Huber <[email protected]>
    Date:   Fri Jun 21 13:44:29 2024 -0400

        Fix and simplify online archiving and reenable METplus jobs (#2687)

        This fixes the online archiving portion of the `*arch` and `*earc00`
        jobs, a prerequisite for running METplus.  This also reenables
        METplus by default.

        The approach previously taken created `FileHandler` dictionaries at
        varying levels within the resulting yaml, which was not properly parsed
        by `exglobal_archive.py`. This approach creates a single `FileHandler`
        dictionary and is much less complicated overall.

        Resolves #2673 #2647

    commit 8993b42cb91144c0ab0501dc7841ea8d675c4701
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 19 21:51:22 2024 -0400

        Eliminate post groups (#2667)

        Eliminates the post groups used for upp and products jobs so that each
        task only processes one forecast hour. This is more efficient and
        greatly simplifies downstream dependencies that depend on a specific
        forecast hour.

        Resolves #2666
        Refs #2642

    commit 0b810c888239853fedd0e4584fe62536c6aaacdf
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 18 20:32:48 2024 -0600

        Removes misleading "No such file or directory" syntax errors from output files (#2688)

        This PR addresses issue #1252. The following is accomplished:

        - Prior to removing files, the existence of a file is checked prior to
        attempting to remove; this is performed as noted
        [here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369);
        this PR only addresses the the `chgrp` issue.

        Refs #1252

        ---------

        Co-authored-by: David Huber <[email protected]>

    commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 18 12:17:59 2024 -0600

        Hotfix for bug in template names. (#2697)

        This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/`
        template.
        Resolves #2696
        Refs #2451

    commit 35d4d99eaac669721add9ddcc793153e5ab3b30a
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 18 08:06:53 2024 -0600

        Update archive job to use COMIN/COMOUT (#2668)

        NCO has requested that each COM variable specify whether it is an input
        or an output. This completes that process for the global-workflow
        archive task.

        Refs #2451
        ---------

        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>
        Co-authored-by: David Huber <[email protected]>

    commit 47b3a581c8257fa24411fb400df8bb0e1e04972a
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jun 17 22:55:38 2024 -0400

        Turn on high-frequency output in extended test (#2679)

        Turns on high-frequency (hourly) output in the extended products test to
        exercise that aspect of the code. This test only runs on WCOSS.

        Also adds the hooks to optionally turn on the metplus jobs, but that is
        deferred as they are not currently working correctly.

    commit 38f2df9fb0c074b1f80d3c637080be79be693161
    Author: David Huber <[email protected]>
    Date:   Mon Jun 17 17:12:55 2024 +0000

        Optimize wavepostpnt (#2657)

        Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs

        This is done by
        1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by
        - performing operations on all files at once instead of looping over
        each file
            - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`)
            - combining `sed` and `grep` calls when possible
            - adding logic to `awk` calls instead of handling that logic in bash
        2) minimizing as much as possible the amount of data on disk that has to
        be read in (e.g. limiting sed to read only the line numbers it needs)
        ---------

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

    commit 5af325a6a4e0a14d180514a418603ca79fada487
    Author: Dan Holdaway <[email protected]>
    Date:   Fri Jun 14 18:05:23 2024 -0400

        Update GDASapp hash to move JCB into GDASapp (#2665)

        This PR moves JCB into GDASapp. The PR
        also bumps up the hash of GDASapp to what is in `feature/move_jcb`,
        which at time of writing is develop plus the absorption of JCB into
        GDASapp.
        Note that I also took the changes from
        https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the
        testing @RussTreadon-NOAA has done.

    commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b
    Author: Yaping Wang <[email protected]>
    Date:   Fri Jun 14 10:18:17 2024 -0500

        Add observation preparation job for aerosols DA to workflow (#2624)

        Add a prepaeroobs job to prepare aerosol obs files for DA.

        This job does quality control of the VIIRS aerosol raw observations and
        convert them to ioda format.

        Resolves #2623
        ---------

        Co-authored-by: ypwang19 <[email protected]>
        Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>
        Co-authored-by: Cory Martin <[email protected]>
        Co-authored-by: David Huber <[email protected]>

    commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4
    Author: Jessica Meixner <[email protected]>
    Date:   Fri Jun 14 11:04:41 2024 -0400

        Remove ocean daily files (#2689)

        This PR removes the ocn_daily files that are produced by the ocean
        component. These files can be recreated by averaging data that exists in
        the 6 hour aveaged files if needed.

        Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675
        Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by
        removing them and making this obsolete)

    commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu Jun 13 12:22:03 2024 -0400

        Update Jenkinsfile

        needed a comma

    commit dc21eac6c3941d7f30803891d91d82f4cc1f8183
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu Jun 13 11:41:14 2024 -0400

        Add Hercules-EMC to the Jenkins configurable parameter list (#2685)

        This quick-fix PR is to update the Jenkins Pipeline's configurable
        parameter list to include the **Hercules-EMC** node.
        This allows Jenkins users to restart Jobs in the controller when no
        updates have been made.

    commit ebacebfbe458634b8c80af6a735d6b6d01e4e406
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Thu Jun 13 11:20:24 2024 -0400

        Update gdas.cd and gsi_utils hashes (#2641)

        This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The
        updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea
        build for gsi_utils.

        Resolves #2640

    commit 34155fb4767769600a1ff95f0a65e37081addc2a
    Author: Neil Barton <[email protected]>
    Date:   Thu Jun 13 11:18:22 2024 -0400

        Add ability to use GEFS replay ICs (#2559)

        The PR allows the use of ICs from PSL's replay analysis. These replay
        ICs will be used for GEFS reforecasting and SFS. Two main changes are
        associated with these updates: (1) replay ICs being valid at 3Z, and (2)
        the use of warm starts.

        Resolves #1838

        ---------

        Co-authored-by: Jessica Meixner <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>

    commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Wed Jun 12 19:25:42 2024 -0600

        Replace `sleep` with `wait_for_file` (#2586)

        This PR addresses issue #2444. The following is accomplished:

        - All `sleep` statements are replaced with `wait_for_file` for the
        relevant scripts beneath `scripts` and `ush`;
        - Indentation and shell-norms are updated where applicable.

        Note: The WAFS scripts are not updated as per @aerorahul direction.

        Resolves #2444

        ---------

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

    commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 12 13:31:55 2024 -0400

        Add COM template for JEDI obs (#2678)

        Adds a COM template to define a path to store obs processed for JEDI.
        This will allow UFSDA to stop writing to COM_OBS, which should be
        read-only as it belongs to obsproc in operations.

        No functional change yet.

    commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed
    Author: Guoqing Ge <[email protected]>
    Date:   Wed Jun 12 09:06:23 2024 -0600

        Link both global-nest fix files and non-nest ones at the same time (#2632)

        This PR enables linking both global-nest fix files and non-nest ones at
        the same time and users can run both nesting and non-nesting experiments
        at the same time without worries about what fix files to be linked.

        Resolves #2631

    commit 61de004d4f9e9edf8a31bb173f2719b46451a36a
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jun 12 11:03:13 2024 -0400

        Update ufs-weather-model  (#2663)

        Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack
        allowing some temporary fixes to be reverted.
        * removes upp submodule
        * uses upp from the ufs-weather-model
        * restores the build and link that were hacked during the Hera Rocky 8
        transition to allow for UPP submodule
        * Removes forecast directories in clean-up

        Resolves #2617
        Resolves #2437

        ---------

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

    commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d
    Author: Eric Sinsky - NOAA <[email protected]>
    Date:   Wed Jun 12 01:15:37 2024 -0400

        Add ability to process ocean/ice products specific to GEFS (#2561)

        This PR begins to add the capability to produce GEFSv13 ocean and ice
        products in the global-workflow according to stakeholder requirements.
        The following features are added.

        - An oceanice prod yaml file has been added to address the ocean and ice
        products specific to GEFSv13.
        - The rocoto dependencies and config.base for GEFS have also been
        modified to allow for 24-hour averaged ocean and ice output.
        - Various scripts have been modified to allow for ocean and ice output
        frequencies of 24 hours.
        - `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN`
        and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`.

        Refs #1878

    commit 6691e7489650e0b738c176fbd096109288dc09b6
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Tue Jun 11 21:15:07 2024 -0600

        Update cleanup job to use COMIN/COMOUT (#2649)

        NCO has requested that each COM variable specify whether it is an input
        or an output. This completes that process for the global-workflow
        clean-up task.

        Refs #2451

        ---------

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

    commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Tue Jun 11 16:17:25 2024 -0400

        Add overwrite to creat experiment in BASH CI (#2676)

        This is a quick hotfix to the CI BASH driver script adding `--overwrite`
        to create experiment script to avoid errors from restarting an
        experiment.

    commit e7909af8d9e1f34140388a3f8556d8e582c58fe5
    Author: emilyhcliu <[email protected]>
    Date:   Mon Jun 10 15:11:27 2024 -0400

        Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py  (#2645)

        This PR proposes updates for the following two scripts:

        1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select
        CRTM cloud optical table based on cloud microphysical scheme indicated
        by `imp_physics'
        The default scheme in the GFS forecast model is Thompson scheme
        (imp_physics = 8).

        2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in
        the script due to increased variables to interplate increments and
        calculate analysis in the netcdf_io routines in GSI-utils.
        Here is the related [PR #46 for
        GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46).

        ---------

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

    commit 9caa51de8fb7be07d2e61775da01937d576964f6
    Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
    Date:   Thu Jun 6 22:15:23 2024 -0600

        Update RDHPCS Hera resource for `eupd` task (#2636)

        As per @wx20jjung, the resource for the `eupd` task have been updated
        for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job
        fails.

        Resolves #2454

        ---------

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

    commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b
    Author: DavidNew-NOAA <[email protected]>
    Date:   Thu Jun 6 11:49:03 2024 -0400

        Parameterize some things in config.atmanl and config.atmensanl (#2661)

        This PR adds some parameters in config.atmanl and config.atmensanl that
        can be altered with the defaults.yaml. The motivation is to make these
        files match those in the GDASApp JJOB tests (example:
        https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl),
        so we can just use the Global Workflow config.atmanl and
        config.atmensanl in the tests rather than custom ones in GDASApp that
        have to be separately updated every time the ones in the Global Workflow
        are updated.

    commit 54ea0b73a07921be5fbb07fe41e976888bd3e549
    Author: Guillaume Vernieres <[email protected]>
    Date:   Thu Jun 6 01:36:02 2024 -0400

        Add links to the ocean insitu obs processing tools (#2644)

        Add links to the marine bufr to ioda converters for the marine insitu
        observations.

        - fixes https://github.com/NOAA-EMC/GDASApp/issues/1106
        - waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135

    commit 205d0c2b13e2d7755cec75bf8c978ab20d453862
    Author: David Huber <[email protected]>
    Date:   Wed Jun 5 17:31:30 2024 +0000

        Update S4 point of contact in docs (#2660)

        Update the point of contact for global workflow issues on S4.

    commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Wed Jun 5 12:50:14 2024 -0400

        Enable wcoss2 ufsda build and module load (#2620)

        This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2.

        Resolves #2602
        Resolves #2579

    commit 67b833e0c7bc390865d453588b4609a1a7ede981
    Author: Jessica Meixner <[email protected]>
    Date:   Tue Jun 4 13:33:43 2024 -0400

        Update ufs-weather-model  (#2646)

        Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6
        This should resolve the issue and allow C768 runs on Hera and allow for CICE
        to run on WCOSS2 (due to library updates to allow linking).

        From what I can tell, all updates needed were done by
        @HenryWinterbottom-NOAA which were updates for CICE

        Fixes #2490

    commit c44d0ac86cfdf78eb87492431bf6d825e8bae637
    Author: GwenChen-NOAA <[email protected]>
    Date:   Tue Jun 4 10:29:49 2024 -0400

        Update wmo parm files to fix WMO header (#2652)

        This PR updates wmo parm files to switch WMO header of precipitation
        type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to
        instantaneous.

        Resolves #2566

    commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60
    Author: Cory Martin <[email protected]>
    Date:   Tue Jun 4 13:55:33 2024 +0000

        Add IAU to snow DA (and its test) (#2610)

        This PR enables IAU for the snow DA which is necessary for GFSv17.

        A snow analysis is created for the center of the window regardless, and
        an additional at the beginning of the window is added if IAU is on. The
        former is needed for UPP and the latter, to initialize the model.

        The increment is valid throughout the window for 3DVar, so the same
        increment is added to both forecasts.

        Additionally, the input file that goes into global_cycle has been
        updated to be the output of the JEDI snow analysis instead of the
        forecast (@jiaruidong2017 I recall discussing this, can you confirm this
        is right or am I mistaken)

        This PR also makes the CI test for snow DA (and aerosol DA) include IAU
        rather than without IAU,.

        ---------

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

    commit c92bf415060750127c9c05a62a1d2851c489551a
    Author: David Huber <[email protected]>
    Date:   Sat Jun 1 05:11:07 2024 +0000

        Archiving cleanup (#2621)

        1) Adds a lot of comments to the jinja templates for archiving
        2) Rearranges the gdas and enkf templates to a more logical order
        3) Fixes a couple of bugs in the enkf archiving of increments and
        analyses
        4) Disables archiving for the half cycle
        5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`,
        instead relying on `DO_FIT2OBS`
        6) Updates wxflow to add the option to not allow undefined variables
        when parsing jinja templates and invokes this feature when running
        archives

        Resolves #2612

    commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri May 31 04:57:08 2024 -0400

        Switch to Rocky 9 built external packages on Hercules (#2608)

        The workflow was updated to use modules built on Rocky 9, but the
        external packages (like prepobs) were still pointing to the versions
        built on CentOS (Orion). This transitions to packages built on Rocky 9.

        Updating of the tracker package has been deferred until later. As such,
        the tracker jobs have been disabled by returning immediately if they are
        on Hercules. Since these jobs are small, resource-wise, it should not
        meaningfully impact turnover time.

    commit 4422550c01c9214a2b3b8890bdcc898123ee216a
    Author: Guoqing Ge <[email protected]>
    Date:   Thu May 30 08:05:23 2024 -0600

        Add the capability to use slurm reservation nodes (#2627)

        Add the capability to use slurm reservation nodes
        Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE

        Resolves #2626

    commit a54153fd9d26126206bc07a1da4e80f50c0c5910
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed May 29 23:24:07 2024 -0400

        Update forecast job to use COMIN/COMOUT (#2622)

        NCO has requested that each COM variable specify whether it is an input
        or an output. This completes that process for the forecast job.

        Refs #2451

        ---------

        Co-authored-by: David Huber <[email protected]>

    commit d69a8af95d492982b918670322ed5c41ab074335
    Author: Jessica Meixner <[email protected]>
    Date:   Wed May 29 21:29:03 2024 -0400

        Update to add 1-deg global wave grid (#2619)

        This PR adds options to use a global 1 deg grid, intended for testing
        with the SFS application.

        Requires new fix file changes NOAA-EMC/global-workflow#2618

    commit 0b4670ecf83b99b72835c8380573b2bca7cf5324
    Author: Jessica Meixner <[email protected]>
    Date:   Wed May 29 17:17:21 2024 -0400

        Add C384mx025_3DVarAOWCDA yamls (#2625)

        Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder.

    commit 2e885d05c64b947f00a3cf055a1277fbfac195c9
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed May 29 13:00:51 2024 -0400

        Script to keep Jenkins Agent persistent from cron (#2634)

        This "persistent" Java Agent launch script can be ran from a cron job:

        - Uses Jenkins Remote API to check the status of the Node connection
        using curl for a given machine.
        - If it is not connected a new agent is launched for that node.

        Resolves #2633

    commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5
    Author: GwenChen-NOAA <[email protected]>
    Date:   Tue May 28 17:17:11 2024 -0400

        Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611)

        Based on users' feedback, this PR do the following:
        1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF
        2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD,
          and VOGRD) from "%g m below water surface" to "%g m below sea level"
        3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m)

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

    commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31
    Author: DavidNew-NOAA <[email protected]>
    Date:   Tue May 28 17:16:23 2024 -0400

        Add atmensanlfv3inc job (#2592)

        This PR creates the atmensanlfv3inc job, the ensemble version of
        atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is
        #[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS
        companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3).

    commit 50c2b8951b29a3c883a778becbf8582f9519eb48
    Author: Anil Kumar <[email protected]>
    Date:   Tue May 28 13:23:53 2024 -0400

        Global-workflow (AR) Generic updates for Gaea C5 (#2515)

        - Port global-workflow’s build and run capability to Gaea-C5
        - Building global-workflow on Gaea-C5
        - Setting up experiments with global-workflow on Gaea-C5

        ---------

        Co-authored-by: AnilKumar-NOAA <[email protected]>
        Co-authored-by: DavidBurrows-NCO <[email protected]>

    commit b6ca771a0c584cbfcbbf9be739765d5f3815df97
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri May 24 10:52:45 2024 -0400

        Update STMP and PTMP settings in host file for Orion and Hercules  (#2614)

        - Updating STMP and PTMP settings in host file for Orion and Hercules
        because they are cross mounted.
        - Also took the opportunity to finally update **SLURM_ACCOUNT** to
        **HPC_ACCOUT** in CI over rides.
        - Added a refactor of the `rocotostat.py` tool that is more pythonic and
        as a execute retry feature because the `rocotostat` utility on Orion has
        been failing sometimes.

    commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f
    Author: Guillaume Vernieres <[email protected]>
    Date:   Tue May 21 23:50:50 2024 -0400

        Sea-ice analysis insertion (#2584)

        Allows cycling and restarting CICE with the sea-ice analysis if the
        marine DA is switched on.

        Resolves #2568
        Resolves NOAA-EMC/GDASApp#1103

    commit 5369a1ff3a3969149fcf32810fad0e50216752b7
    Author: David Huber <[email protected]>
    Date:   Tue May 21 22:12:29 2024 +0000

        Refactored archiving (#2491)

        This provides a new pygfs task, archive.py, that provides all of the
        tools necessary to archive data to the local (`ARCDIR`) and backup
        (`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to
        define the file to be archived or tarred to replace the
        `hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts
        and make it easier to add new data and explicitly handle optional and
        required files.

        For `ATARDIR` archiving, a master jinja template is provided for each
        `RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2,
        master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both
        `enkfgdas` and `enkfgfs` `RUN`s. These templates then include the
        appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on
        experiment, cycle, and coupled parameters. Each of these templates
        corresponds to a single tarball to populate and are tabbed 4 spaces so
        they are defined within the master `datasets` dictionary.

        Future developers should not have to make modifications to archive.py
        unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then
        only a single `elif` needs to be added to the configure method to
        specify the master `ATARDIR` template to archive (e.g.
        `master_gefs.yaml.j2`). If a new component is coming online that needs
        to be archived to `ATARDIR` (e.g. SNOW), then create a new template for
        each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`)
        and reference the template in the appropriate master templates, e.g.

        `master_gdas.yaml:`
        ```jinja
        {% if DO_SNOW %}
        {% include "gdassnow.yaml.j2" %}
        {% endif %}
        ```

        A few other issues were addressed along the way:
        1. Aerosols have been reenabled. Aerosol forecasts should only be
        performed during gdas cycles, but analyses can be performed for both gfs
        and gdas cycles. This was accomplished by setting separate
        `AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs.
        2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`.
        This prevented restarts from being used for cice-enable experiments.
        This feature was not tested.
        3. Create a temporary fix for the `wgrib` utility. For spack-stack
        1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is
        open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in
        existing installations. Once complete, this temporary fix should be
        removed.
        4. The number of `earc` jobs has been reduced for lower resolution
        experiments. Both C48 and C96 experiments will now only have two earc
        jobs (one for the non-member files to archive and another for the member
        files). C192 will have up to 3 earc jobs (one non-member, one for
        members 1-40 and another for members 41-80, if needed).

        Resolves #2345
        Resolves #2318

        ---------

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

    commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri May 17 12:57:59 2024 -0400

         Add remove RUNDIRS step in CI before creating experements (#2607)

        As had been done in Bash CI we need to remove the RUNDIR in Jenkins
        before a creating an experiment in the event that case had beem
        previously ran.

    commit 09333c01dbafddb2d2fe7e181b479af3cc6d3621
    Merge: f7e9f4489 bb930050b
    Author: Janet Derrico <[email protected]>
    Date:   Thu May 16 14:33:19 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit bb930050b3cd51d28ecba6b231c8675f6d11856c
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Thu May 16 12:28:30 2024 -0400

        Adds jjob and other necessities for marine LETKF task (#2564)

        Adds jjob, rocoto script, config file, and other necessities for new
        marine LETKF task.

        Partially addresses NOAA-EMC/GDASApp#1091

    commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu May 16 12:12:06 2024 -0400

        Updating CI Machine configs with redundant PTMP (#2605)

        Quick fix adding PTMP as STMP in Machine configs for CI for completeness

    commit ef340ff33a6f89adf70838206ba3fd56a953fa7a
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Thu May 16 11:37:30 2024 -0400

        Fix race condition in CI between Orion and Hercules (#2604)

        Hotfix to solve race conditions in the CI system due to cross-mounted
        file systems between Orion and Hercules

    commit e8b17e27f719df280170dc3f5bd9f19917cefaf2
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed May 15 17:16:30 2024 -0400

        Remove existing EXPDIRs and COMROTs when CI is re-run (#2601)

        Quick hotfix for having default for re-runing jobs to start clean with
        new EXPDIRs and COMROTs

    commit b5d113efb1970ede5cd1d3d4dff8d96320519c41
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Wed May 15 16:52:49 2024 -0400

        Moving logic for skipping hosts in pr cases (#2573)

        This PR removes the logic of skipping hosts for pr cases from
        `create_experiment.py` and moves it to a test in the cron bash driver
        using a `parse_yaml.py` python tool.

        The Jenkins pipeline was not effected as it uses the
        `get_host_case_list.py` utility to form the cases on a per host bases.

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

    commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Wed May 15 13:13:30 2024 -0400

        Update gsi_utils.fd hash (#2598)

        This PR updates the `gsi_utils.fd` hash to bring in updates which add
        safeguards to
        -
        `src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90`
        - `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90`

        The safeguards are described in GSI-utils PR
        [#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated
        issue.

        Resolves #2597

    commit d5366c66bd67f89d118b18956fe230207cbf0aea
    Author: Kate Friedman <[email protected]>
    Date:   Wed May 15 13:12:56 2024 -0400

        Update CICE and MOM6 fix versions (#2600)

        This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions
        to the newer `20240416` timestamps, which includes updates and fixes to
        the `100` (1-deg) resolution files.

        Resolves #2480
        Resolves #2483
        Resolves #2595

    commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b
    Author: David Huber <[email protected]>
    Date:   Mon May 13 22:57:38 2024 +0000

        Limit gfswavepostpnt to 40 PEs/node (#2588)

        This fixes the slow runtime of the gfswavepostpnt job on Hercules. The
        job is very I/O intensive and does not scale well to large nodes, so
        limit the number of jobs/node to 40.

        Resolves #2587

    commit 4fb7c12c325702a47f27c802a5067efd33d0327c
    Author: Fanglin Yang <[email protected]>
    Date:   Mon May 13 16:37:51 2024 -0400

        Update damping and time-step (#2575)

        Updates the model to use explicit Rayleigh damping for u/v and implicit
        damping to w. This improves model stability and allows for longer
        timesteps. Also unifies the GDAS and GFS to use the same damping.

        Results from a test at the C1152 resolution (coupled model) can be found
        at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/

        Resolves #2574

        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
        Co-authored-by: Lisa Bengtsson <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>

    commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Fri May 10 14:17:13 2024 -0400

        Do not use BUILT_semphore to force rebuilds when re-run (#2593)

        Remove the placement of the `BUILT_semaphore` file after the build in
        the Jenkins Pipeline and force it to rebuild any changes after a PR is
        re-ran.

    commit 2346c6161f75ae02369cbf30f30c6150d3e12b66
    Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com>
    Date:   Thu May 9 21:17:06 2024 -0500

        Migration to Rocky8 spack-stack installations on Jet (#2458)

        # Description
        Migrates Global Workflow to Rocky8 spack-stack installations on Jet.
        Jet has moved from CentOS7 to Rocky8.

        Resolves #2377
        Refs NOAA-EMC/UPP#919
        Refs NOAA-EMC/gfs-utils#60
        Refs NOAA-EMC/GSI#732
        Refs NOAA-EMC/GSI-Monitor#130
        Refs NOAA-EMC/GSI-utils#33

    commit c7b3973014480a20dd8e24edaeb83a9e9e68159f
    Author: Jessica Meixner <[email protected]>
    Date:   Thu May 9 11:36:58 2024 -0400

        Updates for cold start half cycle, then continuing with IAU for WCDA (#2560)

        This PR allows us to run C384 S2S with IAU, but starting with the first
        half-cycle as a cold-start. This will be necessary for cycled testing as
        we build towards the full system for GFSv17. This updates the copying of
        the restarts for RUN=gdas for both ocean and ice copying what the atm
        model is doing. It also reduced the amount of restart files from 4 to 3.

        Other updates:
        * Add DOJEDI ocean triggers for archiving certain files update from:
        @CatherineThomas-NOAA
        * Adds COPY_FINAL_RESTARTS option to turn on/off copying the last
        restart file to COM. Defaults to off...
        * Defines model_start_date_current_cycle & model_start_date_next_cycle
        to help with knowing which IC to grab.

        Refs #2546

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

    commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2
    Author: Dan Holdaway <[email protected]>
    Date:   Wed May 8 20:52:48 2024 -0400

        Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477)

        Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI
        Configuration Builder (JCB) tool so that YAMLs can be made more portable
        and invoke the observation chronicle mechanism.

        Resolves #2476

        Co-authored-by: danholdaway <[email protected]>
        Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

    commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed May 8 02:04:16 2024 -0400

        Add CI test for products (#2567)

        Adds a new version of the atm3DVar test that runs the full forecast
        length and produces most of the secondary products. For now, this test
        will only run on WCOSS due to gempak failures on other machines as well
        as computational needs. On other machines, the original version will run
        (the original version will not run on WCOSS). AWIPS remains off for now
        in this extended test due to a bug involving tocgrib2 and the convective
        precip fields (see #2566).

        The new test runs for 4½ cycles and the full 384-hr forecast length to
        ensure all gempak scripts are exercised. Since the cycle throttle is 3
        and the bulk of the time is in the free forecast, the cycles run mostly
        concurrently so it doesn't exte…
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Modify APP based on RUN WalterKolczynski-NOAA/global-workflow
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