…aram

* origin/develop:
  Remove compiler warnings for CMEPS and CICE; Add traditional threading templates for global apps and append _esmf for templates using ESMF-managed threading (was ufs-community#2179) (ufs-community#2172)

# 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
ufs-community/ufs-weather-model#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]>

Squashed commit of the following:

commit c54fe98c4fe8d811907366d4ba6ff16347bf174c
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Apr 2 15:58:49 2024 -0400

    Move bash utility functions out of preamble (#2447)

    The preamble was accumulating a bunch of utility functions. These
    functions are now moved to a separate file that is sourced by the
    preamble. The only functions remaining in the preamble are those related
    to script control and logging (`set_trace()`, `set_strict()`,
    `postamble()`).

    Resolves #2346

commit 4a39c8afc0555a8f2d621efb55589b9b309a416c
Author: David Huber <[email protected]>
Date:   Tue Apr 2 18:00:21 2024 +0000

    Reenable the minimization monitor on Hera (#2446)

    This allows the minimization monitor to run on Hera Rocky 8.

    A missing perl module was added (List/MoreUtils.pm), but had to be
    installed under the perl/5.38.0 installation, thus that module needs to
    be loaded.

    Resolves #2439

commit 0eaa53771b5e8d476d3b5feabd3181c8dc48629a
Author: Travis Elless <[email protected]>
Date:   Tue Apr 2 00:31:14 2024 -0400

    Fix rotating member bugs (#2443)

    When PR #2427 introduced the rotating subset of member guess states for
    the early-cycle EnKF, the rotating member calculation function was
    omitted from the DOSFCANL_ENKF if block in the enkf surface script. This
    PR adds this feature to this section. This PR also removes hard coded
    values that were included in this function and are replaced with a
    variable equal to the number of late cycle members.

    Resolves #2441

commit 39ba9d720c38ac85239a1eb1696c78df82396644
Author: CatherineThomas-NOAA <[email protected]>
Date:   Mon Apr 1 17:48:42 2024 -0400

    Remove the reset of upper layer humidity (#2449)

    # Description
    The parameter "nudge_qv" resets the upper layer humidity to HALOE
    climatology when cold starting. This parameter has been set to ".true."
    but is no longer needed using v16+ ICs and will now be set to ".false."
    by default.

    Resolves: #2448

commit 7f6bf216566e92bbe072ebe4b64d26cc60fb53f1
Author: Jiarui Dong <[email protected]>
Date:   Mon Apr 1 13:08:33 2024 -0400

    Archive the snow DA analysis into HPSS (#2414)

    This PR adds the capabilities to archive the snow analysis output into
    HPSS. Changes are made to archive the snow stats, letkfoi yaml file and
    snow analysis into HPSS.

commit c1b11a2559e618f61866498b5dad503ba74d8332
Author: Neil Barton <[email protected]>
Date:   Mon Apr 1 13:05:57 2024 -0400

    Add GEFS ENS Atmos options (#2392)

    This PR adds the FV3 atmos perturbation options when running GEFS. This
    is needed for GEFS reforecasts and GEFS operational forecasts.

    This PR continues to address the below issues
    #1720
    #1921

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

commit 834ce31348a627e14d448cdbe33d4ec0dabe99e4
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Mar 29 13:17:08 2024 -0400

    Refactor gempak jobs for new COM and style (#2374)

    Updates the gempak jobs to fit the new COM structure while also
    refactoring them some to improve the style. Despite these technical
    changes, the overall structure is left unchanged for most scripts,
    though some have been rewritten to make the needed changes easier. Some
    of these scripts had already been updated some in the original COM
    refactor and thus needed fewer updates.

    Style updates includes converting all gempak scripts to bash, making
    them shellcheck compliant, and removing trailing whitespace. Further
    refactoring to improve maintainability will be needed in the future (see
    #2341, #2342, #2343, #2348).

    The GFS gif scripts were identical except the forecast hour, so they are
    collapsed down into two: one for f000 and one for other forecast hours.

    The gempak executables have short path limits. To get around this
    without having the gempak module recompiled, target directories (mostly
    relevant for the gempak meta jobs) are symlinked into the working
    directory to drasticly reduce the path lengths.

    Part of this update includes replacing existing MPMD calls with the new
    standard `ush/run_mpmd.sh` script.

    A new function, `wait_for_file()`, is introduced to standardize waiting
    for a file to be available.

    Gempak forecast hours are often hard-coded within scripts. In addition
    to issues with maintainability, this causes problems for shorter
    forecasts, such as we typically run for testing purposes. For now, we
    simply check the values against the forecast length and reduce if
    necessary. Future work (#2348) will be needed to remove these hard-coded
    values with variables set in the config file (or just use update gempak
    products to match standard output time variables).

    One-degree gempak files have been updated to include `1p00` in the
    filename.

    Several gempak job dependencies are corrected.

    Fake gempak data for external models is being staged on tier-1 machines
    to allow testing.

    **Output has not been verified.** Future PRs will likely be needed to
    bring full functionality online.

    Resolves #2158
    Resolves #2152
    Resolves #2151
    Resolves #2249
    Resolves #2247
    Refs #2157
    Refs #2348

commit 20635b0639656769842218d544ec7ce2436337c5
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri Mar 29 08:15:29 2024 +0000

    Turn GEFS CI test on for Hera (#2442)

    Re-enabling gefs case to test gefs system builds in Jenkins on Hera.

    Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>
    Co-authored-by: terrance.mcguinness <[email protected]>
    Co-authored-by: Walter.Kolczynski <[email protected]>

commit ba6a9d5fa6a079b1e3fdd424a493252bbf499c5d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Mar 28 17:34:22 2024 -0400

    Modify APP based on RUN (#2413)

    There is a need to change which coupled components are on depending on
    the current `RUN`. To facilitate this, the `APP` is modified prior to
    the setting of the `DO_<component>` variables based on `RUN`, turning
    off components as desired.

    This new system also replaces the `DO_<component>_ENKF` switches that
    were formerly used to turn components off for the ensemble.

    Also expands allows apps for cycled to include S2SWA.

    Resolves #2318

commit 3ff7a92c25564ddf984cb09cb5667ae8fafe01a0
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Mar 28 17:48:00 2024 +0000

    Fix post log arg check and don't create build semaphore (#2440)

    Two Hot Fixes to Jenkins latest updates:

    1. Logic fixed in checking for mutually exclusive use of gists and repo
    for publishing error files
    2. Removed creation of build success file semaphore forcing complete
    rebuild as the default behavior for rerun/restarts

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

commit d6be3b5c3a1b8fd025a303b40e0660e2914906a7
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Mar 27 20:56:18 2024 -0600

    Update global-workflow and subcomponents to Hera/Rocky 8 partition (#2421)

    This PR addresses issue #2329. The following is accomplished:

    - All submodule RDHPCS Hera stacks are updated to be compatible with the
    Rocky-8 distro spack-stack;
    - The global-workflow version files `versions/build.hera.ver` and
    `versions/run.hera.ver` are updated for Rocky-8;
    - All submodule hashes have been updated to be compliant with the
    Rocky-8 distro spack-stack (see the reference PRs below);
    - Update to `parm/config/config.base` is made for not yet compliant
    packages;
    - Relevant updates are made to `modulefiles/module_base.hera.lua` and
    `modulefiles/module_gwsetup.lua`.

      Resolves #2329
      Refs: [#958](https://github.com/NOAA-EMC/GDASApp/issues/958)
               [#49](https://github.com/NOAA-EMC/gfs-utils/issues/49)
               [#124](https://github.com/NOAA-EMC/GSI-Monitor/issues/124)
               [#31](https://github.com/NOAA-EMC/GSI-utils/issues/31)
    [#2167](https://github.com/ufs-community/ufs-weather-model/issues/2167)
    [#2143](https://github.com/ufs-community/ufs-weather-model/issues/2143)
               [#913](https://github.com/ufs-community/UFS_UTILS/issues/913)

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

commit 47302153f13f6b23539be841b78ed78664599c08
Author: Travis Elless <[email protected]>
Date:   Wed Mar 27 21:14:57 2024 -0400

    Add a rotating subset of members for early-cycle enkf (#2427)

    The early-cycle EnKF needs the ability to run with fewer members than
    the late-cycle due to operational resource constraints. Because of this
    requirement, the introduction of a rotating subset of member first-guess
    states used by the early-cycle ensemble is also needed in order to
    preserve the rotating member initial condition functionality currently
    used by the GEFS.

    Co-authored-by: Travis J Elless <[email protected]>
    Co-authored-by: travis elless <[email protected]>

commit 94c282ef6fdcd47076e932bcadb5bdd55236aa05
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Wed Mar 27 20:28:15 2024 +0000

    Uploading error logs to GitHub from Jenkins CI Runs (#2429)

    This PR enhances the user experience within GitHub for when errors occur
    during build and running of CI cases from within the PR messages. This
    is done by uploading the error logs to GitHub Gists and then publishing
    the links to them along with the full paths of the logs on disk.

    This PR adds the python Class **GitHubPR** in
    `${HOMEgfs}/ci/scripts/utils/githubpr.py` by inhearting the GitHub Class
    from **pyGitHub**. We use this module to introduce a helper python
    utility that can publish a list of log files into a GitHub Gist and/or
    the designated branch **error_logs** in the **emcbot** repo
    **ci-global-workflows** for storing error log files for review from any
    git configured terminal. This upload feature will also create
    persistence of errors over time.

    Also the `build_all.sh -k` script has been updated to support a "quick
    kill" feature (thanks David) that stops the parallel builds whenever one
    fails and creates an error_log file that has the paths to the error
    files that are also uploaded and published in the PR messages in GitHub.

    Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>
    Co-authored-by: terrance.mcguinness <[email protected]>
    Co-authored-by: DavidHuber <[email protected]>
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

commit 6c5065e2e83a45b14505e7575aa4500482ef7452
Author: Rahul Mahajan <[email protected]>
Date:   Wed Mar 27 03:39:16 2024 -0400

    Add option to use traditional threading in the UFS (#2384)

    # Description
    This PR:
    - adds the option of running the ufs-weather-model with traditional
    threading in addition to ESMF-managed threading. See new toggle
    `USE_ESMF_THREADING=YES|NO` set in `config.fcst`
    - does not change the current default of using ESMF-managed threading.
    Traditional threading use might need a little more fine tuning for the
    job-card specification. This will be achieved when the UFSWM RT
    completely switches over to traditional threading
    - updates the hash of the ufs-weather-model to the PR
    https://github.com/ufs-community/ufs-weather-model/pull/2172

    Resolves #2277

    In addition to the above stated objectives, this PR also addresses open
    issues. In particular, this PR:
    - adds a newline at the end of `diag_table_aod`. Fixes #2407
    @zhanglikate
    - reserves more memory on WCOSS2 for offline UPP when running at C768.
    Fixes #2408 @WenMeng-NOAA

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

commit bc1c46dfd7393c5164abcdc2dfa76a9c4bc834b8
Author: RussTreadon-NOAA <[email protected]>
Date:   Tue Mar 26 22:27:30 2024 -0400

    Correct GDASApp paths (#2435)

    The changes in this PR
    - account for changes in GDASApp directory structure
    - generalize how the path to the GDASApp python ioda library is
    specified

    Resolves #2434

commit f0b912be6f2cf2fac590272253f19cb082fbf5f2
Author: David Huber <[email protected]>
Date:   Mon Mar 25 21:46:32 2024 +0000

    Fix *earc jobs where the number of members isn't a multiple of 10 (#2424)

    This limits the earc search for ensemble members to the maximum number
    of members, which prevents attempting to send non-existent members to
    HPSS if the number of ensemble members is not a multiple of 10.

    Resolves #2390s

commit daeb0c855017f8ffd6f06870744b825b276097f3
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri Mar 22 17:40:04 2024 +0000

    hotfix to update full path to error logs on CI case fail (#2425)

    This hotfix PR prepends the full path to the error logs on disk to be
    communitated correctly to the GitHub message to the PR that is being
    processed when there is a failure in from a case.

commit 50f75526549245f2b5d984cdb44e402852e086ec
Author: YaliMao-NOAA <[email protected]>
Date:   Thu Mar 21 16:58:25 2024 +0000

    Add WAFS jobs, scripts and ush to GFS v17 workflow repository (#2412)

    # Description
    This PR adds WAFS jobs, scripts and ush to GFS v17 workflow repository

    ---------

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

commit 03ba78ae3df589211d2776254c6e8584ecdc226f
Author: David Huber <[email protected]>
Date:   Thu Mar 21 13:33:50 2024 +0000

    Hotfix: send the correct number of build jobs for the UFS (#2423)

    This fixes a bug in build_ufs.sh that was causing the UFS to always
    build with 8 jobs (except on the cloud).

commit 4d1bf5266f00b35778ea47896f438e3ef612628d
Author: Kate Friedman <[email protected]>
Date:   Wed Mar 20 14:00:31 2024 -0400

    Updates to RTD documentation (#2418)

    Updates to the RTD documentation include:

    - Textual updates
    - Better definition of GDA subfolder structure
    - Added note about GDAur having been discontinued
    - Adjust copyright and author information
    - Fix Git version table and update its contents
    - Add "Table of Contents" header before table of contents on front page
    - Add AWS ICs path to init page
    - Add link to UFS_UTILS gdas_init RTD documentation
    - Add note about bash to `gw_setup.sh` section and added a warning block

    Refs #2395

commit afe874ee8b28942e459796cd1005ec598458a5b7
Author: Neil Barton <[email protected]>
Date:   Tue Mar 19 14:35:02 2024 -0400

    Add GEFS Ocean Perturbation Options (#2385)

    This PR adds the MOM6 ocean perturbation options when running GEFS. This
    is needed for GEFS reforecasts and GEFS operational forecasts.

    This PR continues to address the below issues
    https://github.com/NOAA-EMC/global-workflow/issues/1720
    https://github.com/NOAA-EMC/global-workflow/issues/1921

    Fixes #2403

commit fa855baa851b0cb635edd1b9ae1bfed5112d41e5
Author: Clara Draper <[email protected]>
Date:   Mon Mar 18 12:49:14 2024 -0600

    Add initial GSI-based soil analysis capability (#2263)

    First set of changes for adding the new soil analysis, from the
    assimilation of screen-level T and q. The changes here enable the
    screen-level observations to be assimilated in the Hybrid (Var and EnKF)
    update, and the soil temperature and soil moisture updates to be made in
    the EnKF only. The functionality is turned on by setting GSI_SOILANAL to
    YES in config.base.

    Resolves #1479

commit e9700d84b521907ee23e1584712f80e25e60f08e
Author: Jessica Meixner <[email protected]>
Date:   Mon Mar 18 09:32:13 2024 -0400

    re-enable ci/cases/pr/C48mx500_3DVarAOWCDA.yaml (#2405)

    Updates to re-enable C48mx500_3DVarAOWCDA CI test after it was disabled
    in https://github.com/NOAA-EMC/global-workflow/pull/2371

    Fixes github.com/NOAA-EMC/global-workflow/issues/2404

commit 3ccffeee120340ab580fc9d96b552970c9f42a8f
Author: Rahul Mahajan <[email protected]>
Date:   Mon Mar 18 09:30:35 2024 -0400

    Parse jediyaml only once (#2387)

    `JEDIYAML` was being parsed 3 times; once in `get_obs_dict`, second in
    `get_bias_dict` and a third time in `initialize` for the specific
    component analysis task.

    This PR:
    - eliminates the duplications and constructs the `jedi_config`
    dictionary just once. The dictionary is written out before calling the
    executable.
    - updates hash to gdasapp
    - updates configs for snow, aerosol, atmvar and atmens JEDI-DA to
    include `JEDI_FIX_YAML` and `CRTM_FIX_YAML` . This allows greater
    flexibility and control over the contents of these fix data sets to be
    copied into the run directory.
    - Combines snowDA and aerosolDA into a single test

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

commit a5f24951c5bef142747c6f6cc6abd474f0b53ac2
Author: CatherineThomas-NOAA <[email protected]>
Date:   Fri Mar 15 14:47:54 2024 -0400

    Fix ensemble archive groups to include all members (#2402)

    The number of groups used in the ensemble archive step (earc) needs to
    include a task for the ensemble stat files such as the mean and the
    spread, resulting in `n_groups+1` tasks for `earc`.

    Resolves: #2390

commit 056cfdca9e7fd7426a315fcbffc38d8ee2891212
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri Mar 15 18:30:23 2024 +0000

    GitHub message error paths (#2401)

    Add feature to message paths to error logs of failed experiments to
    GitHub Messaging the PR from Jenkins.

commit d897ee4936d62160811d936248c8555187f81b65
Author: Rahul Mahajan <[email protected]>
Date:   Thu Mar 14 12:37:49 2024 -0400

    Missed a comma from the hotfix this AM (#2399)

    This PR is a hotfix to the hotfix from earlier this AM. A comma was
    missing.

commit 906540acacf1b2ce4c0489d0d9d4913f53a4e8ad
Author: Rahul Mahajan <[email protected]>
Date:   Thu Mar 14 10:40:03 2024 -0400

    Fix KeyError issue in ocean/ice postprocessing job. (#2398)

    The jjob for ocean and ice pp, only defines the component specific
    history and grib directory. This causes an error in the exscript trying
    to pull keys for both ocean and ice. Fix this. Surprised this has not
    caused failures before today

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

commit c27f243ce24c60261718f15628f6ab30d7b09f7b
Author: Rahul Mahajan <[email protected]>
Date:   Wed Mar 13 13:31:57 2024 -0400

    Remove documentation about generating ICs using global-workflow (#2397)

    Removes instructions on generating ics using global-workflow and
    directs the user to use ufs-utils.

commit 0edbdc197441582f9c402da0f3a7f144b88960c7
Author: DavidNew-NOAA <[email protected]>
Date:   Tue Mar 12 16:30:45 2024 -0400

    Changed config.atmanl to allow non-hybrid background error yamls (#2394)

    # Description

    Makes change so that if DOHYBVAR equals "NO", then the JEDI background
    error yaml is set to staticb_${STATICB_TYPE}.yaml.j2 rather than
    hybvar_${STATICB_TYPE}.yaml.j2. This allows GDAS to run without hybvar,
    which may be necessary for development purposes.

    This is all accomplished by a simple switch in config.atmanl.

commit ccb1f528489e740bb2adc4958146552323dd8709
Author: RussTreadon-NOAA <[email protected]>
Date:   Tue Mar 12 10:45:39 2024 -0400

    Add JEDI atmosphere only CI (#2357)

    The PR contains a minimal set of changes to enable JEDI atmospheric DA
    CI testing. Prototype JEDI atmospheric cycling has begun. The JEDI
    atmosphere DA CI case provides an automated way to see if future PRs
    impact JEDI atmospheric cycling.

    Resolves #2294
    Dependency: GDASApp PR
    [#937](https://github.com/NOAA-EMC/GDASApp/pull/937)

commit b96f5ebbb1968bd539336652b87a2faa8ce68fd4
Author: Kate Friedman <[email protected]>
Date:   Tue Mar 12 07:58:40 2024 -0400

    Add switch to control `debug=true` on WCOSS2 for development testing (#2388)

    Adds a switch (`DEBUG_POSTSCRIPT`) to control whether
    `debug=true` is set when submitting development rocoto jobs to PBS
    schedulers (currently just WCOSS2).

    There isn't an equivalent flag to set for SLURM on the RDHPCS.

    Have added this new switch to documentation.

    Refs #619

commit 02d650500353663d0b193ef14003897daa5dd86c
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Mar 11 21:51:16 2024 +0000

    Rewrote pr_list_database.py to use wxflow's SQLiteDB Class (#2376)

    This PR updates the `pr_list_database.py` code to use **wxflow**
    SQLiteDB Class

    - Improved code's readability
    - Uses better code style matching project's software culture
    - Better docstring standards

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

commit a3374607d01fbdabbec0660afb82b5eb3677b4af
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Fri Mar 8 16:08:42 2024 -0500

    Return ocnanalrun npes resource setting back to previous value (#2386)

    Variable `npes` in `ocnanalrun` entry of `config.resources` was
    erroneously changed in
    https://github.com/NOAA-EMC/global-workflow/pull/2299 and this PR
    changes it back.

    Resolves https://github.com/NOAA-EMC/GDASApp/issues/962

commit d7e9bde84aebe922039589bd2bcd65832c1074eb
Author: BoCui-NOAA <[email protected]>
Date:   Thu Mar 7 16:14:28 2024 -0500

    Add new BUFR table file parm/product/bufr_ij9km.txt for GFSv17 C1152 (#2383)

    This PR will add a new table file parm/product/bufr_ij9km.txt, and
    modify ush/gfs_bufr.sh to choose the different bufr table files based on
    the GFSv17 run resolution, i.e. use file bufr_ij9km.txt for C1152 or
    bufr_ij13km.txt, for C768.

      Resolves #2382

commit 4a525bef3bbed2ea60a71f71b3740c82df125c36
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Thu Mar 7 16:12:31 2024 -0500

    Add global-workflow infrastructure for ocean analysis recentering task (#2299)

    Adds jjob, rocoto script, config file, and basic `config.resources`
    entry for ocean analysis recentering task

    This PR is a dependency for further work on the associated issue within
    global-workflow and GDASApp

    Refs https://github.com/NOAA-EMC/GDASApp/issues/912

commit f83d17a937006add55241ed453e42f4fcbae50aa
Author: Kate Friedman <[email protected]>
Date:   Thu Mar 7 09:29:14 2024 -0500

    Clean out non-gfs top level variables (#2366)

    Clean out non-gfs top level variables that are duplicates or no longer needed.
    Also standardize how we set these variables in scripts.

    Refs #2332

commit c7b306e052497aef0022cd53550a168d2c5b6e5b
Author: Guillaume Vernieres <[email protected]>
Date:   Wed Mar 6 16:16:08 2024 -0500

    Forgotten templated  DO_VRFY_OCEANDA (#2379)

    # Description
    This PR adds the possibility to use the switch for the ocean and sea-ice
    DA verify task from the yaml configuration.

    - fixes
    [GDASApp/issues/954](https://github.com/NOAA-EMC/GDASApp/issues/954)

commit ba6a4fdf6e245b57530f2b20e6f0ccf567115720
Author: David Huber <[email protected]>
Date:   Tue Mar 5 19:09:48 2024 +0000

    Add Hercules support for the GSI monitor (#2373)

    # Description
    This updates the GSI monitor hash and updates the modulefiles to add
    support for the monitor on Hercules.

commit 732a874a2c6793296f136afb23545fab9869b181
Author: Rahul Mahajan <[email protected]>
Date:   Mon Mar 4 16:04:26 2024 -0500

    Reformat snowDA templates to jinja2 (#2371)

    # Description
    This PR:
    - replaces use of non-jinja2 templates in the yaml templates.
    Specifically `$( )` in favor of pure jinja2.
    - uses jinja2's built-in capability to include templates within
    templates, thereby allowing to assemble a completely rendered template
    before passing it to for e.g. yaml loader.
    - requires updates to `wxflow` and `gdasapp`
    - Changes in `wxflow` in `parse_j2yaml` are **not** backwards compatible

    Additionally, this PR:
    - renames `config.base.emc.dyn` to `config.base`.  Resolves #2347

commit d1fa41106e991556606b0f62a15bf45f469f4f79
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Sat Mar 2 04:54:26 2024 +0000

    Reduce Jenkins messaging to GitHub (#2370)

    This PR updates the Jenkins Pipeline code with safeguards against the
    errors caused when Jenkins fails to authenticate with GitHub to message
    or update a label. This was achieved simply by:

    - Reducing the number out messages sent to the GitHub PR
    - Putting try blocks around most of the update label calls

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

commit 52fa3cb32d8b50e47f391b82ea8901435fc88aff
Author: Henry R. Winterbottom <[email protected]>
Date:   Fri Mar 1 12:36:27 2024 -0700

    Adding debug option for all build scripts (#2326)

    This PR addresses issue #300 that allows building in `debug` mode.
    Co-authored-by: David Huber <[email protected]>
    Co-authored-by: Rahul Mahajan <[email protected]>

commit 91738cbf871d8cdce46912e2c11e304d567a2aae
Author: DWesl <[email protected]>
Date:   Fri Mar 1 13:46:42 2024 -0500

    Sort list of coupler restart files for restart time determination (#2360)

    The loop in the following conditional seems to assume the list is
    sorted, so make that explicit in the array construction.

commit 23c25527ad2a62275cd9105bd103b8520a28e573
Author: Neil Barton <[email protected]>
Date:   Fri Mar 1 13:45:39 2024 -0500

    Update stage IC to handle ocean perturbations (#2364)

    This PR adds the option to stage ocean perturbation files for ensemble
    forecasts. These perturbation files are used in GEFS forecasts.
    A new variable is introduced in config.base to use the ocean
    perturbation files.
    This PR does not include using these perturbation files. A future PR
    will address this.

commit 8efe05f475b81e7cf6376745d5f1ce31987cb4eb
Author: Jessica Meixner <[email protected]>
Date:   Fri Mar 1 07:41:56 2024 -0500

    Turn on C48mx500_3DVarAOWCDA test on hera (#2363)

    This PR activates the C48mx500_3DVarAOWCDA test on hera. This required
    an update of the gdas app.

commit 5166593945e9ecc04dfa3409752576c08797d09f
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Feb 29 20:14:41 2024 +0000

    Move Jenkinsfile into ci subdirectory (#2355)

    Just moves the Jenkinsfile into the ci directory

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

commit b7af315bb9dea77b37c6d030b71060b87bedf33e
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Feb 28 22:20:58 2024 +0000

    Fix rocoto forecast hour determination for GEFS (#2351)

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

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

commit d3a49271b6c3816a9feeb7f6fb474797bacf1d7e
Author: Cory Martin <[email protected]>
Date:   Wed Feb 28 09:38:49 2024 -0500

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

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

commit 2693810d6ea9d9b20090777ff3a98e3d072c76d7
Author: Jessica Meixner <[email protected]>
Date:   Tue Feb 27 01:25:51 2024 -0500

    Update ufs-waether-model hash (#2338)

    Routine update of ufs-weather-model hash.

    Other small updates:
    * removes comment referencing closed issue.
    * Updates the CICE diag frequency to once per day as recommend here:
    https://github.com/NOAA-EMC/global-workflow/issues/1810#issuecomment-1686278925
    * Updated amount of time for C384 gdas forecast as it was running out of
    time
    * Removed unused variable wave_sys_ver

commit 9608852784871ebf03d92b53bde891b6dcab8684
Author: RussTreadon-NOAA <[email protected]>
Date:   Mon Feb 26 14:10:01 2024 -0500

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

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

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

    Resolves #2335

commit c5c84660f10f0ef9ce939231b2f7fda498b39a29
Author: Kate Friedman <[email protected]>
Date:   Mon Feb 26 10:18:50 2024 -0500

    Remove FIX* variables for fix subfolders (#2337)

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

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

    Resolves #2184

commit 950c38a093c6a4e2b67e18c76390280d8bfbaef7
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Fri Feb 23 21:15:46 2024 +0000

    Fix several Jenkins issues (#2334)

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

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

commit c67393a203285792b852da0d83fd10fa47155669
Merge: 6f9afff07 79d305e8c
Author: David Huber <[email protected]>
Date:   Fri Feb 23 14:18:15 2024 +0000

    Merge pull request #2239 from DavidHuber-NOAA/ss160

    Update to spack-stack 1.6.0

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

commit 79d305e8cbc339208ea6fe0475ddc56af94a285b
Author: David Huber <[email protected]>
Date:   Thu Feb 22 14:53:57 2024 -0600

    Disable snow DA tests

commit 0459203e97211b041520b39e93a188951396ba33
Author: David Huber <[email protected]>
Date:   Thu Feb 22 12:55:51 2024 -0600

    Update GDASApp hash to current develop

commit 5c96eb2272fe6117f9e4a4c0c790db58e4870d46
Author: David Huber <[email protected]>
Date:   Thu Feb 22 12:37:47 2024 -0600

    Update GDAS hash to allow modified snow DA analysis

commit 79144f2403a33d08140577cc3e8a61d6c4924403
Merge: abbb0b8a7 6f9afff07
Author: DavidHuber <[email protected]>
Date:   Thu Feb 22 15:14:39 2024 +0000

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

commit abbb0b8a76b39d34433802fd4e3d7973fb9f0a39
Merge: 4ad837ea1 4529e8cf3
Author: DavidHuber <[email protected]>
Date:   Thu Feb 22 15:11:03 2024 +0000

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

commit 4ad837ea157b98d2bd173cb696c4d30d142e5540
Merge: 516b2a270 7ca45db8f
Author: DavidHuber <[email protected]>
Date:   Thu Feb 22 15:10:24 2024 +0000

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

commit 516b2a270234bdab5714ef2705c83dd3835b134d
Author: DavidHuber <[email protected]>
Date:   Thu Feb 22 14:19:16 2024 +0000

    Updated GDAS to include rocoto/1.3.6 on Hera.

commit 6f9afff073dd589096f992a3448fb7f0e62c9804
Author: Jessica Meixner <[email protected]>
Date:   Wed Feb 21 13:09:44 2024 -0500

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

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

    Refs #1629

commit f6d3015ab9f9fd23ce0081baa2edbc5d9f5f3e16
Author: David Huber <[email protected]>
Date:   Tue Feb 20 09:53:08 2024 -0600

    Update GDASApp hash to include SS/1.6.0 support.

commit 0bf340bce2f865c582e5305f0c5984cd3affe74e
Author: David Huber <[email protected]>
Date:   Tue Feb 20 09:07:32 2024 -0600

    Construct SS paths from version variables.

commit 3330cd7310bde8090b68720c225656074676d6b2
Author: David Huber <[email protected]>
Date:   Tue Feb 20 09:06:19 2024 -0600

    Removed MET/METplus 'not available' comments

commit fdc638ca1616b347912caec77e5abc2d3e6f18af
Author: David Huber <[email protected]>
Date:   Tue Feb 20 08:35:15 2024 -0600

    Move SS module path to version files.

commit d7d28a6b65b84c8d821abd2c13d0c068bd5ad6d8
Author: David Huber <[email protected]>
Date:   Tue Feb 20 07:53:15 2024 -0600

    Update comment about METplus support.

commit a812f88af3fc043d57494840e81a7527723858e4
Author: David Huber <[email protected]>
Date:   Tue Feb 20 07:45:45 2024 -0600

    Update verif-global to latest WCOSS2 support.

commit d81f07fbf53666a37ab01bd463152e10252869ae
Author: David Huber <[email protected]>
Date:   Tue Feb 20 07:41:38 2024 -0600

    Clean up build_upp.sh.

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

commit ae7eb194cbe2213e564807dd7bc03a28d493eff2
Author: David Huber <[email protected]>
Date:   Fri Feb 16 16:15:40 2024 -0500

    Fix whitespace in build_upp.sh.

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

commit 48b34d0f388a398bb91f7c3b1e5f8338f4beb7b9
Author: David Huber <[email protected]>
Date:   Fri Feb 16 20:56:55 2024 +0000

    Added verif-global support back to WCOSS2.

commit 4529e8cf3736ffbacf615a27e99f4d1beec391aa
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Fri Feb 16 11:12:01 2024 -0700

    Bug fix.

commit 8e4f94d13d32849b2862a9d59aa070f4103c61ae
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Fri Feb 16 11:04:41 2024 -0700

    Updates requested by reviewer Rahul Mahajan.

commit 4624ce21c99ab303afa10c1dd8ddcce7b6f715ca
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Fri Feb 16 10:52:11 2024 -0700

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

commit ed25bbd0b26a893d32ce4a10b368dec2bb722424
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Fri Feb 16 09:33:59 2024 -0700

    Linter corrections.

commit 6a0b7bf214815c13eec98a93bd3abe9978de04e4
Merge: f9fb64ef8 2415b7b4f
Author: David Huber <[email protected]>
Date:   Fri Feb 16 09:50:22 2024 -0600

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

commit f9fb64ef802b683d7b369f8e8268d423ab581481
Merge: 777d97d3a a23b7f2fd
Author: David Huber <[email protected]>
Date:   Fri Feb 16 09:49:42 2024 -0600

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

commit 7ca45db8fa32c84ef117ff2938a650822c81a786
Merge: 73bc76bfd a23b7f2fd
Author: Henry R. Winterbottom <[email protected]>
Date:   Fri Feb 16 07:46:35 2024 -0700

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

commit eb2ed53857eb3387735488a1ce5d701ff680e3db
Merge: 9929277dc a23b7f2fd
Author: Henry R. Winterbottom <[email protected]>
Date:   Fri Feb 16 07:46:24 2024 -0700

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

commit a23b7f2fdca5be700d257e28052a0104f2173a0f
Author: RussTreadon-NOAA <[email protected]>
Date:   Fri Feb 16 09:37:58 2024 -0500

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

commit cf83885548bb3a6740c033f42479ce2ad283a4a9
Author: Jessica Meixner <[email protected]>
Date:   Fri Feb 16 01:55:02 2024 -0500

    Add unstructured grid for HR3/GFS (#2230)

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

    The fix file update is here: NOAA-EMC/global-workflow#2229

    Note: This now means that GFS tests need a new build option:
    `./build_all.sh -w` So that PDLIB=ON is turned on for compiling relevant
    UFS and WW3 codes.

    Resolves NOAA-EMC/global-workflow#1547

commit 9929277dc7d0ad90f5366faf4b5f2278969a0aa2
Merge: eb8791ccb 094e3b86d
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Feb 15 15:05:50 2024 -0700

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

commit 094e3b86da44f1d3fc1d99f68f6fdfcd36deb09f
Author: Cory Martin <[email protected]>
Date:   Thu Feb 15 14:43:55 2024 -0500

    Move IMS remapping files from COM_OBS to FIXgdas (#2322)

    * Add in IMS obs fix directory and update submodule for gdas

commit d465ea06e8b2a8f3a5eb1120647c1e2ce5197d66
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Feb 15 19:25:02 2024 +0000

    Set HOMEgfs for module_setup in CI driver (#2321)

    Hotfixes to  CI Bash system from updates with sourcing
    `detect_machine.sh` in `ush/module-setup.sh` using **HOMEgfs**.

commit 2415b7b4f3e6c376aca27707510001141cc9dd92
Author: David Huber <[email protected]>
Date:   Thu Feb 15 19:21:17 2024 +0000

    Load default rocoto on Jet.

commit eb8791ccbe684828dc529d0e553551969274fc22
Merge: 60d5ee64b 638684e0b
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Feb 15 11:56:40 2024 -0700

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

commit 777d97d3a1c9f5ec5e8af3ca40a41224ec7099a1
Author: David Huber <[email protected]>
Date:   Thu Feb 15 12:34:59 2024 -0600

    Fixed Orion cdo version.

commit ef0723503c72f295de93521c7102c43e75c47417
Author: DavidHuber <[email protected]>
Date:   Thu Feb 15 16:29:32 2024 +0000

    Revert UFS hash.

commit 0ce8c0dbc13227884fef1c637e93616a28c68d34
Author: DavidHuber <[email protected]>
Date:   Thu Feb 15 14:55:48 2024 +0000

    Fix git version in Hera's gwsetup module.

commit 3080a34253e8e24105bf2be72b6a872b1c072935
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 20:52:34 2024 +0000

    Fixed xarray version for SS/1.6.0.

commit 49392dd47ff84b6586052aeae6879d7d8050b746
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 20:29:41 2024 +0000

    Updated GSI-Utils hash to head of develop.

commit c3553f0d8e6a05c6234e7c14a179983aa44fd6f3
Merge: 4568653a6 638684e0b
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 20:28:14 2024 +0000

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

commit 4568653a67aa37c902379db628fb10f69fe7190f
Author: David Huber <[email protected]>
Date:   Wed Feb 14 14:22:13 2024 -0600

    Reupgrade Hercules to SS/1.6.0

commit 638684e0bfcd06700cc8695f09824891a0a1eee1
Author: Kate Friedman <[email protected]>
Date:   Wed Feb 14 14:55:21 2024 -0500

    Remove `finddate.sh` from system (#2308)

    * Retire finddate.sh usage from system
    * Update gfs-utils hash to 7a84c88 - New hash includes removal of finddate.sh

    Refs #2279

commit 2b160f8470bed16c513ca4a5665e2b6d4448c50e
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 18:31:28 2024 +0000

    Reenable METplus jobs on Hercules.

commit 8f5900265a31e894060bbe9c89b262f4df0b1760
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 18:30:23 2024 +0000

    Update GSI hashes.

commit 73bc76bfd47f2cff54df55e15d9ed8969683367d
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 14 09:27:37 2024 -0700

    Updates based on user request.

commit e4bc674cf3b2df10e0b0dfd50a8ecb0f4f7825d8
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 14 08:03:45 2024 -0700

    Corrected based on reviewer review.

commit 60d5ee64bda7a16c1f2dc20c8badcd7c8fc4e592
Merge: 40f2cf6cd 1aaef05d3
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Feb 13 18:08:33 2024 -0700

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

commit 03304112347a673b7a0fcc404703bb10960bc47a
Merge: 929b90330 1aaef05d3
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Feb 13 17:58:12 2024 -0700

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

commit 1aaef05d317cd1eec548ef2b9842679c531cef8b
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Feb 13 18:15:59 2024 -0500

    Jenkins Pipeline updates for Canceling Jobs (#2307)

    Tuning updates for Jenkins Pipeline :
    - Added short circuit for all parallel runs of cases on error of any
    - Fixed canceling of all scheduled jobs on first case error
    - Added feature to save error log files to Jenkins Archive facility on fail

commit 64048926627f8c9edb087de286095e3b93a214c2
Author: Rahul Mahajan <[email protected]>
Date:   Tue Feb 13 14:57:37 2024 -0500

    Ocean/ice product generation for GFS and GEFS (#2286)

    This PR does several things:
    1. the model output for ocean and ice in the `COM/` directory are now
        named per EE2 convention for coupled model.
        E.g `gfs.ocean.t12z.6hr_avg.f120.nc` and `gfs.ocean.t12z.daily.f120.nc`
    2. The products are generated using the `ocnicepost.fd` utility developed
        by @DeniseWorthen in https://github.com/NOAA-EMC/gfs-utils and
        converted to grib2 using example scripts provided by @GwenChen-NOAA
        using `wgrib2`.
    3. NetCDF products on the native grid are also generated by subsetting
        variables from  the raw model output.  This is done with `xarray`.
    4. updates the hash of https://github.com/NOAA-EMC/gfs-utils to include
        fixes in `ocnicepost.fd`
    5. removes NCL related scripting that was previously used for ocean/ice
        interpolation and `reg2grb2` used for converting to grib2.
    6. updates archive scripts to accommodate updated file names
    7. removes intermediate ocean processed files such as 2D/3D/xsect data-
        sets
    8. separate jobs are added for ocean and ice product generation.
    9. removes intermediate restarts for the mediator and only saves the medi-
        ator restart at the end of the forecast in `COM`.
    10. Increases memory for offline UPP when run at C768.  The program
          segfaults with an OOM when memory is self allocated based on PEs by
          the scheduler on Hera.
    11. Enables ocean/ice ensemble product generation for GEFS
    12. Some minor clean-ups

    Fixes #935
    Fixes #1317
    Fixes #1864

commit 40f2cf6cd70ac94e01babc96982f37ae1b0c7e79
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Tue Feb 13 10:18:53 2024 -0700

    Implemented ush/detect_machine.sh for host determination and removed redundant checks for expected file paths.

commit 929b90330c7eb345011c2c850915e0004ca26b11
Merge: 2d08d015a 3f99f700c
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Feb 13 08:31:06 2024 -0700

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

commit 3f99f700c987526c8eb754b3f4c7b698b3e9b1dc
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Feb 13 00:57:18 2024 -0500

    Add wave post jobs to GEFS (#2292)

    Adds the wave post jobs for gridded and points to GEFS. Boundary
    point jobs are added even though the current GEFS buoy file does
    not contain any (tested by manually subbing in the GFS buoy file).

    Resolves #827

commit 842adf38087aec9f1c0bca9567e4b11d494e14c7
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Feb 12 12:50:08 2024 -0500

    Added additional test cases to the pr list in Jenkins (#2306)

    C48mx500_3DVarAOWCDA, C96C48_hybatmDA, and C96_atmsnowDA
    Co-authored-by: terrance.mcguinness <[email protected]>

commit bb4ca65fe5524f76e40b97346339f1dda6680ce1
Author: CatherineThomas-NOAA <[email protected]>
Date:   Mon Feb 12 14:50:41 2024 +0000

    Redo v16.3 config.base changes for DA increments (#2304)

    Include the additional hydrometeors to the
    INCREMENTS_TO_ZERO and INCVARS_ZERO_STRAT
    variables in config.base that were modified
    in v16.3.

    Resolves: #2303

commit 061992bb6160554430cf688adf6184f01b732098
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Sat Feb 10 01:33:36 2024 -0500

    Fix Jenkins success reporting (#2302)

    Moving the post section back outside of main Run Experiments
    stage. This allows the system to correctly report the **Success**
    status until after all tests pass.

    _Had originally moved them in attempts to solve "Not an SCM
    GitHub Job" issue and cause the reporting to misbehave._

    Also ran through Jenkins linter and updated some messaging
    that was incorrectly reporting system build type.

commit 28ccf78073a20ba1e4d3b379d164109b54ff6708
Merge: b972f66fc 54daa31ce
Author: David Huber <[email protected]>
Date:   Fri Feb 9 14:00:43 2024 -0600

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

commit b972f66fc924790c48f38d395e7141fa78ef9d90
Author: David Huber <[email protected]>
Date:   Fri Feb 9 10:47:00 2024 -0600

    Fix SS versions for CI modules.

commit 4b01d8eeca26c3b3d843a4b1e7b1618f281de68f
Author: David Huber <[email protected]>
Date:   Fri Feb 9 10:44:30 2024 -0600

    Revert Hercules modules to SS/1.5.1.

commit 54daa31ce0a3c23d4d74def5e54436a39a899ed4
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Feb 8 15:48:38 2024 -0500

    Jenkins Declartive Pipeline for CI with gfs/gefs multibuilds (#2246)

    Adding top level Jenkins file for CI tests running on Jenkins Controller:

    - Declarative Multi-branch Pipeline (has enhanced restart capabilities
    on a per section bases)
    - Starts Pipeline from Label PR same as BASH system (for now)
    - Progress and restarts can me managed with CAC Login at [EPIC OAR
    Jenkins](https://jenkins.epic.oarcloud.noaa.gov)
    - Has logic for multi **gfs/gefs** system builds (arguments based on a
    configuration file `ci/casts/yamls/build.yaml`)
      - Any number of **systems** may be added by manual adding an ele-
    ment to the matrix in the Jenkinsfile
      - _It may be possible to dynamic add matrix values with a specialty
    plug-in_
    - Currently only runs on **Orion** and **Hera** using `mterry` account

    Resolves #2119
    Resolves #2118

commit 43429e23c12c1f2050b3a3f356abdec98dc73ea0
Author: Rahul Mahajan <[email protected]>
Date:   Thu Feb 8 15:30:28 2024 -0500

    Enable AO WCDA test (#1963)

    This PR:
    - adds GSI + SOCA C48 5-deg ocean 3DVar test (courtesy @guillaumevernieres)
    - adds a toggle to optionally disable ocnanalvrfy job.

commit 2d08d015afb9c850577efd9754add16b10c45ae6
Merge: 4745d4a06 f56352874
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Feb 8 07:24:54 2024 -0700

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

commit f56352874d6dc133a4f1181f77c8f91ca38a6416
Author: Kate Friedman <[email protected]>
Date:   Wed Feb 7 15:09:12 2024 -0500

    Update JGLOBAL_FORECAST for octal error (#2295)

    Add "10#" to ENSMEM value > 0 check to handle octal errors.

commit 4745d4a06148cc6c702c647e12ede4875e3a5862
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 7 08:45:49 2024 -0700

    Removed jlogfile references.

commit 5894ca2bf11e8ab7910c69781a9fbe51352a7e8c
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 7 08:32:16 2024 -0700

    Removed dummy variable passed to perl scripts.

commit dae884a7c48b4a30c1844685c3d0ef50c9b78344
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 7 08:29:49 2024 -0700

    Removed jlogfile and postmsg references within gempak scripts.

commit 801058ffb0cbbfe101fd5b686aed79c5bf7538c1
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Feb 7 00:41:59 2024 -0700

    Consolidate `npe_node_max` (#2289)

    - The environment variable `npe_node_max` is removed from all
    files beneath `global-workflow/env`;
    - The environment variable `npe_node_max` is removed from
    `parm/config/gefs/config.ufs` and `parm/config/gfs/config.ufs`;
    - The environment variable `npe_node_max` is maintained only
    within `parm/config/gefs/config.resources` and
    `parm/config/gfs/config.resources`.

    Resolves #2133

commit b0325e0157598702cbba6c3cc09af0120881e2b4
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Feb 7 00:40:20 2024 -0700

    Removes files module loading file no longer used by the GW (#2281)

    Removes `module-setup.csh.inc` and `module-setup.sh.inc`.

    The module `ush/module-setup.sh` is updated such that it now sources
    `ush/detect_machine.sh` to determine which supported platform the
    global-workflow is being execute on.

    Resolves #2130

commit 1ccc9896b361f2aaef8e6e7592a06ae4cfb7c491
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Feb 5 14:16:07 2024 -0500

    Remove EnKF forecast groups (#2280)

    Removes the grouping of EnKF forecasts so each job only runs
    one forecast. Member and MEMDIR are now set at the workflow
    manager (rocoto) level. This change makes much of the system
    simpler (especially dependencies) and allows the elimination of
    the separate efcs scripts.

    Metatask names of updated jobs have been updated to make
    them a little less opaque by using the same name name as its
    constituent tasks (e.g. the forecast metatask is named
    `enkgdasfcst`, not `enkfgdasefcs`). Metatasks that weren't
    updated retain the same names as before for now.

    Resolves #2254

commit 9f3383fd8d8322428a40b94764a172a16872995e
Author: Henry R. Winterbottom <[email protected]>
Date:   Mon Feb 5 12:15:13 2024 -0700

    Updated detect_machine.sh using that from UFS WM. (#2252)

    Updates `ush/detect_machine.sh` to match the UFS weather-model
    `tests/detect_machine.sh` prepared by @BrianCurtis-NOAA

    Resolves #2228

commit 7d68b0b164f0ffcd56867ae4fdab67905d9589eb
Author: CatherineThomas-NOAA <[email protected]>
Date:   Sun Feb 4 22:02:41 2024 +0000

    Update global_cycle for fractional grid (#2262)

    The hash for ufs_utils is updated to include the changes for
    fractional grid support within global_cycle.  This commit also
    removes the hack to skip global_cycle in cycling mode with
    v17 physics.

    Resolves: #1775
    Refs: ufs-community/UFS_UTILS#815
    Refs: ufs-community/UFS_UTILS#891

commit ed592a6ecfabc0d0b64a6e276531b7bc5ae3b8ea
Author: Kate Friedman <[email protected]>
Date:   Sat Feb 3 02:55:14 2024 -0500

    Retire cycle-specific FHMAX_GFS variables (#2278)

    This PR retires the `FHMAX_GFS_${cyc}` variables that allowed users to specify
    different gfs forecast lengths for each cycle. This function is no longer supported
    in global-workflow. The `FHMAX_GFS_*` variables will be removed and will no
    longer be checked to set the final `FHMAX_GFS` variable. The same forecast
    length will be set for every cycle.

    This PR also includes a small fix to add new post parm files into the `.gitignore`
    file. This was intended to be included in a different PR but that PR is on hold for
    further testing so it is being included here to get it into `develop` sooner.

    Resolves #2218

commit 977e2d67b268477321aa26fc56073dd373e4f979
Author: Henry R. Winterbottom <[email protected]>
Date:   Fri Feb 2 07:49:09 2024 -0700

    New GDASApp hash. (#2285)

commit b5f2bd9ec5632c4be43004604eed0e130dfe1735
Merge: 4d667421d 0400e1f35
Author: David Huber <[email protected]>
Date:   Tue Jan 30 13:55:00 2024 -0600

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

commit 0400e1f3558be8e34c1298d32e14999c9dd46f8c
Author: David Huber <[email protected]>
Date:   Tue Jan 30 09:57:11 2024 -0600

    Fix gfs_utils Orion spack-stack env path.

commit 6bbe823e729291db326d108765d3a92a99552a58
Author: DWesl <[email protected]>
Date:   Mon Jan 29 21:15:30 2024 -0500

    Use seq to generate the list of times, instead of a bash for-loop (#2264)

    I'm running a year-long forecast, which means I get a large portion of the log file dedicated to these loops.

    `seq ${START} ${STEP} ${STOP}` will generate a sequence going from START to STOP by STEP, including STOP if relevant.  That seems to be the purpose of these loops.  It will by default separate the list with newlines, but `seq -s ' ' ${START} ${STEP} ${STOP}` will separate them with spaces instead, more closely mimicing the previous behavior.

    I would like this to be two lines in the log, rather than a few hundred, and this may also be faster, though probably more for reasons of fewer writes to disk than because bash isn't designed for arithmetic.

commit d5bee38979cde547861261d1cd150f3a61601d4b
Author: Kate Friedman <[email protected]>
Date:   Mon Jan 29 14:35:02 2024 -0500

    Correct typos in GFS config.resources (#2267)

    This PR corrects some typos in `parm/config/gfs/config.resources` that were
    introduced in PR #2216. The esfc job was failing in tests on WCOSS2 due to
    insufficient memory. This lead to discovering the other typos. The esfc job
    completes without error after its memory is set back to `80GB` from the
    incorrect `8GB`.

    Resolves #2266

commit 81557beca9eecd878e7b25b3822e30a4276f4a16
Author: David Huber <[email protected]>
Date:   Mon Jan 29 12:13:31 2024 -0600

    Update monitor hash to noaa-emc with SS/1.6.0 support.

commit 2238dd6ac0094ba2ff5e1027e964ef29ad33352c
Author: DavidHuber <[email protected]>
Date:   Mon Jan 29 13:21:30 2024 +0000

    Update Orion, Hercules, S4 modulefiles.

commit 6ffd94fd95f54ceb940f0c9201774ad73fbb055b
Author: DavidHuber <[email protected]>
Date:   Fri Jan 26 16:01:23 2024 +0000

    Update GDAS hash to include SS/1.6.0 support.

commit be11f85f28cf832e5fbb390fdd387f1bdecb5f82
Merge: 56b968080 04e0772d9
Author: DavidHuber <[email protected]>
Date:   Fri Jan 26 15:34:24 2024 +0000

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

commit 8ff344844e28c3b2d03a0356f88b14635f318c12
Author: Rahul Mahajan <[email protected]>
Date:   Fri Jan 26 10:12:18 2024 -0500

    Add a yaml for snow DA testing. (#2199)

    - adds a new test yaml C96_atmsnowDA.yaml for 3DVar atmosphere with GSI and Land (Snow) DA with JEDI
    - moves a few yamls from platforms/ to yamls/
    - adds ability to overwrite a previously created experiment as an addition to user input.
    ---------

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

commit 04e0772d9d3e77ac5a24ce4570d48cb41424a08b
Author: David Huber <[email protected]>
Date:   Fri Jan 26 07:16:25 2024 -0600

    Update ufs_utils hash for spack-stack/1.6.0 support.

commit 3d44ff38c5c3324c22fc104fe3259b4ac864c6d6
Author: Barry Baker <[email protected]>
Date:   Thu Jan 25 14:33:27 2024 -0500

    GOCART ExtData biogenic climatology fix (#2253)

    Updates the ExtData for biogenic emissions to be climatology rather than
    for current time.  Fixes an issue which will crash by default for other years.

commit 66f58b8ab1a9524d6be95271f27a06c2f32e5f78
Author: Guillaume Vernieres <[email protected]>
Date:   Thu Jan 25 13:16:41 2024 -0500

    Added missing container case in gfs/config.resources (#2258)

    fixes  #2257

commit 553b4f2e74ef610115436b75f7f6df100babd8dd
Author: WenMeng-NOAA <[email protected]>
Date:   Thu Jan 25 13:00:45 2024 -0500

    Fix post parm links (#2243)

    Change symbolic links under parm/post with the latest version of develop branch from UPP repository and enable MERRA2 aerosol fields.

    Resolves #2259

commit 4d667421d5eefea2347ea1dd8097e39e167d7201
Merge: 6c058039e afa09e356
Author: David Huber <[email protected]>
Date:   Thu Jan 25 07:49:08 2024 -0600

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

commit 6c058039e209c67ea477d37d2d6f76b7a2fa68ac
Author: David Huber <[email protected]>
Date:   Thu Jan 25 07:48:42 2024 -0600

    Fix wgrib2/gfs_utils on Hercules.

commit ee6f536ea0228c60f5a8bec4037cd6f7ea63b816
Author: Kate Friedman <[email protected]>
Date:   Thu Jan 25 07:43:13 2024 -0500

    Update GFS version to v16.3.13 in index.rst (#2256)

    GFSv16.3.13 WAFS update was implemented

    Refs #2013

commit 2445d44d0d66f35512080b0bd5867501660793bb
Author: RussTreadon-NOAA <[email protected]>
Date:   Thu Jan 25 06:17:11 2024 -0500

    Simplify and extend load_ufsda_modules to Hercules (#2245)

    GDASApp jobs do not run on Hercules because `ush/load_ufsda_modules.sh` does
    not include logic to load the appropriate GDASApp modules on Hercules.  This PR
    extends `load_ufsda_modules.sh` functionality to Hercules, thereby enabling
    GDASApp jobs to run on Hercules.

    Resolves #2244

commit 56b9680803f109720f6439276a0e5783a9c49352
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 19:47:34 2024 +0000

    Update hashes (revert WCOSS2 modules).

commit afa09e356503f1befc162df9a79dc9ce7414dc22
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 18:59:40 2024 +0000

    New (cleaner history) gdas hash.

commit a9eaec23d5103ea766342ff81d77df8e0f6d9a58
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 18:52:27 2024 +0000

    Update gdasapp to include ss/1.6.0 support.

commit 5ef8eb24eeaeaff9c9a03767d929f2114fd4840f
Merge: 4c463548b e400068a2
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 17:08:54 2024 +0000

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

commit 4c463548b0c38f36c13c01716fa0b1e91544e440
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 17:05:12 2024 +0000

    Reenable verif-global support

commit f775755df5f1579edfafbce9a7b47034907d023f
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 16:59:10 2024 +0000

    Assign fcsthrs for awips_g2 job.

commit e400068a2951e5fa3b130369861b4a60ece01491
Author: David Huber <[email protected]>
Date:   Mon Jan 22 15:01:07 2024 -0600

    More gsi-addon path fixes.

commit f663d4786f226f8164d348d403e8d105cc3d801b
Author: David Huber <[email protected]>
Date:   Mon Jan 22 14:41:59 2024 -0600

    Fix gsi-addon paths for hercules, orion, and S4.

commit e304bbeb364067e411fb50801796d000b44d9147
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:59:34 2024 +0000

    Better optimize build jobs (more ufs jobs).

commit ccc6e2d445d4c2e2f44fb907c7bc972b1e69f6ff
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:56:18 2024 +0000

    Reenable verif-global. #2195

commit 3ef3411f856b0c5a9cf51686f3a51a2252596690
Merge: 4365f63e5 f4d187f4e
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:39:10 2024 +0000

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

commit 4365f63e54e2ddb9b88e768a6e88a92504b5d482
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:37:25 2024 +0000

    Corrected the SS env. name in the version files. #2195

commit f4d187f4e45fe89583d18987d68a883490827104
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Mon Jan 22 12:28:28 2024 -0500

    Converts obsproc to obsprep in prepoceanobs config file (#2236)

    Converts obsproc to obsprep in prepoceanobs config file as a compliment to mutually depended GDASApp PR NOAA-EMC/GDASApp#858
    The motivations are explained in refs NOAA-EMC/GDASApp#857

commit 9a09d3082208ad206cf6e7103a53bfb7c4946f4a
Author: DavidHuber <[email protected]>
Date:   Fri Jan 19 21:23:50 2024 +0000

    Corrected gsi-addon-dev spelling.

commit 21ff6458aac9372b26cc223f6a114953a137067e
Author: DavidHuber <[email protected]>
Date:   Fri Jan 19 21:11:34 2024 +0000

    Update modulefiles, submodules to spack-stack 1.6.0. #2195

commit d4c55d1011f8b0385d25b62ac04710837ed8413e
Author: Kate Friedman <[email protected]>
Date:   Fri Jan 19 15:43:37 2024 -0500

    Update typing hint for WCOSS version of python (#2238)

    The typing hint `typing.List` was deprecated with python 3.9 in favor
    of using the primitive `list[str]`, but the functional version of python
    on WCOSS2 is <3.9, causing `setup_xml.py` to fail there. This replaces
    `list[str]` as a typing hint with the deprecated form until the supported
    version on WCOSS2 is >=3.9.

commit 491928712ae1dabac62750450c9cad8f538c2a3e
Author: Barry Baker <[email protected]>
Date:   Thu Jan 18 22:31:27 2024 -0500

    GOCART Emission updates for GEFSv13 and GDAS  (#2201)

    This PR addresses several things needed for more recent simulations using
    GOCART2G as well as preparing for the GEFSv13 30 year run.  The main
    updates are:

    - Update CEDS to use monthly emission files instead of daily.  This will
    drastically reduce the number of files needed. No science change
    - Update biogenic MEGAN inputs to use a climatology rather than the
    offline biogenic previously used.  This is needed to deal with simulations
    where the current dataset is not available.
    - Update volcanic SO4 emissions to use degassing emissions only.  This is
    to support the need for more recent simulations where data is not available.

commit 13d25cfc3614de978bfd4b7f273d1f13cb820878
Author: Kate Friedman <[email protected]>
Date:   Thu Jan 18 22:29:43 2024 -0500

    Add `POSTAMBLE_CMD` into preamble postamble (#2235)

    This PR adds the ability to run a command at the end of jobs via the
    preamble's postamble function. A new command can be set via
    `POSTAMBLE_CMD` and will be invoked at the end of jobs. Users can
    add the command to the top of an env file to have every job run it or
    it can be placed within a job if-block in the env file to run for just that
    job.

    Resolves #1145

commit 7759163c668eb6ccc11dc1ecd39c0dc5d433cdc1
Author: Rahul Mahajan <[email protected]>
Date:   Thu Jan 18 01:13:49 2024 -0500

    Add option to…