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Update realtime branch, gsl_ufs_rtdev1 #65

Merged
merged 8 commits into from
Sep 27, 2024
Merged

Update realtime branch, gsl_ufs_rtdev1 #65

merged 8 commits into from
Sep 27, 2024

Commits on Sep 19, 2024

  1. Update realtime branch, gsl_ufs_rtdev1. 

    Squashed commit of the following:

commit 4e0a81f7acf5ccba5de8d3bdf7ab19cae80812cb
Author: kayee.wong <kayee.wong@noaa.gov>
Date:   Wed Sep 18 18:37:50 2024 +0000

    Fix typos/links/dependancy.

commit d5fdcbf8d6e987dbdfcd6b4da34d0934c8d82c3b
Author: kayee.wong <kayee.wong@noaa.gov>
Date:   Wed Sep 18 07:37:52 2024 +0000

    Fixed missing config.base files.

commit c6239f925369b20fd8488e8537969e2f4f9e7725
Author: kayee.wong <kayee.wong@noaa.gov>
Date:   Wed Sep 18 06:53:47 2024 +0000

    Update submodule hashs.

commit 32bf790f67b818ff50a7f6b74388fb81ed175b3a
Author: kayee.wong <kayee.wong@noaa.gov>
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 <143837053+jderrico-noaa@users.noreply.github.com>
    Date:   Wed Aug 7 11:02:24 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04
    Author: Kate Friedman <kate.friedman@noaa.gov>
    Date:   Wed Aug 7 08:11:21 2024 -0400

        Revert MSU FIX_DIRs back to glopara (#2811)

    commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517
    Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
    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 <aerorahul@users.noreply.github.com>
    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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
        Co-authored-by: David Huber <david.huber@noaa.gov>
        Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>

    commit d599fff4aedd41ae587dbe02226acb12ff48efc1
    Author: HelinWei-NOAA <48133472+HelinWei-NOAA@users.noreply.github.com>
    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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
    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 <terrence.mcguinness@cox.net>
    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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
        Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>

    commit b73b1fd203496db97f8067652659573a632bcc67
    Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
    Date:   Fri Aug 2 07:59:06 2024 -0400

        Fix erroneous cdump addition (#2803)

    commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3
    Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
    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 <52789452+GeorgeGayno-NOAA@users.noreply.github.com>
    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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
    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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
    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 <48259628+EricSinsky-NOAA@users.noreply.github.com>
    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 <aerorahul@users.noreply.github.com>

    commit f156a7894d639f177e3e2588f98eec1f6f59aa68
    Author: Jessica Meixner <jessica.meixner@noaa.gov>
    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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
    Date:   Thu Jul 25 14:26:52 2024 -0400

        Temporarily disable METplus jobs (#2796)

    commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2
    Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
    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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
    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 <48259628+EricSinsky-NOAA@users.noreply.github.com>
    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 <aerorahul@users.noreply.github.com>

    commit 71dc33c6ca991c16ce743760d99feaaf60f2218a
    Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
    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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
    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 <aerorahul@users.noreply.github.com>
    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 <kate.friedman@noaa.gov>
    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 <terrence.mcguinness@cox.net>
    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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
    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 <aerorahul@users.noreply.github.com>
        Co-authored-by: Cory Martin <cory.r.martin@noaa.gov>

    commit 8998ec7b74123e953b97a93fa14cc78d471a1aee
    Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
    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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
    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 <aerorahul@users.noreply.github.com>
    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 <kate.friedman@noaa.gov>

    commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a
    Author: Jessica Meixner <jessica.meixner@noaa.gov>
    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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
    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 <95313292+GwenChen-NOAA@users.noreply.github.com>
    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 <Walter.Kolczynski@noaa.gov>

    commit 8215ae654202186a4f753c3abe937b7b9b91a9c7
    Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
    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 <82525974+DavidBurrows-NCO@users.noreply.github.com>
    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 <26926959+RussTreadon-NOAA@users.noreply.github.com>
    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 <danholdaway@users.noreply.github.com>
        Co-authored-by: DavidNew-NOAA <david.new@noaa.gov>
        Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>
        Co-authored-by: Dan Holdaway <27729500+danholdaway@users.noreply.github.com>

    commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b
    Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
    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 <terrence.mcguinness@cox.net>
    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 <Walter.Kolczynski@noaa.gov>
    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 <aerorahul@users.noreply.github.com>
    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 <jessica.meixner@noaa.gov>
    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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
    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 <143837053+jderrico-noaa@users.noreply.github.com>
    Date:   Mon Jun 24 12:44:05 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit 4e1b937b67ed220120e81925c4507f03b9b8965f
    Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
    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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
    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 <Walter.Kolczynski@noaa.gov>
    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 <69919478+DavidHuber-NOAA@users.noreply.github.com>

    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 <Walter.Kolczynski@noaa.gov>
        Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
        Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>

    commit 47b3a581c8257fa24411fb400df8bb0e1e04972a
    Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
    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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
    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 <Walter.Kolczynski@noaa.gov>

    commit 5af325a6a4e0a14d180514a418603ca79fada487
    Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com>
    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 <49168260+ypwang19@users.noreply.github.com>
    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 <yaping.wang@users.noreply.github.com>
        Co-authored-by: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
        Co-authored-by: Cory Martin <cory.r.martin@noaa.gov>
        Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>

    commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4
    Author: Jessica Meixner <jessica.meixner@noaa.gov>
    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 <terrence.mcguinness@cox.net>
    Date:   Thu Jun 13 12:22:03 2024 -0400

        Update Jenkinsfile

        needed a comma

    commit dc21eac6c3941d7f30803891d91d82f4cc1f8183
    Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
    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 <26926959+RussTreadon-NOAA@users.noreply.github.com>
    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 <103681022+NeilBarton-NOAA@users.noreply.github.com>
    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 <Jessica.Meixner@noaa.gov>
        Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
        Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>

    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 <henry.winterbottom.wxdev@gmail.com>
        Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>

    commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e
    Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
    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 <guoqing.ge@noaa.gov>
    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 <jessica.meixner@noaa.gov>
    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 <aerorahul@users.noreply.github.com>

    commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d
    Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com>
    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 <Walter.Kolczynski@noaa.gov>

    commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0
    Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
    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 <36091766+emilyhcliu@users.noreply.github.com>
    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 <aerorahul@users.noreply.github.com>
        Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>

    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 <Walter.Kolczynski@noaa.gov>

    commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b
    Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>
    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 <guillaume.vernieres@noaa.gov>
    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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
    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 <26926959+RussTreadon-NOAA@users.noreply.github.com>
    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 <jessica.meixner@noaa.gov>
    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 <95313292+GwenChen-NOAA@users.noreply.github.com>
    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 <cory.r.martin@noaa.gov>
    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 <aerorahul@users.noreply.github.com>
        Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>

    commit c92bf415060750127c9c05a62a1d2851c489551a
    Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
    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 <Walter.Kolczynski@noaa.gov>
    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 <guoqing.ge@noaa.gov>
    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 <Walter.Kolczynski@noaa.gov>
    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 <69919478+DavidHuber-NOAA@users.noreply.github.com>

    commit d69a8af95d492982b918670322ed5c41ab074335
    Author: Jessica Meixner <jessica.meixner@noaa.gov>
    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 <jessica.meixner@noaa.gov>
    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 <terrence.mcguinness@cox.net>
    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 <95313292+GwenChen-NOAA@users.noreply.github.com>
    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 <aerorahul@users.noreply.github.com>

    commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31
    Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>
    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 <108816337+AnilKumar-NOAA@users.noreply.github.com>
    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 <Anil.Kumar@gaea53.ncrc.gov>
        Co-authored-by: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com>

    commit b6ca771a0c584cbfcbbf9be739765d5f3815df97
    Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
    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 <guillaume.vernieres@noaa.gov>
    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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
    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 <Walter.Kolczynski@noaa.gov>

    commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c
    Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
    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 <143837053+jderrico-noaa@users.noreply.github.com>
    Date:   Thu May 16 14:33:19 2024 -0600

        Merge branch 'NOAA-EMC:develop' into develop

    commit bb930050b3cd51d28ecba6b231c8675f6d11856c
    Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
    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 <terrence.mcguinness@cox.net>
    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 <terrence.mcguinness@cox.net>
    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 <terrence.mcguinness@cox.net>
    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 <terrence.mcguinness@cox.net>
    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 <aerorahul@users.noreply.github.com>

    commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916
    Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
    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 <kate.friedman@noaa.gov>
    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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
    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 <fanglin.yang@noaa.gov>
    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 <Walter.Kolczynski@noaa.gov>
        Co-authored-by: Lisa Bengtsson <lbengtss@Orion-login-1.HPC.MsState.Edu>
        Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>

    commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6
    Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
    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 <jessica.meixner@noaa.gov>
    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 <aerorahul@users.noreply.github.com>

    commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2
    Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com>
    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 <danholdaway@users.noreply.github.com>
        Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>

    commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95
    Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
    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 <aerorahul@users.noreply.github.com>
    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 <Walter.Kolczynski@noaa.gov>

    commit 233c18815d2e8e6b344f161fd0c102a4fbdfb66d
    Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com>
    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…
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Commits on Sep 20, 2024

  1. Update experiment directory.

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  2. Real time path fix.

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  3. Update realtime xml.

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  1. Resolve unit test and Python conflicts.

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Commits on Sep 26, 2024

  1. Update ufs_model.fd and ufs_utils.fd pointers. 

    Add shal_cnv back to config.fcst.
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  1. Remove extra statement.

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  2. Update pointers and submodules.

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