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Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh… #2212

Merged
merged 1 commit into from
Jan 10, 2024
Merged

Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh… #2212

merged 1 commit into from
Jan 10, 2024

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souopgui
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Fix OpenMP over-allocation of resources running MPMD tasks

Description

  • Prefix the call to "${HOMEgfs}/ush/run_mpmd.sh" by OMP_NUM_THREADS=1.
  • This ensures that OMP_NUM_THREADS is set to 1 only when running MPMD, where multiple instances are being kicked off simultaneously. By only prefixing this call, we are sure that no other run is affected.
  • It prevent the overthreading in OpenMP when running MPMD tasks
  • This fix is transparent to users.
    Resolves A couple of Global Workflow tasks are failing on S4 due to over-threading by OpenMP #2211

Type of change

  • Bug fix (fixes something broken)

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?

Cloned and tested on S4

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

DavidHuber-NOAA
DavidHuber-NOAA approved these changes Jan 10, 2024
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Approve.

scripts/exglobal_atmos_products.sh Show resolved Hide resolved
@aerorahul aerorahul merged commit 4cb5802 into NOAA-EMC:develop Jan 10, 2024
4 checks passed
kayeekayee added a commit to kayeekayee/global-workflow that referenced this pull request Feb 8, 2024
@kayeekayee
Merge to 2024 Jan 12 NOAA-EMC/develop.
9e0d134 
Squashed commit of the following:

commit c590476
Author: Rahul Mahajan <[email protected]>
Date:   Fri Jan 12 19:21:02 2024 -0500

    Update hash to ufs-weather-model. The noahmptable.tbl was reorganized, so update link_workflow.sh to use the same one used in UFSWM RT (NOAA-EMC#2219)

commit c041968
Author: Kate Friedman <[email protected]>
Date:   Fri Jan 12 12:09:35 2024 -0500

    Add ocean resolution to setup_expt invocation and retire/reduce COMROT/ROTDIR usage (NOAA-EMC#2214)

    Two series of updates:

    1) Update setup scripts to now allow users to provide ocean resolution
    2) Housekeeping to retire the `COMROT` variable, replacing it with other variables
    as needed, and reduce the `ROTDIR` variable usage.

    Both updates change options for the workflow setup API.

    Refs NOAA-EMC#2061

commit 997f978
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Fri Jan 12 10:46:36 2024 -0500

    Allow use of ocean obs prep in WCDA cycling and remove R2D2 (NOAA-EMC#2215)

    Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same.
    Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS.
    Replaces the current R2D2 processing.

commit 12a5bb1
Merge: 4cb5802 6492c2d
Author: David Huber <[email protected]>
Date:   Fri Jan 12 09:26:27 2024 -0500

    Merge pull request NOAA-EMC#2217 from DavidHuber-NOAA/update/versions

    Update and clean up version and module files

commit 6492c2d
Author: David Huber <[email protected]>
Date:   Thu Jan 11 11:49:08 2024 -0600

    Update orion module/version files for met/metplus NOAA-EMC#2123

commit 94c9937
Author: DavidHuber <[email protected]>
Date:   Thu Jan 11 17:42:53 2024 +0000

    Comment met/metplus out from Hera modulefile. NOAA-EMC#2123

commit 8c32f8b
Merge: a65e4c6 4cb5802
Author: David Huber <[email protected]>
Date:   Thu Jan 11 11:34:44 2024 -0600

    Merge branch 'develop' of github.com:noaa-emc/global-workflow into develop

commit a65e4c6
Author: David Huber <[email protected]>
Date:   Thu Jan 11 11:34:19 2024 -0600

    Initial update of version/module files NOAA-EMC#2123

commit 4cb5802
Author: souopgui <[email protected]>
Date:   Wed Jan 10 08:30:22 2024 -0600

    Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh when running MPMD tasks (NOAA-EMC#2212)

    Fix OpenMP over-allocation of resources running MPMD tasks
    Co-authored-by: Innocent Souopgui <[email protected]>

commit b056b53
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Jan 8 17:28:05 2024 -0500

    Add Hercules as valid machine in CI scripts (NOAA-EMC#2207)

    Few updates to CI scripts to include names for hercules that where missed
    the first time.

commit 6574d29
Author: Rahul Mahajan <[email protected]>
Date:   Mon Jan 8 17:25:47 2024 -0500

    Fix invalid GH action and restart file name (NOAA-EMC#2210)

    Resolves a typo that leads to an invalid workflow yaml and fixes the restart filename in restart detection.

    Resolves NOAA-EMC#2205

commit 69605ea
Author: Rahul Mahajan <[email protected]>
Date:   Mon Jan 8 17:00:28 2024 -0500

    Stop attempting to comment link to RTD for non-PRs (NOAA-EMC#2209)

    Adds a check so comments with a link to documentation are only generated
    for PRs.

commit 4e160a8
Author: Rahul Mahajan <[email protected]>
Date:   Mon Jan 8 13:10:15 2024 -0500

    Enable UPP for GOES processing (NOAA-EMC#2203)

    Wnables the creation of special master grib2 files from UPP for
    GOES processing

commit c15875b
Author: David Huber <[email protected]>
Date:   Mon Jan 8 09:56:06 2024 -0500

    Port cycling to Hercules (NOAA-EMC#2196)

    Adds cycled support for Hercules (excluding gsi-monitor).
    Partially resolves NOAA-EMC#1588
    GSI monitoring is disabled on Hercules due to missing Perl modules. That will be enabled in a later PR.

commit ef6827d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Jan 8 09:43:12 2024 -0500

    Refactor rocoto task XML creation (NOAA-EMC#2189)

    Refactors the rocoto task generation to be recursive.
    This will allow nested metatasks to loop over multiple variables, which is needed for GEFS product generation.

    As part of this refactor, there is no longer separate arguments to designate metatasks.
    Instead, task dicts can include a nested 'task_dict' as well as a 'var_dict' containing the variables to loop over.
    The nested task dict can then either have another layer, or be the innermost task.

    To accommodate the new recursive nature, some defaults that were previously defined in create_wf_task() had to be pushed down into the function that creates the innermost task.
    Also, former keywords have been absorbed by the task dict.

    Refs NOAA-EMC#823
    Refs NOAA-EMC#827

commit 2b81cfa
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Jan 8 09:41:03 2024 -0500

    Update fix versions (NOAA-EMC#2198)

    Updates fix versions for a few components:
    - Update cice and mom6 versions to support C96/1p00 marine
    - Update wave to change betamax setting for glo_025 waves

    Resolves NOAA-EMC#2004
    Resolves NOAA-EMC#2107
kayeekayee added a commit to kayeekayee/global-workflow that referenced this pull request Mar 1, 2024
@kayeekayee
Squashed commit of the following:
1d2ed1b 
commit d1e8f33
Merge: e2d88dd 5166593
Author: kayee.wong <[email protected]>
Date:   Fri Mar 1 00:01:58 2024 +0000

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

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

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

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

    Just moves the Jenkinsfile into the ci directory

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

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

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

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

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

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

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

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

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

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

    Routine update of ufs-weather-model hash.

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

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

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

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

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

    Resolves NOAA-EMC#2335

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

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

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

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

    Resolves NOAA-EMC#2184

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

    Fix several Jenkins issues (NOAA-EMC#2334)

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

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

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

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

    Update to spack-stack 1.6.0

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

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

    Disable snow DA tests

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

    Update GDASApp hash to current develop

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

    Update GDAS hash to allow modified snow DA analysis

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

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

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

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

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

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

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

    Updated GDAS to include rocoto/1.3.6 on Hera.

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

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

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

    Refs NOAA-EMC#1629

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

    Merge branch 'NOAA-EMC:develop' into develop

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

    Update GDASApp hash to include SS/1.6.0 support.

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

    Construct SS paths from version variables.

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

    Removed MET/METplus 'not available' comments

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

    Move SS module path to version files.

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

    Update comment about METplus support.

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

    Update verif-global to latest WCOSS2 support.

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

    Clean up build_upp.sh.

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

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

    Fix whitespace in build_upp.sh.

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

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

    Added verif-global support back to WCOSS2.

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

    Bug fix.

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

    Updates requested by reviewer Rahul Mahajan.

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

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

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

    Linter corrections.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    Resolves NOAA-EMC#1547

commit 9929277
Merge: eb8791c 094e3b8
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Feb 15 15:05:50 2024 -0700

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

commit 094e3b8
Author: Cory Martin <[email protected]>
Date:   Thu Feb 15 14:43:55 2024 -0500

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

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

commit d465ea0
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Feb 15 19:25:02 2024 +0000

    Set HOMEgfs for module_setup in CI driver (NOAA-EMC#2321)

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

commit 2415b7b
Author: David Huber <[email protected]>
Date:   Thu Feb 15 19:21:17 2024 +0000

    Load default rocoto on Jet.

commit eb8791c
Merge: 60d5ee6 638684e
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Feb 15 11:56:40 2024 -0700

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

commit 777d97d
Author: David Huber <[email protected]>
Date:   Thu Feb 15 12:34:59 2024 -0600

    Fixed Orion cdo version.

commit ef07235
Author: DavidHuber <[email protected]>
Date:   Thu Feb 15 16:29:32 2024 +0000

    Revert UFS hash.

commit 0ce8c0d
Author: DavidHuber <[email protected]>
Date:   Thu Feb 15 14:55:48 2024 +0000

    Fix git version in Hera's gwsetup module.

commit 3080a34
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 20:52:34 2024 +0000

    Fixed xarray version for SS/1.6.0.

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

    Updated GSI-Utils hash to head of develop.

commit c3553f0
Merge: 4568653 638684e
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 20:28:14 2024 +0000

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

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

    Reupgrade Hercules to SS/1.6.0

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

    Remove `finddate.sh` from system (NOAA-EMC#2308)

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

    Refs NOAA-EMC#2279

commit 2b160f8
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 18:31:28 2024 +0000

    Reenable METplus jobs on Hercules.

commit 8f59002
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 18:30:23 2024 +0000

    Update GSI hashes.

commit 73bc76b
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 14 09:27:37 2024 -0700

    Updates based on user request.

commit e4bc674
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 14 08:03:45 2024 -0700

    Corrected based on reviewer review.

commit 60d5ee6
Merge: 40f2cf6 1aaef05
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Feb 13 18:08:33 2024 -0700

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

commit 0330411
Merge: 929b903 1aaef05
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Feb 13 17:58:12 2024 -0700

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

commit 1aaef05
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Feb 13 18:15:59 2024 -0500

    Jenkins Pipeline updates for Canceling Jobs (NOAA-EMC#2307)

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

commit 6404892
Author: Rahul Mahajan <[email protected]>
Date:   Tue Feb 13 14:57:37 2024 -0500

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

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

    Fixes NOAA-EMC#935
    Fixes NOAA-EMC#1317
    Fixes NOAA-EMC#1864

commit 40f2cf6
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Tue Feb 13 10:18:53 2024 -0700

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

commit 929b903
Merge: 2d08d01 3f99f70
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Feb 13 08:31:06 2024 -0700

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

commit 3f99f70
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Feb 13 00:57:18 2024 -0500

    Add wave post jobs to GEFS (NOAA-EMC#2292)

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

    Resolves NOAA-EMC#827

commit 842adf3
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Feb 12 12:50:08 2024 -0500

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

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

commit bb4ca65
Author: CatherineThomas-NOAA <[email protected]>
Date:   Mon Feb 12 14:50:41 2024 +0000

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

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

    Resolves: NOAA-EMC#2303

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

    Fix Jenkins success reporting (NOAA-EMC#2302)

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

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

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

commit 28ccf78
Merge: b972f66 54daa31
Author: David Huber <[email protected]>
Date:   Fri Feb 9 14:00:43 2024 -0600

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

commit b972f66
Author: David Huber <[email protected]>
Date:   Fri Feb 9 10:47:00 2024 -0600

    Fix SS versions for CI modules.

commit 4b01d8e
Author: David Huber <[email protected]>
Date:   Fri Feb 9 10:44:30 2024 -0600

    Revert Hercules modules to SS/1.5.1.

commit 54daa31
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Feb 8 15:48:38 2024 -0500

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

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

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

    Resolves NOAA-EMC#2119
    Resolves NOAA-EMC#2118

commit 43429e2
Author: Rahul Mahajan <[email protected]>
Date:   Thu Feb 8 15:30:28 2024 -0500

    Enable AO WCDA test (NOAA-EMC#1963)

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

commit 2d08d01
Merge: 4745d4a f563528
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Feb 8 07:24:54 2024 -0700

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

commit f563528
Author: Kate Friedman <[email protected]>
Date:   Wed Feb 7 15:09:12 2024 -0500

    Update JGLOBAL_FORECAST for octal error (NOAA-EMC#2295)

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

commit 4745d4a
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 7 08:45:49 2024 -0700

    Removed jlogfile references.

commit 5894ca2
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 7 08:32:16 2024 -0700

    Removed dummy variable passed to perl scripts.

commit dae884a
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 7 08:29:49 2024 -0700

    Removed jlogfile and postmsg references within gempak scripts.

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

    Consolidate `npe_node_max` (NOAA-EMC#2289)

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

    Resolves NOAA-EMC#2133

commit b0325e0
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Feb 7 00:40:20 2024 -0700

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

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

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

    Resolves NOAA-EMC#2130

commit 3e6b1e2
Merge: f4c8e00 1ccc989
Author: Janet Derrico <[email protected]>
Date:   Tue Feb 6 10:43:55 2024 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit 1ccc989
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Feb 5 14:16:07 2024 -0500

    Remove EnKF forecast groups (NOAA-EMC#2280)

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

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

    Resolves NOAA-EMC#2254

commit 9f3383f
Author: Henry R. Winterbottom <[email protected]>
Date:   Mon Feb 5 12:15:13 2024 -0700

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

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

    Resolves NOAA-EMC#2228

commit 7d68b0b
Author: CatherineThomas-NOAA <[email protected]>
Date:   Sun Feb 4 22:02:41 2024 +0000

    Update global_cycle for fractional grid (NOAA-EMC#2262)

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

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

commit ed592a6
Author: Kate Friedman <[email protected]>
Date:   Sat Feb 3 02:55:14 2024 -0500

    Retire cycle-specific FHMAX_GFS variables (NOAA-EMC#2278)

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

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

    Resolves NOAA-EMC#2218

commit 977e2d6
Author: Henry R. Winterbottom <[email protected]>
Date:   Fri Feb 2 07:49:09 2024 -0700

    New GDASApp hash. (NOAA-EMC#2285)

commit b5f2bd9
Merge: 4d66742 0400e1f
Author: David Huber <[email protected]>
Date:   Tue Jan 30 13:55:00 2024 -0600

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

commit 0400e1f
Author: David Huber <[email protected]>
Date:   Tue Jan 30 09:57:11 2024 -0600

    Fix gfs_utils Orion spack-stack env path.

commit 6bbe823
Author: DWesl <[email protected]>
Date:   Mon Jan 29 21:15:30 2024 -0500

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

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

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

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

commit f4c8e00
Merge: 61975cf d5bee38
Author: Janet Derrico <[email protected]>
Date:   Mon Jan 29 15:38:56 2024 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit d5bee38
Author: Kate Friedman <[email protected]>
Date:   Mon Jan 29 14:35:02 2024 -0500

    Correct typos in GFS config.resources (NOAA-EMC#2267)

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

    Resolves NOAA-EMC#2266

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

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

commit 2238dd6
Author: DavidHuber <[email protected]>
Date:   Mon Jan 29 13:21:30 2024 +0000

    Update Orion, Hercules, S4 modulefiles.

commit 6ffd94f
Author: DavidHuber <[email protected]>
Date:   Fri Jan 26 16:01:23 2024 +0000

    Update GDAS hash to include SS/1.6.0 support.

commit be11f85
Merge: 56b9680 04e0772
Author: DavidHuber <[email protected]>
Date:   Fri Jan 26 15:34:24 2024 +0000

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

commit 8ff3448
Author: Rahul Mahajan <[email protected]>
Date:   Fri Jan 26 10:12:18 2024 -0500

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

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

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

commit 04e0772
Author: David Huber <[email protected]>
Date:   Fri Jan 26 07:16:25 2024 -0600

    Update ufs_utils hash for spack-stack/1.6.0 support.

commit 3d44ff3
Author: Barry Baker <[email protected]>
Date:   Thu Jan 25 14:33:27 2024 -0500

    GOCART ExtData biogenic climatology fix (NOAA-EMC#2253)

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

commit 66f58b8
Author: Guillaume Vernieres <[email protected]>
Date:   Thu Jan 25 13:16:41 2024 -0500

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

    fixes  NOAA-EMC#2257

commit 553b4f2
Author: WenMeng-NOAA <[email protected]>
Date:   Thu Jan 25 13:00:45 2024 -0500

    Fix post parm links (NOAA-EMC#2243)

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

    Resolves NOAA-EMC#2259

commit 4d66742
Merge: 6c05803 afa09e3
Author: David Huber <[email protected]>
Date:   Thu Jan 25 07:49:08 2024 -0600

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

commit 6c05803
Author: David Huber <[email protected]>
Date:   Thu Jan 25 07:48:42 2024 -0600

    Fix wgrib2/gfs_utils on Hercules.

commit ee6f536
Author: Kate Friedman <[email protected]>
Date:   Thu Jan 25 07:43:13 2024 -0500

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

    GFSv16.3.13 WAFS update was implemented

    Refs NOAA-EMC#2013

commit 2445d44
Author: RussTreadon-NOAA <[email protected]>
Date:   Thu Jan 25 06:17:11 2024 -0500

    Simplify and extend load_ufsda_modules to Hercules (NOAA-EMC#2245)

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

    Resolves NOAA-EMC#2244

commit 56b9680
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 19:47:34 2024 +0000

    Update hashes (revert WCOSS2 modules).

commit afa09e3
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 18:59:40 2024 +0000

    New (cleaner history) gdas hash.

commit a9eaec2
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 18:52:27 2024 +0000

    Update gdasapp to include ss/1.6.0 support.

commit 5ef8eb2
Merge: 4c46354 e400068
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 17:08:54 2024 +0000

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

commit 4c46354
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 17:05:12 2024 +0000

    Reenable verif-global support

commit f775755
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 16:59:10 2024 +0000

    Assign fcsthrs for awips_g2 job.

commit e400068
Author: David Huber <[email protected]>
Date:   Mon Jan 22 15:01:07 2024 -0600

    More gsi-addon path fixes.

commit f663d47
Author: David Huber <[email protected]>
Date:   Mon Jan 22 14:41:59 2024 -0600

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

commit e304bbe
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:59:34 2024 +0000

    Better optimize build jobs (more ufs jobs).

commit ccc6e2d
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:56:18 2024 +0000

    Reenable verif-global. NOAA-EMC#2195

commit 3ef3411
Merge: 4365f63 f4d187f
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:39:10 2024 +0000

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

commit 4365f63
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:37:25 2024 +0000

    Corrected the SS env. name in the version files. NOAA-EMC#2195

commit f4d187f
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Mon Jan 22 12:28:28 2024 -0500

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

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

commit 9a09d30
Author: DavidHuber <[email protected]>
Date:   Fri Jan 19 21:23:50 2024 +0000

    Corrected gsi-addon-dev spelling.

commit 21ff645
Author: DavidHuber <[email protected]>
Date:   Fri Jan 19 21:11:34 2024 +0000

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

commit d4c55d1
Author: Kate Friedman <[email protected]>
Date:   Fri Jan 19 15:43:37 2024 -0500

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

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

commit 61975cf
Merge: 1344313 4919287
Author: Janet Derrico <[email protected]>
Date:   Fri Jan 19 08:38:17 2024 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit 4919287
Author: Barry Baker <[email protected]>
Date:   Thu Jan 18 22:31:27 2024 -0500

    GOCART Emission updates for GEFSv13 and GDAS  (NOAA-EMC#2201)

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

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

commit 13d25cf
Author: Kate Friedman <[email protected]>
Date:   Thu Jan 18 22:29:43 2024 -0500

    Add `POSTAMBLE_CMD` into preamble postamble (NOAA-EMC#2235)

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

    Resolves NOAA-EMC#1145

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

    Add option to create WGNE atmosphere products (NOAA-EMC#2233)

    Adds option to create WGNE products for the atmosphere.

    Resolves NOAA-EMC#1951
    Resolves NOAA-EMC#2226

commit d95ed85
Author: Rahul Mahajan <[email protected]>
Date:   Wed Jan 17 18:04:56 2024 -0500

    Use ufs.configure, model_configure, MOM_input, data_table, and ice_in templates from UFS-weather-model (NOAA-EMC#2051)

    This PR:
    - links `ufs.configure.*.IN`, `model_configure.IN`, `MOM_input_${OCNRES}.in`,
    `MOM6_data_table.IN`, and `ice_in.IN` from ufs-weather-model into the
    global-workflow `parm/ufs` directory
    - prepares local variables for use in the templates in the respective functions
    for FV3, MOM6, and CICE6
    - uses `atparse.bash` to render these templates into fully formed namelists

    - Work was performed by @DeniseWorthen in the ufs-weather-model to
    templatize several variables that are hard-wired in the ufs-weather-model
    for CICE. See ufs-community/ufs-weather-model/NOAA-EMC#2010

commit 44a66dd
Author: RussTreadon-NOAA <[email protected]>
Date:   Wed Jan 17 13:52:09 2024 -0500

    Update gdas.cd hash to use gsibec tag 1.1.3 (NOAA-EMC#2231) (NOAA-EMC#2234)

commit 9046d97
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Jan 17 10:19:18 2024 -0500

    Add basic atmos products for GEFS and refactor resources (NOAA-EMC#2216)

    * Add basic atmos products for GEFS

    Adds basic atmosphere products for GEFS members (no mean or spread).

    To facilitate the addition of GEFS parameter lists, the existing GFS
    lists are renamed. They are also relocated to `parm/products/` direc
    tory instead of `parm/post/`. GEFS v12 uses different parameter lists
    for different resolutions, but for this implementation, the 0p25 lists
    are used for all resolutions. However, to hedge against the final con-
    figuration, all of the GEFS parameter lists have been added to parm.
    Implementation of different parameter lists for each resolution will
    take additional refactoring of the atmos_products job, as it currently
    assumes all resolutions use the same lists.

    The new GEFS rocoto task is implented as two loops of metatasks (made
    possible by PR NOAA-EMC#2189). The member is set at the rocoto level, so the
    setting in `config.base` had to be updated to accept a pass-through.
    The generation of a forecast hour list is moved up to its own function
    in `rocoto.tasks`, separate from the post groups which are not used.
    This can be used as a model for future metatasks (or refactoring of old
    ones). `rocoto_viewer.py` does function with the nested metatasks,
    though only one level of folding is available and the metatask name
    is that of the lower metatask (though it encompasses the entire outer
    metatask).

    Additionally, the GEFS `config.resources` had diverged from the GFS
    version, which included not having a section for the atm products job.
    This led to the refactoring of the GFS `config.resources`, including
    switching to using a `case` statement instead of sequential `elif`.
    This refactored script was then copied over to GEFS, replacing the old
    one, with all jobs not currently implemented for GEFS removed (except
    wave post, whose inclusion is immenent). New blocks can be copied over
    from GFS as they are added.

    Resolves NOAA-EMC#823

commit fbba174
Author: RussTreadon-NOAA <[email protected]>
Date:   Tue Jan 16 14:05:48 2024 -0500

    Update GDASApp (gdas.cd) hash (NOAA-EMC#2225)

    GDASApp now uses gitsubmodules

commit 1344313
Merge: 4b58891 dddd837
Author: Janet Derrico <[email protected]>
Date:   Tue Jan 16 11:13:59 2024 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit dddd837
Author: Rahul Mahajan <[email protected]>
Date:   Tue Jan 16 12:17:19 2024 -0500

    Fix ocean resolution for the S2SWA test (NOAA-EMC#2223)

commit 83edaf1
Author: David Huber <[email protected]>
Date:   Tue Jan 16 11:07:02 2024 -0500

    Apply fixes to archiving jobs (NOAA-EMC#2221)

    Add checks for potentially missing log/data files and update log names for archiving.

    Missing sflux index files are also added to the products script.

    Resolves NOAA-EMC#2076

commit c590476
Author: Rahul Mahajan <[email protected]>
Date:   Fri Jan 12 19:21:02 2024 -0500

    Update hash to ufs-weather-model. The noahmptable.tbl was reorganized, so update link_workflow.sh to use the same one used in UFSWM RT (NOAA-EMC#2219)

commit c041968
Author: Kate Friedman <[email protected]>
Date:   Fri Jan 12 12:09:35 2024 -0500

    Add ocean resolution to setup_expt invocation and retire/reduce COMROT/ROTDIR usage (NOAA-EMC#2214)

    Two series of updates:

    1) Update setup scripts to now allow users to provide ocean resolution
    2) Housekeeping to retire the `COMROT` variable, replacing it with other variables
    as needed, and reduce the `ROTDIR` variable usage.

    Both updates change options for the workflow setup API.

    Refs NOAA-EMC#2061

commit 997f978
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Fri Jan 12 10:46:36 2024 -0500

    Allow use of ocean obs prep in WCDA cycling and remove R2D2 (NOAA-EMC#2215)

    Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same.
    Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS.
    Replaces the current R2D2 processing.

commit 12a5bb1
Merge: 4cb5802 6492c2d
Author: David Huber <[email protected]>
Date:   Fri Jan 12 09:26:27 2024 -0500

    Merge pull request NOAA-EMC#2217 from DavidHuber-NOAA/update/versions

    Update and clean up version and module files

commit 6492c2d
Author: David Huber <[email protected]>
Date:   Thu Jan 11 11:49:08 2024 -0600

    Update orion module/version files for met/metplus NOAA-EMC#2123

commit 94c9937
Author: DavidHuber <[email protected]>
Date:   Thu Jan 11 17:42:53 2024 +0000

    Comment met/metplus out from Hera modulefile. NOAA-EMC#2123

commit 8c32f8b
Merge: a65e4c6 4cb5802
Author: David Huber <[email protected]>
Date:   Thu Jan 11 11:34:44 2024 -0600

    Merge branch 'develop' of github.com:noaa-emc/global-workflow into develop

commit a65e4c6
Author: David Huber <[email protected]>
Date:   Thu Jan 11 11:34:19 2024 -0600

    Initial update of version/module files NOAA-EMC#2123

commit 4b58891
Merge: a75e73e 4cb5802
Author: Janet Derrico <[email protected]>
Date:   Wed Jan 10 10:15:48 2024 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit 4cb5802
Author: souopgui <[email protected]>
Date:   Wed Jan 10 08:30:22 2024 -0600

    Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh when running MPMD tasks (NOAA-EMC#2212)

    Fix OpenMP over-allocation of resources running MPMD tasks
    Co-authored-by: Innocent Souopgui <[email protected]>

commit b056b53
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Jan 8 17:28:05 2024 -0500

    Add Hercules as valid machine in CI scripts (NOAA-EMC#2207)

    Few updates to CI scripts to include names for hercules that where missed
    the first time.

commit 6574d29
Author: Rahul Mahajan <[email protected]>
Date:   Mon Jan 8 17:25:47 2024 -0500

    Fix invalid GH action and restart file name (NOAA-EMC#2210)

    Resolves a typo that leads to an invalid workflow yaml and fixes the restart filename in restart detection.

    Resolves NOAA-EMC#2205

commit 69605ea
Author: Rahul Mahajan <[email protected]>
Date:   Mon Jan 8 17:00:28 2024 -0500

    Stop attempting to comment link to RTD for non-PRs (NOAA-EMC#2209)

    Adds a check so comments with a link to documentation are only generated
    for PRs.

commit 4e160a8
Author: Rahul Mahajan <[email protected]>
Date:   Mon Jan 8 13:10:15 2024 -0500

    Enable UPP for GOES processing (NOAA-EMC#2203)

    Wnables the creation of special master grib2 files from UPP for
    GOES processing

commit c15875b
Author: David Huber <[email protected]>
Date:   Mon Jan 8 09:56:06 2024 -0500

    Port cycling to Hercules (NOAA-EMC#2196)

    Adds cycled support for Hercules (excluding gsi-monitor).
    Partially resolves NOAA-EMC#1588
    GSI monitoring is disabled on Hercules due to missing Perl modules. That will be enabled in a later PR.

commit ef6827d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Jan 8 09:43:12 2024 -0500

    Refactor rocoto task XML creation (NOAA-EMC#2189)

    Refactors the rocoto task generation to be recursive.
    This will allow nested metatasks to loop over multiple variables, which is needed for GEFS product generation.

    As part of this refactor, there is no longer separate arguments to designate metatasks.
    Instead, task dicts can include a nested 'task_dict' as well as a 'var_dict' containing the variables to loop over.
    The nested task dict can then either have another layer, or be the innermost task.

    To accommodate the new recursive nature, some defaults that were previously defined in create_wf_task() had to be pushed down into the function that creates the innermost task.
    Also, former keywords have been absorbed by the task dict.

    Refs NOAA-EMC#823
    Refs NOAA-EMC#827

commit 2b81cfa
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Jan 8 09:41:03 2024 -0500

    Update fix versions (NOAA-EMC#2198)

    Updates fix versions for a few components:
    - Update cice and mom6 versions to support C96/1p00 marine
    - Update wave to change betamax setting for glo_025 waves

    Resolves NOAA-EMC#2004
    Resolves NOAA-EMC#2107

commit a75e73e
Merge: 5adc47b 9d901db
Author: Janet Derrico <[email protected]>
Date:   Tue Jan 2 12:44:40 2024 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit 5adc47b
Merge: a3ce9db a3c5099
Author: Janet Derrico <[email protected]>
Date:   Tue Dec 26 12:40:08 2023 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit a3ce9db
Merge: 2b1a8e3 a81da33
Author: Janet Derrico <[email protected]>
Date:   Tue Dec 19 09:12:48 2023 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit 2b1a8e3
Merge: 4562dec 9505cb4
Author: Janet Derrico <[email protected]>
Date:   Fri Dec 15 09:50:35 2023 -0700

    Merge branch 'NOAA-EMC:develop' into develop

commit 4562dec
Merge: 9f7eeba 29d3417
Author: Janet Derrico <[email protected]>
Date:   Mon Dec 11 12:10:25 2023 -0700

    Merge pull request NOAA-GSL#34 from NOAA-EMC/develop

    Sync develop branch with EMC develop
kayeekayee added a commit to kayeekayee/global-workflow that referenced this pull request Mar 11, 2024
@kayeekayee
Update realtime branch, gsl_ufs_rt
b992922 
- based on gsl_ufs_dev from NOAA-GSL/gsl_ufs_dev
   29Feb24 global-workflow, 25c026e
   UFS: 29Jan24, 625ac02
   FV3: 06Jan24, 5e7f196
   UPP:  07Nov23, 78f369b

   update pointers for ufs_model and ufs_utils
   remove GSL directories for ufs_model and ufs_utils
   add GSL C3_MYNN xml suite

Squashed commit of the following:

commit 25c026ef03a8d8c0db0b7368d2836f0b2e866eae
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 29 20:35:11 2024 +0000

    update ufs_model pointer

commit a28617a951c46b765aa996bfe4d28b554ec4e0a4
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 22 06:16:26 2024 +0000

    removed unneeded gsl directories

commit 6fb4f90e8572e98c977a1d2ab385f033111f3ea7
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 22 06:08:13 2024 +0000

    update ufs_utils.fd pointer

commit 9264f0c09239d046c5cd862d807e9b82f51dc3bd
Author: jderrico-noaa <[email protected]>
Date:   Wed Feb 21 19:33:26 2024 +0000

    update .gitmodules file

commit f8edfa966147506f2c207728039e3a736cb95415
Author: jderrico-noaa <[email protected]>
Date:   Wed Feb 21 19:30:47 2024 +0000

    update pointer to ufs_utils.fd

commit 5e0d2ab02d58e6a7a40db55a149a93008b28aa8b
Author: jderrico-noaa <[email protected]>
Date:   Wed Feb 21 19:25:52 2024 +0000

    update pointer to ufs_model.fd

commit ebc9e1d02987a1c6aa8cabedf2323642748fab3c
Merge: e7a81511 50cb1e6f
Author: Janet Derrico <[email protected]>
Date:   Thu Feb 15 13:40:33 2024 -0700

    Merge pull request #40 from kayeekayee/gsl_ufs_dev

    Merge to 2024 Jan 12 NOAA-EMC/develop and update to 2024 Jan 29 UFS

commit 50cb1e6f0c661e4c6e2ef0be4527cce58379b2c9
Author: kayee.wong <[email protected]>
Date:   Thu Feb 15 20:30:34 2024 +0000

    Add pygraf workflow.

commit 38b726125d49cff6cae4c0e5fff2438fc33143c5
Author: kayee.wong <[email protected]>
Date:   Wed Feb 14 17:43:15 2024 +0000

    Add double quote for the arguments when calling setup_expt.py.

commit 053f2025fb0b0679c7d4f84958973c1534ec050c
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:57:06 2024 +0000

    more fix.

commit 6f80ea2edc5444e275a79b371d02b6e98e963662
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:50:01 2024 +0000

    more bug fix.

commit 56e283f1f666a38a4a3b30e1528e96eeb5c622e7
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:40:02 2024 +0000

    Minor bug fix.

commit 2dcfed06ff6789eb77cf92e22b80f5475923fafc
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:19:03 2024 +0000

    Update parameter for c3 case
    Add c3 and mynn template

commit cc46b19ccc7cdb54878340eff79dda9e747abdf7
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 20:51:23 2024 +0000

    Update INFO.
    Add c3 SDF in the build.

commit a444ed48a23f24724853036e522b4437bf412c59
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 18:42:33 2024 +0000

    Update to UFS 2024 Jan 29 version.

commit 88595707c7521cdce37ae1cf78720a7827242b24
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 18:16:46 2024 +0000

    Minor bug fix.

commit baa0e9f10b132098d5134efaad712a51ebc26b83
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 17:59:27 2024 +0000

    Update parameters for setup_expt.py in p8_ugwpv1.sh to resdetatmos and comroot.

commit 5875f06903f82a47fafb05f89f840e3b099d18d8
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 17:51:11 2024 +0000

    Remove old gsl SDFs.
    Remove 'rrtmg_lw_pre' from C3 and MYNN SDFs.

commit 9e0d1342f4e1edce96c9b2baeec55c2cffb964cd
Author: kayee.wong <[email protected]>
Date:   Thu Feb 8 22:14:01 2024 +0000

    Merge to 2024 Jan 12 NOAA-EMC/develop.

    Squashed commit of the following:

    commit c59047614c29f6ec15a4d4a6fa1855929287debd
    Author: Rahul Mahajan <[email protected]>
    Date:   Fri Jan 12 19:21:02 2024 -0500

        Update hash to ufs-weather-model. The noahmptable.tbl was reorganized, so update link_workflow.sh to use the same one used in UFSWM RT (#2219)

    commit c041968e165c07da785376f1441374687b55d6cc
    Author: Kate Friedman <[email protected]>
    Date:   Fri Jan 12 12:09:35 2024 -0500

        Add ocean resolution to setup_expt invocation and retire/reduce COMROT/ROTDIR usage (#2214)

        Two series of updates:

        1) Update setup scripts to now allow users to provide ocean resolution
        2) Housekeeping to retire the `COMROT` variable, replacing it with other variables
        as needed, and reduce the `ROTDIR` variable usage.

        Both updates change options for the workflow setup API.

        Refs #2061

    commit 997f97816493d9ed0242e169b6dcf84e5c9338d6
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Fri Jan 12 10:46:36 2024 -0500

        Allow use of ocean obs prep in WCDA cycling and remove R2D2 (#2215)

        Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same.
        Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS.
        Replaces the current R2D2 processing.

    commit 12a5bb192ab6282d44c008c06dc14947abd37249
    Merge: 4cb58020 6492c2da
    Author: David Huber <[email protected]>
    Date:   Fri Jan 12 09:26:27 2024 -0500

        Merge pull request #2217 from DavidHuber-NOAA/update/versions

        Update and clean up version and module files

    commit 6492c2da5f49bd31575d0bef5278c9a7f8ba3412
    Author: David Huber <[email protected]>
    Date:   Thu Jan 11 11:49:08 2024 -0600

        Update orion module/version files for met/metplus #2123

    commit 94c9937f0bff380b0ebd6acdcfd2509e1ae99389
    Author: DavidHuber <[email protected]>
    Date:   Thu Jan 11 17:42:53 2024 +0000

        Comment met/metplus out from Hera modulefile. #2123

    commit 8c32f8b7d00bba6e3e954f149e6548fb27713a3c
    Merge: a65e4c67 4cb58020
    Author: David Huber <[email protected]>
    Date:   Thu Jan 11 11:34:44 2024 -0600

        Merge branch 'develop' of github.com:noaa-emc/global-workflow into develop

    commit a65e4c675f21dbe72198d263e85e894e62b41e13
    Author: David Huber <[email protected]>
    Date:   Thu Jan 11 11:34:19 2024 -0600

        Initial update of version/module files #2123

    commit 4cb580201af68c1c0e2ae19faf0727dcbbe43b4d
    Author: souopgui <[email protected]>
    Date:   Wed Jan 10 08:30:22 2024 -0600

        Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh when running MPMD tasks (#2212)

        Fix OpenMP over-allocation of resources running MPMD tasks
        Co-authored-by: Innocent Souopgui <[email protected]>

    commit b056b531faee6929687cb8a588ffafa1a66426fb
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Mon Jan 8 17:28:05 2024 -0500

        Add Hercules as valid machine in CI scripts (#2207)

        Few updates to CI scripts to include names for hercules that where missed
        the first time.

    commit 6574d29a8c26b0695614874c344bccc5182363f4
    Author: Rahul Mahajan <[email protected]>
    Date:   Mon Jan 8 17:25:47 2024 -0500

        Fix invalid GH action and restart file name (#2210)

        Resolves a typo that leads to an invalid workflow yaml and fixes the restart filename in restart detection.

        Resolves #2205

    commit 69605eac299df381ea9e0e329654487e26380ff5
    Author: Rahul Mahajan <[email protected]>
    Date:   Mon Jan 8 17:00:28 2024 -0500

        Stop attempting to comment link to RTD for non-PRs (#2209)

        Adds a check so comments with a link to documentation are only generated
        for PRs.

    commit 4e160a895bfb31c281e21557dd86c13954a1a967
    Author: Rahul Mahajan <[email protected]>
    Date:   Mon Jan 8 13:10:15 2024 -0500

        Enable UPP for GOES processing (#2203)

        Wnables the creation of special master grib2 files from UPP for
        GOES processing

    commit c15875b6dbf685327af9316ee43b3d01f0fc815e
    Author: David Huber <[email protected]>
    Date:   Mon Jan 8 09:56:06 2024 -0500

        Port cycling to Hercules (#2196)

        Adds cycled support for Hercules (excluding gsi-monitor).
        Partially resolves #1588
        GSI monitoring is disabled on Hercules due to missing Perl modules. That will be enabled in a later PR.

    commit ef6827dd6abdab2996d1e19f9e0ff5d3071e0fdd
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jan 8 09:43:12 2024 -0500

        Refactor rocoto task XML creation (#2189)

        Refactors the rocoto task generation to be recursive.
        This will allow nested metatasks to loop over multiple variables, which is needed for GEFS product generation.

        As part of this refactor, there is no longer separate arguments to designate metatasks.
        Instead, task dicts can include a nested 'task_dict' as well as a 'var_dict' containing the variables to loop over.
        The nested task dict can then either have another layer, or be the innermost task.

        To accommodate the new recursive nature, some defaults that were previously defined in create_wf_task() had to be pushed down into the function that creates the innermost task.
        Also, former keywords have been absorbed by the task dict.

        Refs #823
        Refs #827

    commit 2b81cfac16f103fb29b3aeb9748941787abf7287
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jan 8 09:41:03 2024 -0500

        Update fix versions (#2198)

        Updates fix versions for a few components:
        - Update cice and mom6 versions to support C96/1p00 marine
        - Update wave to change betamax setting for glo_025 waves

        Resolves #2004
        Resolves #2107

commit e7a81511e37f86e881da020e06b95990b470d952
Merge: af47b77c 75ad3754
Author: Janet Derrico <[email protected]>
Date:   Thu Feb 1 13:14:02 2024 -0700

    Merge pull request #37 from jderrico-noaa/gsl_ufs_dev

    Add GSL archive script and correct typos/fixed paths

commit 75ad3754f8bef5411c2570b5e392cd08e95cb6cb
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 1 20:00:52 2024 +0000

    adding consistent [[ ]] for if statements

commit 67b99668c82a5fd8c42479b9b1bfe8b0bad0be25
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Feb 1 19:37:47 2024 +0000

     Updated HOMEgfs in GSL XML templates

commit 4d3719c086e7907a6eeff03112042d392e0d8c5e
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Feb 1 17:27:39 2024 +0000

     Correct syntax errors in GSL scripts

     Add new GSL archive script for archiving grib2 and ICs, but no netcdf files

commit 4309dd0b3b2d5625e7e1740d7cd3e39aacd5bc29
Author: Judy.K.Henderson <[email protected]>
Date:   Mon Jan 29 18:05:45 2024 +0000

     Add GSL diag tables to parm/ufs/fv3

     Update GSL template for hera

     Create EMC and GSL versions of files under workflow/rocoto
      - tasks.py, workflow_tasks.py

commit af47b77c7ee59a11c798995b4362b57e9096b090
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 02:07:43 2024 +0000

     Create GSL version of archive script

commit 529d9f71f97b6e643e76a53bc9871901ae861faf
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 01:37:09 2024 +0000

     Create GSL version of tracker.sh

     - this is a placeholder with changes from last year's HFIP experiment; will likely need to be updated in the future

commit 8457e12c313bee602265b863129734354b019271
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 01:27:42 2024 +0000

     Link config.base.emc.dyn_hera to config.base.emc.dyn

commit 7a05f5bd947944d8c3be828aeef9cc03bf9e073a
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 01:22:54 2024 +0000

     Create GSL version of hpssarch_gen.sh

     - assume we only run cold starts
     - archive only 0p25 grib2 files (no 0p50 opr 1p00)
     - assume no pgrb2b or flux files are created so no need to archive to HPSS

commit 98f5d6b16437e2a340bf16f83187e389a53f8bf0
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 00:24:06 2024 +0000

     Update workflow directory

     - add GSL template for jet (based on last year's experiment)
     - create EMC and GSL versions of yaml files under hosts; defaults point to GSL files

commit 38a7e5629ceeb23d399643a021e9a0a88468a07c
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 25 18:40:37 2024 +0000

     Update atmos_products configuration file for GSL

       - set downset to 1 so pgrb2b files are not created
       - set FLXGF to "NO" so interpolated sflux.1p00 files are not created

commit fe8a953658d092ce2b597e14f31678624606fd8a
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 25 17:02:25 2024 +0000

     Update nodes for gfsfcst task in GSL template for hera to match default configuration in config.ufs
       (12x12, 2 threads, 1 write group, 40 write tasks ==> 56 nodes)

     Increase walltime to 4:10 for gfsfcst task

commit 9d85b0f6d50e8ed142557fcb87c89d2e5d63c617
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 23 19:08:52 2024 +0000

     Added default location for PTMP/STMP in workflow/hosts/hera.yaml

     Added GSL XML template for hera

commit 1cf317d327fae78c5469712c9e5a6aa1ffa4b23b
Author: Judy.K.Henderson <[email protected]>
Date:   Wed Jan 17 22:33:13 2024 +0000

     Add sjet partition

     Make syntax consistent in "if" statements in config.resources

commit 2755e203751f50113849b06769173285e093290b
Author: Judy.K.Henderson <[email protected]>
Date:   Wed Jan 17 22:32:26 2024 +0000

      Update configuration files for GSL

     - create Hera and Jet versions of config.base.emc.dyn
     - correct typo in config.fcst
     - create different versions of config.ufs;
       default is 12x12, 2 threads, 1 write group/40 write tasks (56 nodes)

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

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

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

     Update link script for ufs_utils.fd

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

     Add GSL archive scripts for initial conditions

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

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

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

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

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

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

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

     Change default HPSS_PROJECT to fim

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

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

     Add namelist parameter, nord_tr, for GSL suites

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

     Add changes for running v17p8_mynn

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

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

     Add experiment setup script for p8_ugwpv1

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

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

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

     Updated GSL-specific files under ufs_utils.fd_gsl

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

     Create new branch, gsl_ufs_dev, from dev_02jan24_9d901db

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

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

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

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

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

    Resolves #1224

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

    Reorganize NPOESS scripts (#2166)

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

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

    Resolves #1226

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

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

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

    Changes:

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

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

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

    Resolves #1984
    Resolves #1981
    Resolves #2175

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

    Remove HIRS from GSI processing (#2183)

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

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

    Resolves #2182

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

    Update ufs-weather-model version  (#2186)

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

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

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

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

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

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

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

    ---------

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

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

    Stop calling ufs-utils link script (#2172)

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

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

    Fix handling of excluded hosts list (#2170)

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

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

    Add COMOUT_OBS to marine obs prep (#2173)

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

    Towards resolving NOAA-EMC/GDASApp#815

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

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

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

    Fixes #2168

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

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

    Refs #2096

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

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

    Set job as shared when not exclusive on WCOSS2

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

    Refs #2135

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

    Update gfs-utils version for Hercules (#2163)

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

    Also includes gfs-utils update for new marine post.

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

    CI Updates to support Hercules (#2155)

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

    Resolves #2154

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

    Correct fbwind (#2161)

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

    Add MOS jobs to rocoto mesh (#2148)

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

    Refs #2068

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

    Replace checkout script with submodules (#2142)

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

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

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

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

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

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

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

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

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

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

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

    CI and documentation are also updated to reflect the changes.

    Resolves #2141

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

    Enable radar reflectivity output (#2143)

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

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

    Fix Hercules hostname (#2150)

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

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

    Fix module load typo (#2145)

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

    Refs #2144

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

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

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

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

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

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

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

    Enable forecast-only experiments on Hercules (#2128)

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

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

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

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

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

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

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

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

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

    Refs #1356

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

    Splits AWIPS jobs into seperate tasks (#2094)

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

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

      Resolves #1228

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

    Consolidate VMINMON and cleanup monitor scripts (#2088)

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

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

    Resolves #1925

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

    Robust CI Restarts (#2093)

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

    New Features:

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

    Resolves #2060

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

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

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

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

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

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

    Added variables to config.prepoceanobs (#2101)

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

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

    Refs #2097

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

    Add wave init to GEFS (#2089)

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

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

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

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

    Resolves #2017

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

    Adjust permissions for jobs/JGFS_ATMOS_VERIFICATION (#2095)

    Add execute permissions (755)

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

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

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

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

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

    Refs #1575

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

    Adds FBWINDS support to global-workflow (#2082)

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

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

    Resolves #1221

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

    Adds NPOESS support to global-workflow (#2083)

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

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

    Resolves #1225

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

    Retire vrfy job (#2080)

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

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

    Resolves #2069
    Refs #235

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

    Enable different coupled settings for ensemble (#2030)

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

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

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

    Resolves #1692

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

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

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

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

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

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

    Resolves #2044

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

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

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

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

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

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

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

    Resolves #1942

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

    Fix check for existence of preamble functions (#2066)

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

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

    Update UPP products for GFS v17 (#1973)

    Updates of generating GFS V17 UPP products to support HR3:

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

    Resolves #1965
    Resolves #1994

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

    Fix some rocoto dependencies (#2074)

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

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

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

    Resolves #2075

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

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

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

    Update functionality for Prototype HR3 UGWP (#1987)

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

    Resolves #1986

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

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

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

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

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

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

    Resolves #2038

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

    Resolve ENKF archive script bugs (#2065)

    Fix two bugs in the exgdas_enkf_earc.sh script:

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

    Refs #2064

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

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

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

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

    Changes in this PR:

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

    Refs #235
    Resolves #1988
    Resolves #2048

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

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

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

    Fixes #2016

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

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

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

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

    Refine fit2obs job in rocoto mesh (#2047)

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

    Changes in PR:

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

    Resolves #2043

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

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

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

    Resolves #1444

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

    Update wave IC source for C384 (#2055)

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

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

    Fix analysis and post on Orion (#2046)

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

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

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

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

    Resolves #1996
    Resolves #2041
    Refs #2044

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

    Hack UPP version (#2042)

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

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

    Resolves #2041

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

    Add basic C1152 settings (#2020)

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

    Resolves #2019

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

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

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

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

    Reduce gdas builds to 8 #2029 (#2036)

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

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

    Resolves #2029

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

    Streamline CI reporting to PRs (#2026)

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

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

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

    Resolves #2007

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

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

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

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

    Resolves #1943
    Refs #1776

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

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

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

    Fix staging of MOM data (#2028)

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

    Resolves #2027

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

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

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

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

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

    Changes in this PR:

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

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

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

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

    Lingering work and considerations:

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

    Resolves #1908

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

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

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

    Resolves #1130

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

    Corrects missing local variable reference (#2023)

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

    Resolves #2022

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

    Updates to prep ocean obs task (#1870)

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

    No longer write archive lists COM (#2000)

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

    Resolves #760

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

    Parallelize the build scripts (#1998)

    Optimized/parallelized build scripts.

    A few notes:

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

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

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

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

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

    Resolves #1978

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

    Add missing export for rCDUMP in stage_ic (#2009)

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

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

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

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

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

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

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

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

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

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

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

    Resolves NOAA-EMC/GDASApp/issues/693

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

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

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

    GEFS Staging in exglobal_stage_ic  (#1892)

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

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

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

    Resolves #911

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

    Update GDASApp hash (#1975)

    Update GDASApp hash to bring recent UFSDA development into g-w…
kayeekayee added a commit to kayeekayee/global-workflow that referenced this pull request Mar 12, 2024
@kayeekayee
- based on gsl_ufs_dev from NOAA-GSL/gsl_ufs_dev(29Feb24,25c026e)
2472fa0 
   12Jan24 global-workflow
   UFS: 29Jan24, 625ac02
   FV3: 29Jan24, bd38c56
   UPP: 07Nov23, 78f369b
   UFS_UTILS: 22Dev23, ce385ce

   update pointers for ufs_model and ufs_utils
   add GSL C3_MYNN xml suite

Squashed commit of the following:

commit 25c026ef03a8d8c0db0b7368d2836f0b2e866eae
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 29 20:35:11 2024 +0000

    update ufs_model pointer

commit a28617a951c46b765aa996bfe4d28b554ec4e0a4
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 22 06:16:26 2024 +0000

    removed unneeded gsl directories

commit 6fb4f90e8572e98c977a1d2ab385f033111f3ea7
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 22 06:08:13 2024 +0000

    update ufs_utils.fd pointer

commit 9264f0c09239d046c5cd862d807e9b82f51dc3bd
Author: jderrico-noaa <[email protected]>
Date:   Wed Feb 21 19:33:26 2024 +0000

    update .gitmodules file

commit f8edfa966147506f2c207728039e3a736cb95415
Author: jderrico-noaa <[email protected]>
Date:   Wed Feb 21 19:30:47 2024 +0000

    update pointer to ufs_utils.fd

commit 5e0d2ab02d58e6a7a40db55a149a93008b28aa8b
Author: jderrico-noaa <[email protected]>
Date:   Wed Feb 21 19:25:52 2024 +0000

    update pointer to ufs_model.fd

commit ebc9e1d02987a1c6aa8cabedf2323642748fab3c
Merge: e7a81511 50cb1e6f
Author: Janet Derrico <[email protected]>
Date:   Thu Feb 15 13:40:33 2024 -0700

    Merge pull request #40 from kayeekayee/gsl_ufs_dev

    Merge to 2024 Jan 12 NOAA-EMC/develop and update to 2024 Jan 29 UFS

commit 50cb1e6f0c661e4c6e2ef0be4527cce58379b2c9
Author: kayee.wong <[email protected]>
Date:   Thu Feb 15 20:30:34 2024 +0000

    Add pygraf workflow.

commit 38b726125d49cff6cae4c0e5fff2438fc33143c5
Author: kayee.wong <[email protected]>
Date:   Wed Feb 14 17:43:15 2024 +0000

    Add double quote for the arguments when calling setup_expt.py.

commit 053f2025fb0b0679c7d4f84958973c1534ec050c
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:57:06 2024 +0000

    more fix.

commit 6f80ea2edc5444e275a79b371d02b6e98e963662
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:50:01 2024 +0000

    more bug fix.

commit 56e283f1f666a38a4a3b30e1528e96eeb5c622e7
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:40:02 2024 +0000

    Minor bug fix.

commit 2dcfed06ff6789eb77cf92e22b80f5475923fafc
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:19:03 2024 +0000

    Update parameter for c3 case
    Add c3 and mynn template

commit cc46b19ccc7cdb54878340eff79dda9e747abdf7
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 20:51:23 2024 +0000

    Update INFO.
    Add c3 SDF in the build.

commit a444ed48a23f24724853036e522b4437bf412c59
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 18:42:33 2024 +0000

    Update to UFS 2024 Jan 29 version.

commit 88595707c7521cdce37ae1cf78720a7827242b24
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 18:16:46 2024 +0000

    Minor bug fix.

commit baa0e9f10b132098d5134efaad712a51ebc26b83
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 17:59:27 2024 +0000

    Update parameters for setup_expt.py in p8_ugwpv1.sh to resdetatmos and comroot.

commit 5875f06903f82a47fafb05f89f840e3b099d18d8
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 17:51:11 2024 +0000

    Remove old gsl SDFs.
    Remove 'rrtmg_lw_pre' from C3 and MYNN SDFs.

commit 9e0d1342f4e1edce96c9b2baeec55c2cffb964cd
Author: kayee.wong <[email protected]>
Date:   Thu Feb 8 22:14:01 2024 +0000

    Merge to 2024 Jan 12 NOAA-EMC/develop.

    Squashed commit of the following:

    commit c59047614c29f6ec15a4d4a6fa1855929287debd
    Author: Rahul Mahajan <[email protected]>
    Date:   Fri Jan 12 19:21:02 2024 -0500

        Update hash to ufs-weather-model. The noahmptable.tbl was reorganized, so update link_workflow.sh to use the same one used in UFSWM RT (#2219)

    commit c041968e165c07da785376f1441374687b55d6cc
    Author: Kate Friedman <[email protected]>
    Date:   Fri Jan 12 12:09:35 2024 -0500

        Add ocean resolution to setup_expt invocation and retire/reduce COMROT/ROTDIR usage (#2214)

        Two series of updates:

        1) Update setup scripts to now allow users to provide ocean resolution
        2) Housekeeping to retire the `COMROT` variable, replacing it with other variables
        as needed, and reduce the `ROTDIR` variable usage.

        Both updates change options for the workflow setup API.

        Refs #2061

    commit 997f97816493d9ed0242e169b6dcf84e5c9338d6
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Fri Jan 12 10:46:36 2024 -0500

        Allow use of ocean obs prep in WCDA cycling and remove R2D2 (#2215)

        Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same.
        Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS.
        Replaces the current R2D2 processing.

    commit 12a5bb192ab6282d44c008c06dc14947abd37249
    Merge: 4cb58020 6492c2da
    Author: David Huber <[email protected]>
    Date:   Fri Jan 12 09:26:27 2024 -0500

        Merge pull request #2217 from DavidHuber-NOAA/update/versions

        Update and clean up version and module files

    commit 6492c2da5f49bd31575d0bef5278c9a7f8ba3412
    Author: David Huber <[email protected]>
    Date:   Thu Jan 11 11:49:08 2024 -0600

        Update orion module/version files for met/metplus #2123

    commit 94c9937f0bff380b0ebd6acdcfd2509e1ae99389
    Author: DavidHuber <[email protected]>
    Date:   Thu Jan 11 17:42:53 2024 +0000

        Comment met/metplus out from Hera modulefile. #2123

    commit 8c32f8b7d00bba6e3e954f149e6548fb27713a3c
    Merge: a65e4c67 4cb58020
    Author: David Huber <[email protected]>
    Date:   Thu Jan 11 11:34:44 2024 -0600

        Merge branch 'develop' of github.com:noaa-emc/global-workflow into develop

    commit a65e4c675f21dbe72198d263e85e894e62b41e13
    Author: David Huber <[email protected]>
    Date:   Thu Jan 11 11:34:19 2024 -0600

        Initial update of version/module files #2123

    commit 4cb580201af68c1c0e2ae19faf0727dcbbe43b4d
    Author: souopgui <[email protected]>
    Date:   Wed Jan 10 08:30:22 2024 -0600

        Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh when running MPMD tasks (#2212)

        Fix OpenMP over-allocation of resources running MPMD tasks
        Co-authored-by: Innocent Souopgui <[email protected]>

    commit b056b531faee6929687cb8a588ffafa1a66426fb
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Mon Jan 8 17:28:05 2024 -0500

        Add Hercules as valid machine in CI scripts (#2207)

        Few updates to CI scripts to include names for hercules that where missed
        the first time.

    commit 6574d29a8c26b0695614874c344bccc5182363f4
    Author: Rahul Mahajan <[email protected]>
    Date:   Mon Jan 8 17:25:47 2024 -0500

        Fix invalid GH action and restart file name (#2210)

        Resolves a typo that leads to an invalid workflow yaml and fixes the restart filename in restart detection.

        Resolves #2205

    commit 69605eac299df381ea9e0e329654487e26380ff5
    Author: Rahul Mahajan <[email protected]>
    Date:   Mon Jan 8 17:00:28 2024 -0500

        Stop attempting to comment link to RTD for non-PRs (#2209)

        Adds a check so comments with a link to documentation are only generated
        for PRs.

    commit 4e160a895bfb31c281e21557dd86c13954a1a967
    Author: Rahul Mahajan <[email protected]>
    Date:   Mon Jan 8 13:10:15 2024 -0500

        Enable UPP for GOES processing (#2203)

        Wnables the creation of special master grib2 files from UPP for
        GOES processing

    commit c15875b6dbf685327af9316ee43b3d01f0fc815e
    Author: David Huber <[email protected]>
    Date:   Mon Jan 8 09:56:06 2024 -0500

        Port cycling to Hercules (#2196)

        Adds cycled support for Hercules (excluding gsi-monitor).
        Partially resolves #1588
        GSI monitoring is disabled on Hercules due to missing Perl modules. That will be enabled in a later PR.

    commit ef6827dd6abdab2996d1e19f9e0ff5d3071e0fdd
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jan 8 09:43:12 2024 -0500

        Refactor rocoto task XML creation (#2189)

        Refactors the rocoto task generation to be recursive.
        This will allow nested metatasks to loop over multiple variables, which is needed for GEFS product generation.

        As part of this refactor, there is no longer separate arguments to designate metatasks.
        Instead, task dicts can include a nested 'task_dict' as well as a 'var_dict' containing the variables to loop over.
        The nested task dict can then either have another layer, or be the innermost task.

        To accommodate the new recursive nature, some defaults that were previously defined in create_wf_task() had to be pushed down into the function that creates the innermost task.
        Also, former keywords have been absorbed by the task dict.

        Refs #823
        Refs #827

    commit 2b81cfac16f103fb29b3aeb9748941787abf7287
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jan 8 09:41:03 2024 -0500

        Update fix versions (#2198)

        Updates fix versions for a few components:
        - Update cice and mom6 versions to support C96/1p00 marine
        - Update wave to change betamax setting for glo_025 waves

        Resolves #2004
        Resolves #2107

commit e7a81511e37f86e881da020e06b95990b470d952
Merge: af47b77c 75ad3754
Author: Janet Derrico <[email protected]>
Date:   Thu Feb 1 13:14:02 2024 -0700

    Merge pull request #37 from jderrico-noaa/gsl_ufs_dev

    Add GSL archive script and correct typos/fixed paths

commit 75ad3754f8bef5411c2570b5e392cd08e95cb6cb
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 1 20:00:52 2024 +0000

    adding consistent [[ ]] for if statements

commit 67b99668c82a5fd8c42479b9b1bfe8b0bad0be25
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Feb 1 19:37:47 2024 +0000

     Updated HOMEgfs in GSL XML templates

commit 4d3719c086e7907a6eeff03112042d392e0d8c5e
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Feb 1 17:27:39 2024 +0000

     Correct syntax errors in GSL scripts

     Add new GSL archive script for archiving grib2 and ICs, but no netcdf files

commit 4309dd0b3b2d5625e7e1740d7cd3e39aacd5bc29
Author: Judy.K.Henderson <[email protected]>
Date:   Mon Jan 29 18:05:45 2024 +0000

     Add GSL diag tables to parm/ufs/fv3

     Update GSL template for hera

     Create EMC and GSL versions of files under workflow/rocoto
      - tasks.py, workflow_tasks.py

commit af47b77c7ee59a11c798995b4362b57e9096b090
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 02:07:43 2024 +0000

     Create GSL version of archive script

commit 529d9f71f97b6e643e76a53bc9871901ae861faf
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 01:37:09 2024 +0000

     Create GSL version of tracker.sh

     - this is a placeholder with changes from last year's HFIP experiment; will likely need to be updated in the future

commit 8457e12c313bee602265b863129734354b019271
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 01:27:42 2024 +0000

     Link config.base.emc.dyn_hera to config.base.emc.dyn

commit 7a05f5bd947944d8c3be828aeef9cc03bf9e073a
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 01:22:54 2024 +0000

     Create GSL version of hpssarch_gen.sh

     - assume we only run cold starts
     - archive only 0p25 grib2 files (no 0p50 opr 1p00)
     - assume no pgrb2b or flux files are created so no need to archive to HPSS

commit 98f5d6b16437e2a340bf16f83187e389a53f8bf0
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 00:24:06 2024 +0000

     Update workflow directory

     - add GSL template for jet (based on last year's experiment)
     - create EMC and GSL versions of yaml files under hosts; defaults point to GSL files

commit 38a7e5629ceeb23d399643a021e9a0a88468a07c
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 25 18:40:37 2024 +0000

     Update atmos_products configuration file for GSL

       - set downset to 1 so pgrb2b files are not created
       - set FLXGF to "NO" so interpolated sflux.1p00 files are not created

commit fe8a953658d092ce2b597e14f31678624606fd8a
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 25 17:02:25 2024 +0000

     Update nodes for gfsfcst task in GSL template for hera to match default configuration in config.ufs
       (12x12, 2 threads, 1 write group, 40 write tasks ==> 56 nodes)

     Increase walltime to 4:10 for gfsfcst task

commit 9d85b0f6d50e8ed142557fcb87c89d2e5d63c617
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 23 19:08:52 2024 +0000

     Added default location for PTMP/STMP in workflow/hosts/hera.yaml

     Added GSL XML template for hera

commit 1cf317d327fae78c5469712c9e5a6aa1ffa4b23b
Author: Judy.K.Henderson <[email protected]>
Date:   Wed Jan 17 22:33:13 2024 +0000

     Add sjet partition

     Make syntax consistent in "if" statements in config.resources

commit 2755e203751f50113849b06769173285e093290b
Author: Judy.K.Henderson <[email protected]>
Date:   Wed Jan 17 22:32:26 2024 +0000

      Update configuration files for GSL

     - create Hera and Jet versions of config.base.emc.dyn
     - correct typo in config.fcst
     - create different versions of config.ufs;
       default is 12x12, 2 threads, 1 write group/40 write tasks (56 nodes)

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

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

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

     Update link script for ufs_utils.fd

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

     Add GSL archive scripts for initial conditions

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

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

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

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

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

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

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

     Change default HPSS_PROJECT to fim

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

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

     Add namelist parameter, nord_tr, for GSL suites

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

     Add changes for running v17p8_mynn

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

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

     Add experiment setup script for p8_ugwpv1

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

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

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

     Updated GSL-specific files under ufs_utils.fd_gsl

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

     Create new branch, gsl_ufs_dev, from dev_02jan24_9d901db

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

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

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

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

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

    Resolves #1224

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

    Reorganize NPOESS scripts (#2166)

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

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

    Resolves #1226

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

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

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

    Changes:

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

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

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

    Resolves #1984
    Resolves #1981
    Resolves #2175

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

    Remove HIRS from GSI processing (#2183)

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

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

    Resolves #2182

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

    Update ufs-weather-model version  (#2186)

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

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

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

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

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

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

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

    ---------

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

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

    Stop calling ufs-utils link script (#2172)

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

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

    Fix handling of excluded hosts list (#2170)

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

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

    Add COMOUT_OBS to marine obs prep (#2173)

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

    Towards resolving NOAA-EMC/GDASApp#815

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

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

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

    Fixes #2168

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

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

    Refs #2096

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

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

    Set job as shared when not exclusive on WCOSS2

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

    Refs #2135

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

    Update gfs-utils version for Hercules (#2163)

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

    Also includes gfs-utils update for new marine post.

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

    CI Updates to support Hercules (#2155)

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

    Resolves #2154

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

    Correct fbwind (#2161)

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

    Add MOS jobs to rocoto mesh (#2148)

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

    Refs #2068

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

    Replace checkout script with submodules (#2142)

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

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

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

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

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

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

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

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

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

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

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

    CI and documentation are also updated to reflect the changes.

    Resolves #2141

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

    Enable radar reflectivity output (#2143)

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

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

    Fix Hercules hostname (#2150)

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

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

    Fix module load typo (#2145)

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

    Refs #2144

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

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

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

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

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

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

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

    Enable forecast-only experiments on Hercules (#2128)

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

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

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

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

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

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

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

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

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

    Refs #1356

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

    Splits AWIPS jobs into seperate tasks (#2094)

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

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

      Resolves #1228

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

    Consolidate VMINMON and cleanup monitor scripts (#2088)

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

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

    Resolves #1925

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

    Robust CI Restarts (#2093)

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

    New Features:

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

    Resolves #2060

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

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

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

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

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

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

    Added variables to config.prepoceanobs (#2101)

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

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

    Refs #2097

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

    Add wave init to GEFS (#2089)

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

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

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

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

    Resolves #2017

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

    Adjust permissions for jobs/JGFS_ATMOS_VERIFICATION (#2095)

    Add execute permissions (755)

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

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

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

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

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

    Refs #1575

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

    Adds FBWINDS support to global-workflow (#2082)

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

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

    Resolves #1221

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

    Adds NPOESS support to global-workflow (#2083)

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

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

    Resolves #1225

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

    Retire vrfy job (#2080)

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

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

    Resolves #2069
    Refs #235

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

    Enable different coupled settings for ensemble (#2030)

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

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

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

    Resolves #1692

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

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

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

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

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

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

    Resolves #2044

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

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

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

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

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

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

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

    Resolves #1942

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

    Fix check for existence of preamble functions (#2066)

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

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

    Update UPP products for GFS v17 (#1973)

    Updates of generating GFS V17 UPP products to support HR3:

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

    Resolves #1965
    Resolves #1994

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

    Fix some rocoto dependencies (#2074)

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

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

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

    Resolves #2075

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

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

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

    Update functionality for Prototype HR3 UGWP (#1987)

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

    Resolves #1986

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

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

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

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

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

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

    Resolves #2038

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

    Resolve ENKF archive script bugs (#2065)

    Fix two bugs in the exgdas_enkf_earc.sh script:

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

    Refs #2064

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

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

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

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

    Changes in this PR:

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

    Refs #235
    Resolves #1988
    Resolves #2048

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

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

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

    Fixes #2016

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

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

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

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

    Refine fit2obs job in rocoto mesh (#2047)

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

    Changes in PR:

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

    Resolves #2043

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

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

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

    Resolves #1444

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

    Update wave IC source for C384 (#2055)

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

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

    Fix analysis and post on Orion (#2046)

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

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

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

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

    Resolves #1996
    Resolves #2041
    Refs #2044

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

    Hack UPP version (#2042)

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

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

    Resolves #2041

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

    Add basic C1152 settings (#2020)

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

    Resolves #2019

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

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

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

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

    Reduce gdas builds to 8 #2029 (#2036)

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

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

    Resolves #2029

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

    Streamline CI reporting to PRs (#2026)

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

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

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

    Resolves #2007

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

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

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

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

    Resolves #1943
    Refs #1776

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

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

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

    Fix staging of MOM data (#2028)

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

    Resolves #2027

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

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

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

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

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

    Changes in this PR:

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

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

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

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

    Lingering work and considerations:

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

    Resolves #1908

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

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

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

    Resolves #1130

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

    Corrects missing local variable reference (#2023)

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

    Resolves #2022

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

    Updates to prep ocean obs task (#1870)

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

    No longer write archive lists COM (#2000)

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

    Resolves #760

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

    Parallelize the build scripts (#1998)

    Optimized/parallelized build scripts.

    A few notes:

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

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

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

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

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

    Resolves #1978

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

    Add missing export for rCDUMP in stage_ic (#2009)

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

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

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

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

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

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

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

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

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

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

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

    Resolves NOAA-EMC/GDASApp/issues/693

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

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

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

    GEFS Staging in exglobal_stage_ic  (#1892)

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

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

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

    Resolves #911

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

    Update GDASApp hash (#1975)

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

    Resolves #1972

commit 962368884991670d3a1e…
kayeekayee added a commit to kayeekayee/global-workflow that referenced this pull request Mar 15, 2024
@kayeekayee
Merge gsl_ufs_dev from EMC develop (emc_dev_mar4_732a874a)
a04630c 
   UFS: 21Feb24, 6988662
   FV3: 14Feb24, 0fe9ba3
   UPP: 23Jan23, 945cb2c
   UFS_UTILS: 22Feb24, d805336

Squashed commit of the following:

commit 732a874
Author: Rahul Mahajan <[email protected]>
Date:   Mon Mar 4 16:04:26 2024 -0500

    Reformat snowDA templates to jinja2 (NOAA-EMC#2371)

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

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

commit d1fa411
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Sat Mar 2 04:54:26 2024 +0000

    Reduce Jenkins messaging to GitHub (NOAA-EMC#2370)

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

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

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

commit 52fa3cb
Author: Henry R. Winterbottom <[email protected]>
Date:   Fri Mar 1 12:36:27 2024 -0700

    Adding debug option for all build scripts (NOAA-EMC#2326)

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

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

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

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

commit 23c2552
Author: Neil Barton <[email protected]>
Date:   Fri Mar 1 13:45:39 2024 -0500

    Update stage IC to handle ocean perturbations (NOAA-EMC#2364)

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

commit 8efe05f
Author: Jessica Meixner <[email protected]>
Date:   Fri Mar 1 07:41:56 2024 -0500

    Turn on C48mx500_3DVarAOWCDA test on hera (NOAA-EMC#2363)

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

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

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

    Just moves the Jenkinsfile into the ci directory

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

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

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

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

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

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

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

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

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

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

    Routine update of ufs-weather-model hash.

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

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

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

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

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

    Resolves NOAA-EMC#2335

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

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

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

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

    Resolves NOAA-EMC#2184

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

    Fix several Jenkins issues (NOAA-EMC#2334)

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

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

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

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

    Update to spack-stack 1.6.0

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

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

    Disable snow DA tests

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

    Update GDASApp hash to current develop

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

    Update GDAS hash to allow modified snow DA analysis

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

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

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

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

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

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

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

    Updated GDAS to include rocoto/1.3.6 on Hera.

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

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

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

    Refs NOAA-EMC#1629

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

    Update GDASApp hash to include SS/1.6.0 support.

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

    Construct SS paths from version variables.

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

    Removed MET/METplus 'not available' comments

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

    Move SS module path to version files.

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

    Update comment about METplus support.

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

    Update verif-global to latest WCOSS2 support.

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

    Clean up build_upp.sh.

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

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

    Fix whitespace in build_upp.sh.

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

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

    Added verif-global support back to WCOSS2.

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

    Bug fix.

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

    Updates requested by reviewer Rahul Mahajan.

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

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

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

    Linter corrections.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    Resolves NOAA-EMC#1547

commit 9929277
Merge: eb8791c 094e3b8
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Feb 15 15:05:50 2024 -0700

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

commit 094e3b8
Author: Cory Martin <[email protected]>
Date:   Thu Feb 15 14:43:55 2024 -0500

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

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

commit d465ea0
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Feb 15 19:25:02 2024 +0000

    Set HOMEgfs for module_setup in CI driver (NOAA-EMC#2321)

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

commit 2415b7b
Author: David Huber <[email protected]>
Date:   Thu Feb 15 19:21:17 2024 +0000

    Load default rocoto on Jet.

commit eb8791c
Merge: 60d5ee6 638684e
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Feb 15 11:56:40 2024 -0700

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

commit 777d97d
Author: David Huber <[email protected]>
Date:   Thu Feb 15 12:34:59 2024 -0600

    Fixed Orion cdo version.

commit ef07235
Author: DavidHuber <[email protected]>
Date:   Thu Feb 15 16:29:32 2024 +0000

    Revert UFS hash.

commit 0ce8c0d
Author: DavidHuber <[email protected]>
Date:   Thu Feb 15 14:55:48 2024 +0000

    Fix git version in Hera's gwsetup module.

commit 3080a34
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 20:52:34 2024 +0000

    Fixed xarray version for SS/1.6.0.

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

    Updated GSI-Utils hash to head of develop.

commit c3553f0
Merge: 4568653 638684e
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 20:28:14 2024 +0000

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

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

    Reupgrade Hercules to SS/1.6.0

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

    Remove `finddate.sh` from system (NOAA-EMC#2308)

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

    Refs NOAA-EMC#2279

commit 2b160f8
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 18:31:28 2024 +0000

    Reenable METplus jobs on Hercules.

commit 8f59002
Author: DavidHuber <[email protected]>
Date:   Wed Feb 14 18:30:23 2024 +0000

    Update GSI hashes.

commit 73bc76b
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 14 09:27:37 2024 -0700

    Updates based on user request.

commit e4bc674
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 14 08:03:45 2024 -0700

    Corrected based on reviewer review.

commit 60d5ee6
Merge: 40f2cf6 1aaef05
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Feb 13 18:08:33 2024 -0700

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

commit 0330411
Merge: 929b903 1aaef05
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Feb 13 17:58:12 2024 -0700

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

commit 1aaef05
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Feb 13 18:15:59 2024 -0500

    Jenkins Pipeline updates for Canceling Jobs (NOAA-EMC#2307)

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

commit 6404892
Author: Rahul Mahajan <[email protected]>
Date:   Tue Feb 13 14:57:37 2024 -0500

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

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

    Fixes NOAA-EMC#935
    Fixes NOAA-EMC#1317
    Fixes NOAA-EMC#1864

commit 40f2cf6
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Tue Feb 13 10:18:53 2024 -0700

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

commit 929b903
Merge: 2d08d01 3f99f70
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Feb 13 08:31:06 2024 -0700

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

commit 3f99f70
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Feb 13 00:57:18 2024 -0500

    Add wave post jobs to GEFS (NOAA-EMC#2292)

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

    Resolves NOAA-EMC#827

commit 842adf3
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Feb 12 12:50:08 2024 -0500

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

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

commit bb4ca65
Author: CatherineThomas-NOAA <[email protected]>
Date:   Mon Feb 12 14:50:41 2024 +0000

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

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

    Resolves: NOAA-EMC#2303

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

    Fix Jenkins success reporting (NOAA-EMC#2302)

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

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

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

commit 28ccf78
Merge: b972f66 54daa31
Author: David Huber <[email protected]>
Date:   Fri Feb 9 14:00:43 2024 -0600

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

commit b972f66
Author: David Huber <[email protected]>
Date:   Fri Feb 9 10:47:00 2024 -0600

    Fix SS versions for CI modules.

commit 4b01d8e
Author: David Huber <[email protected]>
Date:   Fri Feb 9 10:44:30 2024 -0600

    Revert Hercules modules to SS/1.5.1.

commit 54daa31
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Feb 8 15:48:38 2024 -0500

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

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

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

    Resolves NOAA-EMC#2119
    Resolves NOAA-EMC#2118

commit 43429e2
Author: Rahul Mahajan <[email protected]>
Date:   Thu Feb 8 15:30:28 2024 -0500

    Enable AO WCDA test (NOAA-EMC#1963)

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

commit 2d08d01
Merge: 4745d4a f563528
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Feb 8 07:24:54 2024 -0700

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

commit f563528
Author: Kate Friedman <[email protected]>
Date:   Wed Feb 7 15:09:12 2024 -0500

    Update JGLOBAL_FORECAST for octal error (NOAA-EMC#2295)

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

commit 4745d4a
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 7 08:45:49 2024 -0700

    Removed jlogfile references.

commit 5894ca2
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 7 08:32:16 2024 -0700

    Removed dummy variable passed to perl scripts.

commit dae884a
Author: henrywinterbottom-wxdev <[email protected]>
Date:   Wed Feb 7 08:29:49 2024 -0700

    Removed jlogfile and postmsg references within gempak scripts.

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

    Consolidate `npe_node_max` (NOAA-EMC#2289)

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

    Resolves NOAA-EMC#2133

commit b0325e0
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Feb 7 00:40:20 2024 -0700

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

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

    The module `ush/module-setup.sh` is updated such that it now sources
    `ush/detect_machine.sh` to determine which supported platform the
    global-workflow is being execute on.

    Resolves NOAA-EMC#2130

commit 1ccc989
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Feb 5 14:16:07 2024 -0500

    Remove EnKF forecast groups (NOAA-EMC#2280)

    Removes the grouping of EnKF forecasts so each job only runs
    one forecast. Member and MEMDIR are now set at the workflow
    manager (rocoto) level. This change makes much of the system
    simpler (especially dependencies) and allows the elimination of
    the separate efcs scripts.

    Metatask names of updated jobs have been updated to make
    them a little less opaque by using the same name name as its
    constituent tasks (e.g. the forecast metatask is named
    `enkgdasfcst`, not `enkfgdasefcs`). Metatasks that weren't
    updated retain the same names as before for now.

    Resolves NOAA-EMC#2254

commit 9f3383f
Author: Henry R. Winterbottom <[email protected]>
Date:   Mon Feb 5 12:15:13 2024 -0700

    Updated detect_machine.sh using that from UFS WM. (NOAA-EMC#2252)

    Updates `ush/detect_machine.sh` to match the UFS weather-model
    `tests/detect_machine.sh` prepared by @BrianCurtis-NOAA

    Resolves NOAA-EMC#2228

commit 7d68b0b
Author: CatherineThomas-NOAA <[email protected]>
Date:   Sun Feb 4 22:02:41 2024 +0000

    Update global_cycle for fractional grid (NOAA-EMC#2262)

    The hash for ufs_utils is updated to include the changes for
    fractional grid support within global_cycle.  This commit also
    removes the hack to skip global_cycle in cycling mode with
    v17 physics.

    Resolves: NOAA-EMC#1775
    Refs: ufs-community/UFS_UTILS#815
    Refs: ufs-community/UFS_UTILS#891

commit ed592a6
Author: Kate Friedman <[email protected]>
Date:   Sat Feb 3 02:55:14 2024 -0500

    Retire cycle-specific FHMAX_GFS variables (NOAA-EMC#2278)

    This PR retires the `FHMAX_GFS_${cyc}` variables that allowed users to specify
    different gfs forecast lengths for each cycle. This function is no longer supported
    in global-workflow. The `FHMAX_GFS_*` variables will be removed and will no
    longer be checked to set the final `FHMAX_GFS` variable. The same forecast
    length will be set for every cycle.

    This PR also includes a small fix to add new post parm files into the `.gitignore`
    file. This was intended to be included in a different PR but that PR is on hold for
    further testing so it is being included here to get it into `develop` sooner.

    Resolves NOAA-EMC#2218

commit 977e2d6
Author: Henry R. Winterbottom <[email protected]>
Date:   Fri Feb 2 07:49:09 2024 -0700

    New GDASApp hash. (NOAA-EMC#2285)

commit b5f2bd9
Merge: 4d66742 0400e1f
Author: David Huber <[email protected]>
Date:   Tue Jan 30 13:55:00 2024 -0600

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit 0400e1f
Author: David Huber <[email protected]>
Date:   Tue Jan 30 09:57:11 2024 -0600

    Fix gfs_utils Orion spack-stack env path.

commit 6bbe823
Author: DWesl <[email protected]>
Date:   Mon Jan 29 21:15:30 2024 -0500

    Use seq to generate the list of times, instead of a bash for-loop (NOAA-EMC#2264)

    I'm running a year-long forecast, which means I get a large portion of the log file dedicated to these loops.

    `seq ${START} ${STEP} ${STOP}` will generate a sequence going from START to STOP by STEP, including STOP if relevant.  That seems to be the purpose of these loops.  It will by default separate the list with newlines, but `seq -s ' ' ${START} ${STEP} ${STOP}` will separate them with spaces instead, more closely mimicing the previous behavior.

    I would like this to be two lines in the log, rather than a few hundred, and this may also be faster, though probably more for reasons of fewer writes to disk than because bash isn't designed for arithmetic.

commit d5bee38
Author: Kate Friedman <[email protected]>
Date:   Mon Jan 29 14:35:02 2024 -0500

    Correct typos in GFS config.resources (NOAA-EMC#2267)

    This PR corrects some typos in `parm/config/gfs/config.resources` that were
    introduced in PR NOAA-EMC#2216. The esfc job was failing in tests on WCOSS2 due to
    insufficient memory. This lead to discovering the other typos. The esfc job
    completes without error after its memory is set back to `80GB` from the
    incorrect `8GB`.

    Resolves NOAA-EMC#2266

commit 81557be
Author: David Huber <[email protected]>
Date:   Mon Jan 29 12:13:31 2024 -0600

    Update monitor hash to noaa-emc with SS/1.6.0 support.

commit 2238dd6
Author: DavidHuber <[email protected]>
Date:   Mon Jan 29 13:21:30 2024 +0000

    Update Orion, Hercules, S4 modulefiles.

commit 6ffd94f
Author: DavidHuber <[email protected]>
Date:   Fri Jan 26 16:01:23 2024 +0000

    Update GDAS hash to include SS/1.6.0 support.

commit be11f85
Merge: 56b9680 04e0772
Author: DavidHuber <[email protected]>
Date:   Fri Jan 26 15:34:24 2024 +0000

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit 8ff3448
Author: Rahul Mahajan <[email protected]>
Date:   Fri Jan 26 10:12:18 2024 -0500

    Add a yaml for snow DA testing. (NOAA-EMC#2199)

    - adds a new test yaml C96_atmsnowDA.yaml for 3DVar atmosphere with GSI and Land (Snow) DA with JEDI
    - moves a few yamls from platforms/ to yamls/
    - adds ability to overwrite a previously created experiment as an addition to user input.
    ---------

    Co-authored-by: Cory Martin <[email protected]>

commit 04e0772
Author: David Huber <[email protected]>
Date:   Fri Jan 26 07:16:25 2024 -0600

    Update ufs_utils hash for spack-stack/1.6.0 support.

commit 3d44ff3
Author: Barry Baker <[email protected]>
Date:   Thu Jan 25 14:33:27 2024 -0500

    GOCART ExtData biogenic climatology fix (NOAA-EMC#2253)

    Updates the ExtData for biogenic emissions to be climatology rather than
    for current time.  Fixes an issue which will crash by default for other years.

commit 66f58b8
Author: Guillaume Vernieres <[email protected]>
Date:   Thu Jan 25 13:16:41 2024 -0500

    Added missing container case in gfs/config.resources (NOAA-EMC#2258)

    fixes  NOAA-EMC#2257

commit 553b4f2
Author: WenMeng-NOAA <[email protected]>
Date:   Thu Jan 25 13:00:45 2024 -0500

    Fix post parm links (NOAA-EMC#2243)

    Change symbolic links under parm/post with the latest version of develop branch from UPP repository and enable MERRA2 aerosol fields.

    Resolves NOAA-EMC#2259

commit 4d66742
Merge: 6c05803 afa09e3
Author: David Huber <[email protected]>
Date:   Thu Jan 25 07:49:08 2024 -0600

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit 6c05803
Author: David Huber <[email protected]>
Date:   Thu Jan 25 07:48:42 2024 -0600

    Fix wgrib2/gfs_utils on Hercules.

commit ee6f536
Author: Kate Friedman <[email protected]>
Date:   Thu Jan 25 07:43:13 2024 -0500

    Update GFS version to v16.3.13 in index.rst (NOAA-EMC#2256)

    GFSv16.3.13 WAFS update was implemented

    Refs NOAA-EMC#2013

commit 2445d44
Author: RussTreadon-NOAA <[email protected]>
Date:   Thu Jan 25 06:17:11 2024 -0500

    Simplify and extend load_ufsda_modules to Hercules (NOAA-EMC#2245)

    GDASApp jobs do not run on Hercules because `ush/load_ufsda_modules.sh` does
    not include logic to load the appropriate GDASApp modules on Hercules.  This PR
    extends `load_ufsda_modules.sh` functionality to Hercules, thereby enabling
    GDASApp jobs to run on Hercules.

    Resolves NOAA-EMC#2244

commit 56b9680
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 19:47:34 2024 +0000

    Update hashes (revert WCOSS2 modules).

commit afa09e3
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 18:59:40 2024 +0000

    New (cleaner history) gdas hash.

commit a9eaec2
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 18:52:27 2024 +0000

    Update gdasapp to include ss/1.6.0 support.

commit 5ef8eb2
Merge: 4c46354 e400068
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 17:08:54 2024 +0000

    Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160

commit 4c46354
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 17:05:12 2024 +0000

    Reenable verif-global support

commit f775755
Author: DavidHuber <[email protected]>
Date:   Wed Jan 24 16:59:10 2024 +0000

    Assign fcsthrs for awips_g2 job.

commit e400068
Author: David Huber <[email protected]>
Date:   Mon Jan 22 15:01:07 2024 -0600

    More gsi-addon path fixes.

commit f663d47
Author: David Huber <[email protected]>
Date:   Mon Jan 22 14:41:59 2024 -0600

    Fix gsi-addon paths for hercules, orion, and S4.

commit e304bbe
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:59:34 2024 +0000

    Better optimize build jobs (more ufs jobs).

commit ccc6e2d
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:56:18 2024 +0000

    Reenable verif-global. NOAA-EMC#2195

commit 3ef3411
Merge: 4365f63 f4d187f
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:39:10 2024 +0000

    Merge remote-tracking branch 'origin/develop' into ss160

commit 4365f63
Author: DavidHuber <[email protected]>
Date:   Mon Jan 22 18:37:25 2024 +0000

    Corrected the SS env. name in the version files. NOAA-EMC#2195

commit f4d187f
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Mon Jan 22 12:28:28 2024 -0500

    Converts obsproc to obsprep in prepoceanobs config file (NOAA-EMC#2236)

    Converts obsproc to obsprep in prepoceanobs config file as a compliment to mutually depended GDASApp PR NOAA-EMC/GDASApp#858
    The motivations are explained in refs NOAA-EMC/GDASApp#857

commit 9a09d30
Author: DavidHuber <[email protected]>
Date:   Fri Jan 19 21:23:50 2024 +0000

    Corrected gsi-addon-dev spelling.

commit 21ff645
Author: DavidHuber <[email protected]>
Date:   Fri Jan 19 21:11:34 2024 +0000

    Update modulefiles, submodules to spack-stack 1.6.0. NOAA-EMC#2195

commit d4c55d1
Author: Kate Friedman <[email protected]>
Date:   Fri Jan 19 15:43:37 2024 -0500

    Update typing hint for WCOSS version of python (NOAA-EMC#2238)

    The typing hint `typing.List` was deprecated with python 3.9 in favor
    of using the primitive `list[str]`, but the functional version of python
    on WCOSS2 is <3.9, causing `setup_xml.py` to fail there. This replaces
    `list[str]` as a typing hint with the deprecated form until the supported
    version on WCOSS2 is >=3.9.

commit 4919287
Author: Barry Baker <[email protected]>
Date:   Thu Jan 18 22:31:27 2024 -0500

    GOCART Emission updates for GEFSv13 and GDAS  (NOAA-EMC#2201)

    This PR addresses several things needed for more recent simulations using
    GOCART2G as well as preparing for the GEFSv13 30 year run.  The main
    updates are:

    - Update CEDS to use monthly emission files instead of daily.  This will
    drastically reduce the number of files needed. No science change
    - Update biogenic MEGAN inputs to use a climatology rather than the
    offline biogenic previously used.  This is needed to deal with simulations
    where the current dataset is not available.
    - Update volcanic SO4 emissions to use degassing emissions only.  This is
    to support the need for more recent simulations where data is not available.

commit 13d25cf
Author: Kate Friedman <[email protected]>
Date:   Thu Jan 18 22:29:43 2024 -0500

    Add `POSTAMBLE_CMD` into preamble postamble (NOAA-EMC#2235)

    This PR adds the ability to run a command at the end of jobs via the
    preamble's postamble function. A new command can be set via
    `POSTAMBLE_CMD` and will be invoked at the end of jobs. Users can
    add the command to the top of an env file to have every job run it or
    it can be placed within a job if-block in the env file to run for just that
    job.

    Resolves NOAA-EMC#1145

commit 7759163
Author: Rahul Mahajan <[email protected]>
Date:   Thu Jan 18 01:13:49 2024 -0500

    Add option to create WGNE atmosphere products (NOAA-EMC#2233)

    Adds option to create WGNE products for the atmosphere.

    Resolves NOAA-EMC#1951
    Resolves NOAA-EMC#2226

commit d95ed85
Author: Rahul Mahajan <[email protected]>
Date:   Wed Jan 17 18:04:56 2024 -0500

    Use ufs.configure, model_configure, MOM_input, data_table, and ice_in templates from UFS-weather-model (NOAA-EMC#2051)

    This PR:
    - links `ufs.configure.*.IN`, `model_configure.IN`, `MOM_input_${OCNRES}.in`,
    `MOM6_data_table.IN`, and `ice_in.IN` from ufs-weather-model into the
    global-workflow `parm/ufs` directory
    - prepares local variables for use in the templates in the respective functions
    for FV3, MOM6, and CICE6
    - uses `atparse.bash` to render these templates into fully formed namelists

    - Work was performed by @DeniseWorthen in the ufs-weather-model to
    templatize several variables that are hard-wired in the ufs-weather-model
    for CICE. See ufs-community/ufs-weather-model/NOAA-EMC#2010

commit 44a66dd
Author: RussTreadon-NOAA <[email protected]>
Date:   Wed Jan 17 13:52:09 2024 -0500

    Update gdas.cd hash to use gsibec tag 1.1.3 (NOAA-EMC#2231) (NOAA-EMC#2234)

commit 9046d97
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Jan 17 10:19:18 2024 -0500

    Add basic atmos products for GEFS and refactor resources (NOAA-EMC#2216)

    * Add basic atmos products for GEFS

    Adds basic atmosphere products for GEFS members (no mean or spread).

    To facilitate the addition of GEFS parameter lists, the existing GFS
    lists are renamed. They are also relocated to `parm/products/` direc
    tory instead of `parm/post/`. GEFS v12 uses different parameter lists
    for different resolutions, but for this implementation, the 0p25 lists
    are used for all resolutions. However, to hedge against the final con-
    figuration, all of the GEFS parameter lists have been added to parm.
    Implementation of different parameter lists for each resolution will
    take additional refactoring of the atmos_products job, as it currently
    assumes all resolutions use the same lists.

    The new GEFS rocoto task is implented as two loops of metatasks (made
    possible by PR NOAA-EMC#2189). The member is set at the rocoto level, so the
    setting in `config.base` had to be updated to accept a pass-through.
    The generation of a forecast hour list is moved up to its own function
    in `rocoto.tasks`, separate from the post groups which are not used.
    This can be used as a model for future metatasks (or refactoring of old
    ones). `rocoto_viewer.py` does function with the nested metatasks,
    though only one level of folding is available and the metatask name
    is that of the lower metatask (though it encompasses the entire outer
    metatask).

    Additionally, the GEFS `config.resources` had diverged from the GFS
    version, which included not having a section for the atm products job.
    This led to the refactoring of the GFS `config.resources`, including
    switching to using a `case` statement instead of sequential `elif`.
    This refactored script was then copied over to GEFS, replacing the old
    one, with all jobs not currently implemented for GEFS removed (except
    wave post, whose inclusion is immenent). New blocks can be copied over
    from GFS as they are added.

    Resolves NOAA-EMC#823

commit fbba174
Author: RussTreadon-NOAA <[email protected]>
Date:   Tue Jan 16 14:05:48 2024 -0500

    Update GDASApp (gdas.cd) hash (NOAA-EMC#2225)

    GDASApp now uses gitsubmodules

commit dddd837
Author: Rahul Mahajan <[email protected]>
Date:   Tue Jan 16 12:17:19 2024 -0500

    Fix ocean resolution for the S2SWA test (NOAA-EMC#2223)

commit 83edaf1
Author: David Huber <[email protected]>
Date:   Tue Jan 16 11:07:02 2024 -0500

    Apply fixes to archiving jobs (NOAA-EMC#2221)

    Add checks for potentially missing log/data files and update log names for archiving.

    Missing sflux index files are also added to the products script.

    Resolves NOAA-EMC#2076

commit c590476
Author: Rahul Mahajan <[email protected]>
Date:   Fri Jan 12 19:21:02 2024 -0500

    Update hash to ufs-weather-model. The noahmptable.tbl was reorganized, so update link_workflow.sh to use the same one used in UFSWM RT (NOAA-EMC#2219)

commit c041968
Author: Kate Friedman <[email protected]>
Date:   Fri Jan 12 12:09:35 2024 -0500

    Add ocean resolution to setup_expt invocation and retire/reduce COMROT/ROTDIR usage (NOAA-EMC#2214)

    Two series of updates:

    1) Update setup scripts to now allow users to provide ocean resolution
    2) Housekeeping to retire the `COMROT` variable, replacing it with other variables
    as needed, and reduce the `ROTDIR` variable usage.

    Both updates change options for the workflow setup API.

    Refs NOAA-EMC#2061

commit 997f978
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Fri Jan 12 10:46:36 2024 -0500

    Allow use of ocean obs prep in WCDA cycling and remove R2D2 (NOAA-EMC#2215)

    Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same.
    Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS.
    Replaces the current R2D2 processing.

commit 12a5bb1
Merge: 4cb5802 6492c2d
Author: David Huber <[email protected]>
Date:   Fri Jan 12 09:26:27 2024 -0500

    Merge pull request NOAA-EMC#2217 from DavidHuber-NOAA/update/versions

    Update and clean up version and module files

commit 6492c2d
Author: David Huber <[email protected]>
Date:   Thu Jan 11 11:49:08 2024 -0600

    Update orion module/version files for met/metplus NOAA-EMC#2123

commit 94c9937
Author: DavidHuber <[email protected]>
Date:   Thu Jan 11 17:42:53 2024 +0000

    Comment met/metplus out from Hera modulefile. NOAA-EMC#2123

commit 8c32f8b
Merge: a65e4c6 4cb5802
Author: David Huber <[email protected]>
Date:   Thu Jan 11 11:34:44 2024 -0600

    Merge branch 'develop' of github.com:noaa-emc/global-workflow into develop

commit a65e4c6
Author: David Huber <[email protected]>
Date:   Thu Jan 11 11:34:19 2024 -0600

    Initial update of version/module files NOAA-EMC#2123

commit 4cb5802
Author: souopgui <[email protected]>
Date:   Wed Jan 10 08:30:22 2024 -0600

    Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh when running MPMD tasks (NOAA-EMC#2212)

    Fix OpenMP over-allocation of resources running MPMD tasks
    Co-authored-by: Innocent Souopgui <[email protected]>

commit b056b53
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Jan 8 17:28:05 2024 -0500

    Add Hercules as valid machine in CI scripts (NOAA-EMC#2207)

    Few updates to CI scripts to include names for hercules that where missed
    the first time.

commit 6574d29
Author: Rahul Mahajan <[email protected]>
Date:   Mon Jan 8 17:25:47 2024 -0500

    Fix invalid GH action and restart file name (NOAA-EMC#2210)

    Resolves a typo that leads to an invalid workflow yaml and fixes the restart filename in restart detection.

    Resolves NOAA-EMC#2205

commit 69605ea
Author: Rahul Mahajan <[email protected]>
Date:   Mon Jan 8 17:00:28 2024 -0500

    Stop attempting to comment link to RTD for non-PRs (NOAA-EMC#2209)

    Adds a check so comments with a link to documentation are only generated
    for PRs.

commit 4e160a8
Author: Rahul Mahajan <[email protected]>
Date:   Mon Jan 8 13:10:15 2024 -0500

    Enable UPP for GOES processing (NOAA-EMC#2203)

    Wnables the creation of special master grib2 files from UPP for
    GOES processing

commit c15875b
Author: David Huber <[email protected]>
Date:   Mon Jan 8 09:56:06 2024 -0500

    Port cycling to Hercules (NOAA-EMC#2196)

    Adds cycled support for Hercules (excluding gsi-monitor).
    Partially resolves NOAA-EMC#1588
    GSI monitoring is disabled on Hercules due to missing Perl modules. That will be enabled in a later PR.

commit ef6827d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Jan 8 09:43:12 2024 -0500

    Refactor rocoto task XML creation (NOAA-EMC#2189)

    Refactors the rocoto task generation to be recursive.
    This will allow nested metatasks to loop over multiple variables, which is needed for GEFS product generation.

    As part of this refactor, there is no longer separate arguments to designate metatasks.
    Instead, task dicts can include a nested 'task_dict' as well as a 'var_dict' containing the variables to loop over.
    The nested task dict can then either have another layer, or be the innermost task.

    To accommodate the new recursive nature, some defaults that were previously defined in create_wf_task() had to be pushed down into the function that creates the innermost task.
    Also, former keywords have been absorbed by the task dict.

    Refs NOAA-EMC#823
    Refs NOAA-EMC#827

commit 2b81cfa
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Jan 8 09:41:03 2024 -0500

    Update fix versions (NOAA-EMC#2198)

    Updates fix versions for a few components:
    - Update cice and mom6 versions to support C96/1p00 marine
    - Update wave to change betamax setting for glo_025 waves

    Resolves NOAA-EMC#2004
    Resolves NOAA-EMC#2107
kayeekayee added a commit to kayeekayee/global-workflow that referenced this pull request Mar 16, 2024
@kayeekayee
- based on gsl_ufs_dev from NOAA-GSL/gsl_ufs_dev(29Feb24,25c026e)
3b558f5 
   12Jan24 global-workflow
   UFS: 29Jan24, 625ac02
   FV3: 29Jan24, bd38c56
   UPP: 07Nov23, 78f369b
   UFS_UTILS: 22Dev23, ce385ce

   update pointers for ufs_model and ufs_utils
   add GSL C3_MYNN xml suite
   Change dt_inner=75 for any configuration running aerosol-aware Thompson (ltaerosol=.true.)

Squashed commit of the following:

commit 25c026ef03a8d8c0db0b7368d2836f0b2e866eae
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 29 20:35:11 2024 +0000

    update ufs_model pointer

commit a28617a951c46b765aa996bfe4d28b554ec4e0a4
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 22 06:16:26 2024 +0000

    removed unneeded gsl directories

commit 6fb4f90e8572e98c977a1d2ab385f033111f3ea7
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 22 06:08:13 2024 +0000

    update ufs_utils.fd pointer

commit 9264f0c09239d046c5cd862d807e9b82f51dc3bd
Author: jderrico-noaa <[email protected]>
Date:   Wed Feb 21 19:33:26 2024 +0000

    update .gitmodules file

commit f8edfa966147506f2c207728039e3a736cb95415
Author: jderrico-noaa <[email protected]>
Date:   Wed Feb 21 19:30:47 2024 +0000

    update pointer to ufs_utils.fd

commit 5e0d2ab02d58e6a7a40db55a149a93008b28aa8b
Author: jderrico-noaa <[email protected]>
Date:   Wed Feb 21 19:25:52 2024 +0000

    update pointer to ufs_model.fd

commit ebc9e1d02987a1c6aa8cabedf2323642748fab3c
Merge: e7a81511 50cb1e6f
Author: Janet Derrico <[email protected]>
Date:   Thu Feb 15 13:40:33 2024 -0700

    Merge pull request #40 from kayeekayee/gsl_ufs_dev

    Merge to 2024 Jan 12 NOAA-EMC/develop and update to 2024 Jan 29 UFS

commit 50cb1e6f0c661e4c6e2ef0be4527cce58379b2c9
Author: kayee.wong <[email protected]>
Date:   Thu Feb 15 20:30:34 2024 +0000

    Add pygraf workflow.

commit 38b726125d49cff6cae4c0e5fff2438fc33143c5
Author: kayee.wong <[email protected]>
Date:   Wed Feb 14 17:43:15 2024 +0000

    Add double quote for the arguments when calling setup_expt.py.

commit 053f2025fb0b0679c7d4f84958973c1534ec050c
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:57:06 2024 +0000

    more fix.

commit 6f80ea2edc5444e275a79b371d02b6e98e963662
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:50:01 2024 +0000

    more bug fix.

commit 56e283f1f666a38a4a3b30e1528e96eeb5c622e7
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:40:02 2024 +0000

    Minor bug fix.

commit 2dcfed06ff6789eb77cf92e22b80f5475923fafc
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:19:03 2024 +0000

    Update parameter for c3 case
    Add c3 and mynn template

commit cc46b19ccc7cdb54878340eff79dda9e747abdf7
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 20:51:23 2024 +0000

    Update INFO.
    Add c3 SDF in the build.

commit a444ed48a23f24724853036e522b4437bf412c59
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 18:42:33 2024 +0000

    Update to UFS 2024 Jan 29 version.

commit 88595707c7521cdce37ae1cf78720a7827242b24
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 18:16:46 2024 +0000

    Minor bug fix.

commit baa0e9f10b132098d5134efaad712a51ebc26b83
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 17:59:27 2024 +0000

    Update parameters for setup_expt.py in p8_ugwpv1.sh to resdetatmos and comroot.

commit 5875f06903f82a47fafb05f89f840e3b099d18d8
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 17:51:11 2024 +0000

    Remove old gsl SDFs.
    Remove 'rrtmg_lw_pre' from C3 and MYNN SDFs.

commit 9e0d1342f4e1edce96c9b2baeec55c2cffb964cd
Author: kayee.wong <[email protected]>
Date:   Thu Feb 8 22:14:01 2024 +0000

    Merge to 2024 Jan 12 NOAA-EMC/develop.

    Squashed commit of the following:

    commit c59047614c29f6ec15a4d4a6fa1855929287debd
    Author: Rahul Mahajan <[email protected]>
    Date:   Fri Jan 12 19:21:02 2024 -0500

        Update hash to ufs-weather-model. The noahmptable.tbl was reorganized, so update link_workflow.sh to use the same one used in UFSWM RT (#2219)

    commit c041968e165c07da785376f1441374687b55d6cc
    Author: Kate Friedman <[email protected]>
    Date:   Fri Jan 12 12:09:35 2024 -0500

        Add ocean resolution to setup_expt invocation and retire/reduce COMROT/ROTDIR usage (#2214)

        Two series of updates:

        1) Update setup scripts to now allow users to provide ocean resolution
        2) Housekeeping to retire the `COMROT` variable, replacing it with other variables
        as needed, and reduce the `ROTDIR` variable usage.

        Both updates change options for the workflow setup API.

        Refs #2061

    commit 997f97816493d9ed0242e169b6dcf84e5c9338d6
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Fri Jan 12 10:46:36 2024 -0500

        Allow use of ocean obs prep in WCDA cycling and remove R2D2 (#2215)

        Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same.
        Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS.
        Replaces the current R2D2 processing.

    commit 12a5bb192ab6282d44c008c06dc14947abd37249
    Merge: 4cb58020 6492c2da
    Author: David Huber <[email protected]>
    Date:   Fri Jan 12 09:26:27 2024 -0500

        Merge pull request #2217 from DavidHuber-NOAA/update/versions

        Update and clean up version and module files

    commit 6492c2da5f49bd31575d0bef5278c9a7f8ba3412
    Author: David Huber <[email protected]>
    Date:   Thu Jan 11 11:49:08 2024 -0600

        Update orion module/version files for met/metplus #2123

    commit 94c9937f0bff380b0ebd6acdcfd2509e1ae99389
    Author: DavidHuber <[email protected]>
    Date:   Thu Jan 11 17:42:53 2024 +0000

        Comment met/metplus out from Hera modulefile. #2123

    commit 8c32f8b7d00bba6e3e954f149e6548fb27713a3c
    Merge: a65e4c67 4cb58020
    Author: David Huber <[email protected]>
    Date:   Thu Jan 11 11:34:44 2024 -0600

        Merge branch 'develop' of github.com:noaa-emc/global-workflow into develop

    commit a65e4c675f21dbe72198d263e85e894e62b41e13
    Author: David Huber <[email protected]>
    Date:   Thu Jan 11 11:34:19 2024 -0600

        Initial update of version/module files #2123

    commit 4cb580201af68c1c0e2ae19faf0727dcbbe43b4d
    Author: souopgui <[email protected]>
    Date:   Wed Jan 10 08:30:22 2024 -0600

        Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh when running MPMD tasks (#2212)

        Fix OpenMP over-allocation of resources running MPMD tasks
        Co-authored-by: Innocent Souopgui <[email protected]>

    commit b056b531faee6929687cb8a588ffafa1a66426fb
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Mon Jan 8 17:28:05 2024 -0500

        Add Hercules as valid machine in CI scripts (#2207)

        Few updates to CI scripts to include names for hercules that where missed
        the first time.

    commit 6574d29a8c26b0695614874c344bccc5182363f4
    Author: Rahul Mahajan <[email protected]>
    Date:   Mon Jan 8 17:25:47 2024 -0500

        Fix invalid GH action and restart file name (#2210)

        Resolves a typo that leads to an invalid workflow yaml and fixes the restart filename in restart detection.

        Resolves #2205

    commit 69605eac299df381ea9e0e329654487e26380ff5
    Author: Rahul Mahajan <[email protected]>
    Date:   Mon Jan 8 17:00:28 2024 -0500

        Stop attempting to comment link to RTD for non-PRs (#2209)

        Adds a check so comments with a link to documentation are only generated
        for PRs.

    commit 4e160a895bfb31c281e21557dd86c13954a1a967
    Author: Rahul Mahajan <[email protected]>
    Date:   Mon Jan 8 13:10:15 2024 -0500

        Enable UPP for GOES processing (#2203)

        Wnables the creation of special master grib2 files from UPP for
        GOES processing

    commit c15875b6dbf685327af9316ee43b3d01f0fc815e
    Author: David Huber <[email protected]>
    Date:   Mon Jan 8 09:56:06 2024 -0500

        Port cycling to Hercules (#2196)

        Adds cycled support for Hercules (excluding gsi-monitor).
        Partially resolves #1588
        GSI monitoring is disabled on Hercules due to missing Perl modules. That will be enabled in a later PR.

    commit ef6827dd6abdab2996d1e19f9e0ff5d3071e0fdd
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jan 8 09:43:12 2024 -0500

        Refactor rocoto task XML creation (#2189)

        Refactors the rocoto task generation to be recursive.
        This will allow nested metatasks to loop over multiple variables, which is needed for GEFS product generation.

        As part of this refactor, there is no longer separate arguments to designate metatasks.
        Instead, task dicts can include a nested 'task_dict' as well as a 'var_dict' containing the variables to loop over.
        The nested task dict can then either have another layer, or be the innermost task.

        To accommodate the new recursive nature, some defaults that were previously defined in create_wf_task() had to be pushed down into the function that creates the innermost task.
        Also, former keywords have been absorbed by the task dict.

        Refs #823
        Refs #827

    commit 2b81cfac16f103fb29b3aeb9748941787abf7287
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jan 8 09:41:03 2024 -0500

        Update fix versions (#2198)

        Updates fix versions for a few components:
        - Update cice and mom6 versions to support C96/1p00 marine
        - Update wave to change betamax setting for glo_025 waves

        Resolves #2004
        Resolves #2107

commit e7a81511e37f86e881da020e06b95990b470d952
Merge: af47b77c 75ad3754
Author: Janet Derrico <[email protected]>
Date:   Thu Feb 1 13:14:02 2024 -0700

    Merge pull request #37 from jderrico-noaa/gsl_ufs_dev

    Add GSL archive script and correct typos/fixed paths

commit 75ad3754f8bef5411c2570b5e392cd08e95cb6cb
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 1 20:00:52 2024 +0000

    adding consistent [[ ]] for if statements

commit 67b99668c82a5fd8c42479b9b1bfe8b0bad0be25
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Feb 1 19:37:47 2024 +0000

     Updated HOMEgfs in GSL XML templates

commit 4d3719c086e7907a6eeff03112042d392e0d8c5e
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Feb 1 17:27:39 2024 +0000

     Correct syntax errors in GSL scripts

     Add new GSL archive script for archiving grib2 and ICs, but no netcdf files

commit 4309dd0b3b2d5625e7e1740d7cd3e39aacd5bc29
Author: Judy.K.Henderson <[email protected]>
Date:   Mon Jan 29 18:05:45 2024 +0000

     Add GSL diag tables to parm/ufs/fv3

     Update GSL template for hera

     Create EMC and GSL versions of files under workflow/rocoto
      - tasks.py, workflow_tasks.py

commit af47b77c7ee59a11c798995b4362b57e9096b090
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 02:07:43 2024 +0000

     Create GSL version of archive script

commit 529d9f71f97b6e643e76a53bc9871901ae861faf
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 01:37:09 2024 +0000

     Create GSL version of tracker.sh

     - this is a placeholder with changes from last year's HFIP experiment; will likely need to be updated in the future

commit 8457e12c313bee602265b863129734354b019271
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 01:27:42 2024 +0000

     Link config.base.emc.dyn_hera to config.base.emc.dyn

commit 7a05f5bd947944d8c3be828aeef9cc03bf9e073a
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 01:22:54 2024 +0000

     Create GSL version of hpssarch_gen.sh

     - assume we only run cold starts
     - archive only 0p25 grib2 files (no 0p50 opr 1p00)
     - assume no pgrb2b or flux files are created so no need to archive to HPSS

commit 98f5d6b16437e2a340bf16f83187e389a53f8bf0
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 00:24:06 2024 +0000

     Update workflow directory

     - add GSL template for jet (based on last year's experiment)
     - create EMC and GSL versions of yaml files under hosts; defaults point to GSL files

commit 38a7e5629ceeb23d399643a021e9a0a88468a07c
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 25 18:40:37 2024 +0000

     Update atmos_products configuration file for GSL

       - set downset to 1 so pgrb2b files are not created
       - set FLXGF to "NO" so interpolated sflux.1p00 files are not created

commit fe8a953658d092ce2b597e14f31678624606fd8a
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 25 17:02:25 2024 +0000

     Update nodes for gfsfcst task in GSL template for hera to match default configuration in config.ufs
       (12x12, 2 threads, 1 write group, 40 write tasks ==> 56 nodes)

     Increase walltime to 4:10 for gfsfcst task

commit 9d85b0f6d50e8ed142557fcb87c89d2e5d63c617
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 23 19:08:52 2024 +0000

     Added default location for PTMP/STMP in workflow/hosts/hera.yaml

     Added GSL XML template for hera

commit 1cf317d327fae78c5469712c9e5a6aa1ffa4b23b
Author: Judy.K.Henderson <[email protected]>
Date:   Wed Jan 17 22:33:13 2024 +0000

     Add sjet partition

     Make syntax consistent in "if" statements in config.resources

commit 2755e203751f50113849b06769173285e093290b
Author: Judy.K.Henderson <[email protected]>
Date:   Wed Jan 17 22:32:26 2024 +0000

      Update configuration files for GSL

     - create Hera and Jet versions of config.base.emc.dyn
     - correct typo in config.fcst
     - create different versions of config.ufs;
       default is 12x12, 2 threads, 1 write group/40 write tasks (56 nodes)

commit 3c0c126a376af31866a93aef4cdd0b4145150c58
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 16 17:32:25 2024 +0000

     Add script for remapping 1/4 degree grib2 grids to other domains

commit f217d4ed9a500e9a1bdcc17548729d972a1763ac
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 16 16:46:25 2024 +0000

     Update link script for ufs_utils.fd

commit 5b21b31900955013b4e8106d3ae906b9da93b361
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 16 16:45:25 2024 +0000

     Add GSL archive scripts for initial conditions

commit abb88baf9dd536a3b2ea1e24eaa99cbfe85af799
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 16 16:42:17 2024 +0000

     Move configuration files for getic and init from jobs/rocoto to parm/config/gfs

commit 45b235180719ab79d2514f0317207fbebfb8aedd
Author: Judy.K.Henderson <[email protected]>
Date:   Sun Jan 14 03:21:15 2024 +0000

     Add suite definition file for v17p8_ugwpv1_c3 to sorc/ufs_model.fd_gsl

commit 147b1fce99254dcb602c333cc559feaa9a396e81
Author: Judy.K.Henderson <[email protected]>
Date:   Sun Jan 14 01:57:22 2024 +0000

     Add getic and init tasks to workflow to create initial conditions in realtime

commit 4e4e50803d95566e1c7967cf4cfa575391d77f25
Author: Judy.K.Henderson <[email protected]>
Date:   Fri Jan 12 00:44:59 2024 +0000

     Change default HPSS_PROJECT to fim

     Change restart_interval_gfs to -1 so no files are written ro RERUN_RESTART directory

commit 791d7a27c6b12f07d9c12ce491338e3da59eb1d8
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 11 23:34:36 2024 +0000

     Add namelist parameter, nord_tr, for GSL suites

commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 11 23:31:22 2024 +0000

     Add changes for running v17p8_mynn

     - new field table, field_table_thompson_aero_tke_progsigma
     - updated namelist parameters in config.fcst

commit 982a1f02e3b880be43f4ae8a3f0ffbb34c056aea
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 02:26:22 2024 +0000

     Add experiment setup script for p8_ugwpv1

commit c5a3697d22fdbb02bb80ddffee2629dddc10c702
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 02:19:13 2024 +0000

     Add memory report to srun command in env/HERA.env

commit ece7e516ca65ec0240899e7d84321310a6887595
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 02:13:42 2024 +0000

     Updated GSL-specific files under ufs_utils.fd_gsl

commit 1b153fc95b93a16eb40b791be7322100fde4a3d4
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 01:52:56 2024 +0000

     Create new branch, gsl_ufs_dev, from dev_02jan24_9d901db

     Add initial GSL modifications
      - changes to workflow files
        * GSL paths, projects, entities
      - new FV3_GFS_v17_p8_ugwpv1_mynn suite definition file (SDF)
      - updated namelist parameters in ush/parsing_namelists_FV3.sh
      - create new GSL directories: ufs_model.fd_gsl and ufs_utils.fd_gsl
        * new SDFs, add instantaneous flux variables to grib2 configuration files
        * add Thompson tracers to initial conditions
      - new sync script: rsync_gsl.sh
      - new job files:  getic.sh, makeinit_link.sh
      - modify build_ufs.sh to include MYNN SDF

commit 9d901dbbff4d41586580316bdc094d24760119e6
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Jan 2 10:30:33 2024 -0700

    Stop Gempak pgrb2 spec from modifying $DATA (#2147)

    This PR addresses issue #1224. The following is accomplished:

    - Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time;
    - Shell linter exceptions are addressed accordingly;
    - The respective GEMPAK tasks is added to the Rocoto mesh.

    Resolves #1224

commit 31ad23527802f7d07171132cc620f7135c4d8cba
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Jan 2 10:27:30 2024 -0700

    Reorganize NPOESS scripts (#2166)

    This PR addresses issue #1226. The following is accomplished:

    - Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure
    of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated;
    - Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh`
    are moved accordingly; this specifically applies to the environment variable `FHOUR`,
    `SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`;
    - The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level
    (if necessary);
    - Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however,
    this may not be necessary (see `TODO` note within draft PR.

    Resolves #1226

commit 22bd82fa93b49e5ce98eb3f69123956dd5018049
Author: Kate Friedman <[email protected]>
Date:   Tue Jan 2 11:55:03 2024 -0500

    Orog fix file reorg and fix directory variable standardization (#2181)

    This PR makes updates to use the newly reorganized `orog/20231027`
    fix file version and standardizes the fix file directory variables.

    Changes:

    1. Update UFS_UTILS hash to ce385ce
    2. Update fix file version file to use new orog timestamp: `orog_ver=20231027`
    3. Add ".mx$(OCNRES)" to `oro_data` filenames in scripts
    4. Remove ".mx$(ocn_res)_frac" from the directory names for atmosphere
    resolutions under the `/orog` folder
    5. Adds fix file directory variables to `config.base`, many of which are pulled
    up out of lower scripts; introduce `FIXcpl`
    6. Renamed/replaced the following fix file directory variables:

    - `FV3JEDI_FIX` --> `FIXgdas`
    - `FIXfv3`, `FIX_orog` and `OROFIX` --> `FIXorog`
    - `FIX_ugwd` and `OROFIX_ugwd` --> `FIXugwd`
    - `FIX_am`, `FIXgsm`, `FIXSYND` --> `FIXam`
    - `FIX_lut` --> `FIXlut`
    - `FIX_aer` --> `FIXaer`
    - `FIX_SFC` --> `FIXsfc`
    - `FIX_DIR` --> `FIXgfs`
    - `RTMFIX` and `FIXCRTM` --> `CRTM_FIX` (is `CRTM_FIX` in crtm module,
    so not using `FIXcrtm`)

    7. Correct the defaults for `FIXwave` in wave JJOB scripts
    8. Update variable names in `*fixed_files.yaml` files, as well as update naming
    convention for `oro_data` files

    Resolves #1984
    Resolves #1981
    Resolves #2175

commit 03d03bf53b43914a55c384cb33eb06f6a9a443a6
Author: Andrew Collard <[email protected]>
Date:   Tue Jan 2 11:53:44 2024 -0500

    Remove HIRS from GSI processing (#2183)

    With the update to CRTM 2.4.0.1, an issue with versioning of CRTM HIRS
    files has been exposed. This is documented in JCSDA/crtm#42.

    As HIRS radiances are no longer used in the GSI, these data should be removed
    from processing until a suitable update to CRTM is available.

    Resolves #2182

commit a3c50998d35525a39a66d5592fbf327ab3569e8b
Author: Jessica Meixner <[email protected]>
Date:   Fri Dec 22 18:07:48 2023 -0500

    Update ufs-weather-model version  (#2186)

    * update model to latest version which includes needed bugfixes for HR3

commit 774c7302e618370ef578bec3ccabc70486d6da1b
Author: David Huber <[email protected]>
Date:   Fri Dec 22 11:34:53 2023 -0500

    Fix analysis post processing's handling of 0-padded negative integers (#2187)

    This screens for the analysis 'forecast' hour (-001) and handles the '-' and circumvents octal issues.

commit d1251360325faf75af9df0608557fcd10202a883
Author: Barry Baker <[email protected]>
Date:   Thu Dec 21 11:23:48 2023 -0500

    Fix for restoring cycling aerosols in fo-mode post COM refactor (#2179)

    - Update to COM reorg aerosol initialization job
    - Address bug in joining paths for data dependency in this job

    ---------

    Co-authored-by: Rahul Mahajan <[email protected]>

commit e55a05980709288d902ad1bd894164bfa5a18a65
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Dec 20 22:14:01 2023 -0500

    Stop calling ufs-utils link script (#2172)

    The `link_workflow.sh` script was calling the ufs_utils version of the
    same. That step is only necessary if a user is going to run one of the
    stand-alone ufs-utils, which is rare.

commit ef3e5ad7c63be1644c82333c95853c3caf2d8995
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Dec 19 22:02:55 2023 -0500

    Fix handling of excluded hosts list (#2170)

    This PR fixes the issue with `create_experment.py` so that the yaml configuration
    file can have a string of list of strings when specifying the host name to exclude
    from the CI tests.

commit ea74a5719efc8f0fe631c5ff93426a4299a614f3
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Tue Dec 19 16:21:41 2023 -0500

    Add COMOUT_OBS to marine obs prep (#2173)

    Adds `COMOUT_OBS` (defined from `COM_OBS_TMPL`) to marine obs prep task to properly handle marine obs prep files. Used to keep obs after IODA conversion, QC, and other prep.

    Towards resolving NOAA-EMC/GDASApp#815

commit c2500feace0bb7c04ce67a90dd3182120ee67b2e
Author: David Huber <[email protected]>
Date:   Tue Dec 19 14:55:20 2023 -0500

    Return failed status if a build fails. (#2171)

    If any of the builds fail, this makes build_all.sh return the sum of the error codes encountered.

    Fixes #2168

commit 76fdd81cd84ed812181996a102379d8d964ba27a
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 19 13:24:34 2023 -0500

    Update index.rst for new GFSv16.3.12 in ops (#2169)

    Refs #2096

commit a81da33e8fe7541a36f68e7a4f14a384cadd36c8
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 19 10:22:21 2023 -0500

    Set place=shared for shared jobs on WCOSS2 (develop) (#2156)

    Set job as shared when not exclusive on WCOSS2

    WCOSS2 defaults to exclusive when it is not specified as
    either exclusive (place=exclhost) or shared (place=shared).
    Now set shared when job should be shared.

    Refs #2135

commit 89aea972f7964dac3f515e8070d7c534812c5fb4
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Dec 15 16:31:06 2023 -0500

    Update gfs-utils version for Hercules (#2163)

    An update of gfs-utils was misssing from the previous PR that added
    initial Hercules support (#2128).

    Also includes gfs-utils update for new marine post.

commit 9505cb4abc6ca2643a8ab254d14ca2000747fa44
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Dec 14 16:15:31 2023 -0500

    CI Updates to support Hercules (#2155)

    If merged, this PR will update the CI scripts so they will run on Hercules for forecast only
    NOTE: This is a stop gap to issue #2131 until its block on #1588 is removed.

    Resolves #2154

commit c5ca82f04a2efae78389dec1c46b94ef4fb5bbe5
Author: Rahul Mahajan <[email protected]>
Date:   Thu Dec 14 16:05:33 2023 -0500

    Correct fbwind (#2161)

commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a
Author: Kate Friedman <[email protected]>
Date:   Thu Dec 14 12:06:23 2023 -0500

    Add MOS jobs to rocoto mesh (#2148)

    Create separate jobs for GFS MOS - extracted from now-retired vrfy job

    Refs #2068

commit bb6151aa50c27253cb9b8f0a6601ddd58526b8b3
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Dec 14 05:38:29 2023 -0500

    Replace checkout script with submodules (#2142)

    Replaces the checkout script with git submodules. This change brings workflow in
    line with other repos and git standards.

    Due to these changes, the build system is updated slightly. First, the options that
    were formerly used with `checkout.sh` to reduce unneeded builds (`-g` for GSI
    and `-u` for UFSDA) are moved to `build_all.sh` instead. This is needed since build
    all will not be able to key off directories existing or not to determine which com-
    ponents to build. Second, the partial build system is removed. It was rarely, if ever,
    used, and parts of it were already ignored with the previous changes to base builds
    off whether directories exist. The manage externals file is also removed since that is
    also not being used.

    Following these changes, clones/checkout will need to either be recursive, or
    `git submodule update` will need to be called separately to make sure components
    are properly checked out (non-exhaustive list):

    ```
    ## Checkout develop (method 1)
    git clone --recursive https://github.com/NOAA-EMC/global-workflow destination

    ## Checkout develop (method 2)
    git clone  --jobs 8 https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git submodule update --init --recursive --jobs 8

    ## Checkout existing branch some_branch (method 1)
    git clone --recursive  --jobs 8 -b some_branch https://github.com/NOAA-EMC/global-workflow destination

    ## Checkout existing branch some_branch (method 2)
    git clone https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git checkout --recurse-submodules some_branch

    ## Checkout existing branch some_branch (method 3)
    git clone https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git checkout some_branch
    git submodule update --init --recursive  --jobs 8

    ## Checkout new branch new_branch
    git clone https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git checkout -b new_branch
    git submodule update --init --recursive  --jobs 8
    ```

    The git ignore list had to be updated to use explicit paths as the wildcard paths pick
    up the ones that are now submodules.

    UFS creates files during the build process that are not in its ignore list, so that sub-
    module ignores the "dirty" state to avoid confusing users running `git status`.

    CI and documentation are also updated to reflect the changes.

    Resolves #2141

commit 1332188ce2409e012ec127d44880e49732f7f379
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Dec 13 09:32:57 2023 -0500

    Enable radar reflectivity output (#2143)

    Turns on radar reflectivity output from FV3. This eliminates missing values appearing in the grib2 files.

commit 24d898ec0ec0c7fcbda6966988f9a986f528ed14
Author: David Huber <[email protected]>
Date:   Wed Dec 13 09:32:24 2023 -0500

    Fix Hercules hostname (#2150)

    * Allow lower or upper hostname on hercules.
    * Add Hercules to issue template.

commit 2896bb8787698be28ad20f2298589e6e95eaf9fb
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 12 09:13:06 2023 -0500

    Fix module load typo (#2145)

    Fix typo with loading the crtm module in the UPP hack for WCOSS2

    Refs #2144

commit 29d34172a67d976f910e78158ff0337e1ef099ca
Author: Cory Martin <[email protected]>
Date:   Thu Dec 7 15:12:05 2023 -0500

    Update GDAS hash to most recent stable versions (#2138)

commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Dec 7 10:41:05 2023 -0700

    Corrected typo in a gempak job gempakncdcupapgif . (#2137)

commit 3483f550db1ae35a680de49f7485ce5a11902dd9
Author: Cory Martin <[email protected]>
Date:   Thu Dec 7 12:34:56 2023 -0500

    Add support for FGAT and IAU for aerosol DA (#1940)

commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9
Author: David Huber <[email protected]>
Date:   Thu Dec 7 12:33:46 2023 -0500

    Enable forecast-only experiments on Hercules (#2128)

    This add forecast-only support for Hercules to the global workflow. Partially satisfies #1588.
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

commit a29f751aed05312da3d80d396159bb5a906d6ce4
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Dec 6 13:45:56 2023 -0700

    Adds GEMPAK and related jobs to rocoto task mesh (#2127)

commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082
Author: Rahul Mahajan <[email protected]>
Date:   Tue Dec 5 15:47:52 2023 -0500

    Separate offline UPP from interpolated grib2 product generation (#2110)

    This PR:
    - Replaces the use of  `JGLOBAL_ATMOS_POST` with `JGLOBAL_ATMOS_UPP`
    and `JGLOBAL_ATMOS_PRODUCTS`.
    - Introduces `JGLOBAL_ATMOS_PRODUCTS` that is responsible for creating
    grib2 products from the master file produced by UPP (inline from the model,
    or offline by running `JGLOBAL_ATMOS_UPP`).  Rocoto job `atmos_products.sh`,
    ex-script `exglobal_atmos_products.sh` are also added along with a
    `config.atmos_products`. Updates are made to the relevant `env` files as well as
    `config.resources` to reflect the addition of this job.
    - reduces the number of cores needed appropriately for forecast products when
    there is no offline UPP necessary.
    - renames older `fv3gfs_dwn_nems.sh` to `interp_atmos_master.sh` and
    `inter_flux.sh` to `interp_atmos_sflux.sh`
    - removes `fv3gfs_downstream_nems.sh` as it is absorbed into
    `exglobal_atmos_products.sh`
    - removes no longer used scripts for `gfs_post.sh`, `gfs_transfer.sh` (DBN alerts
    are absorbed into `exglobal_atmos_products.sh`), `post.sh`,
    `JGLOBAL_ATMOS_POST`, `ex${RUN}_atmos_post.sh` scripts.
    - Rocoto workflow related scripts are updated to add `atmos_products` as a job.
    When `WRITE_DOPOST` is `.false.`, `upp.sh` job to run the UPP offline is also
    added.  Dependencies have been appropriately applied.
    - removes `PGB1F` option that creates 1-degree grib1 products that are no longer
    needed in GFSv17.

    The hacks from (now deleted) `post.sh` had to be reinstated in `upp.sh` to load the
    modules from UPP instead of `load_fv3gfs_modules.sh`.

commit 44186f594aaf5f8feea0eadd4c5c3b59de3a825e
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 5 12:28:08 2023 -0500

    Update index.rst for new GFSv16.3.11 version (#2121)

    Refs #1356

commit e62a3a73cd22701962b7bf210fdfee37f37a5474
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Dec 5 09:08:12 2023 -0700

    Splits AWIPS jobs into seperate tasks (#2094)

    This PR addresses issue #1228. The following is accomplished:

    - Separate rocoto jobs have been created beneath `jobs/rocoto/`
    -- `awips_20sh` and `awips_g2sh`; these jobs replace `awips.sh` which was
    calling multiple J-jobs within the respective `awips.sh` scripts;
    - New tasks has been added to `workflow/rocoto/tasks.py` for the new
    AWIPS scripts;
    - The `gfs_cycled` and `gfs_forecast_only` modules beneath
    `workflow/rocoto` have been updated accordingly.

      Resolves #1228

commit 04d97e9aa7ab84b9754ab670074cfb19d543aa26
Author: Kate Friedman <[email protected]>
Date:   Mon Dec 4 13:38:30 2023 -0500

    Consolidate VMINMON and cleanup monitor scripts (#2088)

    This PR combines the GDAS and GFS versions of the VMINMON JJOB
    and ex-driver scripts into single GLOBAL/global versions. Additionally:

    * some further cleanup of the GSI-Monitor scripts is done; variable
    settings in ex-driver scripts are moved up to the JJOB level
    * the fix symlinks are consolidated into a new `fix/mon` subfolder (formerly
    `fix/gdas`) and copies of the gfs monitor fix files under `fix/products` are
    removed

    Resolves #1925

commit a286a11fdcbc31c8bc6d944890bc56294bc8caf6
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Dec 4 17:48:44 2023 +0000

    Robust CI Restarts (#2093)

    Improved CI robustness for reverting back to **CI-Ready** from any
    given state

    New Features:

    - Improved `scancel` routine (refactored into bash "subroutine")
    - Improved messaging (see below) when ever a user changes state
    - Any and all previous build scripts and running experiments are killed as
    a result of reset to **Ready**

    Resolves #2060

commit 73621e9b20b20f85e8b21e4c1e09ed1d80ecd46f
Author: David Huber <[email protected]>
Date:   Sun Dec 3 11:19:19 2023 -0500

    Upgrade to spack-stack/1.5.1 and Intel 2022 on non-production machines (#2084)

    Update module files to spack-stack/1.5.1 and compilers to Intel 2022+ on all non-production machines.

commit 6d548b250688861eb20a7e0dc852a0e4ba9e64f4
Author: jiandewang <[email protected]>
Date:   Thu Nov 30 12:00:21 2023 -0500

    Add variable tob in diag_table for ocean model output(#2105)

commit c19810cce252fcdb25fd9960c05b08b5f8d8b1ad
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Wed Nov 29 15:17:36 2023 -0500

    Added variables to config.prepoceanobs (#2101)

commit c2d78a61a224678fb804eed19f39d1f07408ae5f
Author: Kate Friedman <[email protected]>
Date:   Wed Nov 29 12:39:08 2023 -0500

    Add missing cut to VDATE setting in JGFS_ATMOS_VERIFICATION (#2098)

    Refs #2097

commit c1c025f91ddac73aea595cc9fa4dd0bea80575fc
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Nov 29 17:15:10 2023 +0000

    Add wave init to GEFS (#2089)

    Adds the wave init job to GEFS. Since the output would be the same for
    every member, the job is only run once for the control, then links are
    created in each of the member directories pointing to that copy.

    New ww3_multi and ww3_shell templates for GEFS are copied from the
    GFS versions.

    The GEFS restart frequency is changed to not be zero, and the comment
    about not setting it to zero is copied from the gfs config.base. The restart
    interval for the GEFS perturbed members is changed to equal that of the
    control.

    Also fixes a bug where `RUNwave` was not defined for ensemble forecasts,
    and another bug in the GEFS stage_ic dependency.

    Resolves #2017

commit 64a2470ce29b7d8d5cb85ebcb4048ff82958f64e
Author: Kate Friedman <[email protected]>
Date:   Wed Nov 29 11:26:34 2023 -0500

    Adjust permissions for jobs/JGFS_ATMOS_VERIFICATION (#2095)

    Add execute permissions (755)

commit 964b77bc6de67291973c2c70598a1f8cb72501c5
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Nov 28 18:45:51 2023 +0000

    Make proper j-job for MET+ (#2090)

    Creates a proper j-job for the metp job, moving much of the material
    from the `jobs/rocoto` script there (some of it within `jjob_header`).

    Also updates the old `COMIN` variable for the COM refactor (although
    it does not appear used in the verify scripts currently).

    This is a partial step towards restoring/improving metp functionality
    and remains untested.

    Refs #1575

commit 8c11eeb8556619e8db4e0efb6394ce5a2c1aae0f
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Nov 23 10:31:32 2023 -0700

    Adds FBWINDS support to global-workflow (#2082)

    This PR addresses issue #1221. The following was accomplished:

    - A new Rocoto job is added; `jobs/rocoto/fbwinds.sh`;
    - `workflow/applications/gfs_cycled.py` is updated to include the `fbwinds` task;
    - `workflow/applications/gfs_forecast_only.py` is updated to include the `fbwinds` task;
    -  A new function is added to `workflow/rocoto/gfs_tasks.py`, `fbwinds` is added as new GFS (only) task;
    - `workflow/rocoto/tasks.py` is updated to include the `fbwinds` task.

    Resolves #1221

commit 513db190d21f9ede0724a2cd5606372b1d7605de
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Nov 21 22:52:58 2023 -0700

    Adds NPOESS support to global-workflow (#2083)

    This PR addresses issue #1225. The following was accomplished:

    - A new Rocoto job is added; `jobs/rocoto/npoess.sh`;
    - `workflow/applications/gfs_cycled.py` is updated to include the `npoess`
    task;
    - `workflow/applications/gfs_forecast_only.py` is updated to include the
    `npoess` task;
    -  A new function is added to `workflow/rocoto/gfs_tasks.py`, `npoess` is
    added as new GFS (only) task;
    - `workflow/rocoto/tasks.py` is updated to include the `npoess` task.

    Resolves #1225

commit 62d8e99e77ffe44784f4c61c3f2296c6d1a72413
Author: Kate Friedman <[email protected]>
Date:   Fri Nov 17 20:25:50 2023 -0500

    Retire vrfy job (#2080)

    Retires the `vrfy` job from the global-workflow system. All associated
    scripts, configs, and references to the job are removed.

    Additionally, the switches listed in RTD were updated to reflect new
    ones added in other PRs for issue #235.

    Resolves #2069
    Refs #235

commit ea386abf11ecbacef407388e8d57e71b30148a35
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Nov 17 23:59:46 2023 +0000

    Enable different coupled settings for ensemble (#2030)

    Adds the ability to turn off some coupled components for the ensemble.

    To enable this, many settings are moved out of `config.fcst` and into `config.ufs`
    so they are calculated after any overrides of `DO_*` have been made. Some
    settings also had to be moved out of `config.base` for the same reason. A
    switch to turn on gocart is added to `config.ufs`, but unlike the other switches
    this one takes no arguments.

    The name of the ufs configure template used is converted from a partial file
    name to the full file name.

    Resolves #1692

commit fe792c0c9a1c46908cbd18c7e71eb836974cf1de
Author: Kate Friedman <[email protected]>
Date:   Fri Nov 17 17:19:16 2023 -0500

    Add --cpus-per-task to srun commands for Hera and Orion (#2077)

    This PR adds the `--cpus-per-task` flag to non-CFP `APRUN`/srun commands
    in the env files for Orion and Hera. This is needed as a result of an upgrade
    to SLURM on Orion that no longer exported the thread value to the
    environment. Issue #1996 was a hotfix to add this flag for the analysis job
    that was suddenly running slowly after the SLURM upgrade. A similar SLURM
    upgrade was done on Hera but the sysadmins there implemented a
    workaround so this issue did not appear there.

    This PR adds the `--cpus-per-task` flag for both machines...needed on Orion
    and as a safety measure on Hera.

    Also included in this PR is a fix to indentations in the
    `scripts/exglobal_diag.sh` script that was noticed during work for this PR.

    Timing differences were not observed for other jobs after adding this srun
    flag. Job timings were of a similar variation between control and test runs.
    Any potential additional speedup was not observed. The test runs also
    reproduced the control runs with `develop`.

    Resolves #2044

commit 42c943be305c297a56b104bb50727938c1ba688f
Author: Kate Friedman <[email protected]>
Date:   Fri Nov 17 15:41:34 2023 -0500

    Adjust modules in post.sh for WCOSS2 (#2079)

    On WCOSS2 the grib_util module is named a bit different and
    needs the libjpeg module loaded beforehand.

commit cd4e6a1987e7fd71dff06766f540b5d32c8b648d
Author: Jessica Meixner <[email protected]>
Date:   Fri Nov 17 11:49:32 2023 -0500

    Update ufs-weather-model and remove upp hack (#2071)

    Updates the model to the most recent commit of ufs-weather-model.  This
    should allow for the removal of the UPP hack that was added in PR #2042

    This required changing nems.configure -> ufs.configure.

    Resolves #1942

commit 5a2d97e142aa4999b122fd5a130c63e59ea9f8e2
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Nov 16 22:15:53 2023 +0000

    Fix check for existence of preamble functions (#2066)

    A few of the setup scripts were checking for the existence of
    functions set by the preamble before calling them so they could
    also be used stand-alone. However, the `type` command returns `1`
    if the function name does not exist, which will cause the script
    to die is `set -e` is on. Now the `type` command fails over to an
    empty string.

commit ed2ee7c2b1457b71b271a2c40f0dfa356e0f52f8
Author: WenMeng-NOAA <[email protected]>
Date:   Thu Nov 16 16:38:11 2023 -0500

    Update UPP products for GFS v17 (#1973)

    Updates of generating GFS V17 UPP products to support HR3:

    - Update g2tmpl to 1.0.12
    - Add changes to launch cfp on WCOSS2 to generate pgrb2/pgrb2b files
    - Changes for generating new products (MERRA2, six winter weather variables,
    1km HLCY, SDEN) in pgrb2 files

    Resolves #1965
    Resolves #1994

commit 635c4719e603538ce7cccf9ea6b31f3f84f20849
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Nov 16 20:35:30 2023 +0000

    Fix some rocoto dependencies (#2074)

    A few small errors/cleanup in the dependencies, mostly in fcst:

    A few small errors/cleanup have crept into the dependencies with recent changes,
    mostly in fcst:

    - Fixed the offset, as it would yield a string rocoto doesn't recognize when the
    interval was 24+ hrs
    - Removed the duplicate wave dependency. When `waveprep` is included, it
    depends on `waveinit` so there is no need to add a `waveinit` dependency.
    - Converted an interval in the archive job that was missed in #2039

    Resolves #2075

commit d4c7508260975c6b94fc92fd085f39d4faf3f027
Author: Rahul Mahajan <[email protected]>
Date:   Wed Nov 15 16:44:03 2023 -0500

    Fix missing _PREV in ocean restart file location (#2070)

commit 255616d37505c785bdddd5d3e39e8399110b626e
Author: mdtoyNOAA <[email protected]>
Date:   Wed Nov 15 12:02:09 2023 -0700

    Update functionality for Prototype HR3 UGWP (#1987)

    This PR adds/modifies namelist options and activates new 'ccpp' suite definition
    files for the updated Unified Gravity Wave Physics (UGWP) in the ufs-weather-
    model recently updated for HR3.  The changes to UGWP are the use of the GSL
    drag suite for orographic gravity wave drag (GWD) and blocking, as well as the
    new UGWP Version 1 non-stationary GWD.  See
    ufs-community/ufs-weather-model#1923 for details.

    Resolves #1986

commit be9085e62aae147e3c74602e2f82a99b374fc783
Author: Guillaume Vernieres <[email protected]>
Date:   Wed Nov 15 13:48:58 2023 -0500

    Save the required CICE history for the sea-ice DA (#2062)

    The hist_avg setting of CICE was changed to be an array.

commit 85f1f5131ffd70061231304ea477bde0559eb67b
Author: Guoqing Ge <[email protected]>
Date:   Wed Nov 15 11:47:21 2023 -0700

    Use assim_freq to configure "offset" in dependencies (#2039)

    Use the assim_freq from config.base to configure "offset" in dependencies
    instead of hard-coding them.

    Resolves #2038

commit 4e3d82ba3a1fa7cdd4443bcd4cf83b2f8835137c
Author: Kate Friedman <[email protected]>
Date:   Wed Nov 15 13:39:14 2023 -0500

    Resolve ENKF archive script bugs (#2065)

    Fix two bugs in the exgdas_enkf_earc.sh script:

    1) Replace ARCH_LIST with DATA to match changes done in PR #2000
    and update path to generated archive list files.
    2) Add status check and exit after script attempts to make tarball on HPSS.

    Refs #2064

commit 42d7f2f0c48fab898b764e09cfbbd7a9fabbae08
Author: Kate Friedman <[email protected]>
Date:   Tue Nov 14 17:54:29 2023 -0500

    Separate tracker and genesis jobs from vrfy job (#2058)

    This PR creates new individual jobs for the tracker and genesis jobs that are being
    pulled out of the `vrfy` job (issue #235). The `tracker` and `genesis` jobs will be on
    by default while the `genesis_fsu` job will be off by default. This mimics the current
    settings in the `vrfy` job.

    No enhancements or upgrades are made to the jobs themselves in this PR, only to
    separate them from the `vrfy` job. However, one change compared to how they
    currently run in the `vrfy` job is to no longer run the `tracker` in the gdas suite. This
    mimics how the `ens_tracker` package is run in operations (gfs only).

    Changes in this PR:

    1. Create rocoto job scripts for tracker/genesis jobs.
    2. Create configs for tracker/genesis jobs, as well as `config.tropcy` for shared
    settings.
    3. Add tracker/genesis jobs to `config.resources`; use resources from the ecf scripts
    for `ens_tracker` jobs in operations
    4. Add tracker/genesis jobs to rocoto setup for both cycled and forecast-only
    modes.
    5. Update arguments for `jjob_header.sh` script in tracker/genesis JJOB scripts to use
    specific job names and configs instead of vrfy.
    6. Rename `tracker_ver` to `ens_tracker_ver` in version files to mimic variable within
    tracker package.
    7. Rename and move tracker/genesis switches to `config.base`.
    8. Remove tracker/genesis jobs from `vrfy` job (`jobs/rocoto/vrfy` and `config.vrfy`).
    9. Reduce vrfy job resources to accommodate tasks having been removed.

    Refs #235
    Resolves #1988
    Resolves #2048

commit 0a0d6984e094d2a551d5d8331102142e7db13fc2
Author: Rahul Mahajan <[email protected]>
Date:   Tue Nov 14 14:08:26 2023 -0500

    Enable warm starting of the model for forecast-only mode (#2031)

    This PR:
    - adds an option to warm|cold start the ufs-weather-model when setting up an experiment for GFS/GEFS
    - adds the capability to stage FV3 restarts when the atmosphere is warm started from FV3 restarts. This would be used in the GEFS free-forecast for part of the reforecast capability.
    - If a coupled model is warm started for the atmosphere, also check if mediator restarts are present. If so, stage mediator restarts to allow restarting the coupled model.

    Fixes #2016

commit 2cd6a589305a9ac9d3a9a0d2136e66e42f09d3bf
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Nov 14 12:05:20 2023 -0700

    Moves UFS WM configuration files to `COM_CONF` (#2054)

    The UFS weather-model (WM) files are place in the COM_CONF path rather than the respective component model COM history paths.
    Resolves #2015

commit 6f1693081662f241fafc930b1afc88125f7f5aff
Author: Kate Friedman <[email protected]>
Date:   Tue Nov 14 11:15:02 2023 -0500

    Refine fit2obs job in rocoto mesh (#2047)

    This PR adjusts the `fit2obs` job in the rocoto mesh to better define when it exists
    and how the archive job dependencies accommodate it not being in the first half
    cycle.

    Changes in PR:

    1. Remove the `fit2obs` job from the first half cycle `cycledef`.
    2. Adjust the archive job dependencies to now include the `fit2obs` job in the new
    logic check added in PR #1983. The `gdasarch` job in the first half cycle will check if
    `gdasfit2obs` is complete OR no prior cycle exists. Also cleaned up this new logic
    check block some to make it a tad simpler.
    3. Also, fix the addition of the `fit2obs` config to the config list in setup scripts. Now
    tied to whether `fit2obs` job is on instead of always adding the config to the list.

    Resolves #2043

commit 5730a71fa5d311e49d9bb11528b500f27f33d69d
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Nov 14 09:13:11 2023 -0700

    Add `waveinit` and `waveprep` to half-cycle. (#2037)

    This PR addresses issue #1444. The `waveinit` and `waveprep` tasks have been added to
    the GDAS have cycle. The downstream dependencies for the respective GFS and GDAS
    forecast tasks have been removed.

    Resolves #1444

commit 28d2e93c3857de95b0309a089cd7dac736ccaded
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Nov 14 16:11:47 2023 +0000

    Update wave IC source for C384 (#2055)

    The default wave grid for C384 has changed since P8, so a single wave
    IC on the new grid is available under a different IC name.

commit 81dd2d9855091315611106a5afbdaeaa15e6e4ae
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Nov 9 17:19:57 2023 +0000

    Fix analysis and post on Orion (#2046)

    Fixes a couple things to get workflow to work on Orion again:

    First, while #2042 allowed post to be built, the `upp.x` executable would fail due
    to a missing library. Now post jobs (temporarily) uses the UPP modules (plus
    others needed for runtime) instead of the normal workflow runtime module. This
    should actually fix #2041. This hack can likely be removed once we move to
    spack-stack.

    Second, the launcher command for the analysis jobs on Orion are updated to
    specify the number of CPUs per task. This was necessary as a recent slurm update
    on Orion discontinued reading that value from the scheduler. Other jobs will be
    handled later (see #2044).

    Additionally, a change is made to `module-setup.sh` that will eliminate the
    annoyance of `gw_setup.sh` breaking tab completion because undefined variable
    checking was turned on for the script but not back off.

    Resolves #1996
    Resolves #2041
    Refs #2044

commit 13d06ded4155cba2d08ef2a2cd553024c5abe29d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Nov 8 18:25:47 2023 +0000

    Hack UPP version (#2042)

    The stack UPP was using on Orion was recently deleted, leaving us
    unable to build the UFS verison of UPP there. UPP has an updated
    version using spack-stack that works, so the checkout script is
    modified to check out that version of UPP after UFS has been
    checked out.

    This temporary hack can be removed once we move to a UFS version
    that advances the UPP version to or beyond 78f369b.

    Resolves #2041

commit 20f6eceb8ff58f84174a27eb849c1d74566a3e03
Author: jiandewang <[email protected]>
Date:   Wed Nov 8 11:14:55 2023 -0500

    Add basic C1152 settings (#2020)

    Adding C1152 setting in host.yaml, config.base and config.stage_ic so that can run C1152 S2SW.

    Resolves #2019

commit 5183c43bbbd07285869feacb49d8680afe85929a
Author: Barry Baker <[email protected]>
Date:   Tue Nov 7 01:14:40 2023 -0500

    Update UFS for dust fix and remove nitrates by default  (#1989)

    This PR updates the `ufs-weather-model` to the latest hash that included the dust fix (PR #1922).
    Along with this I removed the nitrates by default in support of the GEFSv13 EP4 and EP5
    experiments. Removed unneeded inputs that should help with speed improvements.

commit 34a73cf2ed5afefc776d9cc73b6ebf439122a1bb
Author: David Huber <[email protected]>
Date:   Mon Nov 6 14:00:51 2023 -0500

    Reduce gdas builds to 8 #2029 (#2036)

    Reduce the default number of build jobs for the GDASApp to 8 from 16.

    This is needed for Orion as the build crashes during a linking step.  Though not verified, it
    appears this may be caused by using too much memory with 16 builds.  The issue disappears
    when using 8 build jobs.

    Resolves #2029

commit 75269e4bb9764b81589efc7d703825b80e74c8f5
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Nov 6 17:34:47 2023 +0000

    Streamline CI reporting to PRs (#2026)

    Cleaned up the logs for CI PRs sent to the GitHub Messages:

    - Eliminates redundant accumulative reporting
    - Reports on all created or skipped experiment instantiations in a single message
    - Gives one line report once  for each experiment completion
    - Single final report completion of CI

    See some examples in forked [PR 195](https://github.com/TerrenceMcGuinness-NOAA/global-workflow/pull/195)

    Resolves #2007

commit 8d55126bb0b27c79c8bee7f72b014abd34950ff9
Author: Guillaume Vernieres <[email protected]>
Date:   Fri Nov 3 17:06:09 2023 -0400

    Implement IAU Cycling Type with Marine Data Assimilation Enabled (#1944)

    Allows cycling in IAU mode with the S2S UFS model, soca and the GSI.

    Most of the work related to making IAU work was done by @JessicaMeixner-NOAA . Thanks @JessicaMeixner-NOAA !

    Resolves #1943
    Refs #1776

commit 2563806821d4ae3b57120bc61aa0575139a708f0
Author: jiandewang <[email protected]>
Date:   Fri Nov 3 11:49:37 2023 -0400

    Add two ucx modules in load_ufswm_modules.sh to solve C768 and C1152 S2SW job hanging issue on WCOSS2 (#2021)

commit cbdc09711a83493f363a737d1e3e46c48a09719d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Nov 3 04:09:33 2023 +0000

    Fix staging of MOM data (#2028)

    During the update to stage_ic, the copying of the additional res_N files for
    0p25 was omitted. These are now properly copied.

    Resolves #2027

commit bd4c56d99c23c5c41f0bd5f8a980ef99ee160888
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Thu Nov 2 16:09:59 2023 -0400

    changed optional script name vars for ocean analysis (#2025)

commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6
Author: Kate Friedman <[email protected]>
Date:   Thu Nov 2 16:01:18 2023 -0400

    Create separate GSI monitor jobs and remove from vrfy job (#1983)

    This PR will move the GSI monitor tasks from the `vrfy` job into their own separate jobs in
    the rocoto mesh. This takes care of part of issue #235.

    Changes in this PR:

    1. Create new individual GSI monitor jobs in the rocoto mesh to match how it is done in
    operations. The new jobs are: `gdasverfozn`, `gdasverfrad`, `gdasvminmon`, and `gfsvminmon`.
    The names correspond to the names in operations and the ecf script names. The jobs are only
    added to cycled mode, none of the jobs are run in forecast-only mode.
    2. Updates to GSI monitor scripts:
      * Update `ush/jjob_header.sh` arguments in JJOB scripts to call new individual job names and
    configs.
      * Introduce `COM_*` variables and use of the `generate_com` utility. This results in the outputs
    landing in `COM` subfolders, like occurs in operations, instead of landing in the online archive.
      * Some variable cleanup in JJOB and ush scripts, includes cleaning up usage of `DATA` variable
    and its removal at the end of the jobs.
      * Add missing exit statements to `JGFS_ATMOS_VMINMON` and `JGDAS_ATMOS_VERFRAD`.
    3. Create new rocoto job scripts for the new individual GSI monitor jobs.
    4. Create new configs for the new individual GSI monitor jobs.
    5. Add new individual GSI monitor jobs to resource configuration, using the same resources as
    in operations.
    6. Move and rename GSI monitor job switches from `config.vrfy` to `config.base`. Also add
    switches to setup system. New switches to control each job being added to the rocoto mesh
    are: `DO_VERFOZN`, `DO_VERFRAD`, `DO_VMINMON`
    7. Add GSI monitor job output to archival job and into resulting HPSS tarballs or local tarballs.
    This now matches what is done in operations.
    8. Remove the GSI monitor tasks from the rocoto `vrfy` job and associated `config.vrfy`.

    Example output locations and files (not showing contents of oznmon/horiz or oznmon/time for
    brevity, see archival script for full list of output files):
    ```
    kate.friedman@dlogin09:/lfs/h2/emc/ptmp/kate.friedman/comrot/testmonitor2> ll gdas.20211221/00/products/atmos/*mon
    gdas.20211221/00/products/atmos/minmon:
    total 112
    -rw-r--r-- 1 kate.friedman emc 14030 Oct 25 15:00 2021122100.costs.txt
    -rw-r--r-- 1 kate.friedman emc 84932 Oct 25 15:00 2021122100.cost_terms.txt
    -rw-r--r-- 1 kate.friedman emc   808 Oct 25 15:00 2021122100.gnorms.ieee_d
    -rw-r--r-- 1 kate.friedman emc   808 Oct 25 15:00 2021122100.reduction.ieee_d
    -rw-r--r-- 1 kate.friedman emc    80 Oct 25 15:00 gnorm_data.txt

    gdas.20211221/00/products/atmos/oznmon:
    total 8
    drwxr-sr-x 2 kate.friedman emc 4096 Oct 25 15:05 horiz
    drwxr-sr-x 2 kate.friedman emc 4096 Oct 25 15:05 time

    gdas.20211221/00/products/atmos/radmon:
    total 21036
    -rw-r--r-- 1 kate.friedman emc      231 Oct 25 15:12 bad_diag.2021122100
    -rw-r--r-- 1 kate.friedman emc     9035 Oct 25 15:12 bad_pen.2021122100
    -rw-r--r-- 1 kate.friedman emc     1449 Oct 25 15:12 low_count.2021122100
    -rw-r--r-- 1 kate.friedman emc 20523403 Oct 25 15:07 radmon_angle.tar.gz
    -rw-r--r-- 1 kate.friedman emc   217272 Oct 25 15:08 radmon_bcoef.tar.gz
    -rw-r--r-- 1 kate.friedman emc   502151 Oct 25 15:10 radmon_bcor.tar.gz
    -rw-r--r-- 1 kate.friedman emc   264480 Oct 25 15:12 radmon_time.tar.gz
    -rw-r--r-- 1 kate.friedman emc      684 Oct 25 15:12 warning.2021122100
    kate.friedman@dlogin09:/lfs/h2/emc/ptmp/kate.friedman/comrot/testmonitor2> ll gfs.20211221/00/products/atmos/minmon/
    total 88
    -rw-r--r-- 1 kate.friedman emc 10530 Oct 25 14:55 2021122100.costs.txt
    -rw-r--r-- 1 kate.friedman emc 63882 Oct 25 14:55 2021122100.cost_terms.txt
    -rw-r--r-- 1 kate.friedman emc   808 Oct 25 14:55 2021122100.gnorms.ieee_d
    -rw-r--r-- 1 kate.friedman emc   608 Oct 25 14:55 2021122100.reduction.ieee_d
    -rw-r--r-- 1 kate.friedman emc    80 Oct 25 14:55 gnorm_data.txt
    ```

    Lingering work and considerations:

    1. Issue #1925
    2. Consider not hardcoding the list of types in archival and perhaps tie it to something reliable or
    configurable (maybe into `config.verfozn`?):
    `subtyplist="gome_metop-b omi_aura ompslp_npp ompsnp_n20 ompsnp_npp ompstc8_n20 ompstc8_npp sbuv2_n19"`

    Resolves #1908

commit 31b05a99b77d0f6eaa8b116485a41a43867d20e1
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Nov 2 12:23:32 2023 -0600

    Move analysis post to new stand-alone task (#1979)

    This PR addresses issue #1130. A new task `postanl.sh` has been added such that the
    `anl` post-processing is not it's own task within the Rocoto workflow. This change
    prevents the GDAS experiment from breaking due to failures caused by the `anl` not
    being available for the first cycle.

    Resolves #1130

commit 247cdf8c7e10e6c98f782799fc51c069b6474e70
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Nov 2 11:18:53 2023 -0600

    Corrects missing local variable reference (#2023)

    Fixes missing `$` in variable reference in archive job.

    Resolves #2022

commit 241742b246da1794646b68e41c3d6fe00b95dd07
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Wed Nov 1 14:19:55 2023 -0400

    Updates to prep ocean obs task (#1870)

commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Nov 1 12:09:33 2023 -0600

    No longer write archive lists COM (#2000)

    Changes the respective `.txt` files used for the HPSS archive to the `DATA` path. Each
    defined text file has been updated to explicitly write to `DATA` rather than `COM` such
    that the files are deleted rather than being archived.

    Resolves #760

commit 517b92f9c20c9e44abba3183325e35a95a7334a5
Author: David Huber <[email protected]>
Date:   Tue Oct 31 16:33:11 2023 -0400

    Parallelize the build scripts (#1998)

    Optimized/parallelized build scripts.

    A few notes:

    1) The default number of build jobs is 20, but one could argue for using 40.  When researching
    this, I looked up what the SRW is compiling with.  That system uses 40 cores, which seems a
    little excessive, but on testing the global workflow, the actual number of cores being used at
    any given time rarely exceeds 16 when running with 40 cores.  This is because the builds tend to
    use multiple threads in the beginning when compiling low-level modules while the higher-level
    modules are more or less serial AND because the GDASApp takes several minutes to initialize
    all of its subrepositories by which time the smaller builds are complete.

    2) I also updated checkout.sh so that all checkouts are simultaneous.  The CPU load for
    `git submodule` is quite low, so running 16 instead of 8 jobs at once is not much more expensive.

    3) To make this work, I had to add `-j` options to most of the build scripts.  The only exception is
    build_upp, for which the build script within the UPP is hard coded to use 6 cores.

    4) I fixed a few small bugs in the build scripts along the way.

    5) Lastly, this reduce the total build time from ~2.5 hours for the entire system (including GDAS
    and GSI in the same build) to ~40 minutes when running with `-j 40`.

    Resolves #1978

commit 67c050c201f92e855d09211e41a5f51ee1cb5230
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Oct 31 19:00:47 2023 +0000

    Add missing export for rCDUMP in stage_ic (#2009)

    rCDUMP is needed by the exscript but was never exported by the jjob.

commit 872068cb5ea78b311f7a77e97ee1428ae027cb61
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Oct 31 14:37:55 2023 +0000

    Add output error log to user for create_experiment.py on fail in CI (#1974)

    Small changes to driver CI bash scripts to recapture error log from `create_experment.py` logger
    Fixes #1939

commit b2e4a2e9d269842acbb1b37dd563ee5dee2adf0f
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Oct 31 13:57:02 2023 +0000

    Allow CI case to exclude running on certain platforms (#2001)

commit 7cc137116f1619bf1e5a12eaacb98d17da97c223
Author: Jeff Whitaker <[email protected]>
Date:   Tue Oct 31 07:54:24 2023 -0600

    Add initial C96/1 deg coupled model support (#1991)

commit 7086ddc4bece6fb2a8c1c2e6090800d4293e410e
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Mon Oct 30 19:58:43 2023 -0400

    Add ocean analysis files to HPSS archiving task (#1985)

    This PR adds the files under `analysis/ocean` (except those in `bump` and `vrfy`) to the
    HPSS archiving job, in `gdasocean_analysis.tar`, which were previously not archived.

    Resolves NOAA-EMC/GDASApp/issues/693

commit eabc82ad30c118645c0e6e216162d823882a8139
Author: Guillaume Vernieres <[email protected]>
Date:   Mon Oct 30 10:31:27 2023 -0400

    Make the early cycle work with the coupled UFS configured as S2S  (#1954)

commit aff6ca7ae559e424dae128d6cfd5da4a4e3049e7
Author: Anil Kumar <[email protected]>
Date:   Fri Oct 27 14:11:55 2023 -0400

    GEFS Staging in exglobal_stage_ic  (#1892)

    Adjusts source paths for forecast-only ICs in support of extension to ensembles.
    New paths omit the resolution (that is captured by the IC id name) and allow for
    a member level.

    Directories with the reorganized ICs have been added to the three tier-1 machines
    under glopara space.

    Building on this, also adds capability to stage GEFS ICs.

    Resolves #911

commit 77c1ff2bfa26b341b01f41e50ee0ecb31cc4f661
Author: RussTreadon-NOAA <[email protected]>
Date:   Thu Oct 26 23:44:27 2023 -0400

    Update GDASApp hash (#1975)

    Update GDASApp hash…
kayeekayee added a commit to kayeekayee/global-workflow that referenced this pull request Mar 20, 2024
@kayeekayee
Update realtime branch, gsl_ufs_rt
03291a6 
   12Jan24 global-workflow
   UFS: 29Jan24, 625ac02
   FV3: 29Jan24, bd38c56 (GSL: 28Feb24 , a439cc7)
   UPP: 07Nov23, 78f369b
   UFS_UTILS: 22Dev23, ce385ce

   update pointers for ufs_model and ufs_utils
   add GSL C3_MYNN xml suite

Squashed commit of the following:

commit db6a85e0ce36cec28714a4c9d6e13565253cf7bb
Author: jderrico-noaa <[email protected]>
Date:   Tue Mar 19 19:33:28 2024 +0000

    29Jan ufs_model.fd, 29Jan FV3 with C3 files

commit de7b382c4b259d99d39e8857cbcee7efe64c1956
Author: jderrico-noaa <[email protected]>
Date:   Mon Mar 18 16:23:05 2024 +0000

    update pointer for atmos_cubed_sphere to Feb 1 hash

commit 0fc27835205aaf57bdba228b1769e0ac7b37712e
Merge: b2c8ef81 db06f7c5
Author: jderrico-noaa <[email protected]>
Date:   Thu Mar 14 00:17:24 2024 +0000

    Merge branch 'gsl_ufs_dev' of https://github.com/NOAA-GSL/global-workflow into gsl_ufs_dev

commit b2c8ef81229b5e9b8e7592cb12c2f3e8e3179d92
Author: jderrico-noaa <[email protected]>
Date:   Wed Mar 13 23:51:45 2024 +0000

    ccpp pointer updates to framework and physics

commit 484a18df8c9022190c8900c80e40507a6771e314
Author: jderrico-noaa <[email protected]>
Date:   Wed Mar 13 23:43:18 2024 +0000

    ccpp pointer update in ufs_model.fd/FV3

commit db06f7c57d4cfc863352a4613c8260b0dffd9afe
Merge: 579f90c1 2dbd12a6
Author: Janet Derrico <[email protected]>
Date:   Wed Mar 13 15:55:48 2024 -0600

    Merge pull request #43 from kayeekayee/gsl_ufs_dev

    update GSL C3_MYNN files and change dt_inner=75

commit 2dbd12a695c4349071ee8470e597540e71bc0292
Author: kayee.wong <[email protected]>
Date:   Wed Mar 13 03:48:51 2024 +0000

    update GSL C3_MYNN files

commit 579f90c1e0e2896710046c1885f68560ea435fa6
Author: jderrico-noaa <[email protected]>
Date:   Thu Mar 7 19:20:46 2024 +0000

    update ufs_model.fd submodule pointer

commit 2f2622d68eb8444afde9c1ddad470cfee1b63b99
Author: jderrico-noaa <[email protected]>
Date:   Thu Mar 7 19:15:23 2024 +0000

    update ufs_model.fd submod pointer

commit 706a0c52bb11af78e016014550ebd6847cc0ee19
Author: jderrico-noaa <[email protected]>
Date:   Thu Mar 7 19:12:35 2024 +0000

    update ufs_model.fd/FV3 path

commit 352f188f095e19442ade1f3fd167ff2fed501cd2
Merge: 5a8edc76 96545dcb
Author: jderrico-noaa <[email protected]>
Date:   Thu Mar 7 17:58:38 2024 +0000

    update ufs model pointer

commit 5a8edc766f2f4d3e12c692069d46c02fd766c354
Author: jderrico-noaa <[email protected]>
Date:   Thu Mar 7 17:42:00 2024 +0000

    update FV3 and UPP

commit 96545dcb63e3f8f7dfc036961d818db15fa1a003
Author: jderrico-noaa <[email protected]>
Date:   Wed Mar 6 10:05:39 2024 -0700

    update pointer for ufs_model.fd

commit 25c026ef03a8d8c0db0b7368d2836f0b2e866eae
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 29 20:35:11 2024 +0000

    update ufs_model pointer

commit a28617a951c46b765aa996bfe4d28b554ec4e0a4
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 22 06:16:26 2024 +0000

    removed unneeded gsl directories

commit 6fb4f90e8572e98c977a1d2ab385f033111f3ea7
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 22 06:08:13 2024 +0000

    update ufs_utils.fd pointer

commit 9264f0c09239d046c5cd862d807e9b82f51dc3bd
Author: jderrico-noaa <[email protected]>
Date:   Wed Feb 21 19:33:26 2024 +0000

    update .gitmodules file

commit f8edfa966147506f2c207728039e3a736cb95415
Author: jderrico-noaa <[email protected]>
Date:   Wed Feb 21 19:30:47 2024 +0000

    update pointer to ufs_utils.fd

commit 5e0d2ab02d58e6a7a40db55a149a93008b28aa8b
Author: jderrico-noaa <[email protected]>
Date:   Wed Feb 21 19:25:52 2024 +0000

    update pointer to ufs_model.fd

commit ebc9e1d02987a1c6aa8cabedf2323642748fab3c
Merge: e7a81511 50cb1e6f
Author: Janet Derrico <[email protected]>
Date:   Thu Feb 15 13:40:33 2024 -0700

    Merge pull request #40 from kayeekayee/gsl_ufs_dev

    Merge to 2024 Jan 12 NOAA-EMC/develop and update to 2024 Jan 29 UFS

commit 50cb1e6f0c661e4c6e2ef0be4527cce58379b2c9
Author: kayee.wong <[email protected]>
Date:   Thu Feb 15 20:30:34 2024 +0000

    Add pygraf workflow.

commit 38b726125d49cff6cae4c0e5fff2438fc33143c5
Author: kayee.wong <[email protected]>
Date:   Wed Feb 14 17:43:15 2024 +0000

    Add double quote for the arguments when calling setup_expt.py.

commit 053f2025fb0b0679c7d4f84958973c1534ec050c
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:57:06 2024 +0000

    more fix.

commit 6f80ea2edc5444e275a79b371d02b6e98e963662
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:50:01 2024 +0000

    more bug fix.

commit 56e283f1f666a38a4a3b30e1528e96eeb5c622e7
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:40:02 2024 +0000

    Minor bug fix.

commit 2dcfed06ff6789eb77cf92e22b80f5475923fafc
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:19:03 2024 +0000

    Update parameter for c3 case
    Add c3 and mynn template

commit cc46b19ccc7cdb54878340eff79dda9e747abdf7
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 20:51:23 2024 +0000

    Update INFO.
    Add c3 SDF in the build.

commit a444ed48a23f24724853036e522b4437bf412c59
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 18:42:33 2024 +0000

    Update to UFS 2024 Jan 29 version.

commit 88595707c7521cdce37ae1cf78720a7827242b24
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 18:16:46 2024 +0000

    Minor bug fix.

commit baa0e9f10b132098d5134efaad712a51ebc26b83
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 17:59:27 2024 +0000

    Update parameters for setup_expt.py in p8_ugwpv1.sh to resdetatmos and comroot.

commit 5875f06903f82a47fafb05f89f840e3b099d18d8
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 17:51:11 2024 +0000

    Remove old gsl SDFs.
    Remove 'rrtmg_lw_pre' from C3 and MYNN SDFs.

commit 9e0d1342f4e1edce96c9b2baeec55c2cffb964cd
Author: kayee.wong <[email protected]>
Date:   Thu Feb 8 22:14:01 2024 +0000

    Merge to 2024 Jan 12 NOAA-EMC/develop.

    Squashed commit of the following:

    commit c59047614c29f6ec15a4d4a6fa1855929287debd
    Author: Rahul Mahajan <[email protected]>
    Date:   Fri Jan 12 19:21:02 2024 -0500

        Update hash to ufs-weather-model. The noahmptable.tbl was reorganized, so update link_workflow.sh to use the same one used in UFSWM RT (#2219)

    commit c041968e165c07da785376f1441374687b55d6cc
    Author: Kate Friedman <[email protected]>
    Date:   Fri Jan 12 12:09:35 2024 -0500

        Add ocean resolution to setup_expt invocation and retire/reduce COMROT/ROTDIR usage (#2214)

        Two series of updates:

        1) Update setup scripts to now allow users to provide ocean resolution
        2) Housekeeping to retire the `COMROT` variable, replacing it with other variables
        as needed, and reduce the `ROTDIR` variable usage.

        Both updates change options for the workflow setup API.

        Refs #2061

    commit 997f97816493d9ed0242e169b6dcf84e5c9338d6
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Fri Jan 12 10:46:36 2024 -0500

        Allow use of ocean obs prep in WCDA cycling and remove R2D2 (#2215)

        Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same.
        Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS.
        Replaces the current R2D2 processing.

    commit 12a5bb192ab6282d44c008c06dc14947abd37249
    Merge: 4cb58020 6492c2da
    Author: David Huber <[email protected]>
    Date:   Fri Jan 12 09:26:27 2024 -0500

        Merge pull request #2217 from DavidHuber-NOAA/update/versions

        Update and clean up version and module files

    commit 6492c2da5f49bd31575d0bef5278c9a7f8ba3412
    Author: David Huber <[email protected]>
    Date:   Thu Jan 11 11:49:08 2024 -0600

        Update orion module/version files for met/metplus #2123

    commit 94c9937f0bff380b0ebd6acdcfd2509e1ae99389
    Author: DavidHuber <[email protected]>
    Date:   Thu Jan 11 17:42:53 2024 +0000

        Comment met/metplus out from Hera modulefile. #2123

    commit 8c32f8b7d00bba6e3e954f149e6548fb27713a3c
    Merge: a65e4c67 4cb58020
    Author: David Huber <[email protected]>
    Date:   Thu Jan 11 11:34:44 2024 -0600

        Merge branch 'develop' of github.com:noaa-emc/global-workflow into develop

    commit a65e4c675f21dbe72198d263e85e894e62b41e13
    Author: David Huber <[email protected]>
    Date:   Thu Jan 11 11:34:19 2024 -0600

        Initial update of version/module files #2123

    commit 4cb580201af68c1c0e2ae19faf0727dcbbe43b4d
    Author: souopgui <[email protected]>
    Date:   Wed Jan 10 08:30:22 2024 -0600

        Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh when running MPMD tasks (#2212)

        Fix OpenMP over-allocation of resources running MPMD tasks
        Co-authored-by: Innocent Souopgui <[email protected]>

    commit b056b531faee6929687cb8a588ffafa1a66426fb
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Mon Jan 8 17:28:05 2024 -0500

        Add Hercules as valid machine in CI scripts (#2207)

        Few updates to CI scripts to include names for hercules that where missed
        the first time.

    commit 6574d29a8c26b0695614874c344bccc5182363f4
    Author: Rahul Mahajan <[email protected]>
    Date:   Mon Jan 8 17:25:47 2024 -0500

        Fix invalid GH action and restart file name (#2210)

        Resolves a typo that leads to an invalid workflow yaml and fixes the restart filename in restart detection.

        Resolves #2205

    commit 69605eac299df381ea9e0e329654487e26380ff5
    Author: Rahul Mahajan <[email protected]>
    Date:   Mon Jan 8 17:00:28 2024 -0500

        Stop attempting to comment link to RTD for non-PRs (#2209)

        Adds a check so comments with a link to documentation are only generated
        for PRs.

    commit 4e160a895bfb31c281e21557dd86c13954a1a967
    Author: Rahul Mahajan <[email protected]>
    Date:   Mon Jan 8 13:10:15 2024 -0500

        Enable UPP for GOES processing (#2203)

        Wnables the creation of special master grib2 files from UPP for
        GOES processing

    commit c15875b6dbf685327af9316ee43b3d01f0fc815e
    Author: David Huber <[email protected]>
    Date:   Mon Jan 8 09:56:06 2024 -0500

        Port cycling to Hercules (#2196)

        Adds cycled support for Hercules (excluding gsi-monitor).
        Partially resolves #1588
        GSI monitoring is disabled on Hercules due to missing Perl modules. That will be enabled in a later PR.

    commit ef6827dd6abdab2996d1e19f9e0ff5d3071e0fdd
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jan 8 09:43:12 2024 -0500

        Refactor rocoto task XML creation (#2189)

        Refactors the rocoto task generation to be recursive.
        This will allow nested metatasks to loop over multiple variables, which is needed for GEFS product generation.

        As part of this refactor, there is no longer separate arguments to designate metatasks.
        Instead, task dicts can include a nested 'task_dict' as well as a 'var_dict' containing the variables to loop over.
        The nested task dict can then either have another layer, or be the innermost task.

        To accommodate the new recursive nature, some defaults that were previously defined in create_wf_task() had to be pushed down into the function that creates the innermost task.
        Also, former keywords have been absorbed by the task dict.

        Refs #823
        Refs #827

    commit 2b81cfac16f103fb29b3aeb9748941787abf7287
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jan 8 09:41:03 2024 -0500

        Update fix versions (#2198)

        Updates fix versions for a few components:
        - Update cice and mom6 versions to support C96/1p00 marine
        - Update wave to change betamax setting for glo_025 waves

        Resolves #2004
        Resolves #2107

commit e7a81511e37f86e881da020e06b95990b470d952
Merge: af47b77c 75ad3754
Author: Janet Derrico <[email protected]>
Date:   Thu Feb 1 13:14:02 2024 -0700

    Merge pull request #37 from jderrico-noaa/gsl_ufs_dev

    Add GSL archive script and correct typos/fixed paths

commit 75ad3754f8bef5411c2570b5e392cd08e95cb6cb
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 1 20:00:52 2024 +0000

    adding consistent [[ ]] for if statements

commit 67b99668c82a5fd8c42479b9b1bfe8b0bad0be25
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Feb 1 19:37:47 2024 +0000

     Updated HOMEgfs in GSL XML templates

commit 4d3719c086e7907a6eeff03112042d392e0d8c5e
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Feb 1 17:27:39 2024 +0000

     Correct syntax errors in GSL scripts

     Add new GSL archive script for archiving grib2 and ICs, but no netcdf files

commit 4309dd0b3b2d5625e7e1740d7cd3e39aacd5bc29
Author: Judy.K.Henderson <[email protected]>
Date:   Mon Jan 29 18:05:45 2024 +0000

     Add GSL diag tables to parm/ufs/fv3

     Update GSL template for hera

     Create EMC and GSL versions of files under workflow/rocoto
      - tasks.py, workflow_tasks.py

commit af47b77c7ee59a11c798995b4362b57e9096b090
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 02:07:43 2024 +0000

     Create GSL version of archive script

commit 529d9f71f97b6e643e76a53bc9871901ae861faf
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 01:37:09 2024 +0000

     Create GSL version of tracker.sh

     - this is a placeholder with changes from last year's HFIP experiment; will likely need to be updated in the future

commit 8457e12c313bee602265b863129734354b019271
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 01:27:42 2024 +0000

     Link config.base.emc.dyn_hera to config.base.emc.dyn

commit 7a05f5bd947944d8c3be828aeef9cc03bf9e073a
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 01:22:54 2024 +0000

     Create GSL version of hpssarch_gen.sh

     - assume we only run cold starts
     - archive only 0p25 grib2 files (no 0p50 opr 1p00)
     - assume no pgrb2b or flux files are created so no need to archive to HPSS

commit 98f5d6b16437e2a340bf16f83187e389a53f8bf0
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 00:24:06 2024 +0000

     Update workflow directory

     - add GSL template for jet (based on last year's experiment)
     - create EMC and GSL versions of yaml files under hosts; defaults point to GSL files

commit 38a7e5629ceeb23d399643a021e9a0a88468a07c
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 25 18:40:37 2024 +0000

     Update atmos_products configuration file for GSL

       - set downset to 1 so pgrb2b files are not created
       - set FLXGF to "NO" so interpolated sflux.1p00 files are not created

commit fe8a953658d092ce2b597e14f31678624606fd8a
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 25 17:02:25 2024 +0000

     Update nodes for gfsfcst task in GSL template for hera to match default configuration in config.ufs
       (12x12, 2 threads, 1 write group, 40 write tasks ==> 56 nodes)

     Increase walltime to 4:10 for gfsfcst task

commit 9d85b0f6d50e8ed142557fcb87c89d2e5d63c617
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 23 19:08:52 2024 +0000

     Added default location for PTMP/STMP in workflow/hosts/hera.yaml

     Added GSL XML template for hera

commit 1cf317d327fae78c5469712c9e5a6aa1ffa4b23b
Author: Judy.K.Henderson <[email protected]>
Date:   Wed Jan 17 22:33:13 2024 +0000

     Add sjet partition

     Make syntax consistent in "if" statements in config.resources

commit 2755e203751f50113849b06769173285e093290b
Author: Judy.K.Henderson <[email protected]>
Date:   Wed Jan 17 22:32:26 2024 +0000

      Update configuration files for GSL

     - create Hera and Jet versions of config.base.emc.dyn
     - correct typo in config.fcst
     - create different versions of config.ufs;
       default is 12x12, 2 threads, 1 write group/40 write tasks (56 nodes)

commit 3c0c126a376af31866a93aef4cdd0b4145150c58
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 16 17:32:25 2024 +0000

     Add script for remapping 1/4 degree grib2 grids to other domains

commit f217d4ed9a500e9a1bdcc17548729d972a1763ac
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 16 16:46:25 2024 +0000

     Update link script for ufs_utils.fd

commit 5b21b31900955013b4e8106d3ae906b9da93b361
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 16 16:45:25 2024 +0000

     Add GSL archive scripts for initial conditions

commit abb88baf9dd536a3b2ea1e24eaa99cbfe85af799
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 16 16:42:17 2024 +0000

     Move configuration files for getic and init from jobs/rocoto to parm/config/gfs

commit 45b235180719ab79d2514f0317207fbebfb8aedd
Author: Judy.K.Henderson <[email protected]>
Date:   Sun Jan 14 03:21:15 2024 +0000

     Add suite definition file for v17p8_ugwpv1_c3 to sorc/ufs_model.fd_gsl

commit 147b1fce99254dcb602c333cc559feaa9a396e81
Author: Judy.K.Henderson <[email protected]>
Date:   Sun Jan 14 01:57:22 2024 +0000

     Add getic and init tasks to workflow to create initial conditions in realtime

commit 4e4e50803d95566e1c7967cf4cfa575391d77f25
Author: Judy.K.Henderson <[email protected]>
Date:   Fri Jan 12 00:44:59 2024 +0000

     Change default HPSS_PROJECT to fim

     Change restart_interval_gfs to -1 so no files are written ro RERUN_RESTART directory

commit 791d7a27c6b12f07d9c12ce491338e3da59eb1d8
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 11 23:34:36 2024 +0000

     Add namelist parameter, nord_tr, for GSL suites

commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 11 23:31:22 2024 +0000

     Add changes for running v17p8_mynn

     - new field table, field_table_thompson_aero_tke_progsigma
     - updated namelist parameters in config.fcst

commit 982a1f02e3b880be43f4ae8a3f0ffbb34c056aea
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 02:26:22 2024 +0000

     Add experiment setup script for p8_ugwpv1

commit c5a3697d22fdbb02bb80ddffee2629dddc10c702
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 02:19:13 2024 +0000

     Add memory report to srun command in env/HERA.env

commit ece7e516ca65ec0240899e7d84321310a6887595
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 02:13:42 2024 +0000

     Updated GSL-specific files under ufs_utils.fd_gsl

commit 1b153fc95b93a16eb40b791be7322100fde4a3d4
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 01:52:56 2024 +0000

     Create new branch, gsl_ufs_dev, from dev_02jan24_9d901db

     Add initial GSL modifications
      - changes to workflow files
        * GSL paths, projects, entities
      - new FV3_GFS_v17_p8_ugwpv1_mynn suite definition file (SDF)
      - updated namelist parameters in ush/parsing_namelists_FV3.sh
      - create new GSL directories: ufs_model.fd_gsl and ufs_utils.fd_gsl
        * new SDFs, add instantaneous flux variables to grib2 configuration files
        * add Thompson tracers to initial conditions
      - new sync script: rsync_gsl.sh
      - new job files:  getic.sh, makeinit_link.sh
      - modify build_ufs.sh to include MYNN SDF

commit 9d901dbbff4d41586580316bdc094d24760119e6
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Jan 2 10:30:33 2024 -0700

    Stop Gempak pgrb2 spec from modifying $DATA (#2147)

    This PR addresses issue #1224. The following is accomplished:

    - Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time;
    - Shell linter exceptions are addressed accordingly;
    - The respective GEMPAK tasks is added to the Rocoto mesh.

    Resolves #1224

commit 31ad23527802f7d07171132cc620f7135c4d8cba
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Jan 2 10:27:30 2024 -0700

    Reorganize NPOESS scripts (#2166)

    This PR addresses issue #1226. The following is accomplished:

    - Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure
    of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated;
    - Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh`
    are moved accordingly; this specifically applies to the environment variable `FHOUR`,
    `SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`;
    - The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level
    (if necessary);
    - Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however,
    this may not be necessary (see `TODO` note within draft PR.

    Resolves #1226

commit 22bd82fa93b49e5ce98eb3f69123956dd5018049
Author: Kate Friedman <[email protected]>
Date:   Tue Jan 2 11:55:03 2024 -0500

    Orog fix file reorg and fix directory variable standardization (#2181)

    This PR makes updates to use the newly reorganized `orog/20231027`
    fix file version and standardizes the fix file directory variables.

    Changes:

    1. Update UFS_UTILS hash to ce385ce
    2. Update fix file version file to use new orog timestamp: `orog_ver=20231027`
    3. Add ".mx$(OCNRES)" to `oro_data` filenames in scripts
    4. Remove ".mx$(ocn_res)_frac" from the directory names for atmosphere
    resolutions under the `/orog` folder
    5. Adds fix file directory variables to `config.base`, many of which are pulled
    up out of lower scripts; introduce `FIXcpl`
    6. Renamed/replaced the following fix file directory variables:

    - `FV3JEDI_FIX` --> `FIXgdas`
    - `FIXfv3`, `FIX_orog` and `OROFIX` --> `FIXorog`
    - `FIX_ugwd` and `OROFIX_ugwd` --> `FIXugwd`
    - `FIX_am`, `FIXgsm`, `FIXSYND` --> `FIXam`
    - `FIX_lut` --> `FIXlut`
    - `FIX_aer` --> `FIXaer`
    - `FIX_SFC` --> `FIXsfc`
    - `FIX_DIR` --> `FIXgfs`
    - `RTMFIX` and `FIXCRTM` --> `CRTM_FIX` (is `CRTM_FIX` in crtm module,
    so not using `FIXcrtm`)

    7. Correct the defaults for `FIXwave` in wave JJOB scripts
    8. Update variable names in `*fixed_files.yaml` files, as well as update naming
    convention for `oro_data` files

    Resolves #1984
    Resolves #1981
    Resolves #2175

commit 03d03bf53b43914a55c384cb33eb06f6a9a443a6
Author: Andrew Collard <[email protected]>
Date:   Tue Jan 2 11:53:44 2024 -0500

    Remove HIRS from GSI processing (#2183)

    With the update to CRTM 2.4.0.1, an issue with versioning of CRTM HIRS
    files has been exposed. This is documented in JCSDA/crtm#42.

    As HIRS radiances are no longer used in the GSI, these data should be removed
    from processing until a suitable update to CRTM is available.

    Resolves #2182

commit a3c50998d35525a39a66d5592fbf327ab3569e8b
Author: Jessica Meixner <[email protected]>
Date:   Fri Dec 22 18:07:48 2023 -0500

    Update ufs-weather-model version  (#2186)

    * update model to latest version which includes needed bugfixes for HR3

commit 774c7302e618370ef578bec3ccabc70486d6da1b
Author: David Huber <[email protected]>
Date:   Fri Dec 22 11:34:53 2023 -0500

    Fix analysis post processing's handling of 0-padded negative integers (#2187)

    This screens for the analysis 'forecast' hour (-001) and handles the '-' and circumvents octal issues.

commit d1251360325faf75af9df0608557fcd10202a883
Author: Barry Baker <[email protected]>
Date:   Thu Dec 21 11:23:48 2023 -0500

    Fix for restoring cycling aerosols in fo-mode post COM refactor (#2179)

    - Update to COM reorg aerosol initialization job
    - Address bug in joining paths for data dependency in this job

    ---------

    Co-authored-by: Rahul Mahajan <[email protected]>

commit e55a05980709288d902ad1bd894164bfa5a18a65
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Dec 20 22:14:01 2023 -0500

    Stop calling ufs-utils link script (#2172)

    The `link_workflow.sh` script was calling the ufs_utils version of the
    same. That step is only necessary if a user is going to run one of the
    stand-alone ufs-utils, which is rare.

commit ef3e5ad7c63be1644c82333c95853c3caf2d8995
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Dec 19 22:02:55 2023 -0500

    Fix handling of excluded hosts list (#2170)

    This PR fixes the issue with `create_experment.py` so that the yaml configuration
    file can have a string of list of strings when specifying the host name to exclude
    from the CI tests.

commit ea74a5719efc8f0fe631c5ff93426a4299a614f3
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Tue Dec 19 16:21:41 2023 -0500

    Add COMOUT_OBS to marine obs prep (#2173)

    Adds `COMOUT_OBS` (defined from `COM_OBS_TMPL`) to marine obs prep task to properly handle marine obs prep files. Used to keep obs after IODA conversion, QC, and other prep.

    Towards resolving NOAA-EMC/GDASApp#815

commit c2500feace0bb7c04ce67a90dd3182120ee67b2e
Author: David Huber <[email protected]>
Date:   Tue Dec 19 14:55:20 2023 -0500

    Return failed status if a build fails. (#2171)

    If any of the builds fail, this makes build_all.sh return the sum of the error codes encountered.

    Fixes #2168

commit 76fdd81cd84ed812181996a102379d8d964ba27a
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 19 13:24:34 2023 -0500

    Update index.rst for new GFSv16.3.12 in ops (#2169)

    Refs #2096

commit a81da33e8fe7541a36f68e7a4f14a384cadd36c8
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 19 10:22:21 2023 -0500

    Set place=shared for shared jobs on WCOSS2 (develop) (#2156)

    Set job as shared when not exclusive on WCOSS2

    WCOSS2 defaults to exclusive when it is not specified as
    either exclusive (place=exclhost) or shared (place=shared).
    Now set shared when job should be shared.

    Refs #2135

commit 89aea972f7964dac3f515e8070d7c534812c5fb4
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Dec 15 16:31:06 2023 -0500

    Update gfs-utils version for Hercules (#2163)

    An update of gfs-utils was misssing from the previous PR that added
    initial Hercules support (#2128).

    Also includes gfs-utils update for new marine post.

commit 9505cb4abc6ca2643a8ab254d14ca2000747fa44
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Dec 14 16:15:31 2023 -0500

    CI Updates to support Hercules (#2155)

    If merged, this PR will update the CI scripts so they will run on Hercules for forecast only
    NOTE: This is a stop gap to issue #2131 until its block on #1588 is removed.

    Resolves #2154

commit c5ca82f04a2efae78389dec1c46b94ef4fb5bbe5
Author: Rahul Mahajan <[email protected]>
Date:   Thu Dec 14 16:05:33 2023 -0500

    Correct fbwind (#2161)

commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a
Author: Kate Friedman <[email protected]>
Date:   Thu Dec 14 12:06:23 2023 -0500

    Add MOS jobs to rocoto mesh (#2148)

    Create separate jobs for GFS MOS - extracted from now-retired vrfy job

    Refs #2068

commit bb6151aa50c27253cb9b8f0a6601ddd58526b8b3
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Dec 14 05:38:29 2023 -0500

    Replace checkout script with submodules (#2142)

    Replaces the checkout script with git submodules. This change brings workflow in
    line with other repos and git standards.

    Due to these changes, the build system is updated slightly. First, the options that
    were formerly used with `checkout.sh` to reduce unneeded builds (`-g` for GSI
    and `-u` for UFSDA) are moved to `build_all.sh` instead. This is needed since build
    all will not be able to key off directories existing or not to determine which com-
    ponents to build. Second, the partial build system is removed. It was rarely, if ever,
    used, and parts of it were already ignored with the previous changes to base builds
    off whether directories exist. The manage externals file is also removed since that is
    also not being used.

    Following these changes, clones/checkout will need to either be recursive, or
    `git submodule update` will need to be called separately to make sure components
    are properly checked out (non-exhaustive list):

    ```
    ## Checkout develop (method 1)
    git clone --recursive https://github.com/NOAA-EMC/global-workflow destination

    ## Checkout develop (method 2)
    git clone  --jobs 8 https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git submodule update --init --recursive --jobs 8

    ## Checkout existing branch some_branch (method 1)
    git clone --recursive  --jobs 8 -b some_branch https://github.com/NOAA-EMC/global-workflow destination

    ## Checkout existing branch some_branch (method 2)
    git clone https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git checkout --recurse-submodules some_branch

    ## Checkout existing branch some_branch (method 3)
    git clone https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git checkout some_branch
    git submodule update --init --recursive  --jobs 8

    ## Checkout new branch new_branch
    git clone https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git checkout -b new_branch
    git submodule update --init --recursive  --jobs 8
    ```

    The git ignore list had to be updated to use explicit paths as the wildcard paths pick
    up the ones that are now submodules.

    UFS creates files during the build process that are not in its ignore list, so that sub-
    module ignores the "dirty" state to avoid confusing users running `git status`.

    CI and documentation are also updated to reflect the changes.

    Resolves #2141

commit 1332188ce2409e012ec127d44880e49732f7f379
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Dec 13 09:32:57 2023 -0500

    Enable radar reflectivity output (#2143)

    Turns on radar reflectivity output from FV3. This eliminates missing values appearing in the grib2 files.

commit 24d898ec0ec0c7fcbda6966988f9a986f528ed14
Author: David Huber <[email protected]>
Date:   Wed Dec 13 09:32:24 2023 -0500

    Fix Hercules hostname (#2150)

    * Allow lower or upper hostname on hercules.
    * Add Hercules to issue template.

commit 2896bb8787698be28ad20f2298589e6e95eaf9fb
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 12 09:13:06 2023 -0500

    Fix module load typo (#2145)

    Fix typo with loading the crtm module in the UPP hack for WCOSS2

    Refs #2144

commit 29d34172a67d976f910e78158ff0337e1ef099ca
Author: Cory Martin <[email protected]>
Date:   Thu Dec 7 15:12:05 2023 -0500

    Update GDAS hash to most recent stable versions (#2138)

commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Dec 7 10:41:05 2023 -0700

    Corrected typo in a gempak job gempakncdcupapgif . (#2137)

commit 3483f550db1ae35a680de49f7485ce5a11902dd9
Author: Cory Martin <[email protected]>
Date:   Thu Dec 7 12:34:56 2023 -0500

    Add support for FGAT and IAU for aerosol DA (#1940)

commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9
Author: David Huber <[email protected]>
Date:   Thu Dec 7 12:33:46 2023 -0500

    Enable forecast-only experiments on Hercules (#2128)

    This add forecast-only support for Hercules to the global workflow. Partially satisfies #1588.
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

commit a29f751aed05312da3d80d396159bb5a906d6ce4
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Dec 6 13:45:56 2023 -0700

    Adds GEMPAK and related jobs to rocoto task mesh (#2127)

commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082
Author: Rahul Mahajan <[email protected]>
Date:   Tue Dec 5 15:47:52 2023 -0500

    Separate offline UPP from interpolated grib2 product generation (#2110)

    This PR:
    - Replaces the use of  `JGLOBAL_ATMOS_POST` with `JGLOBAL_ATMOS_UPP`
    and `JGLOBAL_ATMOS_PRODUCTS`.
    - Introduces `JGLOBAL_ATMOS_PRODUCTS` that is responsible for creating
    grib2 products from the master file produced by UPP (inline from the model,
    or offline by running `JGLOBAL_ATMOS_UPP`).  Rocoto job `atmos_products.sh`,
    ex-script `exglobal_atmos_products.sh` are also added along with a
    `config.atmos_products`. Updates are made to the relevant `env` files as well as
    `config.resources` to reflect the addition of this job.
    - reduces the number of cores needed appropriately for forecast products when
    there is no offline UPP necessary.
    - renames older `fv3gfs_dwn_nems.sh` to `interp_atmos_master.sh` and
    `inter_flux.sh` to `interp_atmos_sflux.sh`
    - removes `fv3gfs_downstream_nems.sh` as it is absorbed into
    `exglobal_atmos_products.sh`
    - removes no longer used scripts for `gfs_post.sh`, `gfs_transfer.sh` (DBN alerts
    are absorbed into `exglobal_atmos_products.sh`), `post.sh`,
    `JGLOBAL_ATMOS_POST`, `ex${RUN}_atmos_post.sh` scripts.
    - Rocoto workflow related scripts are updated to add `atmos_products` as a job.
    When `WRITE_DOPOST` is `.false.`, `upp.sh` job to run the UPP offline is also
    added.  Dependencies have been appropriately applied.
    - removes `PGB1F` option that creates 1-degree grib1 products that are no longer
    needed in GFSv17.

    The hacks from (now deleted) `post.sh` had to be reinstated in `upp.sh` to load the
    modules from UPP instead of `load_fv3gfs_modules.sh`.

commit 44186f594aaf5f8feea0eadd4c5c3b59de3a825e
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 5 12:28:08 2023 -0500

    Update index.rst for new GFSv16.3.11 version (#2121)

    Refs #1356

commit e62a3a73cd22701962b7bf210fdfee37f37a5474
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Dec 5 09:08:12 2023 -0700

    Splits AWIPS jobs into seperate tasks (#2094)

    This PR addresses issue #1228. The following is accomplished:

    - Separate rocoto jobs have been created beneath `jobs/rocoto/`
    -- `awips_20sh` and `awips_g2sh`; these jobs replace `awips.sh` which was
    calling multiple J-jobs within the respective `awips.sh` scripts;
    - New tasks has been added to `workflow/rocoto/tasks.py` for the new
    AWIPS scripts;
    - The `gfs_cycled` and `gfs_forecast_only` modules beneath
    `workflow/rocoto` have been updated accordingly.

      Resolves #1228

commit 04d97e9aa7ab84b9754ab670074cfb19d543aa26
Author: Kate Friedman <[email protected]>
Date:   Mon Dec 4 13:38:30 2023 -0500

    Consolidate VMINMON and cleanup monitor scripts (#2088)

    This PR combines the GDAS and GFS versions of the VMINMON JJOB
    and ex-driver scripts into single GLOBAL/global versions. Additionally:

    * some further cleanup of the GSI-Monitor scripts is done; variable
    settings in ex-driver scripts are moved up to the JJOB level
    * the fix symlinks are consolidated into a new `fix/mon` subfolder (formerly
    `fix/gdas`) and copies of the gfs monitor fix files under `fix/products` are
    removed

    Resolves #1925

commit a286a11fdcbc31c8bc6d944890bc56294bc8caf6
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Dec 4 17:48:44 2023 +0000

    Robust CI Restarts (#2093)

    Improved CI robustness for reverting back to **CI-Ready** from any
    given state

    New Features:

    - Improved `scancel` routine (refactored into bash "subroutine")
    - Improved messaging (see below) when ever a user changes state
    - Any and all previous build scripts and running experiments are killed as
    a result of reset to **Ready**

    Resolves #2060

commit 73621e9b20b20f85e8b21e4c1e09ed1d80ecd46f
Author: David Huber <[email protected]>
Date:   Sun Dec 3 11:19:19 2023 -0500

    Upgrade to spack-stack/1.5.1 and Intel 2022 on non-production machines (#2084)

    Update module files to spack-stack/1.5.1 and compilers to Intel 2022+ on all non-production machines.

commit 6d548b250688861eb20a7e0dc852a0e4ba9e64f4
Author: jiandewang <[email protected]>
Date:   Thu Nov 30 12:00:21 2023 -0500

    Add variable tob in diag_table for ocean model output(#2105)

commit c19810cce252fcdb25fd9960c05b08b5f8d8b1ad
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Wed Nov 29 15:17:36 2023 -0500

    Added variables to config.prepoceanobs (#2101)

commit c2d78a61a224678fb804eed19f39d1f07408ae5f
Author: Kate Friedman <[email protected]>
Date:   Wed Nov 29 12:39:08 2023 -0500

    Add missing cut to VDATE setting in JGFS_ATMOS_VERIFICATION (#2098)

    Refs #2097

commit c1c025f91ddac73aea595cc9fa4dd0bea80575fc
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Nov 29 17:15:10 2023 +0000

    Add wave init to GEFS (#2089)

    Adds the wave init job to GEFS. Since the output would be the same for
    every member, the job is only run once for the control, then links are
    created in each of the member directories pointing to that copy.

    New ww3_multi and ww3_shell templates for GEFS are copied from the
    GFS versions.

    The GEFS restart frequency is changed to not be zero, and the comment
    about not setting it to zero is copied from the gfs config.base. The restart
    interval for the GEFS perturbed members is changed to equal that of the
    control.

    Also fixes a bug where `RUNwave` was not defined for ensemble forecasts,
    and another bug in the GEFS stage_ic dependency.

    Resolves #2017

commit 64a2470ce29b7d8d5cb85ebcb4048ff82958f64e
Author: Kate Friedman <[email protected]>
Date:   Wed Nov 29 11:26:34 2023 -0500

    Adjust permissions for jobs/JGFS_ATMOS_VERIFICATION (#2095)

    Add execute permissions (755)

commit 964b77bc6de67291973c2c70598a1f8cb72501c5
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Nov 28 18:45:51 2023 +0000

    Make proper j-job for MET+ (#2090)

    Creates a proper j-job for the metp job, moving much of the material
    from the `jobs/rocoto` script there (some of it within `jjob_header`).

    Also updates the old `COMIN` variable for the COM refactor (although
    it does not appear used in the verify scripts currently).

    This is a partial step towards restoring/improving metp functionality
    and remains untested.

    Refs #1575

commit 8c11eeb8556619e8db4e0efb6394ce5a2c1aae0f
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Nov 23 10:31:32 2023 -0700

    Adds FBWINDS support to global-workflow (#2082)

    This PR addresses issue #1221. The following was accomplished:

    - A new Rocoto job is added; `jobs/rocoto/fbwinds.sh`;
    - `workflow/applications/gfs_cycled.py` is updated to include the `fbwinds` task;
    - `workflow/applications/gfs_forecast_only.py` is updated to include the `fbwinds` task;
    -  A new function is added to `workflow/rocoto/gfs_tasks.py`, `fbwinds` is added as new GFS (only) task;
    - `workflow/rocoto/tasks.py` is updated to include the `fbwinds` task.

    Resolves #1221

commit 513db190d21f9ede0724a2cd5606372b1d7605de
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Nov 21 22:52:58 2023 -0700

    Adds NPOESS support to global-workflow (#2083)

    This PR addresses issue #1225. The following was accomplished:

    - A new Rocoto job is added; `jobs/rocoto/npoess.sh`;
    - `workflow/applications/gfs_cycled.py` is updated to include the `npoess`
    task;
    - `workflow/applications/gfs_forecast_only.py` is updated to include the
    `npoess` task;
    -  A new function is added to `workflow/rocoto/gfs_tasks.py`, `npoess` is
    added as new GFS (only) task;
    - `workflow/rocoto/tasks.py` is updated to include the `npoess` task.

    Resolves #1225

commit 62d8e99e77ffe44784f4c61c3f2296c6d1a72413
Author: Kate Friedman <[email protected]>
Date:   Fri Nov 17 20:25:50 2023 -0500

    Retire vrfy job (#2080)

    Retires the `vrfy` job from the global-workflow system. All associated
    scripts, configs, and references to the job are removed.

    Additionally, the switches listed in RTD were updated to reflect new
    ones added in other PRs for issue #235.

    Resolves #2069
    Refs #235

commit ea386abf11ecbacef407388e8d57e71b30148a35
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Nov 17 23:59:46 2023 +0000

    Enable different coupled settings for ensemble (#2030)

    Adds the ability to turn off some coupled components for the ensemble.

    To enable this, many settings are moved out of `config.fcst` and into `config.ufs`
    so they are calculated after any overrides of `DO_*` have been made. Some
    settings also had to be moved out of `config.base` for the same reason. A
    switch to turn on gocart is added to `config.ufs`, but unlike the other switches
    this one takes no arguments.

    The name of the ufs configure template used is converted from a partial file
    name to the full file name.

    Resolves #1692

commit fe792c0c9a1c46908cbd18c7e71eb836974cf1de
Author: Kate Friedman <[email protected]>
Date:   Fri Nov 17 17:19:16 2023 -0500

    Add --cpus-per-task to srun commands for Hera and Orion (#2077)

    This PR adds the `--cpus-per-task` flag to non-CFP `APRUN`/srun commands
    in the env files for Orion and Hera. This is needed as a result of an upgrade
    to SLURM on Orion that no longer exported the thread value to the
    environment. Issue #1996 was a hotfix to add this flag for the analysis job
    that was suddenly running slowly after the SLURM upgrade. A similar SLURM
    upgrade was done on Hera but the sysadmins there implemented a
    workaround so this issue did not appear there.

    This PR adds the `--cpus-per-task` flag for both machines...needed on Orion
    and as a safety measure on Hera.

    Also included in this PR is a fix to indentations in the
    `scripts/exglobal_diag.sh` script that was noticed during work for this PR.

    Timing differences were not observed for other jobs after adding this srun
    flag. Job timings were of a similar variation between control and test runs.
    Any potential additional speedup was not observed. The test runs also
    reproduced the control runs with `develop`.

    Resolves #2044

commit 42c943be305c297a56b104bb50727938c1ba688f
Author: Kate Friedman <[email protected]>
Date:   Fri Nov 17 15:41:34 2023 -0500

    Adjust modules in post.sh for WCOSS2 (#2079)

    On WCOSS2 the grib_util module is named a bit different and
    needs the libjpeg module loaded beforehand.

commit cd4e6a1987e7fd71dff06766f540b5d32c8b648d
Author: Jessica Meixner <[email protected]>
Date:   Fri Nov 17 11:49:32 2023 -0500

    Update ufs-weather-model and remove upp hack (#2071)

    Updates the model to the most recent commit of ufs-weather-model.  This
    should allow for the removal of the UPP hack that was added in PR #2042

    This required changing nems.configure -> ufs.configure.

    Resolves #1942

commit 5a2d97e142aa4999b122fd5a130c63e59ea9f8e2
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Nov 16 22:15:53 2023 +0000

    Fix check for existence of preamble functions (#2066)

    A few of the setup scripts were checking for the existence of
    functions set by the preamble before calling them so they could
    also be used stand-alone. However, the `type` command returns `1`
    if the function name does not exist, which will cause the script
    to die is `set -e` is on. Now the `type` command fails over to an
    empty string.

commit ed2ee7c2b1457b71b271a2c40f0dfa356e0f52f8
Author: WenMeng-NOAA <[email protected]>
Date:   Thu Nov 16 16:38:11 2023 -0500

    Update UPP products for GFS v17 (#1973)

    Updates of generating GFS V17 UPP products to support HR3:

    - Update g2tmpl to 1.0.12
    - Add changes to launch cfp on WCOSS2 to generate pgrb2/pgrb2b files
    - Changes for generating new products (MERRA2, six winter weather variables,
    1km HLCY, SDEN) in pgrb2 files

    Resolves #1965
    Resolves #1994

commit 635c4719e603538ce7cccf9ea6b31f3f84f20849
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Nov 16 20:35:30 2023 +0000

    Fix some rocoto dependencies (#2074)

    A few small errors/cleanup in the dependencies, mostly in fcst:

    A few small errors/cleanup have crept into the dependencies with recent changes,
    mostly in fcst:

    - Fixed the offset, as it would yield a string rocoto doesn't recognize when the
    interval was 24+ hrs
    - Removed the duplicate wave dependency. When `waveprep` is included, it
    depends on `waveinit` so there is no need to add a `waveinit` dependency.
    - Converted an interval in the archive job that was missed in #2039

    Resolves #2075

commit d4c7508260975c6b94fc92fd085f39d4faf3f027
Author: Rahul Mahajan <[email protected]>
Date:   Wed Nov 15 16:44:03 2023 -0500

    Fix missing _PREV in ocean restart file location (#2070)

commit 255616d37505c785bdddd5d3e39e8399110b626e
Author: mdtoyNOAA <[email protected]>
Date:   Wed Nov 15 12:02:09 2023 -0700

    Update functionality for Prototype HR3 UGWP (#1987)

    This PR adds/modifies namelist options and activates new 'ccpp' suite definition
    files for the updated Unified Gravity Wave Physics (UGWP) in the ufs-weather-
    model recently updated for HR3.  The changes to UGWP are the use of the GSL
    drag suite for orographic gravity wave drag (GWD) and blocking, as well as the
    new UGWP Version 1 non-stationary GWD.  See
    ufs-community/ufs-weather-model#1923 for details.

    Resolves #1986

commit be9085e62aae147e3c74602e2f82a99b374fc783
Author: Guillaume Vernieres <[email protected]>
Date:   Wed Nov 15 13:48:58 2023 -0500

    Save the required CICE history for the sea-ice DA (#2062)

    The hist_avg setting of CICE was changed to be an array.

commit 85f1f5131ffd70061231304ea477bde0559eb67b
Author: Guoqing Ge <[email protected]>
Date:   Wed Nov 15 11:47:21 2023 -0700

    Use assim_freq to configure "offset" in dependencies (#2039)

    Use the assim_freq from config.base to configure "offset" in dependencies
    instead of hard-coding them.

    Resolves #2038

commit 4e3d82ba3a1fa7cdd4443bcd4cf83b2f8835137c
Author: Kate Friedman <[email protected]>
Date:   Wed Nov 15 13:39:14 2023 -0500

    Resolve ENKF archive script bugs (#2065)

    Fix two bugs in the exgdas_enkf_earc.sh script:

    1) Replace ARCH_LIST with DATA to match changes done in PR #2000
    and update path to generated archive list files.
    2) Add status check and exit after script attempts to make tarball on HPSS.

    Refs #2064

commit 42d7f2f0c48fab898b764e09cfbbd7a9fabbae08
Author: Kate Friedman <[email protected]>
Date:   Tue Nov 14 17:54:29 2023 -0500

    Separate tracker and genesis jobs from vrfy job (#2058)

    This PR creates new individual jobs for the tracker and genesis jobs that are being
    pulled out of the `vrfy` job (issue #235). The `tracker` and `genesis` jobs will be on
    by default while the `genesis_fsu` job will be off by default. This mimics the current
    settings in the `vrfy` job.

    No enhancements or upgrades are made to the jobs themselves in this PR, only to
    separate them from the `vrfy` job. However, one change compared to how they
    currently run in the `vrfy` job is to no longer run the `tracker` in the gdas suite. This
    mimics how the `ens_tracker` package is run in operations (gfs only).

    Changes in this PR:

    1. Create rocoto job scripts for tracker/genesis jobs.
    2. Create configs for tracker/genesis jobs, as well as `config.tropcy` for shared
    settings.
    3. Add tracker/genesis jobs to `config.resources`; use resources from the ecf scripts
    for `ens_tracker` jobs in operations
    4. Add tracker/genesis jobs to rocoto setup for both cycled and forecast-only
    modes.
    5. Update arguments for `jjob_header.sh` script in tracker/genesis JJOB scripts to use
    specific job names and configs instead of vrfy.
    6. Rename `tracker_ver` to `ens_tracker_ver` in version files to mimic variable within
    tracker package.
    7. Rename and move tracker/genesis switches to `config.base`.
    8. Remove tracker/genesis jobs from `vrfy` job (`jobs/rocoto/vrfy` and `config.vrfy`).
    9. Reduce vrfy job resources to accommodate tasks having been removed.

    Refs #235
    Resolves #1988
    Resolves #2048

commit 0a0d6984e094d2a551d5d8331102142e7db13fc2
Author: Rahul Mahajan <[email protected]>
Date:   Tue Nov 14 14:08:26 2023 -0500

    Enable warm starting of the model for forecast-only mode (#2031)

    This PR:
    - adds an option to warm|cold start the ufs-weather-model when setting up an experiment for GFS/GEFS
    - adds the capability to stage FV3 restarts when the atmosphere is warm started from FV3 restarts. This would be used in the GEFS free-forecast for part of the reforecast capability.
    - If a coupled model is warm started for the atmosphere, also check if mediator restarts are present. If so, stage mediator restarts to allow restarting the coupled model.

    Fixes #2016

commit 2cd6a589305a9ac9d3a9a0d2136e66e42f09d3bf
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Nov 14 12:05:20 2023 -0700

    Moves UFS WM configuration files to `COM_CONF` (#2054)

    The UFS weather-model (WM) files are place in the COM_CONF path rather than the respective component model COM history paths.
    Resolves #2015

commit 6f1693081662f241fafc930b1afc88125f7f5aff
Author: Kate Friedman <[email protected]>
Date:   Tue Nov 14 11:15:02 2023 -0500

    Refine fit2obs job in rocoto mesh (#2047)

    This PR adjusts the `fit2obs` job in the rocoto mesh to better define when it exists
    and how the archive job dependencies accommodate it not being in the first half
    cycle.

    Changes in PR:

    1. Remove the `fit2obs` job from the first half cycle `cycledef`.
    2. Adjust the archive job dependencies to now include the `fit2obs` job in the new
    logic check added in PR #1983. The `gdasarch` job in the first half cycle will check if
    `gdasfit2obs` is complete OR no prior cycle exists. Also cleaned up this new logic
    check block some to make it a tad simpler.
    3. Also, fix the addition of the `fit2obs` config to the config list in setup scripts. Now
    tied to whether `fit2obs` job is on instead of always adding the config to the list.

    Resolves #2043

commit 5730a71fa5d311e49d9bb11528b500f27f33d69d
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Nov 14 09:13:11 2023 -0700

    Add `waveinit` and `waveprep` to half-cycle. (#2037)

    This PR addresses issue #1444. The `waveinit` and `waveprep` tasks have been added to
    the GDAS have cycle. The downstream dependencies for the respective GFS and GDAS
    forecast tasks have been removed.

    Resolves #1444

commit 28d2e93c3857de95b0309a089cd7dac736ccaded
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Nov 14 16:11:47 2023 +0000

    Update wave IC source for C384 (#2055)

    The default wave grid for C384 has changed since P8, so a single wave
    IC on the new grid is available under a different IC name.

commit 81dd2d9855091315611106a5afbdaeaa15e6e4ae
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Nov 9 17:19:57 2023 +0000

    Fix analysis and post on Orion (#2046)

    Fixes a couple things to get workflow to work on Orion again:

    First, while #2042 allowed post to be built, the `upp.x` executable would fail due
    to a missing library. Now post jobs (temporarily) uses the UPP modules (plus
    others needed for runtime) instead of the normal workflow runtime module. This
    should actually fix #2041. This hack can likely be removed once we move to
    spack-stack.

    Second, the launcher command for the analysis jobs on Orion are updated to
    specify the number of CPUs per task. This was necessary as a recent slurm update
    on Orion discontinued reading that value from the scheduler. Other jobs will be
    handled later (see #2044).

    Additionally, a change is made to `module-setup.sh` that will eliminate the
    annoyance of `gw_setup.sh` breaking tab completion because undefined variable
    checking was turned on for the script but not back off.

    Resolves #1996
    Resolves #2041
    Refs #2044

commit 13d06ded4155cba2d08ef2a2cd553024c5abe29d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Nov 8 18:25:47 2023 +0000

    Hack UPP version (#2042)

    The stack UPP was using on Orion was recently deleted, leaving us
    unable to build the UFS verison of UPP there. UPP has an updated
    version using spack-stack that works, so the checkout script is
    modified to check out that version of UPP after UFS has been
    checked out.

    This temporary hack can be removed once we move to a UFS version
    that advances the UPP version to or beyond 78f369b.

    Resolves #2041

commit 20f6eceb8ff58f84174a27eb849c1d74566a3e03
Author: jiandewang <[email protected]>
Date:   Wed Nov 8 11:14:55 2023 -0500

    Add basic C1152 settings (#2020)

    Adding C1152 setting in host.yaml, config.base and config.stage_ic so that can run C1152 S2SW.

    Resolves #2019

commit 5183c43bbbd07285869feacb49d8680afe85929a
Author: Barry Baker <[email protected]>
Date:   Tue Nov 7 01:14:40 2023 -0500

    Update UFS for dust fix and remove nitrates by default  (#1989)

    This PR updates the `ufs-weather-model` to the latest hash that included the dust fix (PR #1922).
    Along with this I removed the nitrates by default in support of the GEFSv13 EP4 and EP5
    experiments. Removed unneeded inputs that should help with speed improvements.

commit 34a73cf2ed5afefc776d9cc73b6ebf439122a1bb
Author: David Huber <[email protected]>
Date:   Mon Nov 6 14:00:51 2023 -0500

    Reduce gdas builds to 8 #2029 (#2036)

    Reduce the default number of build jobs for the GDASApp to 8 from 16.

    This is needed for Orion as the build crashes during a linking step.  Though not verified, it
    appears this may be caused by using too much memory with 16 builds.  The issue disappears
    when using 8 build jobs.

    Resolves #2029

commit 75269e4bb9764b81589efc7d703825b80e74c8f5
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Nov 6 17:34:47 2023 +0000

    Streamline CI reporting to PRs (#2026)

    Cleaned up the logs for CI PRs sent to the GitHub Messages:

    - Eliminates redundant accumulative reporting
    - Reports on all created or skipped experiment instantiations in a single message
    - Gives one line report once  for each experiment completion
    - Single final report completion of CI

    See some examples in forked [PR 195](https://github.com/TerrenceMcGuinness-NOAA/global-workflow/pull/195)

    Resolves #2007

commit 8d55126bb0b27c79c8bee7f72b014abd34950ff9
Author: Guillaume Vernieres <[email protected]>
Date:   Fri Nov 3 17:06:09 2023 -0400

    Implement IAU Cycling Type with Marine Data Assimilation Enabled (#1944)

    Allows cycling in IAU mode with the S2S UFS model, soca and the GSI.

    Most of the work related to making IAU work was done by @JessicaMeixner-NOAA . Thanks @JessicaMeixner-NOAA !

    Resolves #1943
    Refs #1776

commit 2563806821d4ae3b57120bc61aa0575139a708f0
Author: jiandewang <[email protected]>
Date:   Fri Nov 3 11:49:37 2023 -0400

    Add two ucx modules in load_ufswm_modules.sh to solve C768 and C1152 S2SW job hanging issue on WCOSS2 (#2021)

commit cbdc09711a83493f363a737d1e3e46c48a09719d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Nov 3 04:09:33 2023 +0000

    Fix staging of MOM data (#2028)

    During the update to stage_ic, the copying of the additional res_N files for
    0p25 was omitted. These are now properly copied.

    Resolves #2027

commit bd4c56d99c23c5c41f0bd5f8a980ef99ee160888
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Thu Nov 2 16:09:59 2023 -0400

    changed optional script name vars for ocean analysis (#2025)

commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6
Author: Kate Friedman <[email protected]>
Date:   Thu Nov 2 16:01:18 2023 -0400

    Create separate GSI monitor jobs and remove from vrfy job (#1983)

    This PR will move the GSI monitor tasks from the `vrfy` job into their own separate jobs in
    the rocoto mesh. This takes care of part of issue #235.

    Changes in this PR:

    1. Create new individual GSI monitor jobs in the rocoto mesh to match how it is done in
    operations. The new jobs are: `gdasverfozn`, `gdasverfrad`, `gdasvminmon`, and `gfsvminmon`.
    The names correspond to the names in operations and the ecf script names. The jobs are only
    added to cycled mode, none of the jobs are run in forecast-only mode.
    2. Updates to GSI monitor scripts:
      * Update `ush/jjob_header.sh` arguments in JJOB scripts to call new individual job names and
    configs.
      * Introduce `COM_*` variables and use of the `generate_com` utility. This results in the outputs
    landing in `COM` subfolders, like occurs in operations, instead of landing in the online archive.
      * Some variable cleanup in JJOB and ush scripts, includes cleaning up usage of `DATA` variable
    and its removal at the end of the jobs.
      * Add missing exit statements to `JGFS_ATMOS_VMINMON` and `JGDAS_ATMOS_VERFRAD`.
    3. Create new rocoto job scripts for the new individual GSI monitor jobs.
    4. Create new configs for the new individual GSI monitor jobs.
    5. Add new individual GSI monitor jobs to resource configuration, using the same resources as
    in operations.
    6. Move and rename GSI monitor job switches from `config.vrfy` to `config.base`. Also add
    switches to setup system. New switches to control each job being added to the rocoto mesh
    are: `DO_VERFOZN`, `DO_VERFRAD`, `DO_VMINMON`
    7. Add GSI monitor job output to archival job and into resulting HPSS tarballs or local tarballs.
    This now matches what is done in operations.
    8. Remove the GSI monitor tasks from the rocoto `vrfy` job and associated `config.vrfy`.

    Example output locations and files (not showing contents of oznmon/horiz or oznmon/time for
    brevity, see archival script for full list of output files):
    ```
    kate.friedman@dlogin09:/lfs/h2/emc/ptmp/kate.friedman/comrot/testmonitor2> ll gdas.20211221/00/products/atmos/*mon
    gdas.20211221/00/products/atmos/minmon:
    total 112
    -rw-r--r-- 1 kate.friedman emc 14030 Oct 25 15:00 2021122100.costs.txt
    -rw-r--r-- 1 kate.friedman emc 84932 Oct 25 15:00 2021122100.cost_terms.txt
    -rw-r--r-- 1 kate.friedman emc   808 Oct 25 15:00 2021122100.gnorms.ieee_d
    -rw-r--r-- 1 kate.friedman emc   808 Oct 25 15:00 2021122100.reduction.ieee_d
    -rw-r--r-- 1 kate.friedman emc    80 Oct 25 15:00 gnorm_data.txt

    gdas.20211221/00/products/atmos/oznmon:
    total 8
    drwxr-sr-x 2 kate.friedman emc 4096 Oct 25 15:05 horiz
    drwxr-sr-x 2 kate.friedman emc 4096 Oct 25 15:05 time

    gdas.20211221/00/products/atmos/radmon:
    total 21036
    -rw-r--r-- 1 kate.friedman emc      231 Oct 25 15:12 bad_diag.2021122100
    -rw-r--r-- 1 kate.friedman emc     9035 Oct 25 15:12 bad_pen.2021122100
    -rw-r--r-- 1 kate.friedman emc     1449 Oct 25 15:12 low_count.2021122100
    -rw-r--r-- 1 kate.friedman emc 20523403 Oct 25 15:07 radmon_angle.tar.gz
    -rw-r--r-- 1 kate.friedman emc   217272 Oct 25 15:08 radmon_bcoef.tar.gz
    -rw-r--r-- 1 kate.friedman emc   502151 Oct 25 15:10 radmon_bcor.tar.gz
    -rw-r--r-- 1 kate.friedman emc   264480 Oct 25 15:12 radmon_time.tar.gz
    -rw-r--r-- 1 kate.friedman emc      684 Oct 25 15:12 warning.2021122100
    kate.friedman@dlogin09:/lfs/h2/emc/ptmp/kate.friedman/comrot/testmonitor2> ll gfs.20211221/00/products/atmos/minmon/
    total 88
    -rw-r--r-- 1 kate.friedman emc 10530 Oct 25 14:55 2021122100.costs.txt
    -rw-r--r-- 1 kate.friedman emc 63882 Oct 25 14:55 2021122100.cost_terms.txt
    -rw-r--r-- 1 kate.friedman emc   808 Oct 25 14:55 2021122100.gnorms.ieee_d
    -rw-r--r-- 1 kate.friedman emc   608 Oct 25 14:55 2021122100.reduction.ieee_d
    -rw-r--r-- 1 kate.friedman emc    80 Oct 25 14:55 gnorm_data.txt
    ```

    Lingering work and considerations:

    1. Issue #1925
    2. Consider not hardcoding the list of types in archival and perhaps tie it to something reliable or
    configurable (maybe into `config.verfozn`?):
    `subtyplist="gome_metop-b omi_aura ompslp_npp ompsnp_n20 ompsnp_npp ompstc8_n20 ompstc8_npp sbuv2_n19"`

    Resolves #1908

commit 31b05a99b77d0f6eaa8b116485a41a43867d20e1
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Nov 2 12:23:32 2023 -0600

    Move analysis post to new stand-alone task (#1979)

    This PR addresses issue #1130. A new task `postanl.sh` has been added such that the
    `anl` post-processing is not it's own task within the Rocoto workflow. This change
    prevents the GDAS experiment from breaking due to failures caused by the `anl` not
    being available for the first cycle.

    Resolves #1130

commit 247cdf8c7e10e6c98f782799fc51c069b6474e70
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Nov 2 11:18:53 2023 -0600

    Corrects missing local variable reference (#2023)

    Fixes missing `$` in variable reference in archive job.

    Resolves #2022

commit 241742b246da1794646b68e41c3d6fe00b95dd07
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Wed Nov 1 14:19:55 2023 -0400

    Updates to prep ocean obs task (#1870)

commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Nov 1 12:09:33 2023 -0600

    No longer write archive lists COM (#2000)

    Changes the respective `.txt` files used for the HPSS archive to the `DATA` path. Each
    defined text file has been updated to explicitly write to `DATA` rather than `COM` such
    that the files are deleted rather than being archived.

    Resolves #760

commit 517b92f9c20c9e44abba3183325e35a95a7334a5
Author: David Huber <[email protected]>
Date:   Tue Oct 31 16:33:11 2023 -0400

    Parallelize the build scripts (#1998)

    Optimized/parallelized build scripts.

    A few notes:

    1) The default number of build jobs is 20, but one could argue for using 40.  When researching
    this, I looked up what the SRW is compiling with.  That system uses 40 cores, which seems a
    little excessive, but on testing the global workflow, the actual number of cores being used at
    any given time rarely exceeds 16 when running with 40 cores.  This is because the builds tend to
    use multiple threads in the beginning when compiling low-level modules while the higher-level
    modules are more or less serial AND because the GDASApp takes several minutes to initialize
    all of its subrepositories by which time the smaller builds are complete.

    2) I also updated checkout.sh so that all checkouts are simultaneous.  The CPU load for
    `git submodule` is quite low, so running 16 instead of 8 jobs at once is not much more expensive.

    3) To make this work, I had to add `-j` options to most of the build scripts.  The only exception is
    build_upp, for which the build script within the UPP is hard coded to use 6 cores.

    4) I fixed a few small bugs in the build scripts along the way.

    5) Lastly, this reduce the total build time from ~2.5 hours for the entire system (including GDAS
    and GSI in the same build) to ~40 minutes when running with `-j 40`.

    Resolves #1978

commit 67c050c201f92e855d09211e41a5f51ee1cb5230
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tu…
kayeekayee added a commit to kayeekayee/global-workflow that referenced this pull request Mar 20, 2024
@kayeekayee
Update realtime branch, gsl_ufs_rtdev1
3027db7 
   12Jan24 global-workflow
   UFS: 29Jan24, 625ac02
   FV3: 29Jan24, bd38c56 (GSL: 28Feb24 , a439cc7)
   UPP: 07Nov23, 78f369b
   UFS_UTILS: 22Dev23, ce385ce

   update pointers for ufs_model and ufs_utils
   add GSL C3_MYNN xml suite
   Change dt_inner=75 for any configuration running aerosol-aware Thompson (ltaerosol=.true.)

Squashed commit of the following:

commit db6a85e0ce36cec28714a4c9d6e13565253cf7bb
Author: jderrico-noaa <[email protected]>
Date:   Tue Mar 19 19:33:28 2024 +0000

    29Jan ufs_model.fd, 29Jan FV3 with C3 files

commit de7b382c4b259d99d39e8857cbcee7efe64c1956
Author: jderrico-noaa <[email protected]>
Date:   Mon Mar 18 16:23:05 2024 +0000

    update pointer for atmos_cubed_sphere to Feb 1 hash

commit 0fc27835205aaf57bdba228b1769e0ac7b37712e
Merge: b2c8ef81 db06f7c5
Author: jderrico-noaa <[email protected]>
Date:   Thu Mar 14 00:17:24 2024 +0000

    Merge branch 'gsl_ufs_dev' of https://github.com/NOAA-GSL/global-workflow into gsl_ufs_dev

commit b2c8ef81229b5e9b8e7592cb12c2f3e8e3179d92
Author: jderrico-noaa <[email protected]>
Date:   Wed Mar 13 23:51:45 2024 +0000

    ccpp pointer updates to framework and physics

commit 484a18df8c9022190c8900c80e40507a6771e314
Author: jderrico-noaa <[email protected]>
Date:   Wed Mar 13 23:43:18 2024 +0000

    ccpp pointer update in ufs_model.fd/FV3

commit db06f7c57d4cfc863352a4613c8260b0dffd9afe
Merge: 579f90c1 2dbd12a6
Author: Janet Derrico <[email protected]>
Date:   Wed Mar 13 15:55:48 2024 -0600

    Merge pull request #43 from kayeekayee/gsl_ufs_dev

    update GSL C3_MYNN files and change dt_inner=75

commit 2dbd12a695c4349071ee8470e597540e71bc0292
Author: kayee.wong <[email protected]>
Date:   Wed Mar 13 03:48:51 2024 +0000

    update GSL C3_MYNN files

commit 579f90c1e0e2896710046c1885f68560ea435fa6
Author: jderrico-noaa <[email protected]>
Date:   Thu Mar 7 19:20:46 2024 +0000

    update ufs_model.fd submodule pointer

commit 2f2622d68eb8444afde9c1ddad470cfee1b63b99
Author: jderrico-noaa <[email protected]>
Date:   Thu Mar 7 19:15:23 2024 +0000

    update ufs_model.fd submod pointer

commit 706a0c52bb11af78e016014550ebd6847cc0ee19
Author: jderrico-noaa <[email protected]>
Date:   Thu Mar 7 19:12:35 2024 +0000

    update ufs_model.fd/FV3 path

commit 352f188f095e19442ade1f3fd167ff2fed501cd2
Merge: 5a8edc76 96545dcb
Author: jderrico-noaa <[email protected]>
Date:   Thu Mar 7 17:58:38 2024 +0000

    update ufs model pointer

commit 5a8edc766f2f4d3e12c692069d46c02fd766c354
Author: jderrico-noaa <[email protected]>
Date:   Thu Mar 7 17:42:00 2024 +0000

    update FV3 and UPP

commit 96545dcb63e3f8f7dfc036961d818db15fa1a003
Author: jderrico-noaa <[email protected]>
Date:   Wed Mar 6 10:05:39 2024 -0700

    update pointer for ufs_model.fd

commit 25c026ef03a8d8c0db0b7368d2836f0b2e866eae
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 29 20:35:11 2024 +0000

    update ufs_model pointer

commit a28617a951c46b765aa996bfe4d28b554ec4e0a4
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 22 06:16:26 2024 +0000

    removed unneeded gsl directories

commit 6fb4f90e8572e98c977a1d2ab385f033111f3ea7
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 22 06:08:13 2024 +0000

    update ufs_utils.fd pointer

commit 9264f0c09239d046c5cd862d807e9b82f51dc3bd
Author: jderrico-noaa <[email protected]>
Date:   Wed Feb 21 19:33:26 2024 +0000

    update .gitmodules file

commit f8edfa966147506f2c207728039e3a736cb95415
Author: jderrico-noaa <[email protected]>
Date:   Wed Feb 21 19:30:47 2024 +0000

    update pointer to ufs_utils.fd

commit 5e0d2ab02d58e6a7a40db55a149a93008b28aa8b
Author: jderrico-noaa <[email protected]>
Date:   Wed Feb 21 19:25:52 2024 +0000

    update pointer to ufs_model.fd

commit ebc9e1d02987a1c6aa8cabedf2323642748fab3c
Merge: e7a81511 50cb1e6f
Author: Janet Derrico <[email protected]>
Date:   Thu Feb 15 13:40:33 2024 -0700

    Merge pull request #40 from kayeekayee/gsl_ufs_dev

    Merge to 2024 Jan 12 NOAA-EMC/develop and update to 2024 Jan 29 UFS

commit 50cb1e6f0c661e4c6e2ef0be4527cce58379b2c9
Author: kayee.wong <[email protected]>
Date:   Thu Feb 15 20:30:34 2024 +0000

    Add pygraf workflow.

commit 38b726125d49cff6cae4c0e5fff2438fc33143c5
Author: kayee.wong <[email protected]>
Date:   Wed Feb 14 17:43:15 2024 +0000

    Add double quote for the arguments when calling setup_expt.py.

commit 053f2025fb0b0679c7d4f84958973c1534ec050c
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:57:06 2024 +0000

    more fix.

commit 6f80ea2edc5444e275a79b371d02b6e98e963662
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:50:01 2024 +0000

    more bug fix.

commit 56e283f1f666a38a4a3b30e1528e96eeb5c622e7
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:40:02 2024 +0000

    Minor bug fix.

commit 2dcfed06ff6789eb77cf92e22b80f5475923fafc
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 23:19:03 2024 +0000

    Update parameter for c3 case
    Add c3 and mynn template

commit cc46b19ccc7cdb54878340eff79dda9e747abdf7
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 20:51:23 2024 +0000

    Update INFO.
    Add c3 SDF in the build.

commit a444ed48a23f24724853036e522b4437bf412c59
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 18:42:33 2024 +0000

    Update to UFS 2024 Jan 29 version.

commit 88595707c7521cdce37ae1cf78720a7827242b24
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 18:16:46 2024 +0000

    Minor bug fix.

commit baa0e9f10b132098d5134efaad712a51ebc26b83
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 17:59:27 2024 +0000

    Update parameters for setup_expt.py in p8_ugwpv1.sh to resdetatmos and comroot.

commit 5875f06903f82a47fafb05f89f840e3b099d18d8
Author: kayee.wong <[email protected]>
Date:   Tue Feb 13 17:51:11 2024 +0000

    Remove old gsl SDFs.
    Remove 'rrtmg_lw_pre' from C3 and MYNN SDFs.

commit 9e0d1342f4e1edce96c9b2baeec55c2cffb964cd
Author: kayee.wong <[email protected]>
Date:   Thu Feb 8 22:14:01 2024 +0000

    Merge to 2024 Jan 12 NOAA-EMC/develop.

    Squashed commit of the following:

    commit c59047614c29f6ec15a4d4a6fa1855929287debd
    Author: Rahul Mahajan <[email protected]>
    Date:   Fri Jan 12 19:21:02 2024 -0500

        Update hash to ufs-weather-model. The noahmptable.tbl was reorganized, so update link_workflow.sh to use the same one used in UFSWM RT (#2219)

    commit c041968e165c07da785376f1441374687b55d6cc
    Author: Kate Friedman <[email protected]>
    Date:   Fri Jan 12 12:09:35 2024 -0500

        Add ocean resolution to setup_expt invocation and retire/reduce COMROT/ROTDIR usage (#2214)

        Two series of updates:

        1) Update setup scripts to now allow users to provide ocean resolution
        2) Housekeeping to retire the `COMROT` variable, replacing it with other variables
        as needed, and reduce the `ROTDIR` variable usage.

        Both updates change options for the workflow setup API.

        Refs #2061

    commit 997f97816493d9ed0242e169b6dcf84e5c9338d6
    Author: AndrewEichmann-NOAA <[email protected]>
    Date:   Fri Jan 12 10:46:36 2024 -0500

        Allow use of ocean obs prep in WCDA cycling and remove R2D2 (#2215)

        Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same.
        Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS.
        Replaces the current R2D2 processing.

    commit 12a5bb192ab6282d44c008c06dc14947abd37249
    Merge: 4cb58020 6492c2da
    Author: David Huber <[email protected]>
    Date:   Fri Jan 12 09:26:27 2024 -0500

        Merge pull request #2217 from DavidHuber-NOAA/update/versions

        Update and clean up version and module files

    commit 6492c2da5f49bd31575d0bef5278c9a7f8ba3412
    Author: David Huber <[email protected]>
    Date:   Thu Jan 11 11:49:08 2024 -0600

        Update orion module/version files for met/metplus #2123

    commit 94c9937f0bff380b0ebd6acdcfd2509e1ae99389
    Author: DavidHuber <[email protected]>
    Date:   Thu Jan 11 17:42:53 2024 +0000

        Comment met/metplus out from Hera modulefile. #2123

    commit 8c32f8b7d00bba6e3e954f149e6548fb27713a3c
    Merge: a65e4c67 4cb58020
    Author: David Huber <[email protected]>
    Date:   Thu Jan 11 11:34:44 2024 -0600

        Merge branch 'develop' of github.com:noaa-emc/global-workflow into develop

    commit a65e4c675f21dbe72198d263e85e894e62b41e13
    Author: David Huber <[email protected]>
    Date:   Thu Jan 11 11:34:19 2024 -0600

        Initial update of version/module files #2123

    commit 4cb580201af68c1c0e2ae19faf0727dcbbe43b4d
    Author: souopgui <[email protected]>
    Date:   Wed Jan 10 08:30:22 2024 -0600

        Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh when running MPMD tasks (#2212)

        Fix OpenMP over-allocation of resources running MPMD tasks
        Co-authored-by: Innocent Souopgui <[email protected]>

    commit b056b531faee6929687cb8a588ffafa1a66426fb
    Author: TerrenceMcGuinness-NOAA <[email protected]>
    Date:   Mon Jan 8 17:28:05 2024 -0500

        Add Hercules as valid machine in CI scripts (#2207)

        Few updates to CI scripts to include names for hercules that where missed
        the first time.

    commit 6574d29a8c26b0695614874c344bccc5182363f4
    Author: Rahul Mahajan <[email protected]>
    Date:   Mon Jan 8 17:25:47 2024 -0500

        Fix invalid GH action and restart file name (#2210)

        Resolves a typo that leads to an invalid workflow yaml and fixes the restart filename in restart detection.

        Resolves #2205

    commit 69605eac299df381ea9e0e329654487e26380ff5
    Author: Rahul Mahajan <[email protected]>
    Date:   Mon Jan 8 17:00:28 2024 -0500

        Stop attempting to comment link to RTD for non-PRs (#2209)

        Adds a check so comments with a link to documentation are only generated
        for PRs.

    commit 4e160a895bfb31c281e21557dd86c13954a1a967
    Author: Rahul Mahajan <[email protected]>
    Date:   Mon Jan 8 13:10:15 2024 -0500

        Enable UPP for GOES processing (#2203)

        Wnables the creation of special master grib2 files from UPP for
        GOES processing

    commit c15875b6dbf685327af9316ee43b3d01f0fc815e
    Author: David Huber <[email protected]>
    Date:   Mon Jan 8 09:56:06 2024 -0500

        Port cycling to Hercules (#2196)

        Adds cycled support for Hercules (excluding gsi-monitor).
        Partially resolves #1588
        GSI monitoring is disabled on Hercules due to missing Perl modules. That will be enabled in a later PR.

    commit ef6827dd6abdab2996d1e19f9e0ff5d3071e0fdd
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jan 8 09:43:12 2024 -0500

        Refactor rocoto task XML creation (#2189)

        Refactors the rocoto task generation to be recursive.
        This will allow nested metatasks to loop over multiple variables, which is needed for GEFS product generation.

        As part of this refactor, there is no longer separate arguments to designate metatasks.
        Instead, task dicts can include a nested 'task_dict' as well as a 'var_dict' containing the variables to loop over.
        The nested task dict can then either have another layer, or be the innermost task.

        To accommodate the new recursive nature, some defaults that were previously defined in create_wf_task() had to be pushed down into the function that creates the innermost task.
        Also, former keywords have been absorbed by the task dict.

        Refs #823
        Refs #827

    commit 2b81cfac16f103fb29b3aeb9748941787abf7287
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jan 8 09:41:03 2024 -0500

        Update fix versions (#2198)

        Updates fix versions for a few components:
        - Update cice and mom6 versions to support C96/1p00 marine
        - Update wave to change betamax setting for glo_025 waves

        Resolves #2004
        Resolves #2107

commit e7a81511e37f86e881da020e06b95990b470d952
Merge: af47b77c 75ad3754
Author: Janet Derrico <[email protected]>
Date:   Thu Feb 1 13:14:02 2024 -0700

    Merge pull request #37 from jderrico-noaa/gsl_ufs_dev

    Add GSL archive script and correct typos/fixed paths

commit 75ad3754f8bef5411c2570b5e392cd08e95cb6cb
Author: jderrico-noaa <[email protected]>
Date:   Thu Feb 1 20:00:52 2024 +0000

    adding consistent [[ ]] for if statements

commit 67b99668c82a5fd8c42479b9b1bfe8b0bad0be25
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Feb 1 19:37:47 2024 +0000

     Updated HOMEgfs in GSL XML templates

commit 4d3719c086e7907a6eeff03112042d392e0d8c5e
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Feb 1 17:27:39 2024 +0000

     Correct syntax errors in GSL scripts

     Add new GSL archive script for archiving grib2 and ICs, but no netcdf files

commit 4309dd0b3b2d5625e7e1740d7cd3e39aacd5bc29
Author: Judy.K.Henderson <[email protected]>
Date:   Mon Jan 29 18:05:45 2024 +0000

     Add GSL diag tables to parm/ufs/fv3

     Update GSL template for hera

     Create EMC and GSL versions of files under workflow/rocoto
      - tasks.py, workflow_tasks.py

commit af47b77c7ee59a11c798995b4362b57e9096b090
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 02:07:43 2024 +0000

     Create GSL version of archive script

commit 529d9f71f97b6e643e76a53bc9871901ae861faf
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 01:37:09 2024 +0000

     Create GSL version of tracker.sh

     - this is a placeholder with changes from last year's HFIP experiment; will likely need to be updated in the future

commit 8457e12c313bee602265b863129734354b019271
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 01:27:42 2024 +0000

     Link config.base.emc.dyn_hera to config.base.emc.dyn

commit 7a05f5bd947944d8c3be828aeef9cc03bf9e073a
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 01:22:54 2024 +0000

     Create GSL version of hpssarch_gen.sh

     - assume we only run cold starts
     - archive only 0p25 grib2 files (no 0p50 opr 1p00)
     - assume no pgrb2b or flux files are created so no need to archive to HPSS

commit 98f5d6b16437e2a340bf16f83187e389a53f8bf0
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jan 27 00:24:06 2024 +0000

     Update workflow directory

     - add GSL template for jet (based on last year's experiment)
     - create EMC and GSL versions of yaml files under hosts; defaults point to GSL files

commit 38a7e5629ceeb23d399643a021e9a0a88468a07c
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 25 18:40:37 2024 +0000

     Update atmos_products configuration file for GSL

       - set downset to 1 so pgrb2b files are not created
       - set FLXGF to "NO" so interpolated sflux.1p00 files are not created

commit fe8a953658d092ce2b597e14f31678624606fd8a
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 25 17:02:25 2024 +0000

     Update nodes for gfsfcst task in GSL template for hera to match default configuration in config.ufs
       (12x12, 2 threads, 1 write group, 40 write tasks ==> 56 nodes)

     Increase walltime to 4:10 for gfsfcst task

commit 9d85b0f6d50e8ed142557fcb87c89d2e5d63c617
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 23 19:08:52 2024 +0000

     Added default location for PTMP/STMP in workflow/hosts/hera.yaml

     Added GSL XML template for hera

commit 1cf317d327fae78c5469712c9e5a6aa1ffa4b23b
Author: Judy.K.Henderson <[email protected]>
Date:   Wed Jan 17 22:33:13 2024 +0000

     Add sjet partition

     Make syntax consistent in "if" statements in config.resources

commit 2755e203751f50113849b06769173285e093290b
Author: Judy.K.Henderson <[email protected]>
Date:   Wed Jan 17 22:32:26 2024 +0000

      Update configuration files for GSL

     - create Hera and Jet versions of config.base.emc.dyn
     - correct typo in config.fcst
     - create different versions of config.ufs;
       default is 12x12, 2 threads, 1 write group/40 write tasks (56 nodes)

commit 3c0c126a376af31866a93aef4cdd0b4145150c58
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 16 17:32:25 2024 +0000

     Add script for remapping 1/4 degree grib2 grids to other domains

commit f217d4ed9a500e9a1bdcc17548729d972a1763ac
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 16 16:46:25 2024 +0000

     Update link script for ufs_utils.fd

commit 5b21b31900955013b4e8106d3ae906b9da93b361
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 16 16:45:25 2024 +0000

     Add GSL archive scripts for initial conditions

commit abb88baf9dd536a3b2ea1e24eaa99cbfe85af799
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 16 16:42:17 2024 +0000

     Move configuration files for getic and init from jobs/rocoto to parm/config/gfs

commit 45b235180719ab79d2514f0317207fbebfb8aedd
Author: Judy.K.Henderson <[email protected]>
Date:   Sun Jan 14 03:21:15 2024 +0000

     Add suite definition file for v17p8_ugwpv1_c3 to sorc/ufs_model.fd_gsl

commit 147b1fce99254dcb602c333cc559feaa9a396e81
Author: Judy.K.Henderson <[email protected]>
Date:   Sun Jan 14 01:57:22 2024 +0000

     Add getic and init tasks to workflow to create initial conditions in realtime

commit 4e4e50803d95566e1c7967cf4cfa575391d77f25
Author: Judy.K.Henderson <[email protected]>
Date:   Fri Jan 12 00:44:59 2024 +0000

     Change default HPSS_PROJECT to fim

     Change restart_interval_gfs to -1 so no files are written ro RERUN_RESTART directory

commit 791d7a27c6b12f07d9c12ce491338e3da59eb1d8
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 11 23:34:36 2024 +0000

     Add namelist parameter, nord_tr, for GSL suites

commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jan 11 23:31:22 2024 +0000

     Add changes for running v17p8_mynn

     - new field table, field_table_thompson_aero_tke_progsigma
     - updated namelist parameters in config.fcst

commit 982a1f02e3b880be43f4ae8a3f0ffbb34c056aea
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 02:26:22 2024 +0000

     Add experiment setup script for p8_ugwpv1

commit c5a3697d22fdbb02bb80ddffee2629dddc10c702
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 02:19:13 2024 +0000

     Add memory report to srun command in env/HERA.env

commit ece7e516ca65ec0240899e7d84321310a6887595
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 02:13:42 2024 +0000

     Updated GSL-specific files under ufs_utils.fd_gsl

commit 1b153fc95b93a16eb40b791be7322100fde4a3d4
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jan 9 01:52:56 2024 +0000

     Create new branch, gsl_ufs_dev, from dev_02jan24_9d901db

     Add initial GSL modifications
      - changes to workflow files
        * GSL paths, projects, entities
      - new FV3_GFS_v17_p8_ugwpv1_mynn suite definition file (SDF)
      - updated namelist parameters in ush/parsing_namelists_FV3.sh
      - create new GSL directories: ufs_model.fd_gsl and ufs_utils.fd_gsl
        * new SDFs, add instantaneous flux variables to grib2 configuration files
        * add Thompson tracers to initial conditions
      - new sync script: rsync_gsl.sh
      - new job files:  getic.sh, makeinit_link.sh
      - modify build_ufs.sh to include MYNN SDF

commit 9d901dbbff4d41586580316bdc094d24760119e6
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Jan 2 10:30:33 2024 -0700

    Stop Gempak pgrb2 spec from modifying $DATA (#2147)

    This PR addresses issue #1224. The following is accomplished:

    - Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time;
    - Shell linter exceptions are addressed accordingly;
    - The respective GEMPAK tasks is added to the Rocoto mesh.

    Resolves #1224

commit 31ad23527802f7d07171132cc620f7135c4d8cba
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Jan 2 10:27:30 2024 -0700

    Reorganize NPOESS scripts (#2166)

    This PR addresses issue #1226. The following is accomplished:

    - Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure
    of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated;
    - Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh`
    are moved accordingly; this specifically applies to the environment variable `FHOUR`,
    `SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`;
    - The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level
    (if necessary);
    - Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however,
    this may not be necessary (see `TODO` note within draft PR.

    Resolves #1226

commit 22bd82fa93b49e5ce98eb3f69123956dd5018049
Author: Kate Friedman <[email protected]>
Date:   Tue Jan 2 11:55:03 2024 -0500

    Orog fix file reorg and fix directory variable standardization (#2181)

    This PR makes updates to use the newly reorganized `orog/20231027`
    fix file version and standardizes the fix file directory variables.

    Changes:

    1. Update UFS_UTILS hash to ce385ce
    2. Update fix file version file to use new orog timestamp: `orog_ver=20231027`
    3. Add ".mx$(OCNRES)" to `oro_data` filenames in scripts
    4. Remove ".mx$(ocn_res)_frac" from the directory names for atmosphere
    resolutions under the `/orog` folder
    5. Adds fix file directory variables to `config.base`, many of which are pulled
    up out of lower scripts; introduce `FIXcpl`
    6. Renamed/replaced the following fix file directory variables:

    - `FV3JEDI_FIX` --> `FIXgdas`
    - `FIXfv3`, `FIX_orog` and `OROFIX` --> `FIXorog`
    - `FIX_ugwd` and `OROFIX_ugwd` --> `FIXugwd`
    - `FIX_am`, `FIXgsm`, `FIXSYND` --> `FIXam`
    - `FIX_lut` --> `FIXlut`
    - `FIX_aer` --> `FIXaer`
    - `FIX_SFC` --> `FIXsfc`
    - `FIX_DIR` --> `FIXgfs`
    - `RTMFIX` and `FIXCRTM` --> `CRTM_FIX` (is `CRTM_FIX` in crtm module,
    so not using `FIXcrtm`)

    7. Correct the defaults for `FIXwave` in wave JJOB scripts
    8. Update variable names in `*fixed_files.yaml` files, as well as update naming
    convention for `oro_data` files

    Resolves #1984
    Resolves #1981
    Resolves #2175

commit 03d03bf53b43914a55c384cb33eb06f6a9a443a6
Author: Andrew Collard <[email protected]>
Date:   Tue Jan 2 11:53:44 2024 -0500

    Remove HIRS from GSI processing (#2183)

    With the update to CRTM 2.4.0.1, an issue with versioning of CRTM HIRS
    files has been exposed. This is documented in JCSDA/crtm#42.

    As HIRS radiances are no longer used in the GSI, these data should be removed
    from processing until a suitable update to CRTM is available.

    Resolves #2182

commit a3c50998d35525a39a66d5592fbf327ab3569e8b
Author: Jessica Meixner <[email protected]>
Date:   Fri Dec 22 18:07:48 2023 -0500

    Update ufs-weather-model version  (#2186)

    * update model to latest version which includes needed bugfixes for HR3

commit 774c7302e618370ef578bec3ccabc70486d6da1b
Author: David Huber <[email protected]>
Date:   Fri Dec 22 11:34:53 2023 -0500

    Fix analysis post processing's handling of 0-padded negative integers (#2187)

    This screens for the analysis 'forecast' hour (-001) and handles the '-' and circumvents octal issues.

commit d1251360325faf75af9df0608557fcd10202a883
Author: Barry Baker <[email protected]>
Date:   Thu Dec 21 11:23:48 2023 -0500

    Fix for restoring cycling aerosols in fo-mode post COM refactor (#2179)

    - Update to COM reorg aerosol initialization job
    - Address bug in joining paths for data dependency in this job

    ---------

    Co-authored-by: Rahul Mahajan <[email protected]>

commit e55a05980709288d902ad1bd894164bfa5a18a65
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Dec 20 22:14:01 2023 -0500

    Stop calling ufs-utils link script (#2172)

    The `link_workflow.sh` script was calling the ufs_utils version of the
    same. That step is only necessary if a user is going to run one of the
    stand-alone ufs-utils, which is rare.

commit ef3e5ad7c63be1644c82333c95853c3caf2d8995
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Tue Dec 19 22:02:55 2023 -0500

    Fix handling of excluded hosts list (#2170)

    This PR fixes the issue with `create_experment.py` so that the yaml configuration
    file can have a string of list of strings when specifying the host name to exclude
    from the CI tests.

commit ea74a5719efc8f0fe631c5ff93426a4299a614f3
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Tue Dec 19 16:21:41 2023 -0500

    Add COMOUT_OBS to marine obs prep (#2173)

    Adds `COMOUT_OBS` (defined from `COM_OBS_TMPL`) to marine obs prep task to properly handle marine obs prep files. Used to keep obs after IODA conversion, QC, and other prep.

    Towards resolving NOAA-EMC/GDASApp#815

commit c2500feace0bb7c04ce67a90dd3182120ee67b2e
Author: David Huber <[email protected]>
Date:   Tue Dec 19 14:55:20 2023 -0500

    Return failed status if a build fails. (#2171)

    If any of the builds fail, this makes build_all.sh return the sum of the error codes encountered.

    Fixes #2168

commit 76fdd81cd84ed812181996a102379d8d964ba27a
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 19 13:24:34 2023 -0500

    Update index.rst for new GFSv16.3.12 in ops (#2169)

    Refs #2096

commit a81da33e8fe7541a36f68e7a4f14a384cadd36c8
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 19 10:22:21 2023 -0500

    Set place=shared for shared jobs on WCOSS2 (develop) (#2156)

    Set job as shared when not exclusive on WCOSS2

    WCOSS2 defaults to exclusive when it is not specified as
    either exclusive (place=exclhost) or shared (place=shared).
    Now set shared when job should be shared.

    Refs #2135

commit 89aea972f7964dac3f515e8070d7c534812c5fb4
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Dec 15 16:31:06 2023 -0500

    Update gfs-utils version for Hercules (#2163)

    An update of gfs-utils was misssing from the previous PR that added
    initial Hercules support (#2128).

    Also includes gfs-utils update for new marine post.

commit 9505cb4abc6ca2643a8ab254d14ca2000747fa44
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Thu Dec 14 16:15:31 2023 -0500

    CI Updates to support Hercules (#2155)

    If merged, this PR will update the CI scripts so they will run on Hercules for forecast only
    NOTE: This is a stop gap to issue #2131 until its block on #1588 is removed.

    Resolves #2154

commit c5ca82f04a2efae78389dec1c46b94ef4fb5bbe5
Author: Rahul Mahajan <[email protected]>
Date:   Thu Dec 14 16:05:33 2023 -0500

    Correct fbwind (#2161)

commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a
Author: Kate Friedman <[email protected]>
Date:   Thu Dec 14 12:06:23 2023 -0500

    Add MOS jobs to rocoto mesh (#2148)

    Create separate jobs for GFS MOS - extracted from now-retired vrfy job

    Refs #2068

commit bb6151aa50c27253cb9b8f0a6601ddd58526b8b3
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Dec 14 05:38:29 2023 -0500

    Replace checkout script with submodules (#2142)

    Replaces the checkout script with git submodules. This change brings workflow in
    line with other repos and git standards.

    Due to these changes, the build system is updated slightly. First, the options that
    were formerly used with `checkout.sh` to reduce unneeded builds (`-g` for GSI
    and `-u` for UFSDA) are moved to `build_all.sh` instead. This is needed since build
    all will not be able to key off directories existing or not to determine which com-
    ponents to build. Second, the partial build system is removed. It was rarely, if ever,
    used, and parts of it were already ignored with the previous changes to base builds
    off whether directories exist. The manage externals file is also removed since that is
    also not being used.

    Following these changes, clones/checkout will need to either be recursive, or
    `git submodule update` will need to be called separately to make sure components
    are properly checked out (non-exhaustive list):

    ```
    ## Checkout develop (method 1)
    git clone --recursive https://github.com/NOAA-EMC/global-workflow destination

    ## Checkout develop (method 2)
    git clone  --jobs 8 https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git submodule update --init --recursive --jobs 8

    ## Checkout existing branch some_branch (method 1)
    git clone --recursive  --jobs 8 -b some_branch https://github.com/NOAA-EMC/global-workflow destination

    ## Checkout existing branch some_branch (method 2)
    git clone https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git checkout --recurse-submodules some_branch

    ## Checkout existing branch some_branch (method 3)
    git clone https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git checkout some_branch
    git submodule update --init --recursive  --jobs 8

    ## Checkout new branch new_branch
    git clone https://github.com/NOAA-EMC/global-workflow destination
    cd destination
    git checkout -b new_branch
    git submodule update --init --recursive  --jobs 8
    ```

    The git ignore list had to be updated to use explicit paths as the wildcard paths pick
    up the ones that are now submodules.

    UFS creates files during the build process that are not in its ignore list, so that sub-
    module ignores the "dirty" state to avoid confusing users running `git status`.

    CI and documentation are also updated to reflect the changes.

    Resolves #2141

commit 1332188ce2409e012ec127d44880e49732f7f379
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Dec 13 09:32:57 2023 -0500

    Enable radar reflectivity output (#2143)

    Turns on radar reflectivity output from FV3. This eliminates missing values appearing in the grib2 files.

commit 24d898ec0ec0c7fcbda6966988f9a986f528ed14
Author: David Huber <[email protected]>
Date:   Wed Dec 13 09:32:24 2023 -0500

    Fix Hercules hostname (#2150)

    * Allow lower or upper hostname on hercules.
    * Add Hercules to issue template.

commit 2896bb8787698be28ad20f2298589e6e95eaf9fb
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 12 09:13:06 2023 -0500

    Fix module load typo (#2145)

    Fix typo with loading the crtm module in the UPP hack for WCOSS2

    Refs #2144

commit 29d34172a67d976f910e78158ff0337e1ef099ca
Author: Cory Martin <[email protected]>
Date:   Thu Dec 7 15:12:05 2023 -0500

    Update GDAS hash to most recent stable versions (#2138)

commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Dec 7 10:41:05 2023 -0700

    Corrected typo in a gempak job gempakncdcupapgif . (#2137)

commit 3483f550db1ae35a680de49f7485ce5a11902dd9
Author: Cory Martin <[email protected]>
Date:   Thu Dec 7 12:34:56 2023 -0500

    Add support for FGAT and IAU for aerosol DA (#1940)

commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9
Author: David Huber <[email protected]>
Date:   Thu Dec 7 12:33:46 2023 -0500

    Enable forecast-only experiments on Hercules (#2128)

    This add forecast-only support for Hercules to the global workflow. Partially satisfies #1588.
    Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

commit a29f751aed05312da3d80d396159bb5a906d6ce4
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Dec 6 13:45:56 2023 -0700

    Adds GEMPAK and related jobs to rocoto task mesh (#2127)

commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082
Author: Rahul Mahajan <[email protected]>
Date:   Tue Dec 5 15:47:52 2023 -0500

    Separate offline UPP from interpolated grib2 product generation (#2110)

    This PR:
    - Replaces the use of  `JGLOBAL_ATMOS_POST` with `JGLOBAL_ATMOS_UPP`
    and `JGLOBAL_ATMOS_PRODUCTS`.
    - Introduces `JGLOBAL_ATMOS_PRODUCTS` that is responsible for creating
    grib2 products from the master file produced by UPP (inline from the model,
    or offline by running `JGLOBAL_ATMOS_UPP`).  Rocoto job `atmos_products.sh`,
    ex-script `exglobal_atmos_products.sh` are also added along with a
    `config.atmos_products`. Updates are made to the relevant `env` files as well as
    `config.resources` to reflect the addition of this job.
    - reduces the number of cores needed appropriately for forecast products when
    there is no offline UPP necessary.
    - renames older `fv3gfs_dwn_nems.sh` to `interp_atmos_master.sh` and
    `inter_flux.sh` to `interp_atmos_sflux.sh`
    - removes `fv3gfs_downstream_nems.sh` as it is absorbed into
    `exglobal_atmos_products.sh`
    - removes no longer used scripts for `gfs_post.sh`, `gfs_transfer.sh` (DBN alerts
    are absorbed into `exglobal_atmos_products.sh`), `post.sh`,
    `JGLOBAL_ATMOS_POST`, `ex${RUN}_atmos_post.sh` scripts.
    - Rocoto workflow related scripts are updated to add `atmos_products` as a job.
    When `WRITE_DOPOST` is `.false.`, `upp.sh` job to run the UPP offline is also
    added.  Dependencies have been appropriately applied.
    - removes `PGB1F` option that creates 1-degree grib1 products that are no longer
    needed in GFSv17.

    The hacks from (now deleted) `post.sh` had to be reinstated in `upp.sh` to load the
    modules from UPP instead of `load_fv3gfs_modules.sh`.

commit 44186f594aaf5f8feea0eadd4c5c3b59de3a825e
Author: Kate Friedman <[email protected]>
Date:   Tue Dec 5 12:28:08 2023 -0500

    Update index.rst for new GFSv16.3.11 version (#2121)

    Refs #1356

commit e62a3a73cd22701962b7bf210fdfee37f37a5474
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Dec 5 09:08:12 2023 -0700

    Splits AWIPS jobs into seperate tasks (#2094)

    This PR addresses issue #1228. The following is accomplished:

    - Separate rocoto jobs have been created beneath `jobs/rocoto/`
    -- `awips_20sh` and `awips_g2sh`; these jobs replace `awips.sh` which was
    calling multiple J-jobs within the respective `awips.sh` scripts;
    - New tasks has been added to `workflow/rocoto/tasks.py` for the new
    AWIPS scripts;
    - The `gfs_cycled` and `gfs_forecast_only` modules beneath
    `workflow/rocoto` have been updated accordingly.

      Resolves #1228

commit 04d97e9aa7ab84b9754ab670074cfb19d543aa26
Author: Kate Friedman <[email protected]>
Date:   Mon Dec 4 13:38:30 2023 -0500

    Consolidate VMINMON and cleanup monitor scripts (#2088)

    This PR combines the GDAS and GFS versions of the VMINMON JJOB
    and ex-driver scripts into single GLOBAL/global versions. Additionally:

    * some further cleanup of the GSI-Monitor scripts is done; variable
    settings in ex-driver scripts are moved up to the JJOB level
    * the fix symlinks are consolidated into a new `fix/mon` subfolder (formerly
    `fix/gdas`) and copies of the gfs monitor fix files under `fix/products` are
    removed

    Resolves #1925

commit a286a11fdcbc31c8bc6d944890bc56294bc8caf6
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Dec 4 17:48:44 2023 +0000

    Robust CI Restarts (#2093)

    Improved CI robustness for reverting back to **CI-Ready** from any
    given state

    New Features:

    - Improved `scancel` routine (refactored into bash "subroutine")
    - Improved messaging (see below) when ever a user changes state
    - Any and all previous build scripts and running experiments are killed as
    a result of reset to **Ready**

    Resolves #2060

commit 73621e9b20b20f85e8b21e4c1e09ed1d80ecd46f
Author: David Huber <[email protected]>
Date:   Sun Dec 3 11:19:19 2023 -0500

    Upgrade to spack-stack/1.5.1 and Intel 2022 on non-production machines (#2084)

    Update module files to spack-stack/1.5.1 and compilers to Intel 2022+ on all non-production machines.

commit 6d548b250688861eb20a7e0dc852a0e4ba9e64f4
Author: jiandewang <[email protected]>
Date:   Thu Nov 30 12:00:21 2023 -0500

    Add variable tob in diag_table for ocean model output(#2105)

commit c19810cce252fcdb25fd9960c05b08b5f8d8b1ad
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Wed Nov 29 15:17:36 2023 -0500

    Added variables to config.prepoceanobs (#2101)

commit c2d78a61a224678fb804eed19f39d1f07408ae5f
Author: Kate Friedman <[email protected]>
Date:   Wed Nov 29 12:39:08 2023 -0500

    Add missing cut to VDATE setting in JGFS_ATMOS_VERIFICATION (#2098)

    Refs #2097

commit c1c025f91ddac73aea595cc9fa4dd0bea80575fc
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Nov 29 17:15:10 2023 +0000

    Add wave init to GEFS (#2089)

    Adds the wave init job to GEFS. Since the output would be the same for
    every member, the job is only run once for the control, then links are
    created in each of the member directories pointing to that copy.

    New ww3_multi and ww3_shell templates for GEFS are copied from the
    GFS versions.

    The GEFS restart frequency is changed to not be zero, and the comment
    about not setting it to zero is copied from the gfs config.base. The restart
    interval for the GEFS perturbed members is changed to equal that of the
    control.

    Also fixes a bug where `RUNwave` was not defined for ensemble forecasts,
    and another bug in the GEFS stage_ic dependency.

    Resolves #2017

commit 64a2470ce29b7d8d5cb85ebcb4048ff82958f64e
Author: Kate Friedman <[email protected]>
Date:   Wed Nov 29 11:26:34 2023 -0500

    Adjust permissions for jobs/JGFS_ATMOS_VERIFICATION (#2095)

    Add execute permissions (755)

commit 964b77bc6de67291973c2c70598a1f8cb72501c5
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Nov 28 18:45:51 2023 +0000

    Make proper j-job for MET+ (#2090)

    Creates a proper j-job for the metp job, moving much of the material
    from the `jobs/rocoto` script there (some of it within `jjob_header`).

    Also updates the old `COMIN` variable for the COM refactor (although
    it does not appear used in the verify scripts currently).

    This is a partial step towards restoring/improving metp functionality
    and remains untested.

    Refs #1575

commit 8c11eeb8556619e8db4e0efb6394ce5a2c1aae0f
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Nov 23 10:31:32 2023 -0700

    Adds FBWINDS support to global-workflow (#2082)

    This PR addresses issue #1221. The following was accomplished:

    - A new Rocoto job is added; `jobs/rocoto/fbwinds.sh`;
    - `workflow/applications/gfs_cycled.py` is updated to include the `fbwinds` task;
    - `workflow/applications/gfs_forecast_only.py` is updated to include the `fbwinds` task;
    -  A new function is added to `workflow/rocoto/gfs_tasks.py`, `fbwinds` is added as new GFS (only) task;
    - `workflow/rocoto/tasks.py` is updated to include the `fbwinds` task.

    Resolves #1221

commit 513db190d21f9ede0724a2cd5606372b1d7605de
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Nov 21 22:52:58 2023 -0700

    Adds NPOESS support to global-workflow (#2083)

    This PR addresses issue #1225. The following was accomplished:

    - A new Rocoto job is added; `jobs/rocoto/npoess.sh`;
    - `workflow/applications/gfs_cycled.py` is updated to include the `npoess`
    task;
    - `workflow/applications/gfs_forecast_only.py` is updated to include the
    `npoess` task;
    -  A new function is added to `workflow/rocoto/gfs_tasks.py`, `npoess` is
    added as new GFS (only) task;
    - `workflow/rocoto/tasks.py` is updated to include the `npoess` task.

    Resolves #1225

commit 62d8e99e77ffe44784f4c61c3f2296c6d1a72413
Author: Kate Friedman <[email protected]>
Date:   Fri Nov 17 20:25:50 2023 -0500

    Retire vrfy job (#2080)

    Retires the `vrfy` job from the global-workflow system. All associated
    scripts, configs, and references to the job are removed.

    Additionally, the switches listed in RTD were updated to reflect new
    ones added in other PRs for issue #235.

    Resolves #2069
    Refs #235

commit ea386abf11ecbacef407388e8d57e71b30148a35
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Nov 17 23:59:46 2023 +0000

    Enable different coupled settings for ensemble (#2030)

    Adds the ability to turn off some coupled components for the ensemble.

    To enable this, many settings are moved out of `config.fcst` and into `config.ufs`
    so they are calculated after any overrides of `DO_*` have been made. Some
    settings also had to be moved out of `config.base` for the same reason. A
    switch to turn on gocart is added to `config.ufs`, but unlike the other switches
    this one takes no arguments.

    The name of the ufs configure template used is converted from a partial file
    name to the full file name.

    Resolves #1692

commit fe792c0c9a1c46908cbd18c7e71eb836974cf1de
Author: Kate Friedman <[email protected]>
Date:   Fri Nov 17 17:19:16 2023 -0500

    Add --cpus-per-task to srun commands for Hera and Orion (#2077)

    This PR adds the `--cpus-per-task` flag to non-CFP `APRUN`/srun commands
    in the env files for Orion and Hera. This is needed as a result of an upgrade
    to SLURM on Orion that no longer exported the thread value to the
    environment. Issue #1996 was a hotfix to add this flag for the analysis job
    that was suddenly running slowly after the SLURM upgrade. A similar SLURM
    upgrade was done on Hera but the sysadmins there implemented a
    workaround so this issue did not appear there.

    This PR adds the `--cpus-per-task` flag for both machines...needed on Orion
    and as a safety measure on Hera.

    Also included in this PR is a fix to indentations in the
    `scripts/exglobal_diag.sh` script that was noticed during work for this PR.

    Timing differences were not observed for other jobs after adding this srun
    flag. Job timings were of a similar variation between control and test runs.
    Any potential additional speedup was not observed. The test runs also
    reproduced the control runs with `develop`.

    Resolves #2044

commit 42c943be305c297a56b104bb50727938c1ba688f
Author: Kate Friedman <[email protected]>
Date:   Fri Nov 17 15:41:34 2023 -0500

    Adjust modules in post.sh for WCOSS2 (#2079)

    On WCOSS2 the grib_util module is named a bit different and
    needs the libjpeg module loaded beforehand.

commit cd4e6a1987e7fd71dff06766f540b5d32c8b648d
Author: Jessica Meixner <[email protected]>
Date:   Fri Nov 17 11:49:32 2023 -0500

    Update ufs-weather-model and remove upp hack (#2071)

    Updates the model to the most recent commit of ufs-weather-model.  This
    should allow for the removal of the UPP hack that was added in PR #2042

    This required changing nems.configure -> ufs.configure.

    Resolves #1942

commit 5a2d97e142aa4999b122fd5a130c63e59ea9f8e2
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Nov 16 22:15:53 2023 +0000

    Fix check for existence of preamble functions (#2066)

    A few of the setup scripts were checking for the existence of
    functions set by the preamble before calling them so they could
    also be used stand-alone. However, the `type` command returns `1`
    if the function name does not exist, which will cause the script
    to die is `set -e` is on. Now the `type` command fails over to an
    empty string.

commit ed2ee7c2b1457b71b271a2c40f0dfa356e0f52f8
Author: WenMeng-NOAA <[email protected]>
Date:   Thu Nov 16 16:38:11 2023 -0500

    Update UPP products for GFS v17 (#1973)

    Updates of generating GFS V17 UPP products to support HR3:

    - Update g2tmpl to 1.0.12
    - Add changes to launch cfp on WCOSS2 to generate pgrb2/pgrb2b files
    - Changes for generating new products (MERRA2, six winter weather variables,
    1km HLCY, SDEN) in pgrb2 files

    Resolves #1965
    Resolves #1994

commit 635c4719e603538ce7cccf9ea6b31f3f84f20849
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Nov 16 20:35:30 2023 +0000

    Fix some rocoto dependencies (#2074)

    A few small errors/cleanup in the dependencies, mostly in fcst:

    A few small errors/cleanup have crept into the dependencies with recent changes,
    mostly in fcst:

    - Fixed the offset, as it would yield a string rocoto doesn't recognize when the
    interval was 24+ hrs
    - Removed the duplicate wave dependency. When `waveprep` is included, it
    depends on `waveinit` so there is no need to add a `waveinit` dependency.
    - Converted an interval in the archive job that was missed in #2039

    Resolves #2075

commit d4c7508260975c6b94fc92fd085f39d4faf3f027
Author: Rahul Mahajan <[email protected]>
Date:   Wed Nov 15 16:44:03 2023 -0500

    Fix missing _PREV in ocean restart file location (#2070)

commit 255616d37505c785bdddd5d3e39e8399110b626e
Author: mdtoyNOAA <[email protected]>
Date:   Wed Nov 15 12:02:09 2023 -0700

    Update functionality for Prototype HR3 UGWP (#1987)

    This PR adds/modifies namelist options and activates new 'ccpp' suite definition
    files for the updated Unified Gravity Wave Physics (UGWP) in the ufs-weather-
    model recently updated for HR3.  The changes to UGWP are the use of the GSL
    drag suite for orographic gravity wave drag (GWD) and blocking, as well as the
    new UGWP Version 1 non-stationary GWD.  See
    ufs-community/ufs-weather-model#1923 for details.

    Resolves #1986

commit be9085e62aae147e3c74602e2f82a99b374fc783
Author: Guillaume Vernieres <[email protected]>
Date:   Wed Nov 15 13:48:58 2023 -0500

    Save the required CICE history for the sea-ice DA (#2062)

    The hist_avg setting of CICE was changed to be an array.

commit 85f1f5131ffd70061231304ea477bde0559eb67b
Author: Guoqing Ge <[email protected]>
Date:   Wed Nov 15 11:47:21 2023 -0700

    Use assim_freq to configure "offset" in dependencies (#2039)

    Use the assim_freq from config.base to configure "offset" in dependencies
    instead of hard-coding them.

    Resolves #2038

commit 4e3d82ba3a1fa7cdd4443bcd4cf83b2f8835137c
Author: Kate Friedman <[email protected]>
Date:   Wed Nov 15 13:39:14 2023 -0500

    Resolve ENKF archive script bugs (#2065)

    Fix two bugs in the exgdas_enkf_earc.sh script:

    1) Replace ARCH_LIST with DATA to match changes done in PR #2000
    and update path to generated archive list files.
    2) Add status check and exit after script attempts to make tarball on HPSS.

    Refs #2064

commit 42d7f2f0c48fab898b764e09cfbbd7a9fabbae08
Author: Kate Friedman <[email protected]>
Date:   Tue Nov 14 17:54:29 2023 -0500

    Separate tracker and genesis jobs from vrfy job (#2058)

    This PR creates new individual jobs for the tracker and genesis jobs that are being
    pulled out of the `vrfy` job (issue #235). The `tracker` and `genesis` jobs will be on
    by default while the `genesis_fsu` job will be off by default. This mimics the current
    settings in the `vrfy` job.

    No enhancements or upgrades are made to the jobs themselves in this PR, only to
    separate them from the `vrfy` job. However, one change compared to how they
    currently run in the `vrfy` job is to no longer run the `tracker` in the gdas suite. This
    mimics how the `ens_tracker` package is run in operations (gfs only).

    Changes in this PR:

    1. Create rocoto job scripts for tracker/genesis jobs.
    2. Create configs for tracker/genesis jobs, as well as `config.tropcy` for shared
    settings.
    3. Add tracker/genesis jobs to `config.resources`; use resources from the ecf scripts
    for `ens_tracker` jobs in operations
    4. Add tracker/genesis jobs to rocoto setup for both cycled and forecast-only
    modes.
    5. Update arguments for `jjob_header.sh` script in tracker/genesis JJOB scripts to use
    specific job names and configs instead of vrfy.
    6. Rename `tracker_ver` to `ens_tracker_ver` in version files to mimic variable within
    tracker package.
    7. Rename and move tracker/genesis switches to `config.base`.
    8. Remove tracker/genesis jobs from `vrfy` job (`jobs/rocoto/vrfy` and `config.vrfy`).
    9. Reduce vrfy job resources to accommodate tasks having been removed.

    Refs #235
    Resolves #1988
    Resolves #2048

commit 0a0d6984e094d2a551d5d8331102142e7db13fc2
Author: Rahul Mahajan <[email protected]>
Date:   Tue Nov 14 14:08:26 2023 -0500

    Enable warm starting of the model for forecast-only mode (#2031)

    This PR:
    - adds an option to warm|cold start the ufs-weather-model when setting up an experiment for GFS/GEFS
    - adds the capability to stage FV3 restarts when the atmosphere is warm started from FV3 restarts. This would be used in the GEFS free-forecast for part of the reforecast capability.
    - If a coupled model is warm started for the atmosphere, also check if mediator restarts are present. If so, stage mediator restarts to allow restarting the coupled model.

    Fixes #2016

commit 2cd6a589305a9ac9d3a9a0d2136e66e42f09d3bf
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Nov 14 12:05:20 2023 -0700

    Moves UFS WM configuration files to `COM_CONF` (#2054)

    The UFS weather-model (WM) files are place in the COM_CONF path rather than the respective component model COM history paths.
    Resolves #2015

commit 6f1693081662f241fafc930b1afc88125f7f5aff
Author: Kate Friedman <[email protected]>
Date:   Tue Nov 14 11:15:02 2023 -0500

    Refine fit2obs job in rocoto mesh (#2047)

    This PR adjusts the `fit2obs` job in the rocoto mesh to better define when it exists
    and how the archive job dependencies accommodate it not being in the first half
    cycle.

    Changes in PR:

    1. Remove the `fit2obs` job from the first half cycle `cycledef`.
    2. Adjust the archive job dependencies to now include the `fit2obs` job in the new
    logic check added in PR #1983. The `gdasarch` job in the first half cycle will check if
    `gdasfit2obs` is complete OR no prior cycle exists. Also cleaned up this new logic
    check block some to make it a tad simpler.
    3. Also, fix the addition of the `fit2obs` config to the config list in setup scripts. Now
    tied to whether `fit2obs` job is on instead of always adding the config to the list.

    Resolves #2043

commit 5730a71fa5d311e49d9bb11528b500f27f33d69d
Author: Henry R. Winterbottom <[email protected]>
Date:   Tue Nov 14 09:13:11 2023 -0700

    Add `waveinit` and `waveprep` to half-cycle. (#2037)

    This PR addresses issue #1444. The `waveinit` and `waveprep` tasks have been added to
    the GDAS have cycle. The downstream dependencies for the respective GFS and GDAS
    forecast tasks have been removed.

    Resolves #1444

commit 28d2e93c3857de95b0309a089cd7dac736ccaded
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Nov 14 16:11:47 2023 +0000

    Update wave IC source for C384 (#2055)

    The default wave grid for C384 has changed since P8, so a single wave
    IC on the new grid is available under a different IC name.

commit 81dd2d9855091315611106a5afbdaeaa15e6e4ae
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Nov 9 17:19:57 2023 +0000

    Fix analysis and post on Orion (#2046)

    Fixes a couple things to get workflow to work on Orion again:

    First, while #2042 allowed post to be built, the `upp.x` executable would fail due
    to a missing library. Now post jobs (temporarily) uses the UPP modules (plus
    others needed for runtime) instead of the normal workflow runtime module. This
    should actually fix #2041. This hack can likely be removed once we move to
    spack-stack.

    Second, the launcher command for the analysis jobs on Orion are updated to
    specify the number of CPUs per task. This was necessary as a recent slurm update
    on Orion discontinued reading that value from the scheduler. Other jobs will be
    handled later (see #2044).

    Additionally, a change is made to `module-setup.sh` that will eliminate the
    annoyance of `gw_setup.sh` breaking tab completion because undefined variable
    checking was turned on for the script but not back off.

    Resolves #1996
    Resolves #2041
    Refs #2044

commit 13d06ded4155cba2d08ef2a2cd553024c5abe29d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Nov 8 18:25:47 2023 +0000

    Hack UPP version (#2042)

    The stack UPP was using on Orion was recently deleted, leaving us
    unable to build the UFS verison of UPP there. UPP has an updated
    version using spack-stack that works, so the checkout script is
    modified to check out that version of UPP after UFS has been
    checked out.

    This temporary hack can be removed once we move to a UFS version
    that advances the UPP version to or beyond 78f369b.

    Resolves #2041

commit 20f6eceb8ff58f84174a27eb849c1d74566a3e03
Author: jiandewang <[email protected]>
Date:   Wed Nov 8 11:14:55 2023 -0500

    Add basic C1152 settings (#2020)

    Adding C1152 setting in host.yaml, config.base and config.stage_ic so that can run C1152 S2SW.

    Resolves #2019

commit 5183c43bbbd07285869feacb49d8680afe85929a
Author: Barry Baker <[email protected]>
Date:   Tue Nov 7 01:14:40 2023 -0500

    Update UFS for dust fix and remove nitrates by default  (#1989)

    This PR updates the `ufs-weather-model` to the latest hash that included the dust fix (PR #1922).
    Along with this I removed the nitrates by default in support of the GEFSv13 EP4 and EP5
    experiments. Removed unneeded inputs that should help with speed improvements.

commit 34a73cf2ed5afefc776d9cc73b6ebf439122a1bb
Author: David Huber <[email protected]>
Date:   Mon Nov 6 14:00:51 2023 -0500

    Reduce gdas builds to 8 #2029 (#2036)

    Reduce the default number of build jobs for the GDASApp to 8 from 16.

    This is needed for Orion as the build crashes during a linking step.  Though not verified, it
    appears this may be caused by using too much memory with 16 builds.  The issue disappears
    when using 8 build jobs.

    Resolves #2029

commit 75269e4bb9764b81589efc7d703825b80e74c8f5
Author: TerrenceMcGuinness-NOAA <[email protected]>
Date:   Mon Nov 6 17:34:47 2023 +0000

    Streamline CI reporting to PRs (#2026)

    Cleaned up the logs for CI PRs sent to the GitHub Messages:

    - Eliminates redundant accumulative reporting
    - Reports on all created or skipped experiment instantiations in a single message
    - Gives one line report once  for each experiment completion
    - Single final report completion of CI

    See some examples in forked [PR 195](https://github.com/TerrenceMcGuinness-NOAA/global-workflow/pull/195)

    Resolves #2007

commit 8d55126bb0b27c79c8bee7f72b014abd34950ff9
Author: Guillaume Vernieres <[email protected]>
Date:   Fri Nov 3 17:06:09 2023 -0400

    Implement IAU Cycling Type with Marine Data Assimilation Enabled (#1944)

    Allows cycling in IAU mode with the S2S UFS model, soca and the GSI.

    Most of the work related to making IAU work was done by @JessicaMeixner-NOAA . Thanks @JessicaMeixner-NOAA !

    Resolves #1943
    Refs #1776

commit 2563806821d4ae3b57120bc61aa0575139a708f0
Author: jiandewang <[email protected]>
Date:   Fri Nov 3 11:49:37 2023 -0400

    Add two ucx modules in load_ufswm_modules.sh to solve C768 and C1152 S2SW job hanging issue on WCOSS2 (#2021)

commit cbdc09711a83493f363a737d1e3e46c48a09719d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Nov 3 04:09:33 2023 +0000

    Fix staging of MOM data (#2028)

    During the update to stage_ic, the copying of the additional res_N files for
    0p25 was omitted. These are now properly copied.

    Resolves #2027

commit bd4c56d99c23c5c41f0bd5f8a980ef99ee160888
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Thu Nov 2 16:09:59 2023 -0400

    changed optional script name vars for ocean analysis (#2025)

commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6
Author: Kate Friedman <[email protected]>
Date:   Thu Nov 2 16:01:18 2023 -0400

    Create separate GSI monitor jobs and remove from vrfy job (#1983)

    This PR will move the GSI monitor tasks from the `vrfy` job into their own separate jobs in
    the rocoto mesh. This takes care of part of issue #235.

    Changes in this PR:

    1. Create new individual GSI monitor jobs in the rocoto mesh to match how it is done in
    operations. The new jobs are: `gdasverfozn`, `gdasverfrad`, `gdasvminmon`, and `gfsvminmon`.
    The names correspond to the names in operations and the ecf script names. The jobs are only
    added to cycled mode, none of the jobs are run in forecast-only mode.
    2. Updates to GSI monitor scripts:
      * Update `ush/jjob_header.sh` arguments in JJOB scripts to call new individual job names and
    configs.
      * Introduce `COM_*` variables and use of the `generate_com` utility. This results in the outputs
    landing in `COM` subfolders, like occurs in operations, instead of landing in the online archive.
      * Some variable cleanup in JJOB and ush scripts, includes cleaning up usage of `DATA` variable
    and its removal at the end of the jobs.
      * Add missing exit statements to `JGFS_ATMOS_VMINMON` and `JGDAS_ATMOS_VERFRAD`.
    3. Create new rocoto job scripts for the new individual GSI monitor jobs.
    4. Create new configs for the new individual GSI monitor jobs.
    5. Add new individual GSI monitor jobs to resource configuration, using the same resources as
    in operations.
    6. Move and rename GSI monitor job switches from `config.vrfy` to `config.base`. Also add
    switches to setup system. New switches to control each job being added to the rocoto mesh
    are: `DO_VERFOZN`, `DO_VERFRAD`, `DO_VMINMON`
    7. Add GSI monitor job output to archival job and into resulting HPSS tarballs or local tarballs.
    This now matches what is done in operations.
    8. Remove the GSI monitor tasks from the rocoto `vrfy` job and associated `config.vrfy`.

    Example output locations and files (not showing contents of oznmon/horiz or oznmon/time for
    brevity, see archival script for full list of output files):
    ```
    kate.friedman@dlogin09:/lfs/h2/emc/ptmp/kate.friedman/comrot/testmonitor2> ll gdas.20211221/00/products/atmos/*mon
    gdas.20211221/00/products/atmos/minmon:
    total 112
    -rw-r--r-- 1 kate.friedman emc 14030 Oct 25 15:00 2021122100.costs.txt
    -rw-r--r-- 1 kate.friedman emc 84932 Oct 25 15:00 2021122100.cost_terms.txt
    -rw-r--r-- 1 kate.friedman emc   808 Oct 25 15:00 2021122100.gnorms.ieee_d
    -rw-r--r-- 1 kate.friedman emc   808 Oct 25 15:00 2021122100.reduction.ieee_d
    -rw-r--r-- 1 kate.friedman emc    80 Oct 25 15:00 gnorm_data.txt

    gdas.20211221/00/products/atmos/oznmon:
    total 8
    drwxr-sr-x 2 kate.friedman emc 4096 Oct 25 15:05 horiz
    drwxr-sr-x 2 kate.friedman emc 4096 Oct 25 15:05 time

    gdas.20211221/00/products/atmos/radmon:
    total 21036
    -rw-r--r-- 1 kate.friedman emc      231 Oct 25 15:12 bad_diag.2021122100
    -rw-r--r-- 1 kate.friedman emc     9035 Oct 25 15:12 bad_pen.2021122100
    -rw-r--r-- 1 kate.friedman emc     1449 Oct 25 15:12 low_count.2021122100
    -rw-r--r-- 1 kate.friedman emc 20523403 Oct 25 15:07 radmon_angle.tar.gz
    -rw-r--r-- 1 kate.friedman emc   217272 Oct 25 15:08 radmon_bcoef.tar.gz
    -rw-r--r-- 1 kate.friedman emc   502151 Oct 25 15:10 radmon_bcor.tar.gz
    -rw-r--r-- 1 kate.friedman emc   264480 Oct 25 15:12 radmon_time.tar.gz
    -rw-r--r-- 1 kate.friedman emc      684 Oct 25 15:12 warning.2021122100
    kate.friedman@dlogin09:/lfs/h2/emc/ptmp/kate.friedman/comrot/testmonitor2> ll gfs.20211221/00/products/atmos/minmon/
    total 88
    -rw-r--r-- 1 kate.friedman emc 10530 Oct 25 14:55 2021122100.costs.txt
    -rw-r--r-- 1 kate.friedman emc 63882 Oct 25 14:55 2021122100.cost_terms.txt
    -rw-r--r-- 1 kate.friedman emc   808 Oct 25 14:55 2021122100.gnorms.ieee_d
    -rw-r--r-- 1 kate.friedman emc   608 Oct 25 14:55 2021122100.reduction.ieee_d
    -rw-r--r-- 1 kate.friedman emc    80 Oct 25 14:55 gnorm_data.txt
    ```

    Lingering work and considerations:

    1. Issue #1925
    2. Consider not hardcoding the list of types in archival and perhaps tie it to something reliable or
    configurable (maybe into `config.verfozn`?):
    `subtyplist="gome_metop-b omi_aura ompslp_npp ompsnp_n20 ompsnp_npp ompstc8_n20 ompstc8_npp sbuv2_n19"`

    Resolves #1908

commit 31b05a99b77d0f6eaa8b116485a41a43867d20e1
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Nov 2 12:23:32 2023 -0600

    Move analysis post to new stand-alone task (#1979)

    This PR addresses issue #1130. A new task `postanl.sh` has been added such that the
    `anl` post-processing is not it's own task within the Rocoto workflow. This change
    prevents the GDAS experiment from breaking due to failures caused by the `anl` not
    being available for the first cycle.

    Resolves #1130

commit 247cdf8c7e10e6c98f782799fc51c069b6474e70
Author: Henry R. Winterbottom <[email protected]>
Date:   Thu Nov 2 11:18:53 2023 -0600

    Corrects missing local variable reference (#2023)

    Fixes missing `$` in variable reference in archive job.

    Resolves #2022

commit 241742b246da1794646b68e41c3d6fe00b95dd07
Author: AndrewEichmann-NOAA <[email protected]>
Date:   Wed Nov 1 14:19:55 2023 -0400

    Updates to prep ocean obs task (#1870)

commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd
Author: Henry R. Winterbottom <[email protected]>
Date:   Wed Nov 1 12:09:33 2023 -0600

    No longer write archive lists COM (#2000)

    Changes the respective `.txt` files used for the HPSS archive to the `DATA` path. Each
    defined text file has been updated to explicitly write to `DATA` rather than `COM` such
    that the files are deleted rather than being archived.

    Resolves #760

commit 517b92f9c20c9e44abba3183325e35a95a7334a5
Author: David Huber <[email protected]>
Date:   Tue Oct 31 16:33:11 2023 -0400

    Parallelize the build scripts (#1998)

    Optimized/parallelized build scripts.

    A few notes:

    1) The default number of build jobs is 20, but one could argue for using 40.  When researching
    this, I looked up what the SRW is compiling with.  That system uses 40 cores, which seems a
    little excessive, but on testing the global workflow, the actual number of cores being used at
    any given time rarely exceeds 16 when running with 40 cores.  This is because the builds tend to
    use multiple threads in the beginning when compiling low-level modules while the higher-level
    modules are more or less serial AND because the GDASApp takes several minutes to initialize
    all of its subrepositories by which time the smaller builds are complete.

    2) I also updated checkout.sh so that all checkouts are simultaneous.  The CPU load for
    `git submodule` is quite low, so running 16 instead of 8 jobs at once is not much more expensive.

    3) To make this work, I had to add `-j` options to most of the build scripts.  The only exception is
    build_upp, for which the build script within the UPP is hard coded to use 6 cores.

    4) I fixed a few small bugs in the build scripts along the way.

    5) Lastly, this reduce the total build time from ~2.5 hours for the entire system (including GDAS
    and GSI in the same build) to ~40 minutes when running with `-j 40`.

    Resolves #1978

commit 67c050c201f92e8…
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A couple of Global Workflow tasks are failing on S4 due to over-threading by OpenMP
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