Update realtime branch, gsl_ufs_rt

- 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…

.github/workflows/docs.yaml

@@ -17,7 +17,7 @@ on:
 jobs:
 
   documentation:
-    
+
     permissions:
       pull-requests: 'write'
 
@@ -56,7 +56,8 @@ jobs:
         path: artifact/doc_warnings.log
         if-no-files-found: ignore
 
-    - name: Comment ReadDocs
+    - name: Comment ReadDocs Link in PR
+      if: github.event_name == 'pull_request'
       uses: actions/github-script@v6
       with:
         script: |
@@ -68,5 +69,5 @@ jobs:
            issue_number: context.issue.number,
            owner: context.repo.owner,
            repo: context.repo.repo,
-           body: message 
-          })     
+           body: message
+          })

.gitmodules

@@ -1,6 +1,6 @@
 [submodule "sorc/ufs_model.fd"]
 	path = sorc/ufs_model.fd
-	url = https://github.com/ufs-community/ufs-weather-model
+	url = https://github.com/NOAA-GSL/ufs-weather-model
 	ignore = dirty
 [submodule "sorc/wxflow"]
 	path = sorc/wxflow
@@ -10,7 +10,7 @@
 	url = https://github.com/NOAA-EMC/gfs-utils
 [submodule "sorc/ufs_utils.fd"]
 	path = sorc/ufs_utils.fd
-	url = https://github.com/ufs-community/UFS_UTILS.git
+	url = https://github.com/NOAA-GSL/UFS_UTILS.git
 [submodule "sorc/verif-global.fd"]
 	path = sorc/verif-global.fd
 	url = https://github.com/NOAA-EMC/EMC_verif-global.git

INFO

@@ -0,0 +1,25 @@
+03-13-24
+========
+   29Feb24 global-workflow
+   UFS: 29Jan24, 625ac02
+   FV3: 06Jan24, 5e7f196
+   UPP:  07Nov23, 78f369b
+
+   update pointers to FV3 and UPP
+   add GSL C3_MYNN xml suite
+
+02-13-24
+========
+   12Jan24 global-workflow
+   UFS: 29Jan24, 625ac02
+   FV3: 06Jan24, 5e7f196
+   UPP:  07Nov23, 78f369b
+
+01-08-24
+========
+  02Jan24 global-workflow
+  UFS: 21Dec23, 991d652
+  UPP:  07Nov23, 78f369b
+
+  use submodules instead of checkout.sh
+  gfsatmos_products replaces gfspost tasks

ci/cases/pr/C48_ATM.yaml

@@ -5,8 +5,8 @@ experiment:
 arguments:
   pslot: {{ 'pslot' | getenv }}
   app: ATM
-  resdet: 48
-  comrot: {{ 'RUNTESTS' | getenv }}/COMROT
+  resdetatmos: 48
+  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   idate: 2021032312
   edate: 2021032312

ci/cases/pr/C48_S2SW.yaml

@@ -5,8 +5,9 @@ experiment:
 arguments:
   pslot: {{ 'pslot' | getenv }}
   app: S2SW
-  resdet: 48
-  comrot: {{ 'RUNTESTS' | getenv }}/COMROT
+  resdetatmos: 48
+  resdetocean: 5.0
+  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   idate: 2021032312
   edate: 2021032312

ci/cases/pr/C48_S2SWA_gefs.yaml

@@ -5,12 +5,13 @@ experiment:
 arguments:
   pslot: {{ 'pslot' | getenv }}
   app: S2SWA
-  resdet: 48
-  resens: 48
+  resdetatmos: 48
+  resdetocean: 5.0
+  resensatmos: 48
   nens: 2
   gfs_cyc: 1
   start: cold
-  comrot: {{ 'RUNTESTS' | getenv }}/COMROT
+  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   idate: 2021032312
   edate: 2021032312

ci/cases/pr/C96C48_hybatmDA.yaml

@@ -5,9 +5,10 @@ experiment:
 arguments:
   pslot: {{ 'pslot' | getenv }}
   app: ATM
-  resdet: 96
-  resens: 48
-  comrot: {{ 'RUNTESTS' | getenv }}/COMROT
+  resdetatmos: 96
+  resdetocean: 5.0
+  resensatmos: 48
+  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48
   idate: 2021122018
@@ -16,6 +17,3 @@ arguments:
   gfs_cyc: 1
   start: cold
   yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
-
-skip_ci_on_hosts:
-  - hercules

ci/cases/pr/C96_atm3DVar.yaml

@@ -5,16 +5,13 @@ experiment:
 arguments:
   pslot: {{ 'pslot' | getenv }}
   app: ATM
-  resdet: 96
-  comrot: {{ 'RUNTESTS' | getenv }}/COMROT
+  resdetatmos: 96
+  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  icsdir: ${ICSDIR_ROOT}/C96C48
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48
   idate: 2021122018
   edate: 2021122106
   nens: 0
   gfs_cyc: 1
   start: cold
   yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
-
-skip_ci_on_hosts:
-  - hercules

ci/cases/weekly/C384C192_hybatmda.yaml

@@ -5,9 +5,10 @@ experiment:
 arguments:
   pslot: {{ 'pslot' | getenv }}
   app: ATM
-  resdet: 384
-  resens: 192
-  comrot: {{ 'RUNTESTS' | getenv }}/COMROT
+  resdetatmos: 384
+  resdetocean: 0.25
+  resensatmos: 192
+  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C384C192
   idate: 2023040118

ci/cases/weekly/C384_S2SWA.yaml

@@ -5,8 +5,9 @@ experiment:
 arguments:
   pslot: {{ 'pslot' | getenv }}
   app: S2SWA
-  resdet: 384
-  comrot: {{ 'RUNTESTS' | getenv }}/COMROT
+  resdetatmos: 384
+  resdetocean: 0.5
+  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   idate: 2016070100
   edate: 2016070100

ci/cases/weekly/C384_atm3DVar.yaml

@@ -5,9 +5,10 @@ experiment:
 arguments:
   pslot: {{ 'pslot' | getenv }}
   app: ATM
-  resdet: 384
-  resens: 192
-  comrot: {{ 'RUNTESTS' | getenv }}/COMROT
+  resdetatmos: 384
+  resdetocean: 0.25
+  resensatmos: 192
+  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C384C192
   idate: 2023040118

ci/platforms/gefs_ci_defaults.yaml

@@ -1,4 +1,4 @@
 defaults:
   !INC {{ HOMEgfs }}/parm/config/gefs/yaml/defaults.yaml
 base:
-  ACCOUNT: ${SLURM_ACCOUNT}
+  ACCOUNT: {{ 'SLURM_ACCOUNT' | getenv }}

ci/platforms/gfs_defaults_ci.yaml

@@ -1,4 +1,4 @@
 defaults:
   !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
 base:
-  ACCOUNT: ${SLURM_ACCOUNT}
+  ACCOUNT: {{ 'SLURM_ACCOUNT' | getenv }}

ci/scripts/check_ci.sh

@@ -22,7 +22,7 @@ REPO_URL="https://github.com/NOAA-EMC/global-workflow.git"
 
 source "${ROOT_DIR}/ush/detect_machine.sh"
 case ${MACHINE_ID} in
-  hera | orion)
+  hera | orion | hercules)
    echo "Running Automated Testing on ${MACHINE_ID}"
    source "${ROOT_DIR}/ci/platforms/config.${MACHINE_ID}"
    ;;
@@ -149,7 +149,7 @@ for pr in ${pr_list}; do
     if [[ "${num_done}" -eq  "${num_cycles}" ]]; then
       #Remove Experment cases that completed successfully
       rm -Rf "${pslot_dir}"
-      rm -Rf "${pr_dir}/RUNTESTS/COMROT/${pslot}"
+      rm -Rf "${pr_dir}/RUNTESTS/COMROOT/${pslot}"
       rm -f "${output_ci_single}"
       # echo "\`\`\`" > "${output_ci_single}"
       DATE=$(date +'%D %r')

ci/scripts/driver.sh

@@ -34,7 +34,7 @@ export PS4='+ $(basename ${BASH_SOURCE})[${LINENO}]'
 
 source "${ROOT_DIR}/ush/detect_machine.sh"
 case ${MACHINE_ID} in
-  hera | orion)
+  hera | orion | hercules)
     echo "Running Automated Testing on ${MACHINE_ID}"
     source "${ROOT_DIR}/ci/platforms/config.${MACHINE_ID}"
     ;;
@@ -173,7 +173,7 @@ for pr in ${pr_list}; do
   # we need to exit this instance of the driver script
   #################################################################
   if [[ ${ci_status} -ne 0 ]]; then
-     build_PID_check=$("${ROOT_DIR}/ci/scripts/pr_list_database.py" --display "{pr}" --dbfile "${pr_list_dbfile}" | awk '{print $4}' | cut -d":" -f1) || true
+     build_PID_check=$("${ROOT_DIR}/ci/scripts/pr_list_database.py" --display "${pr}" --dbfile "${pr_list_dbfile}" | awk '{print $4}' | cut -d":" -f1) || true
      if [[ "${build_PID_check}" -ne "$$" ]]; then
         echo "Driver build PID: ${build_PID_check} no longer running this build ... exiting"
         exit 0

ci/scripts/driver_weekly.sh

@@ -38,7 +38,7 @@ export PS4='+ $(basename ${BASH_SOURCE[0]})[${LINENO}]'
 
 source "${ROOT_DIR}/ush/detect_machine.sh"
 case ${MACHINE_ID} in
-  hera | orion)
+  hera | orion | hercules)
     echo "Running Automated Testing on ${MACHINE_ID}"
     source "${ROOT_DIR}/ci/platforms/config.${MACHINE_ID}"
     ;;

ci/scripts/run-check_ci.sh

@@ -12,12 +12,12 @@ pslot=${2:-${pslot:-?}}        # Name of the experiment being tested by this scr
 
 # TEST_DIR contains 2 directories;
 # 1. HOMEgfs: clone of the global-workflow
-# 2. RUNTESTS: A directory containing EXPDIR and COMROT for experiments
+# 2. RUNTESTS: A directory containing EXPDIR and COMROOT for experiments
 # # e.g. $> tree ./TEST_DIR
 # ./TEST_DIR
 # ├── HOMEgfs
 # └── RUNTESTS
-#     ├── COMROT
+#     ├── COMROOT
 #     │   └── ${pslot}
 #     └── EXPDIR
 #         └── ${pslot}

ci/scripts/run_ci.sh

@@ -20,7 +20,7 @@ export PS4='+ $(basename ${BASH_SOURCE})[${LINENO}]'
 
 source "${ROOT_DIR}/ush/detect_machine.sh"
 case ${MACHINE_ID} in
-  hera | orion)
+  hera | orion | hercules)
    echo "Running Automated Testing on ${MACHINE_ID}"
    source "${ROOT_DIR}/ci/platforms/config.${MACHINE_ID}"
    ;;

docs/doxygen/mainpage.h

@@ -12,7 +12,7 @@
 With the FV3GFS system, a Rocoto driven workflow is being used. This workflow builds on the experiences and work of Kate.Howard and Terry.McGuinness for the GSM, but strips down a lot of complications arising from the use of a cumbersome <b>\c para_config</b>. The <b>\c para_config</b> no longer exists in the workflow and instead a number of <b> \c config </b> files are added, one each for an individual task e.g. <b>\p config.anal</b> contains the analysis specific information. A base config called as <b>\c config.base</b> contains
 information related to the machine, super-structure, etc. The idea behind splitting the <b>\p para_config</b> into individual, smaller and managable configs is to provide a means to run any chosen task without the overhead of the full cycling framework. All the configs are located under <b>\c fv3gfs/config</b>
 
-Additionally, the structure of the <b>\c COMROT</b> directory is now modified to look like operations. This enables the use of the workflow much closer to the operational environment, with the exception of the workflow manager.
+Additionally, the structure of the <b>\c ROTDIR</b> directory is now modified to look like operations. This enables the use of the workflow much closer to the operational environment, with the exception of the workflow manager.
 
 This is a very much a work in progress and any issues should be reported back and are greatly appreciated.
 
@@ -23,12 +23,12 @@ To setup an experiment, a python script <b>\c setup_expt.py</b> (located in <b>\
     $> setup_expt.py -h
     usage: setup_expt.py [-h] --pslot PSLOT
                      [--configdir CONFIGDIR] [--idate IDATE] [--icsdir ICSDIR]
-                     [--resdet RESDET] [--resens RESENS] [--comrot COMROT]
+                     [--resdetatmos RESDET] [--resensatmos RESENS] [--comroot COMROOT]
                      [--expdir EXPDIR] [--nens NENS] [--cdump CDUMP]
 
     Setup files and directories to start a GFS parallel. Create EXPDIR, copy
-    config files Create COMROT experiment directory structure, link initial
-    condition files from $ICSDIR to $COMROT
+    config files Create ROTDIR experiment directory structure, link initial
+    condition files from $ICSDIR to $ROTDIR
 
     optional arguments:
         -h, --help   show this help message and exit
@@ -40,11 +40,13 @@ To setup an experiment, a python script <b>\c setup_expt.py</b> (located in <b>\
                         (default: 2016100100)
         --icsdir     full path to initial condition directory
                         (default: /scratch4/NCEPDEV/da/noscrub/Rahul.Mahajan/ICS)
-        --resdet     resolution of the deterministic model forecast
+        --resdetatmos atmosphere resolution of the deterministic model forecast
                         (default: 384)
-        --resens     resolution of the ensemble model forecast
+        --resdetocean ocean resolution of the deterministic model forecast
+                        (default: 0. [determined automatically based on atmosphere resolution])
+        --resensatmos     resolution of the ensemble model forecast
                         (default: 192)
-        --comrot     full path to COMROT
+        --comroot    full path to COMROOT, where ROTDIR (COMROOT+PSLOT) will be created
                         (default: None)
         --expdir     full path to EXPDIR
                         (default: None)
@@ -53,7 +55,7 @@ To setup an experiment, a python script <b>\c setup_expt.py</b> (located in <b>\
         --cdump      CDUMP to start the experiment
                         (default: gdas)
 
-The above script creates directories <b>\c EXPDIR</b> and <b>\c COMROT</b>. It will make links for initial conditions from a location provided via the <b>\c --icsdir</b> argument for a chosen resolution for the control <b>\c --resdet</b> and the ensemble <b>\c --resens</b>. Experiment name is controlled by the input argument <b>\c --pslot</b>. The script will ask user input in case any of the directories already exist. It will copy experiment configuration files into the <b>\c EXPDIR</b> from <b>\c CONFIGDIR</b>.
+The above script creates directories <b>\c EXPDIR</b> and <b>\c ROTDIR</b>. It will make links for initial conditions from a location provided via the <b>\c --icsdir</b> argument for a chosen resolution for the control <b>\c --resdetatmos</b> and the ensemble <b>\c --resensatmos</b>. Experiment name is controlled by the input argument <b>\c --pslot</b>. The script will ask user input in case any of the directories already exist. It will copy experiment configuration files into the <b>\c EXPDIR</b> from <b>\c CONFIGDIR</b>.
 
 Sample initial conditions for a few resolutions are available at:<br>
 <b>Hera:</b> TODO: /path/here/for/initial/conditions<br>

docs/source/errors_faq.rst

@@ -36,10 +36,10 @@ Example::
 **Solution:** set TERM to "xterm" (bash: export TERM=xterm ; csh/tcsh: setenv TERM xterm)
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Issue: Directory name change for EnKF folder in COMROT
+Issue: Directory name change for EnKF folder in ROTDIR
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-**Issue:** The EnKF COMROT folders were renamed during the GFS v15 development process to remove the period between "enkf" and "gdas": enkf.gdas.$PDY → enkfgdas.$PDY
+**Issue:** The EnKF ROTDIR folders were renamed during the GFS v15 development process to remove the period between "enkf" and "gdas": enkf.gdas.$PDY → enkfgdas.$PDY
 
 **Fix:** Older tarballs on HPSS will have the older directory name with the period between 'enkf' and 'gdas'. Make sure to rename folder to 'enkfgdas.$PDY' after obtaining. Only an issue for the initial cycle.
 

docs/source/init.rst

@@ -391,7 +391,7 @@ The chgres jobs will have a dependency on the data-pull jobs and will wait to ru
 
 5. Check output:
 
-In the config you will have defined an output folder called ``$OUTDIR``. The converted output will be found there, including the needed abias and radstat initial condition files (if CDUMP=gdas). The files will be in the needed directory structure for the global-workflow system, therefore a user can move the contents of their ``$OUTDIR`` directly into their ``$ROTDIR/$COMROT``.
+In the config you will have defined an output folder called ``$OUTDIR``. The converted output will be found there, including the needed abias and radstat initial condition files (if CDUMP=gdas). The files will be in the needed directory structure for the global-workflow system, therefore a user can move the contents of their ``$OUTDIR`` directly into their ``$ROTDIR``.
 
 Please report bugs to George Gayno ([email protected]) and Kate Friedman ([email protected]).
 
@@ -449,7 +449,7 @@ The warm starts and other output from production are at C768 deterministic and C
 What files should you pull for starting a new experiment with warm starts from production?
 ------------------------------------------------------------------------------------------
 
-That depends on what mode you want to run -- forecast-only or cycled. Whichever mode, navigate to the top of your ``COMROT`` and pull the entirety of the tarball(s) listed below for your mode. The files within the tarball are already in the ``$CDUMP.$PDY/$CYC/$ATMOS`` folder format expected by the system.
+That depends on what mode you want to run -- forecast-only or cycled. Whichever mode, navigate to the top of your ``ROTDIR`` and pull the entirety of the tarball(s) listed below for your mode. The files within the tarball are already in the ``$CDUMP.$PDY/$CYC/$ATMOS`` folder format expected by the system.
 
 For forecast-only there are two tarballs to pull
 
@@ -489,7 +489,7 @@ Tarballs per cycle:
    com_gfs_vGFSVER_enkfgdas.YYYYMMDD_CC.enkfgdas_restart_grp7.tar
    com_gfs_vGFSVER_enkfgdas.YYYYMMDD_CC.enkfgdas_restart_grp8.tar
 
-Go to the top of your ``COMROT/ROTDIR`` and pull the contents of all tarballs there. The tarballs already contain the needed directory structure.
+Go to the top of your ``ROTDIR`` and pull the contents of all tarballs there. The tarballs already contain the needed directory structure.
 
 .. _warmstarts-preprod-parallels:
 
@@ -514,7 +514,7 @@ Recent pre-implementation parallel series was for GFS v16 (implemented March 202
     + ../$GDATE/gdas_restartb.tar
     + ../$GDATE/enkfgdas_restartb_grp##.tar (where ## is 01 through 08) (note, older tarballs may include a period between enkf and gdas: "enkf.gdas")
 
-* **Where do I put the warm-start initial conditions?** Extraction should occur right inside your COMROT. You may need to rename the enkf folder (enkf.gdas.$PDY -> enkfgdas.$PDY).
+* **Where do I put the warm-start initial conditions?** Extraction should occur right inside your ROTDIR. You may need to rename the enkf folder (enkf.gdas.$PDY -> enkfgdas.$PDY).
 
 Due to a recent change in the dycore, you may also need an additional offline step to fix the checksum of the NetCDF files for warm start. See the :ref:`Fix netcdf checksum section <gfsv17-checksum>`.
 
@@ -602,5 +602,5 @@ And then on all platforms:
 
 ::
 
-   cd $COMROT
+   cd $ROTDIR
    for f in $(find ./ -name *tile*.nc); do echo $f; ncatted -a checksum,,d,, $f; done