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Merge to 2024 Jan 12 NOAA-EMC/develop.
Squashed commit of the following: commit c590476 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <david.huber@noaa.gov> Date: Thu Jan 11 11:49:08 2024 -0600 Update orion module/version files for met/metplus NOAA-EMC#2123 commit 94c9937 Author: DavidHuber <david.huber@noaa.gov> 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 <david.huber@noaa.gov> 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 <david.huber@noaa.gov> Date: Thu Jan 11 11:34:19 2024 -0600 Initial update of version/module files NOAA-EMC#2123 commit 4cb5802 Author: souopgui <souopgui@users.noreply.github.com> 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 <isouopgui@redlineperf.com> commit b056b53 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> 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 <aerorahul@users.noreply.github.com> 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 <aerorahul@users.noreply.github.com> 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 <aerorahul@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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
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‎.github/workflows/docs.yaml

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

‎ci/cases/pr/C48_ATM.yaml

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arguments:
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pslot: {{ 'pslot' | getenv }}
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app: ATM
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resdet: 48
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comrot: {{ 'RUNTESTS' | getenv }}/COMROT
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resdetatmos: 48
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comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
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expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
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idate: 2021032312
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edate: 2021032312

‎ci/cases/pr/C48_S2SW.yaml

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arguments:
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pslot: {{ 'pslot' | getenv }}
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app: S2SW
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resdet: 48
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comrot: {{ 'RUNTESTS' | getenv }}/COMROT
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resdetatmos: 48
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resdetocean: 5.0
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comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
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expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
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idate: 2021032312
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edate: 2021032312

‎ci/cases/pr/C48_S2SWA_gefs.yaml

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

‎ci/cases/pr/C96C48_hybatmDA.yaml

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

‎ci/cases/pr/C96_atm3DVar.yaml

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

‎ci/cases/weekly/C384C192_hybatmda.yaml

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arguments:
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pslot: {{ 'pslot' | getenv }}
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app: ATM
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resdet: 384
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resens: 192
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comrot: {{ 'RUNTESTS' | getenv }}/COMROT
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resdetatmos: 384
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resdetocean: 0.25
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resensatmos: 192
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comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
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expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
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icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C384C192
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idate: 2023040118

‎ci/cases/weekly/C384_S2SWA.yaml

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arguments:
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pslot: {{ 'pslot' | getenv }}
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app: S2SWA
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resdet: 384
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comrot: {{ 'RUNTESTS' | getenv }}/COMROT
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resdetatmos: 384
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resdetocean: 0.5
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comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
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expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
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idate: 2016070100
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edate: 2016070100

‎ci/cases/weekly/C384_atm3DVar.yaml

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arguments:
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pslot: {{ 'pslot' | getenv }}
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app: ATM
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resdet: 384
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resens: 192
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comrot: {{ 'RUNTESTS' | getenv }}/COMROT
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resdetatmos: 384
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resdetocean: 0.25
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resensatmos: 192
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comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
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expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
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icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C384C192
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idate: 2023040118

‎ci/platforms/gefs_ci_defaults.yaml

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defaults:
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!INC {{ HOMEgfs }}/parm/config/gefs/yaml/defaults.yaml
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base:
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ACCOUNT: ${SLURM_ACCOUNT}
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ACCOUNT: {{ 'SLURM_ACCOUNT' | getenv }}

‎ci/platforms/gfs_defaults_ci.yaml

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defaults:
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!INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
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base:
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ACCOUNT: ${SLURM_ACCOUNT}
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ACCOUNT: {{ 'SLURM_ACCOUNT' | getenv }}

‎ci/scripts/check_ci.sh

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source "${ROOT_DIR}/ush/detect_machine.sh"
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case ${MACHINE_ID} in
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hera | orion)
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hera | orion | hercules)
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echo "Running Automated Testing on ${MACHINE_ID}"
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source "${ROOT_DIR}/ci/platforms/config.${MACHINE_ID}"
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;;
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if [[ "${num_done}" -eq "${num_cycles}" ]]; then
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#Remove Experment cases that completed successfully
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rm -Rf "${pslot_dir}"
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rm -Rf "${pr_dir}/RUNTESTS/COMROT/${pslot}"
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rm -Rf "${pr_dir}/RUNTESTS/COMROOT/${pslot}"
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rm -f "${output_ci_single}"
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# echo "\`\`\`" > "${output_ci_single}"
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DATE=$(date +'%D %r')

‎ci/scripts/driver.sh

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source "${ROOT_DIR}/ush/detect_machine.sh"
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case ${MACHINE_ID} in
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echo "Running Automated Testing on ${MACHINE_ID}"
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# we need to exit this instance of the driver script
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#################################################################
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if [[ ${ci_status} -ne 0 ]]; then
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build_PID_check=$("${ROOT_DIR}/ci/scripts/pr_list_database.py" --display "{pr}" --dbfile "${pr_list_dbfile}" | awk '{print $4}' | cut -d":" -f1) || true
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build_PID_check=$("${ROOT_DIR}/ci/scripts/pr_list_database.py" --display "${pr}" --dbfile "${pr_list_dbfile}" | awk '{print $4}' | cut -d":" -f1) || true
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if [[ "${build_PID_check}" -ne "$$" ]]; then
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echo "Driver build PID: ${build_PID_check} no longer running this build ... exiting"
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‎ci/scripts/driver_weekly.sh

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source "${ROOT_DIR}/ush/detect_machine.sh"
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case ${MACHINE_ID} in
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echo "Running Automated Testing on ${MACHINE_ID}"
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source "${ROOT_DIR}/ci/platforms/config.${MACHINE_ID}"
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;;

‎ci/scripts/run-check_ci.sh

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# TEST_DIR contains 2 directories;
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# 1. HOMEgfs: clone of the global-workflow
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# 2. RUNTESTS: A directory containing EXPDIR and COMROT for experiments
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# 2. RUNTESTS: A directory containing EXPDIR and COMROOT for experiments
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# # e.g. $> tree ./TEST_DIR
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# ./TEST_DIR
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# ├── HOMEgfs
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# └── RUNTESTS
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# ├── COMROT
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# ├── COMROOT
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# │   └── ${pslot}
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# └── ${pslot}

‎ci/scripts/run_ci.sh

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source "${ROOT_DIR}/ush/detect_machine.sh"
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case ${MACHINE_ID} in
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hera | orion | hercules)
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echo "Running Automated Testing on ${MACHINE_ID}"
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‎docs/doxygen/mainpage.h

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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
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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>
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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.
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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.
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This is a very much a work in progress and any issues should be reported back and are greatly appreciated.
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$> setup_expt.py -h
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usage: setup_expt.py [-h] --pslot PSLOT
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[--configdir CONFIGDIR] [--idate IDATE] [--icsdir ICSDIR]
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[--resdet RESDET] [--resens RESENS] [--comrot COMROT]
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[--resdetatmos RESDET] [--resensatmos RESENS] [--comroot COMROOT]
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[--expdir EXPDIR] [--nens NENS] [--cdump CDUMP]
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Setup files and directories to start a GFS parallel. Create EXPDIR, copy
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config files Create COMROT experiment directory structure, link initial
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condition files from $ICSDIR to $COMROT
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config files Create ROTDIR experiment directory structure, link initial
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condition files from $ICSDIR to $ROTDIR
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optional arguments:
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-h, --help show this help message and exit
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(default: 2016100100)
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--icsdir full path to initial condition directory
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(default: /scratch4/NCEPDEV/da/noscrub/Rahul.Mahajan/ICS)
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--resdet resolution of the deterministic model forecast
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--resdetatmos atmosphere resolution of the deterministic model forecast
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(default: 384)
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--resens resolution of the ensemble model forecast
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--resdetocean ocean resolution of the deterministic model forecast
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(default: 0. [determined automatically based on atmosphere resolution])
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--resensatmos resolution of the ensemble model forecast
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(default: 192)
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--comrot full path to COMROT
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--comroot full path to COMROOT, where ROTDIR (COMROOT+PSLOT) will be created
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(default: None)
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--expdir full path to EXPDIR
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--cdump CDUMP to start the experiment
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(default: gdas)
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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>.
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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>.
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Sample initial conditions for a few resolutions are available at:<br>
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<b>Hera:</b> TODO: /path/here/for/initial/conditions<br>

‎docs/source/errors_faq.rst

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**Solution:** set TERM to "xterm" (bash: export TERM=xterm ; csh/tcsh: setenv TERM xterm)
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Issue: Directory name change for EnKF folder in COMROT
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Issue: Directory name change for EnKF folder in ROTDIR
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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**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
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**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
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**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.
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‎docs/source/init.rst

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5. Check output:
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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``.
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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 ``$ROTDIR``.
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Please report bugs to George Gayno (george.gayno@noaa.gov) and Kate Friedman (kate.friedman@noaa.gov).
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What files should you pull for starting a new experiment with warm starts from production?
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------------------------------------------------------------------------------------------
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That depends on what mode you want to run -- forecast-only or cycled. Whichever mode, navigate to the top of your ``COMROT`` and pull the entirety of the tarball(s) listed below for your mode. The files within the tarball are already in the ``$CDUMP.$PDY/$CYC/$ATMOS`` folder format expected by the system.
452+
That depends on what mode you want to run -- forecast-only or cycled. Whichever mode, navigate to the top of your ``ROTDIR`` and pull the entirety of the tarball(s) listed below for your mode. The files within the tarball are already in the ``$CDUMP.$PDY/$CYC/$ATMOS`` folder format expected by the system.
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For forecast-only there are two tarballs to pull
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@@ -489,7 +489,7 @@ Tarballs per cycle:
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com_gfs_vGFSVER_enkfgdas.YYYYMMDD_CC.enkfgdas_restart_grp7.tar
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com_gfs_vGFSVER_enkfgdas.YYYYMMDD_CC.enkfgdas_restart_grp8.tar
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Go to the top of your ``COMROT/ROTDIR`` and pull the contents of all tarballs there. The tarballs already contain the needed directory structure.
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Go to the top of your ``ROTDIR`` and pull the contents of all tarballs there. The tarballs already contain the needed directory structure.
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.. _warmstarts-preprod-parallels:
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@@ -514,7 +514,7 @@ Recent pre-implementation parallel series was for GFS v16 (implemented March 202
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+ ../$GDATE/gdas_restartb.tar
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+ ../$GDATE/enkfgdas_restartb_grp##.tar (where ## is 01 through 08) (note, older tarballs may include a period between enkf and gdas: "enkf.gdas")
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* **Where do I put the warm-start initial conditions?** Extraction should occur right inside your COMROT. You may need to rename the enkf folder (enkf.gdas.$PDY -> enkfgdas.$PDY).
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* **Where do I put the warm-start initial conditions?** Extraction should occur right inside your ROTDIR. You may need to rename the enkf folder (enkf.gdas.$PDY -> enkfgdas.$PDY).
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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>`.
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@@ -602,5 +602,5 @@ And then on all platforms:
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::
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cd $COMROT
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cd $ROTDIR
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for f in $(find ./ -name *tile*.nc); do echo $f; ncatted -a checksum,,d,, $f; done

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