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

AndrewEichmann-NOAA · 2024-01-10T20:43:04Z

Description

Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same. Experiment setup is same as before, but runs task gdasprepoceanobs before gdasocnanalprep. This obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS. This replaces the current R2D2 processing.

This PR resolves NOAA-EMC/GDASApp#815 and is mutual dependent on the recently merged to GDASApp NOAA-EMC/GDASApp#836

Type of change

New feature (adds functionality)

Change characteristics

Is this a breaking change (a change in existing functionality)? YES
Does this change require a documentation update? NO

How has this been tested?

WCDA cycling on Hera

Checklist

Any dependent changes have been merged and published
My code follows the style guidelines of this project
I have performed a self-review of my own code
I have commented my code, particularly in hard-to-understand areas
My changes generate no new warnings
New and existing tests pass with my changes
I have made corresponding changes to the documentation if necessary

AndrewEichmann-NOAA · 2024-01-10T20:47:23Z

FYI @guillaumevernieres and @CoryMartin-NOAA

guillaumevernieres

Thanks for doing this @AndrewEichmann-NOAA . See comment.

parm/config/gfs/config.prepoceanobs

workflow/rocoto/gfs_tasks.py

guillaumevernieres

Looks good to me, thanks @AndrewEichmann-NOAA .

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

@DeniseWorthen

commit d1e8f33 Merge: e2d88dd 5166593 Author: kayee.wong <kayee.wong@noaa.gov> Date: Fri Mar 1 00:01:58 2024 +0000 Merge remote-tracking branch 'emcgw/develop' into develop remote: https://github.com/NOAA-EMC/global-workflow.git develop (Feb 29, commit 5166593) origin: https://github.com/kayeekayee/global-workflow.git gsl_ufs_dev (Feb 29,commit e0c3e4d) commit 5166593 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Feb 29 20:14:41 2024 +0000 Move Jenkinsfile into ci subdirectory (NOAA-EMC#2355) Just moves the Jenkinsfile into the ci directory Co-authored-by: tmcguinness <terry.mcguinness@noaa.gov> commit b7af315 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 28 22:20:58 2024 +0000 Fix rocoto forecast hour determination for GEFS (NOAA-EMC#2351) The function that generates the list of forecast hours for rocoto was trying to use variables that are not defined for GEFS, causing workflow generation to fail. The function is updated to not try to load these variables before loading the ones actually used for GFS/ GEFS. Also turns GEFS CI test back on and adds an entry to stage C192 ICs (note: these have not been placed in the centralized location.) commit d3a4927 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Wed Feb 28 09:38:49 2024 -0500 Rename the land DA jobs to snow DA to better reflect what they are doing (NOAA-EMC#2330) This PR renames all of the land DA jobs to snow DA to better reflect that this is a JEDI-based snow analysis capability and not a more generic land surface analysis. commit 2693810 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Tue Feb 27 01:25:51 2024 -0500 Update ufs-waether-model hash (NOAA-EMC#2338) Routine update of ufs-weather-model hash. Other small updates: * removes comment referencing closed issue. * Updates the CICE diag frequency to once per day as recommend here: NOAA-EMC#1810 (comment) * Updated amount of time for C384 gdas forecast as it was running out of time * Removed unused variable wave_sys_ver commit 9608852 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon Feb 26 14:10:01 2024 -0500 Update JEDI ATM to use .nc for obs and generalize x,y layout (NOAA-EMC#2336) # Description The changes in this PR are twofold 1. replace `.nc4` suffix for JEDI ATM observation related files with `.nc` 2. use templated variables to specify `{layout_x, layout_y}` for JEDI ATM variational and local ensemble apps The first change conforms with the Unidata recommendation that netCDF files end with the suffix `.nc`. The second change replaces hardwired JEDI ATM var and ens `{layout_x, layout_y}` in `config.resources` with a more flexible approach. Resolves NOAA-EMC#2335 commit c5c8466 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Feb 26 10:18:50 2024 -0500 Remove FIX* variables for fix subfolders (NOAA-EMC#2337) Remove `FIX*` variables for fix subfolders and replace them with the remaining `FIXgfs` variable and the subfolder name (e.g. `${FIXam}` -> `${FIXgfs}/am`). The UFS_UTILS and GDASApp repos were similarly updated. This PR includes a new UFS_UTILS hash. The updated GDASAPP hash was already committed within the spack-stack/1.6.0 PR NOAA-EMC#2239. Resolves NOAA-EMC#2184 commit 950c38a Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri Feb 23 21:15:46 2024 +0000 Fix several Jenkins issues (NOAA-EMC#2334) Jenkins Updates Resolving final kinks: - Removed all `git` shell commands and now exclusively use Software Control Manger (**scm**) plugin. - Add feature for skipping hosts per configuration specified in case yaml files. - Solved and tested false positive builds and experiments. - Tested archiving of task error log on case fail - First case fail quits pipeline and cancels all pending scheduled jobs - Duel build per yaml configuration arguments supported - All designated case files in PR directory pass on intended host (fully tested on Hera) Remaining updates: - Fist build fail short circuit when building sub-modules and archiving build error log. - Re-build/no-build built in logic for Replay and Rerunning previously failed experiments. commit c67393a Merge: 6f9afff 79d305e Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Feb 23 14:18:15 2024 +0000 Merge pull request NOAA-EMC#2239 from DavidHuber-NOAA/ss160 Update to spack-stack 1.6.0 Includes all submodules except the UFS, which will be updated at a later time. commit 79d305e Author: David Huber <david.huber@noaa.gov> Date: Thu Feb 22 14:53:57 2024 -0600 Disable snow DA tests commit 0459203 Author: David Huber <david.huber@noaa.gov> Date: Thu Feb 22 12:55:51 2024 -0600 Update GDASApp hash to current develop commit 5c96eb2 Author: David Huber <david.huber@noaa.gov> Date: Thu Feb 22 12:37:47 2024 -0600 Update GDAS hash to allow modified snow DA analysis commit 79144f2 Merge: abbb0b8 6f9afff Author: DavidHuber <david.huber@noaa.gov> Date: Thu Feb 22 15:14:39 2024 +0000 Merge remote-tracking branch 'origin/develop' into ss160 commit abbb0b8 Merge: 4ad837e 4529e8c Author: DavidHuber <david.huber@noaa.gov> Date: Thu Feb 22 15:11:03 2024 +0000 Merge remote-tracking branch 'henry/feature/gwdev_issue_2129' into ss160 commit 4ad837e Merge: 516b2a2 7ca45db Author: DavidHuber <david.huber@noaa.gov> Date: Thu Feb 22 15:10:24 2024 +0000 Merge remote-tracking branch 'henry/feature/gfsv17_issue_2125' into ss160 commit 516b2a2 Author: DavidHuber <david.huber@noaa.gov> Date: Thu Feb 22 14:19:16 2024 +0000 Updated GDAS to include rocoto/1.3.6 on Hera. commit 6f9afff Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Feb 21 13:09:44 2024 -0500 Add some flexibility for ocean/ice output (NOAA-EMC#2327) This adds functionality to have ocean/ice output frequency be separate from the atm model. One time was created because there's an assumption in the post that these are the same. This could be further modified to remove this assumption. Refs NOAA-EMC#1629 commit e2d88dd Merge: 3e6b1e2 a23b7f2 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Tue Feb 20 16:08:46 2024 -0700 Merge branch 'NOAA-EMC:develop' into develop commit f6d3015 Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 09:53:08 2024 -0600 Update GDASApp hash to include SS/1.6.0 support. commit 0bf340b Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 09:07:32 2024 -0600 Construct SS paths from version variables. commit 3330cd7 Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 09:06:19 2024 -0600 Removed MET/METplus 'not available' comments commit fdc638c Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 08:35:15 2024 -0600 Move SS module path to version files. commit d7d28a6 Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 07:53:15 2024 -0600 Update comment about METplus support. commit a812f88 Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 07:45:45 2024 -0600 Update verif-global to latest WCOSS2 support. commit d81f07f Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 07:41:38 2024 -0600 Clean up build_upp.sh. -Corrected whitespace (tabs instead of spaces) -Removed debug print statement -Alphebetized flags commit ae7eb19 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Feb 16 16:15:40 2024 -0500 Fix whitespace in build_upp.sh. Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 48b34d0 Author: David Huber <david.huber@dlogin05.dogwood.wcoss2.ncep.noaa.gov> Date: Fri Feb 16 20:56:55 2024 +0000 Added verif-global support back to WCOSS2. commit 4529e8c Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Fri Feb 16 11:12:01 2024 -0700 Bug fix. commit 8e4f94d Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Fri Feb 16 11:04:41 2024 -0700 Updates requested by reviewer Rahul Mahajan. commit 4624ce2 Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Fri Feb 16 10:52:11 2024 -0700 Updates requested by reviewer; testing -- DO NOT REVIEW. commit ed25bbd Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Fri Feb 16 09:33:59 2024 -0700 Linter corrections. commit 6a0b7bf Merge: f9fb64e 2415b7b Author: David Huber <david.huber@noaa.gov> Date: Fri Feb 16 09:50:22 2024 -0600 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit f9fb64e Merge: 777d97d a23b7f2 Author: David Huber <david.huber@noaa.gov> Date: Fri Feb 16 09:49:42 2024 -0600 Merge remote-tracking branch 'emc/develop' into ss160 commit 7ca45db Merge: 73bc76b a23b7f2 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Fri Feb 16 07:46:35 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit eb2ed53 Merge: 9929277 a23b7f2 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Fri Feb 16 07:46:24 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit a23b7f2 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Fri Feb 16 09:37:58 2024 -0500 Add JEDI 3DEnVar atmosphere only CI test stub (NOAA-EMC#2309) commit cf83885 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Feb 16 01:55:02 2024 -0500 Add unstructured grid for HR3/GFS (NOAA-EMC#2230) This adds the capability to use unstructured grids in the global workflow, which will be used in HR3. There are new fix files for a low-resolution 100km grid and a grid closer to our targeted GFSv17 grid which has the resolution combined from the older multi_1 and GFSv16 grids. The fix file update is here: NOAA-EMC#2229 Note: This now means that GFS tests need a new build option: `./build_all.sh -w` So that PDLIB=ON is turned on for compiling relevant UFS and WW3 codes. Resolves NOAA-EMC#1547 commit 9929277 Merge: eb8791c 094e3b8 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Feb 15 15:05:50 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit 094e3b8 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Thu Feb 15 14:43:55 2024 -0500 Move IMS remapping files from COM_OBS to FIXgdas (NOAA-EMC#2322) * Add in IMS obs fix directory and update submodule for gdas commit d465ea0 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Feb 15 19:25:02 2024 +0000 Set HOMEgfs for module_setup in CI driver (NOAA-EMC#2321) Hotfixes to CI Bash system from updates with sourcing `detect_machine.sh` in `ush/module-setup.sh` using **HOMEgfs**. commit 2415b7b Author: David Huber <david.huber@noaa.gov> Date: Thu Feb 15 19:21:17 2024 +0000 Load default rocoto on Jet. commit eb8791c Merge: 60d5ee6 638684e Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Feb 15 11:56:40 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit 777d97d Author: David Huber <david.huber@noaa.gov> Date: Thu Feb 15 12:34:59 2024 -0600 Fixed Orion cdo version. commit ef07235 Author: DavidHuber <david.huber@noaa.gov> Date: Thu Feb 15 16:29:32 2024 +0000 Revert UFS hash. commit 0ce8c0d Author: DavidHuber <david.huber@noaa.gov> Date: Thu Feb 15 14:55:48 2024 +0000 Fix git version in Hera's gwsetup module. commit 3080a34 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Feb 14 20:52:34 2024 +0000 Fixed xarray version for SS/1.6.0. commit 49392dd Author: DavidHuber <david.huber@noaa.gov> Date: Wed Feb 14 20:29:41 2024 +0000 Updated GSI-Utils hash to head of develop. commit c3553f0 Merge: 4568653 638684e Author: DavidHuber <david.huber@noaa.gov> Date: Wed Feb 14 20:28:14 2024 +0000 Merge remote-tracking branch 'origin/develop' into ss160 commit 4568653 Author: David Huber <david.huber@noaa.gov> Date: Wed Feb 14 14:22:13 2024 -0600 Reupgrade Hercules to SS/1.6.0 commit 638684e Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Feb 14 14:55:21 2024 -0500 Remove `finddate.sh` from system (NOAA-EMC#2308) * Retire finddate.sh usage from system * Update gfs-utils hash to 7a84c88 - New hash includes removal of finddate.sh Refs NOAA-EMC#2279 commit 2b160f8 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Feb 14 18:31:28 2024 +0000 Reenable METplus jobs on Hercules. commit 8f59002 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Feb 14 18:30:23 2024 +0000 Update GSI hashes. commit 73bc76b Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Wed Feb 14 09:27:37 2024 -0700 Updates based on user request. commit e4bc674 Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Wed Feb 14 08:03:45 2024 -0700 Corrected based on reviewer review. commit 60d5ee6 Merge: 40f2cf6 1aaef05 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Feb 13 18:08:33 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit 0330411 Merge: 929b903 1aaef05 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Feb 13 17:58:12 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit 1aaef05 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Feb 13 18:15:59 2024 -0500 Jenkins Pipeline updates for Canceling Jobs (NOAA-EMC#2307) Tuning updates for Jenkins Pipeline : - Added short circuit for all parallel runs of cases on error of any - Fixed canceling of all scheduled jobs on first case error - Added feature to save error log files to Jenkins Archive facility on fail commit 6404892 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Feb 13 14:57:37 2024 -0500 Ocean/ice product generation for GFS and GEFS (NOAA-EMC#2286) This PR does several things: 1. the model output for ocean and ice in the `COM/` directory are now named per EE2 convention for coupled model. E.g `gfs.ocean.t12z.6hr_avg.f120.nc` and `gfs.ocean.t12z.daily.f120.nc` 2. The products are generated using the `ocnicepost.fd` utility developed by @DeniseWorthen in https://github.com/NOAA-EMC/gfs-utils and converted to grib2 using example scripts provided by @GwenChen-NOAA using `wgrib2`. 3. NetCDF products on the native grid are also generated by subsetting variables from the raw model output. This is done with `xarray`. 4. updates the hash of https://github.com/NOAA-EMC/gfs-utils to include fixes in `ocnicepost.fd` 5. removes NCL related scripting that was previously used for ocean/ice interpolation and `reg2grb2` used for converting to grib2. 6. updates archive scripts to accommodate updated file names 7. removes intermediate ocean processed files such as 2D/3D/xsect data- sets 8. separate jobs are added for ocean and ice product generation. 9. removes intermediate restarts for the mediator and only saves the medi- ator restart at the end of the forecast in `COM`. 10. Increases memory for offline UPP when run at C768. The program segfaults with an OOM when memory is self allocated based on PEs by the scheduler on Hera. 11. Enables ocean/ice ensemble product generation for GEFS 12. Some minor clean-ups Fixes NOAA-EMC#935 Fixes NOAA-EMC#1317 Fixes NOAA-EMC#1864 commit 40f2cf6 Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Tue Feb 13 10:18:53 2024 -0700 Implemented ush/detect_machine.sh for host determination and removed redundant checks for expected file paths. commit 929b903 Merge: 2d08d01 3f99f70 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Feb 13 08:31:06 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit 3f99f70 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Feb 13 00:57:18 2024 -0500 Add wave post jobs to GEFS (NOAA-EMC#2292) Adds the wave post jobs for gridded and points to GEFS. Boundary point jobs are added even though the current GEFS buoy file does not contain any (tested by manually subbing in the GFS buoy file). Resolves NOAA-EMC#827 commit 842adf3 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Mon Feb 12 12:50:08 2024 -0500 Added additional test cases to the pr list in Jenkins (NOAA-EMC#2306) C48mx500_3DVarAOWCDA, C96C48_hybatmDA, and C96_atmsnowDA Co-authored-by: terrance.mcguinness <terrance.mcguinness@noaa.gov> commit bb4ca65 Author: CatherineThomas-NOAA <59020064+CatherineThomas-NOAA@users.noreply.github.com> Date: Mon Feb 12 14:50:41 2024 +0000 Redo v16.3 config.base changes for DA increments (NOAA-EMC#2304) Include the additional hydrometeors to the INCREMENTS_TO_ZERO and INCVARS_ZERO_STRAT variables in config.base that were modified in v16.3. Resolves: NOAA-EMC#2303 commit 061992b Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Sat Feb 10 01:33:36 2024 -0500 Fix Jenkins success reporting (NOAA-EMC#2302) Moving the post section back outside of main Run Experiments stage. This allows the system to correctly report the **Success** status until after all tests pass. _Had originally moved them in attempts to solve "Not an SCM GitHub Job" issue and cause the reporting to misbehave._ Also ran through Jenkins linter and updated some messaging that was incorrectly reporting system build type. commit 28ccf78 Merge: b972f66 54daa31 Author: David Huber <david.huber@noaa.gov> Date: Fri Feb 9 14:00:43 2024 -0600 Merge remote-tracking branch 'emc/develop' into ss160 commit b972f66 Author: David Huber <david.huber@noaa.gov> Date: Fri Feb 9 10:47:00 2024 -0600 Fix SS versions for CI modules. commit 4b01d8e Author: David Huber <david.huber@noaa.gov> Date: Fri Feb 9 10:44:30 2024 -0600 Revert Hercules modules to SS/1.5.1. commit 54daa31 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Feb 8 15:48:38 2024 -0500 Jenkins Declartive Pipeline for CI with gfs/gefs multibuilds (NOAA-EMC#2246) Adding top level Jenkins file for CI tests running on Jenkins Controller: - Declarative Multi-branch Pipeline (has enhanced restart capabilities on a per section bases) - Starts Pipeline from Label PR same as BASH system (for now) - Progress and restarts can me managed with CAC Login at [EPIC OAR Jenkins](https://jenkins.epic.oarcloud.noaa.gov) - Has logic for multi **gfs/gefs** system builds (arguments based on a configuration file `ci/casts/yamls/build.yaml`) - Any number of **systems** may be added by manual adding an ele- ment to the matrix in the Jenkinsfile - _It may be possible to dynamic add matrix values with a specialty plug-in_ - Currently only runs on **Orion** and **Hera** using `mterry` account Resolves NOAA-EMC#2119 Resolves NOAA-EMC#2118 commit 43429e2 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Feb 8 15:30:28 2024 -0500 Enable AO WCDA test (NOAA-EMC#1963) This PR: - adds GSI + SOCA C48 5-deg ocean 3DVar test (courtesy @guillaumevernieres) - adds a toggle to optionally disable ocnanalvrfy job. commit 2d08d01 Merge: 4745d4a f563528 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Feb 8 07:24:54 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit f563528 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Feb 7 15:09:12 2024 -0500 Update JGLOBAL_FORECAST for octal error (NOAA-EMC#2295) Add "10#" to ENSMEM value > 0 check to handle octal errors. commit 4745d4a Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Wed Feb 7 08:45:49 2024 -0700 Removed jlogfile references. commit 5894ca2 Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Wed Feb 7 08:32:16 2024 -0700 Removed dummy variable passed to perl scripts. commit dae884a Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Wed Feb 7 08:29:49 2024 -0700 Removed jlogfile and postmsg references within gempak scripts. commit 801058f Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Feb 7 00:41:59 2024 -0700 Consolidate `npe_node_max` (NOAA-EMC#2289) - The environment variable `npe_node_max` is removed from all files beneath `global-workflow/env`; - The environment variable `npe_node_max` is removed from `parm/config/gefs/config.ufs` and `parm/config/gfs/config.ufs`; - The environment variable `npe_node_max` is maintained only within `parm/config/gefs/config.resources` and `parm/config/gfs/config.resources`. Resolves NOAA-EMC#2133 commit b0325e0 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Feb 7 00:40:20 2024 -0700 Removes files module loading file no longer used by the GW (NOAA-EMC#2281) Removes `module-setup.csh.inc` and `module-setup.sh.inc`. The module `ush/module-setup.sh` is updated such that it now sources `ush/detect_machine.sh` to determine which supported platform the global-workflow is being execute on. Resolves NOAA-EMC#2130 commit 3e6b1e2 Merge: f4c8e00 1ccc989 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Tue Feb 6 10:43:55 2024 -0700 Merge branch 'NOAA-EMC:develop' into develop commit 1ccc989 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Feb 5 14:16:07 2024 -0500 Remove EnKF forecast groups (NOAA-EMC#2280) Removes the grouping of EnKF forecasts so each job only runs one forecast. Member and MEMDIR are now set at the workflow manager (rocoto) level. This change makes much of the system simpler (especially dependencies) and allows the elimination of the separate efcs scripts. Metatask names of updated jobs have been updated to make them a little less opaque by using the same name name as its constituent tasks (e.g. the forecast metatask is named `enkgdasfcst`, not `enkfgdasefcs`). Metatasks that weren't updated retain the same names as before for now. Resolves NOAA-EMC#2254 commit 9f3383f Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Mon Feb 5 12:15:13 2024 -0700 Updated detect_machine.sh using that from UFS WM. (NOAA-EMC#2252) Updates `ush/detect_machine.sh` to match the UFS weather-model `tests/detect_machine.sh` prepared by @BrianCurtis-NOAA Resolves NOAA-EMC#2228 commit 7d68b0b Author: CatherineThomas-NOAA <59020064+CatherineThomas-NOAA@users.noreply.github.com> Date: Sun Feb 4 22:02:41 2024 +0000 Update global_cycle for fractional grid (NOAA-EMC#2262) The hash for ufs_utils is updated to include the changes for fractional grid support within global_cycle. This commit also removes the hack to skip global_cycle in cycling mode with v17 physics. Resolves: NOAA-EMC#1775 Refs: ufs-community/UFS_UTILS#815 Refs: ufs-community/UFS_UTILS#891 commit ed592a6 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Sat Feb 3 02:55:14 2024 -0500 Retire cycle-specific FHMAX_GFS variables (NOAA-EMC#2278) This PR retires the `FHMAX_GFS_${cyc}` variables that allowed users to specify different gfs forecast lengths for each cycle. This function is no longer supported in global-workflow. The `FHMAX_GFS_*` variables will be removed and will no longer be checked to set the final `FHMAX_GFS` variable. The same forecast length will be set for every cycle. This PR also includes a small fix to add new post parm files into the `.gitignore` file. This was intended to be included in a different PR but that PR is on hold for further testing so it is being included here to get it into `develop` sooner. Resolves NOAA-EMC#2218 commit 977e2d6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Fri Feb 2 07:49:09 2024 -0700 New GDASApp hash. (NOAA-EMC#2285) commit b5f2bd9 Merge: 4d66742 0400e1f Author: David Huber <david.huber@noaa.gov> Date: Tue Jan 30 13:55:00 2024 -0600 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 0400e1f Author: David Huber <david.huber@noaa.gov> Date: Tue Jan 30 09:57:11 2024 -0600 Fix gfs_utils Orion spack-stack env path. commit 6bbe823 Author: DWesl <22566757+DWesl@users.noreply.github.com> Date: Mon Jan 29 21:15:30 2024 -0500 Use seq to generate the list of times, instead of a bash for-loop (NOAA-EMC#2264) I'm running a year-long forecast, which means I get a large portion of the log file dedicated to these loops. `seq ${START} ${STEP} ${STOP}` will generate a sequence going from START to STOP by STEP, including STOP if relevant. That seems to be the purpose of these loops. It will by default separate the list with newlines, but `seq -s ' ' ${START} ${STEP} ${STOP}` will separate them with spaces instead, more closely mimicing the previous behavior. I would like this to be two lines in the log, rather than a few hundred, and this may also be faster, though probably more for reasons of fewer writes to disk than because bash isn't designed for arithmetic. commit f4c8e00 Merge: 61975cf d5bee38 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Mon Jan 29 15:38:56 2024 -0700 Merge branch 'NOAA-EMC:develop' into develop commit d5bee38 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Jan 29 14:35:02 2024 -0500 Correct typos in GFS config.resources (NOAA-EMC#2267) This PR corrects some typos in `parm/config/gfs/config.resources` that were introduced in PR NOAA-EMC#2216. The esfc job was failing in tests on WCOSS2 due to insufficient memory. This lead to discovering the other typos. The esfc job completes without error after its memory is set back to `80GB` from the incorrect `8GB`. Resolves NOAA-EMC#2266 commit 81557be Author: David Huber <david.huber@noaa.gov> Date: Mon Jan 29 12:13:31 2024 -0600 Update monitor hash to noaa-emc with SS/1.6.0 support. commit 2238dd6 Author: DavidHuber <david.huber@noaa.gov> Date: Mon Jan 29 13:21:30 2024 +0000 Update Orion, Hercules, S4 modulefiles. commit 6ffd94f Author: DavidHuber <david.huber@noaa.gov> Date: Fri Jan 26 16:01:23 2024 +0000 Update GDAS hash to include SS/1.6.0 support. commit be11f85 Merge: 56b9680 04e0772 Author: DavidHuber <david.huber@noaa.gov> Date: Fri Jan 26 15:34:24 2024 +0000 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 8ff3448 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jan 26 10:12:18 2024 -0500 Add a yaml for snow DA testing. (NOAA-EMC#2199) - adds a new test yaml C96_atmsnowDA.yaml for 3DVar atmosphere with GSI and Land (Snow) DA with JEDI - moves a few yamls from platforms/ to yamls/ - adds ability to overwrite a previously created experiment as an addition to user input. --------- Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> commit 04e0772 Author: David Huber <david.huber@noaa.gov> Date: Fri Jan 26 07:16:25 2024 -0600 Update ufs_utils hash for spack-stack/1.6.0 support. commit 3d44ff3 Author: Barry Baker <bbakernoaa@users.noreply.github.com> Date: Thu Jan 25 14:33:27 2024 -0500 GOCART ExtData biogenic climatology fix (NOAA-EMC#2253) Updates the ExtData for biogenic emissions to be climatology rather than for current time. Fixes an issue which will crash by default for other years. commit 66f58b8 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Thu Jan 25 13:16:41 2024 -0500 Added missing container case in gfs/config.resources (NOAA-EMC#2258) fixes NOAA-EMC#2257 commit 553b4f2 Author: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com> Date: Thu Jan 25 13:00:45 2024 -0500 Fix post parm links (NOAA-EMC#2243) Change symbolic links under parm/post with the latest version of develop branch from UPP repository and enable MERRA2 aerosol fields. Resolves NOAA-EMC#2259 commit 4d66742 Merge: 6c05803 afa09e3 Author: David Huber <david.huber@noaa.gov> Date: Thu Jan 25 07:49:08 2024 -0600 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 6c05803 Author: David Huber <david.huber@noaa.gov> Date: Thu Jan 25 07:48:42 2024 -0600 Fix wgrib2/gfs_utils on Hercules. commit ee6f536 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Jan 25 07:43:13 2024 -0500 Update GFS version to v16.3.13 in index.rst (NOAA-EMC#2256) GFSv16.3.13 WAFS update was implemented Refs NOAA-EMC#2013 commit 2445d44 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Thu Jan 25 06:17:11 2024 -0500 Simplify and extend load_ufsda_modules to Hercules (NOAA-EMC#2245) GDASApp jobs do not run on Hercules because `ush/load_ufsda_modules.sh` does not include logic to load the appropriate GDASApp modules on Hercules. This PR extends `load_ufsda_modules.sh` functionality to Hercules, thereby enabling GDASApp jobs to run on Hercules. Resolves NOAA-EMC#2244 commit 56b9680 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Jan 24 19:47:34 2024 +0000 Update hashes (revert WCOSS2 modules). commit afa09e3 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Jan 24 18:59:40 2024 +0000 New (cleaner history) gdas hash. commit a9eaec2 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Jan 24 18:52:27 2024 +0000 Update gdasapp to include ss/1.6.0 support. commit 5ef8eb2 Merge: 4c46354 e400068 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Jan 24 17:08:54 2024 +0000 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 4c46354 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Jan 24 17:05:12 2024 +0000 Reenable verif-global support commit f775755 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Jan 24 16:59:10 2024 +0000 Assign fcsthrs for awips_g2 job. commit e400068 Author: David Huber <david.huber@noaa.gov> Date: Mon Jan 22 15:01:07 2024 -0600 More gsi-addon path fixes. commit f663d47 Author: David Huber <david.huber@noaa.gov> Date: Mon Jan 22 14:41:59 2024 -0600 Fix gsi-addon paths for hercules, orion, and S4. commit e304bbe Author: DavidHuber <david.huber@noaa.gov> Date: Mon Jan 22 18:59:34 2024 +0000 Better optimize build jobs (more ufs jobs). commit ccc6e2d Author: DavidHuber <david.huber@noaa.gov> Date: Mon Jan 22 18:56:18 2024 +0000 Reenable verif-global. NOAA-EMC#2195 commit 3ef3411 Merge: 4365f63 f4d187f Author: DavidHuber <david.huber@noaa.gov> Date: Mon Jan 22 18:39:10 2024 +0000 Merge remote-tracking branch 'origin/develop' into ss160 commit 4365f63 Author: DavidHuber <david.huber@noaa.gov> Date: Mon Jan 22 18:37:25 2024 +0000 Corrected the SS env. name in the version files. NOAA-EMC#2195 commit f4d187f Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Mon Jan 22 12:28:28 2024 -0500 Converts obsproc to obsprep in prepoceanobs config file (NOAA-EMC#2236) Converts obsproc to obsprep in prepoceanobs config file as a compliment to mutually depended GDASApp PR NOAA-EMC/GDASApp#858 The motivations are explained in refs NOAA-EMC/GDASApp#857 commit 9a09d30 Author: DavidHuber <david.huber@noaa.gov> Date: Fri Jan 19 21:23:50 2024 +0000 Corrected gsi-addon-dev spelling. commit 21ff645 Author: DavidHuber <david.huber@noaa.gov> Date: Fri Jan 19 21:11:34 2024 +0000 Update modulefiles, submodules to spack-stack 1.6.0. NOAA-EMC#2195 commit d4c55d1 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Fri Jan 19 15:43:37 2024 -0500 Update typing hint for WCOSS version of python (NOAA-EMC#2238) The typing hint `typing.List` was deprecated with python 3.9 in favor of using the primitive `list[str]`, but the functional version of python on WCOSS2 is <3.9, causing `setup_xml.py` to fail there. This replaces `list[str]` as a typing hint with the deprecated form until the supported version on WCOSS2 is >=3.9. commit 61975cf Merge: 1344313 4919287 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Fri Jan 19 08:38:17 2024 -0700 Merge branch 'NOAA-EMC:develop' into develop commit 4919287 Author: Barry Baker <bbakernoaa@users.noreply.github.com> Date: Thu Jan 18 22:31:27 2024 -0500 GOCART Emission updates for GEFSv13 and GDAS (NOAA-EMC#2201) This PR addresses several things needed for more recent simulations using GOCART2G as well as preparing for the GEFSv13 30 year run. The main updates are: - Update CEDS to use monthly emission files instead of daily. This will drastically reduce the number of files needed. No science change - Update biogenic MEGAN inputs to use a climatology rather than the offline biogenic previously used. This is needed to deal with simulations where the current dataset is not available. - Update volcanic SO4 emissions to use degassing emissions only. This is to support the need for more recent simulations where data is not available. commit 13d25cf Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Jan 18 22:29:43 2024 -0500 Add `POSTAMBLE_CMD` into preamble postamble (NOAA-EMC#2235) This PR adds the ability to run a command at the end of jobs via the preamble's postamble function. A new command can be set via `POSTAMBLE_CMD` and will be invoked at the end of jobs. Users can add the command to the top of an env file to have every job run it or it can be placed within a job if-block in the env file to run for just that job. Resolves NOAA-EMC#1145 commit 7759163 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Jan 18 01:13:49 2024 -0500 Add option to create WGNE atmosphere products (NOAA-EMC#2233) Adds option to create WGNE products for the atmosphere. Resolves NOAA-EMC#1951 Resolves NOAA-EMC#2226 commit d95ed85 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 17 18:04:56 2024 -0500 Use ufs.configure, model_configure, MOM_input, data_table, and ice_in templates from UFS-weather-model (NOAA-EMC#2051) This PR: - links `ufs.configure.*.IN`, `model_configure.IN`, `MOM_input_${OCNRES}.in`, `MOM6_data_table.IN`, and `ice_in.IN` from ufs-weather-model into the global-workflow `parm/ufs` directory - prepares local variables for use in the templates in the respective functions for FV3, MOM6, and CICE6 - uses `atparse.bash` to render these templates into fully formed namelists - Work was performed by @DeniseWorthen in the ufs-weather-model to templatize several variables that are hard-wired in the ufs-weather-model for CICE. See ufs-community/ufs-weather-model/NOAA-EMC#2010 commit 44a66dd Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed Jan 17 13:52:09 2024 -0500 Update gdas.cd hash to use gsibec tag 1.1.3 (NOAA-EMC#2231) (NOAA-EMC#2234) commit 9046d97 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jan 17 10:19:18 2024 -0500 Add basic atmos products for GEFS and refactor resources (NOAA-EMC#2216) * Add basic atmos products for GEFS Adds basic atmosphere products for GEFS members (no mean or spread). To facilitate the addition of GEFS parameter lists, the existing GFS lists are renamed. They are also relocated to `parm/products/` direc tory instead of `parm/post/`. GEFS v12 uses different parameter lists for different resolutions, but for this implementation, the 0p25 lists are used for all resolutions. However, to hedge against the final con- figuration, all of the GEFS parameter lists have been added to parm. Implementation of different parameter lists for each resolution will take additional refactoring of the atmos_products job, as it currently assumes all resolutions use the same lists. The new GEFS rocoto task is implented as two loops of metatasks (made possible by PR NOAA-EMC#2189). The member is set at the rocoto level, so the setting in `config.base` had to be updated to accept a pass-through. The generation of a forecast hour list is moved up to its own function in `rocoto.tasks`, separate from the post groups which are not used. This can be used as a model for future metatasks (or refactoring of old ones). `rocoto_viewer.py` does function with the nested metatasks, though only one level of folding is available and the metatask name is that of the lower metatask (though it encompasses the entire outer metatask). Additionally, the GEFS `config.resources` had diverged from the GFS version, which included not having a section for the atm products job. This led to the refactoring of the GFS `config.resources`, including switching to using a `case` statement instead of sequential `elif`. This refactored script was then copied over to GEFS, replacing the old one, with all jobs not currently implemented for GEFS removed (except wave post, whose inclusion is immenent). New blocks can be copied over from GFS as they are added. Resolves NOAA-EMC#823 commit fbba174 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Tue Jan 16 14:05:48 2024 -0500 Update GDASApp (gdas.cd) hash (NOAA-EMC#2225) GDASApp now uses gitsubmodules commit 1344313 Merge: 4b58891 dddd837 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Tue Jan 16 11:13:59 2024 -0700 Merge branch 'NOAA-EMC:develop' into develop commit dddd837 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 16 12:17:19 2024 -0500 Fix ocean resolution for the S2SWA test (NOAA-EMC#2223) commit 83edaf1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jan 16 11:07:02 2024 -0500 Apply fixes to archiving jobs (NOAA-EMC#2221) Add checks for potentially missing log/data files and update log names for archiving. Missing sflux index files are also added to the products script. Resolves NOAA-EMC#2076 commit c590476 Author: Rahul Mahajan <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 4b58891 Merge: a75e73e 4cb5802 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Wed Jan 10 10:15:48 2024 -0700 Merge branch 'NOAA-EMC:develop' into develop 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 commit a75e73e Merge: 5adc47b 9d901db Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Tue Jan 2 12:44:40 2024 -0700 Merge branch 'NOAA-EMC:develop' into develop commit 5adc47b Merge: a3ce9db a3c5099 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Tue Dec 26 12:40:08 2023 -0700 Merge branch 'NOAA-EMC:develop' into develop commit a3ce9db Merge: 2b1a8e3 a81da33 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Tue Dec 19 09:12:48 2023 -0700 Merge branch 'NOAA-EMC:develop' into develop commit 2b1a8e3 Merge: 4562dec 9505cb4 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Fri Dec 15 09:50:35 2023 -0700 Merge branch 'NOAA-EMC:develop' into develop commit 4562dec Merge: 9f7eeba 29d3417 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Mon Dec 11 12:10:25 2023 -0700 Merge pull request NOAA-GSL#34 from NOAA-EMC/develop Sync develop branch with EMC develop

- 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 <janet.m.derrico@noaa.gov> Date: Thu Feb 29 20:35:11 2024 +0000 update ufs_model pointer commit a28617a951c46b765aa996bfe4d28b554ec4e0a4 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Feb 22 06:16:26 2024 +0000 removed unneeded gsl directories commit 6fb4f90e8572e98c977a1d2ab385f033111f3ea7 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Feb 22 06:08:13 2024 +0000 update ufs_utils.fd pointer commit 9264f0c09239d046c5cd862d807e9b82f51dc3bd Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Feb 21 19:33:26 2024 +0000 update .gitmodules file commit f8edfa966147506f2c207728039e3a736cb95415 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Feb 21 19:30:47 2024 +0000 update pointer to ufs_utils.fd commit 5e0d2ab02d58e6a7a40db55a149a93008b28aa8b Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Feb 21 19:25:52 2024 +0000 update pointer to ufs_model.fd commit ebc9e1d02987a1c6aa8cabedf2323642748fab3c Merge: e7a81511 50cb1e6f Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> 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 <kayee.wong@noaa.gov> Date: Thu Feb 15 20:30:34 2024 +0000 Add pygraf workflow. commit 38b726125d49cff6cae4c0e5fff2438fc33143c5 Author: kayee.wong <kayee.wong@noaa.gov> 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 <kayee.wong@noaa.gov> Date: Tue Feb 13 23:57:06 2024 +0000 more fix. commit 6f80ea2edc5444e275a79b371d02b6e98e963662 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 23:50:01 2024 +0000 more bug fix. commit 56e283f1f666a38a4a3b30e1528e96eeb5c622e7 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 23:40:02 2024 +0000 Minor bug fix. commit 2dcfed06ff6789eb77cf92e22b80f5475923fafc Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 23:19:03 2024 +0000 Update parameter for c3 case Add c3 and mynn template commit cc46b19ccc7cdb54878340eff79dda9e747abdf7 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 20:51:23 2024 +0000 Update INFO. Add c3 SDF in the build. commit a444ed48a23f24724853036e522b4437bf412c59 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 18:42:33 2024 +0000 Update to UFS 2024 Jan 29 version. commit 88595707c7521cdce37ae1cf78720a7827242b24 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 18:16:46 2024 +0000 Minor bug fix. commit baa0e9f10b132098d5134efaad712a51ebc26b83 Author: kayee.wong <kayee.wong@noaa.gov> 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 <kayee.wong@noaa.gov> 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 <kayee.wong@noaa.gov> 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 <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 (#2219) commit c041968e165c07da785376f1441374687b55d6cc 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 (#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 <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 (#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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <david.huber@noaa.gov> Date: Thu Jan 11 11:49:08 2024 -0600 Update orion module/version files for met/metplus #2123 commit 94c9937f0bff380b0ebd6acdcfd2509e1ae99389 Author: DavidHuber <david.huber@noaa.gov> 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 <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 a65e4c675f21dbe72198d263e85e894e62b41e13 Author: David Huber <david.huber@noaa.gov> Date: Thu Jan 11 11:34:19 2024 -0600 Initial update of version/module files #2123 commit 4cb580201af68c1c0e2ae19faf0727dcbbe43b4d 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 (#2212) Fix OpenMP over-allocation of resources running MPMD tasks Co-authored-by: Innocent Souopgui <isouopgui@redlineperf.com> commit b056b531faee6929687cb8a588ffafa1a66426fb Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> 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 <aerorahul@users.noreply.github.com> 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 <aerorahul@users.noreply.github.com> 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 <aerorahul@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <143837053+jderrico-noaa@users.noreply.github.com> 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 <janet.m.derrico@noaa.gov> Date: Thu Feb 1 20:00:52 2024 +0000 adding consistent [[ ]] for if statements commit 67b99668c82a5fd8c42479b9b1bfe8b0bad0be25 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Feb 1 19:37:47 2024 +0000 Updated HOMEgfs in GSL XML templates commit 4d3719c086e7907a6eeff03112042d392e0d8c5e Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Sat Jan 27 02:07:43 2024 +0000 Create GSL version of archive script commit 529d9f71f97b6e643e76a53bc9871901ae861faf Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Tue Jan 16 16:46:25 2024 +0000 Update link script for ufs_utils.fd commit 5b21b31900955013b4e8106d3ae906b9da93b361 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Jan 16 16:45:25 2024 +0000 Add GSL archive scripts for initial conditions commit abb88baf9dd536a3b2ea1e24eaa99cbfe85af799 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Thu Jan 11 23:34:36 2024 +0000 Add namelist parameter, nord_tr, for GSL suites commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Tue Jan 9 02:26:22 2024 +0000 Add experiment setup script for p8_ugwpv1 commit c5a3697d22fdbb02bb80ddffee2629dddc10c702 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Tue Jan 9 02:13:42 2024 +0000 Updated GSL-specific files under ufs_utils.fd_gsl commit 1b153fc95b93a16eb40b791be7322100fde4a3d4 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jan 2 10:30:33 2024 -0700 Stop Gempak pgrb2 spec from modifying $DATA (#2147) This PR addresses issue #1224. The following is accomplished: - Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time; - Shell linter exceptions are addressed accordingly; - The respective GEMPAK tasks is added to the Rocoto mesh. Resolves #1224 commit 31ad23527802f7d07171132cc620f7135c4d8cba Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jan 2 10:27:30 2024 -0700 Reorganize NPOESS scripts (#2166) This PR addresses issue #1226. The following is accomplished: - Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated; - Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh` are moved accordingly; this specifically applies to the environment variable `FHOUR`, `SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`; - The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level (if necessary); - Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however, this may not be necessary (see `TODO` note within draft PR. Resolves #1226 commit 22bd82fa93b49e5ce98eb3f69123956dd5018049 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Jan 2 11:55:03 2024 -0500 Orog fix file reorg and fix directory variable standardization (#2181) This PR makes updates to use the newly reorganized `orog/20231027` fix file version and standardizes the fix file directory variables. Changes: 1. Update UFS_UTILS hash to ce385ce 2. Update fix file version file to use new orog timestamp: `orog_ver=20231027` 3. Add ".mx$(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 <40322596+ADCollard@users.noreply.github.com> 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 <jessica.meixner@noaa.gov> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <bbakernoaa@users.noreply.github.com> 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 <aerorahul@users.noreply.github.com> commit e55a05980709288d902ad1bd894164bfa5a18a65 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> 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 <terrence.mcguinness@cox.net> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <terrence.mcguinness@cox.net> 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 <aerorahul@users.noreply.github.com> Date: Thu Dec 14 16:05:33 2023 -0500 Correct fbwind (#2161) commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a Author: Kate Friedman <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <cory.r.martin@noaa.gov> Date: Thu Dec 7 15:12:05 2023 -0500 Update GDAS hash to most recent stable versions (#2138) commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Dec 7 10:41:05 2023 -0700 Corrected typo in a gempak job gempakncdcupapgif . (#2137) commit 3483f550db1ae35a680de49f7485ce5a11902dd9 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Thu Dec 7 12:34:56 2023 -0500 Add support for FGAT and IAU for aerosol DA (#1940) commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> commit a29f751aed05312da3d80d396159bb5a906d6ce4 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Dec 6 13:45:56 2023 -0700 Adds GEMPAK and related jobs to rocoto task mesh (#2127) commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <terrence.mcguinness@cox.net> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <jiande.wang@noaa.gov> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Wed Nov 29 15:17:36 2023 -0500 Added variables to config.prepoceanobs (#2101) commit c2d78a61a224678fb804eed19f39d1f07408ae5f Author: Kate Friedman <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <jessica.meixner@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <48260754+WenMeng-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <aerorahul@users.noreply.github.com> Date: Wed Nov 15 16:44:03 2023 -0500 Fix missing _PREV in ocean restart file location (#2070) commit 255616d37505c785bdddd5d3e39e8399110b626e Author: mdtoyNOAA <73618848+mdtoyNOAA@users.noreply.github.com> 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 <guillaume.vernieres@noaa.gov> 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 <guoqing.ge@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <aerorahul@users.noreply.github.com> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <jiande.wang@noaa.gov> 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 <bbakernoaa@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <terrence.mcguinness@cox.net> 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 <guillaume.vernieres@noaa.gov> 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 <jiande.wang@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu Nov 2 16:09:59 2023 -0400 changed optional script name vars for ocean analysis (#2025) commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6 Author: Kate Friedman <kate.friedman@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Wed Nov 1 14:19:55 2023 -0400 Updates to prep ocean obs task (#1870) commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <terrence.mcguinness@cox.net> 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 <terrence.mcguinness@cox.net> Date: Tue Oct 31 13:57:02 2023 +0000 Allow CI case to exclude running on certain platforms (#2001) commit 7cc137116f1619bf1e5a12eaacb98d17da97c223 Author: Jeff Whitaker <jswhit@fastmail.fm> Date: Tue Oct 31 07:54:24 2023 -0600 Add initial C96/1 deg coupled model support (#1991) commit 7086ddc4bece6fb2a8c1c2e6090800d4293e410e Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> 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 <guillaume.vernieres@noaa.gov> 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 <108816337+AnilKumar-NOAA@users.noreply.github.com> 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 <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Thu Oct 26 23:44:27 2023 -0400 Update GDASApp hash (#1975) Update GDASApp hash to bring recent UFSDA development into g-w…

12Jan24 global-workflow UFS: 29Jan24, 625ac02 FV3: 29Jan24, bd38c56 UPP: 07Nov23, 78f369b UFS_UTILS: 22Dev23, ce385ce update pointers for ufs_model and ufs_utils add GSL C3_MYNN xml suite Squashed commit of the following: commit 25c026ef03a8d8c0db0b7368d2836f0b2e866eae Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Feb 29 20:35:11 2024 +0000 update ufs_model pointer commit a28617a951c46b765aa996bfe4d28b554ec4e0a4 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Feb 22 06:16:26 2024 +0000 removed unneeded gsl directories commit 6fb4f90e8572e98c977a1d2ab385f033111f3ea7 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Feb 22 06:08:13 2024 +0000 update ufs_utils.fd pointer commit 9264f0c09239d046c5cd862d807e9b82f51dc3bd Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Feb 21 19:33:26 2024 +0000 update .gitmodules file commit f8edfa966147506f2c207728039e3a736cb95415 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Feb 21 19:30:47 2024 +0000 update pointer to ufs_utils.fd commit 5e0d2ab02d58e6a7a40db55a149a93008b28aa8b Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Feb 21 19:25:52 2024 +0000 update pointer to ufs_model.fd commit ebc9e1d02987a1c6aa8cabedf2323642748fab3c Merge: e7a81511 50cb1e6f Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> 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 <kayee.wong@noaa.gov> Date: Thu Feb 15 20:30:34 2024 +0000 Add pygraf workflow. commit 38b726125d49cff6cae4c0e5fff2438fc33143c5 Author: kayee.wong <kayee.wong@noaa.gov> 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 <kayee.wong@noaa.gov> Date: Tue Feb 13 23:57:06 2024 +0000 more fix. commit 6f80ea2edc5444e275a79b371d02b6e98e963662 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 23:50:01 2024 +0000 more bug fix. commit 56e283f1f666a38a4a3b30e1528e96eeb5c622e7 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 23:40:02 2024 +0000 Minor bug fix. commit 2dcfed06ff6789eb77cf92e22b80f5475923fafc Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 23:19:03 2024 +0000 Update parameter for c3 case Add c3 and mynn template commit cc46b19ccc7cdb54878340eff79dda9e747abdf7 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 20:51:23 2024 +0000 Update INFO. Add c3 SDF in the build. commit a444ed48a23f24724853036e522b4437bf412c59 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 18:42:33 2024 +0000 Update to UFS 2024 Jan 29 version. commit 88595707c7521cdce37ae1cf78720a7827242b24 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 18:16:46 2024 +0000 Minor bug fix. commit baa0e9f10b132098d5134efaad712a51ebc26b83 Author: kayee.wong <kayee.wong@noaa.gov> 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 <kayee.wong@noaa.gov> 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 <kayee.wong@noaa.gov> 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 <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 (#2219) commit c041968e165c07da785376f1441374687b55d6cc 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 (#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 <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 (#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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <david.huber@noaa.gov> Date: Thu Jan 11 11:49:08 2024 -0600 Update orion module/version files for met/metplus #2123 commit 94c9937f0bff380b0ebd6acdcfd2509e1ae99389 Author: DavidHuber <david.huber@noaa.gov> 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 <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 a65e4c675f21dbe72198d263e85e894e62b41e13 Author: David Huber <david.huber@noaa.gov> Date: Thu Jan 11 11:34:19 2024 -0600 Initial update of version/module files #2123 commit 4cb580201af68c1c0e2ae19faf0727dcbbe43b4d 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 (#2212) Fix OpenMP over-allocation of resources running MPMD tasks Co-authored-by: Innocent Souopgui <isouopgui@redlineperf.com> commit b056b531faee6929687cb8a588ffafa1a66426fb Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> 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 <aerorahul@users.noreply.github.com> 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 <aerorahul@users.noreply.github.com> 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 <aerorahul@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <143837053+jderrico-noaa@users.noreply.github.com> 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 <janet.m.derrico@noaa.gov> Date: Thu Feb 1 20:00:52 2024 +0000 adding consistent [[ ]] for if statements commit 67b99668c82a5fd8c42479b9b1bfe8b0bad0be25 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Feb 1 19:37:47 2024 +0000 Updated HOMEgfs in GSL XML templates commit 4d3719c086e7907a6eeff03112042d392e0d8c5e Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Sat Jan 27 02:07:43 2024 +0000 Create GSL version of archive script commit 529d9f71f97b6e643e76a53bc9871901ae861faf Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Tue Jan 16 16:46:25 2024 +0000 Update link script for ufs_utils.fd commit 5b21b31900955013b4e8106d3ae906b9da93b361 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Jan 16 16:45:25 2024 +0000 Add GSL archive scripts for initial conditions commit abb88baf9dd536a3b2ea1e24eaa99cbfe85af799 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Thu Jan 11 23:34:36 2024 +0000 Add namelist parameter, nord_tr, for GSL suites commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Tue Jan 9 02:26:22 2024 +0000 Add experiment setup script for p8_ugwpv1 commit c5a3697d22fdbb02bb80ddffee2629dddc10c702 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Tue Jan 9 02:13:42 2024 +0000 Updated GSL-specific files under ufs_utils.fd_gsl commit 1b153fc95b93a16eb40b791be7322100fde4a3d4 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jan 2 10:30:33 2024 -0700 Stop Gempak pgrb2 spec from modifying $DATA (#2147) This PR addresses issue #1224. The following is accomplished: - Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time; - Shell linter exceptions are addressed accordingly; - The respective GEMPAK tasks is added to the Rocoto mesh. Resolves #1224 commit 31ad23527802f7d07171132cc620f7135c4d8cba Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jan 2 10:27:30 2024 -0700 Reorganize NPOESS scripts (#2166) This PR addresses issue #1226. The following is accomplished: - Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated; - Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh` are moved accordingly; this specifically applies to the environment variable `FHOUR`, `SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`; - The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level (if necessary); - Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however, this may not be necessary (see `TODO` note within draft PR. Resolves #1226 commit 22bd82fa93b49e5ce98eb3f69123956dd5018049 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Jan 2 11:55:03 2024 -0500 Orog fix file reorg and fix directory variable standardization (#2181) This PR makes updates to use the newly reorganized `orog/20231027` fix file version and standardizes the fix file directory variables. Changes: 1. Update UFS_UTILS hash to ce385ce 2. Update fix file version file to use new orog timestamp: `orog_ver=20231027` 3. Add ".mx$(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 <40322596+ADCollard@users.noreply.github.com> 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 <jessica.meixner@noaa.gov> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <bbakernoaa@users.noreply.github.com> 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 <aerorahul@users.noreply.github.com> commit e55a05980709288d902ad1bd894164bfa5a18a65 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> 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 <terrence.mcguinness@cox.net> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <terrence.mcguinness@cox.net> 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 <aerorahul@users.noreply.github.com> Date: Thu Dec 14 16:05:33 2023 -0500 Correct fbwind (#2161) commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a Author: Kate Friedman <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <cory.r.martin@noaa.gov> Date: Thu Dec 7 15:12:05 2023 -0500 Update GDAS hash to most recent stable versions (#2138) commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Dec 7 10:41:05 2023 -0700 Corrected typo in a gempak job gempakncdcupapgif . (#2137) commit 3483f550db1ae35a680de49f7485ce5a11902dd9 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Thu Dec 7 12:34:56 2023 -0500 Add support for FGAT and IAU for aerosol DA (#1940) commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> commit a29f751aed05312da3d80d396159bb5a906d6ce4 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Dec 6 13:45:56 2023 -0700 Adds GEMPAK and related jobs to rocoto task mesh (#2127) commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <terrence.mcguinness@cox.net> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <jiande.wang@noaa.gov> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Wed Nov 29 15:17:36 2023 -0500 Added variables to config.prepoceanobs (#2101) commit c2d78a61a224678fb804eed19f39d1f07408ae5f Author: Kate Friedman <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <jessica.meixner@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <48260754+WenMeng-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <aerorahul@users.noreply.github.com> Date: Wed Nov 15 16:44:03 2023 -0500 Fix missing _PREV in ocean restart file location (#2070) commit 255616d37505c785bdddd5d3e39e8399110b626e Author: mdtoyNOAA <73618848+mdtoyNOAA@users.noreply.github.com> 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 <guillaume.vernieres@noaa.gov> 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 <guoqing.ge@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <aerorahul@users.noreply.github.com> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <jiande.wang@noaa.gov> 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 <bbakernoaa@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <terrence.mcguinness@cox.net> 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 <guillaume.vernieres@noaa.gov> 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 <jiande.wang@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu Nov 2 16:09:59 2023 -0400 changed optional script name vars for ocean analysis (#2025) commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6 Author: Kate Friedman <kate.friedman@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Wed Nov 1 14:19:55 2023 -0400 Updates to prep ocean obs task (#1870) commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <terrence.mcguinness@cox.net> 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 <terrence.mcguinness@cox.net> Date: Tue Oct 31 13:57:02 2023 +0000 Allow CI case to exclude running on certain platforms (#2001) commit 7cc137116f1619bf1e5a12eaacb98d17da97c223 Author: Jeff Whitaker <jswhit@fastmail.fm> Date: Tue Oct 31 07:54:24 2023 -0600 Add initial C96/1 deg coupled model support (#1991) commit 7086ddc4bece6fb2a8c1c2e6090800d4293e410e Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> 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 <guillaume.vernieres@noaa.gov> 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 <108816337+AnilKumar-NOAA@users.noreply.github.com> 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 <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Thu Oct 26 23:44:27 2023 -0400 Update GDASApp hash (#1975) Update GDASApp hash to bring recent UFSDA development into g-w. Resolves #1972 commit 962368884991670d3a1e…

@DeniseWorthen

UFS: 21Feb24, 6988662 FV3: 14Feb24, 0fe9ba3 UPP: 23Jan23, 945cb2c UFS_UTILS: 22Feb24, d805336 Squashed commit of the following: commit 732a874 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Mon Mar 4 16:04:26 2024 -0500 Reformat snowDA templates to jinja2 (NOAA-EMC#2371) # Description This PR: - replaces use of non-jinja2 templates in the yaml templates. Specifically `$( )` in favor of pure jinja2. - uses jinja2's built-in capability to include templates within templates, thereby allowing to assemble a completely rendered template before passing it to for e.g. yaml loader. - requires updates to `wxflow` and `gdasapp` - Changes in `wxflow` in `parse_j2yaml` are **not** backwards compatible Additionally, this PR: - renames `config.base.emc.dyn` to `config.base`. Resolves NOAA-EMC#2347 commit d1fa411 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Sat Mar 2 04:54:26 2024 +0000 Reduce Jenkins messaging to GitHub (NOAA-EMC#2370) This PR updates the Jenkins Pipeline code with safeguards against the errors caused when Jenkins fails to authenticate with GitHub to message or update a label. This was achieved simply by: - Reducing the number out messages sent to the GitHub PR - Putting try blocks around most of the update label calls Co-authored-by: tmcguinness <terry.mcguinness@noaa.gov> commit 52fa3cb Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Fri Mar 1 12:36:27 2024 -0700 Adding debug option for all build scripts (NOAA-EMC#2326) This PR addresses issue NOAA-EMC#300 that allows building in `debug` mode. Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 91738cb Author: DWesl <22566757+DWesl@users.noreply.github.com> Date: Fri Mar 1 13:46:42 2024 -0500 Sort list of coupler restart files for restart time determination (NOAA-EMC#2360) The loop in the following conditional seems to assume the list is sorted, so make that explicit in the array construction. commit 23c2552 Author: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com> Date: Fri Mar 1 13:45:39 2024 -0500 Update stage IC to handle ocean perturbations (NOAA-EMC#2364) This PR adds the option to stage ocean perturbation files for ensemble forecasts. These perturbation files are used in GEFS forecasts. A new variable is introduced in config.base to use the ocean perturbation files. This PR does not include using these perturbation files. A future PR will address this. commit 8efe05f Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Mar 1 07:41:56 2024 -0500 Turn on C48mx500_3DVarAOWCDA test on hera (NOAA-EMC#2363) This PR activates the C48mx500_3DVarAOWCDA test on hera. This required an update of the gdas app. commit 5166593 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Feb 29 20:14:41 2024 +0000 Move Jenkinsfile into ci subdirectory (NOAA-EMC#2355) Just moves the Jenkinsfile into the ci directory Co-authored-by: tmcguinness <terry.mcguinness@noaa.gov> commit b7af315 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 28 22:20:58 2024 +0000 Fix rocoto forecast hour determination for GEFS (NOAA-EMC#2351) The function that generates the list of forecast hours for rocoto was trying to use variables that are not defined for GEFS, causing workflow generation to fail. The function is updated to not try to load these variables before loading the ones actually used for GFS/ GEFS. Also turns GEFS CI test back on and adds an entry to stage C192 ICs (note: these have not been placed in the centralized location.) commit d3a4927 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Wed Feb 28 09:38:49 2024 -0500 Rename the land DA jobs to snow DA to better reflect what they are doing (NOAA-EMC#2330) This PR renames all of the land DA jobs to snow DA to better reflect that this is a JEDI-based snow analysis capability and not a more generic land surface analysis. commit 2693810 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Tue Feb 27 01:25:51 2024 -0500 Update ufs-waether-model hash (NOAA-EMC#2338) Routine update of ufs-weather-model hash. Other small updates: * removes comment referencing closed issue. * Updates the CICE diag frequency to once per day as recommend here: NOAA-EMC#1810 (comment) * Updated amount of time for C384 gdas forecast as it was running out of time * Removed unused variable wave_sys_ver commit 9608852 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon Feb 26 14:10:01 2024 -0500 Update JEDI ATM to use .nc for obs and generalize x,y layout (NOAA-EMC#2336) # Description The changes in this PR are twofold 1. replace `.nc4` suffix for JEDI ATM observation related files with `.nc` 2. use templated variables to specify `{layout_x, layout_y}` for JEDI ATM variational and local ensemble apps The first change conforms with the Unidata recommendation that netCDF files end with the suffix `.nc`. The second change replaces hardwired JEDI ATM var and ens `{layout_x, layout_y}` in `config.resources` with a more flexible approach. Resolves NOAA-EMC#2335 commit c5c8466 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Feb 26 10:18:50 2024 -0500 Remove FIX* variables for fix subfolders (NOAA-EMC#2337) Remove `FIX*` variables for fix subfolders and replace them with the remaining `FIXgfs` variable and the subfolder name (e.g. `${FIXam}` -> `${FIXgfs}/am`). The UFS_UTILS and GDASApp repos were similarly updated. This PR includes a new UFS_UTILS hash. The updated GDASAPP hash was already committed within the spack-stack/1.6.0 PR NOAA-EMC#2239. Resolves NOAA-EMC#2184 commit 950c38a Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri Feb 23 21:15:46 2024 +0000 Fix several Jenkins issues (NOAA-EMC#2334) Jenkins Updates Resolving final kinks: - Removed all `git` shell commands and now exclusively use Software Control Manger (**scm**) plugin. - Add feature for skipping hosts per configuration specified in case yaml files. - Solved and tested false positive builds and experiments. - Tested archiving of task error log on case fail - First case fail quits pipeline and cancels all pending scheduled jobs - Duel build per yaml configuration arguments supported - All designated case files in PR directory pass on intended host (fully tested on Hera) Remaining updates: - Fist build fail short circuit when building sub-modules and archiving build error log. - Re-build/no-build built in logic for Replay and Rerunning previously failed experiments. commit c67393a Merge: 6f9afff 79d305e Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Feb 23 14:18:15 2024 +0000 Merge pull request NOAA-EMC#2239 from DavidHuber-NOAA/ss160 Update to spack-stack 1.6.0 Includes all submodules except the UFS, which will be updated at a later time. commit 79d305e Author: David Huber <david.huber@noaa.gov> Date: Thu Feb 22 14:53:57 2024 -0600 Disable snow DA tests commit 0459203 Author: David Huber <david.huber@noaa.gov> Date: Thu Feb 22 12:55:51 2024 -0600 Update GDASApp hash to current develop commit 5c96eb2 Author: David Huber <david.huber@noaa.gov> Date: Thu Feb 22 12:37:47 2024 -0600 Update GDAS hash to allow modified snow DA analysis commit 79144f2 Merge: abbb0b8 6f9afff Author: DavidHuber <david.huber@noaa.gov> Date: Thu Feb 22 15:14:39 2024 +0000 Merge remote-tracking branch 'origin/develop' into ss160 commit abbb0b8 Merge: 4ad837e 4529e8c Author: DavidHuber <david.huber@noaa.gov> Date: Thu Feb 22 15:11:03 2024 +0000 Merge remote-tracking branch 'henry/feature/gwdev_issue_2129' into ss160 commit 4ad837e Merge: 516b2a2 7ca45db Author: DavidHuber <david.huber@noaa.gov> Date: Thu Feb 22 15:10:24 2024 +0000 Merge remote-tracking branch 'henry/feature/gfsv17_issue_2125' into ss160 commit 516b2a2 Author: DavidHuber <david.huber@noaa.gov> Date: Thu Feb 22 14:19:16 2024 +0000 Updated GDAS to include rocoto/1.3.6 on Hera. commit 6f9afff Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Feb 21 13:09:44 2024 -0500 Add some flexibility for ocean/ice output (NOAA-EMC#2327) This adds functionality to have ocean/ice output frequency be separate from the atm model. One time was created because there's an assumption in the post that these are the same. This could be further modified to remove this assumption. Refs NOAA-EMC#1629 commit f6d3015 Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 09:53:08 2024 -0600 Update GDASApp hash to include SS/1.6.0 support. commit 0bf340b Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 09:07:32 2024 -0600 Construct SS paths from version variables. commit 3330cd7 Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 09:06:19 2024 -0600 Removed MET/METplus 'not available' comments commit fdc638c Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 08:35:15 2024 -0600 Move SS module path to version files. commit d7d28a6 Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 07:53:15 2024 -0600 Update comment about METplus support. commit a812f88 Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 07:45:45 2024 -0600 Update verif-global to latest WCOSS2 support. commit d81f07f Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 07:41:38 2024 -0600 Clean up build_upp.sh. -Corrected whitespace (tabs instead of spaces) -Removed debug print statement -Alphebetized flags commit ae7eb19 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Feb 16 16:15:40 2024 -0500 Fix whitespace in build_upp.sh. Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 48b34d0 Author: David Huber <david.huber@dlogin05.dogwood.wcoss2.ncep.noaa.gov> Date: Fri Feb 16 20:56:55 2024 +0000 Added verif-global support back to WCOSS2. commit 4529e8c Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Fri Feb 16 11:12:01 2024 -0700 Bug fix. commit 8e4f94d Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Fri Feb 16 11:04:41 2024 -0700 Updates requested by reviewer Rahul Mahajan. commit 4624ce2 Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Fri Feb 16 10:52:11 2024 -0700 Updates requested by reviewer; testing -- DO NOT REVIEW. commit ed25bbd Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Fri Feb 16 09:33:59 2024 -0700 Linter corrections. commit 6a0b7bf Merge: f9fb64e 2415b7b Author: David Huber <david.huber@noaa.gov> Date: Fri Feb 16 09:50:22 2024 -0600 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit f9fb64e Merge: 777d97d a23b7f2 Author: David Huber <david.huber@noaa.gov> Date: Fri Feb 16 09:49:42 2024 -0600 Merge remote-tracking branch 'emc/develop' into ss160 commit 7ca45db Merge: 73bc76b a23b7f2 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Fri Feb 16 07:46:35 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit eb2ed53 Merge: 9929277 a23b7f2 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Fri Feb 16 07:46:24 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit a23b7f2 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Fri Feb 16 09:37:58 2024 -0500 Add JEDI 3DEnVar atmosphere only CI test stub (NOAA-EMC#2309) commit cf83885 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Feb 16 01:55:02 2024 -0500 Add unstructured grid for HR3/GFS (NOAA-EMC#2230) This adds the capability to use unstructured grids in the global workflow, which will be used in HR3. There are new fix files for a low-resolution 100km grid and a grid closer to our targeted GFSv17 grid which has the resolution combined from the older multi_1 and GFSv16 grids. The fix file update is here: NOAA-EMC#2229 Note: This now means that GFS tests need a new build option: `./build_all.sh -w` So that PDLIB=ON is turned on for compiling relevant UFS and WW3 codes. Resolves NOAA-EMC#1547 commit 9929277 Merge: eb8791c 094e3b8 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Feb 15 15:05:50 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit 094e3b8 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Thu Feb 15 14:43:55 2024 -0500 Move IMS remapping files from COM_OBS to FIXgdas (NOAA-EMC#2322) * Add in IMS obs fix directory and update submodule for gdas commit d465ea0 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Feb 15 19:25:02 2024 +0000 Set HOMEgfs for module_setup in CI driver (NOAA-EMC#2321) Hotfixes to CI Bash system from updates with sourcing `detect_machine.sh` in `ush/module-setup.sh` using **HOMEgfs**. commit 2415b7b Author: David Huber <david.huber@noaa.gov> Date: Thu Feb 15 19:21:17 2024 +0000 Load default rocoto on Jet. commit eb8791c Merge: 60d5ee6 638684e Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Feb 15 11:56:40 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit 777d97d Author: David Huber <david.huber@noaa.gov> Date: Thu Feb 15 12:34:59 2024 -0600 Fixed Orion cdo version. commit ef07235 Author: DavidHuber <david.huber@noaa.gov> Date: Thu Feb 15 16:29:32 2024 +0000 Revert UFS hash. commit 0ce8c0d Author: DavidHuber <david.huber@noaa.gov> Date: Thu Feb 15 14:55:48 2024 +0000 Fix git version in Hera's gwsetup module. commit 3080a34 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Feb 14 20:52:34 2024 +0000 Fixed xarray version for SS/1.6.0. commit 49392dd Author: DavidHuber <david.huber@noaa.gov> Date: Wed Feb 14 20:29:41 2024 +0000 Updated GSI-Utils hash to head of develop. commit c3553f0 Merge: 4568653 638684e Author: DavidHuber <david.huber@noaa.gov> Date: Wed Feb 14 20:28:14 2024 +0000 Merge remote-tracking branch 'origin/develop' into ss160 commit 4568653 Author: David Huber <david.huber@noaa.gov> Date: Wed Feb 14 14:22:13 2024 -0600 Reupgrade Hercules to SS/1.6.0 commit 638684e Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Feb 14 14:55:21 2024 -0500 Remove `finddate.sh` from system (NOAA-EMC#2308) * Retire finddate.sh usage from system * Update gfs-utils hash to 7a84c88 - New hash includes removal of finddate.sh Refs NOAA-EMC#2279 commit 2b160f8 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Feb 14 18:31:28 2024 +0000 Reenable METplus jobs on Hercules. commit 8f59002 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Feb 14 18:30:23 2024 +0000 Update GSI hashes. commit 73bc76b Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Wed Feb 14 09:27:37 2024 -0700 Updates based on user request. commit e4bc674 Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Wed Feb 14 08:03:45 2024 -0700 Corrected based on reviewer review. commit 60d5ee6 Merge: 40f2cf6 1aaef05 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Feb 13 18:08:33 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit 0330411 Merge: 929b903 1aaef05 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Feb 13 17:58:12 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit 1aaef05 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Feb 13 18:15:59 2024 -0500 Jenkins Pipeline updates for Canceling Jobs (NOAA-EMC#2307) Tuning updates for Jenkins Pipeline : - Added short circuit for all parallel runs of cases on error of any - Fixed canceling of all scheduled jobs on first case error - Added feature to save error log files to Jenkins Archive facility on fail commit 6404892 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Feb 13 14:57:37 2024 -0500 Ocean/ice product generation for GFS and GEFS (NOAA-EMC#2286) This PR does several things: 1. the model output for ocean and ice in the `COM/` directory are now named per EE2 convention for coupled model. E.g `gfs.ocean.t12z.6hr_avg.f120.nc` and `gfs.ocean.t12z.daily.f120.nc` 2. The products are generated using the `ocnicepost.fd` utility developed by @DeniseWorthen in https://github.com/NOAA-EMC/gfs-utils and converted to grib2 using example scripts provided by @GwenChen-NOAA using `wgrib2`. 3. NetCDF products on the native grid are also generated by subsetting variables from the raw model output. This is done with `xarray`. 4. updates the hash of https://github.com/NOAA-EMC/gfs-utils to include fixes in `ocnicepost.fd` 5. removes NCL related scripting that was previously used for ocean/ice interpolation and `reg2grb2` used for converting to grib2. 6. updates archive scripts to accommodate updated file names 7. removes intermediate ocean processed files such as 2D/3D/xsect data- sets 8. separate jobs are added for ocean and ice product generation. 9. removes intermediate restarts for the mediator and only saves the medi- ator restart at the end of the forecast in `COM`. 10. Increases memory for offline UPP when run at C768. The program segfaults with an OOM when memory is self allocated based on PEs by the scheduler on Hera. 11. Enables ocean/ice ensemble product generation for GEFS 12. Some minor clean-ups Fixes NOAA-EMC#935 Fixes NOAA-EMC#1317 Fixes NOAA-EMC#1864 commit 40f2cf6 Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Tue Feb 13 10:18:53 2024 -0700 Implemented ush/detect_machine.sh for host determination and removed redundant checks for expected file paths. commit 929b903 Merge: 2d08d01 3f99f70 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Feb 13 08:31:06 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit 3f99f70 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Feb 13 00:57:18 2024 -0500 Add wave post jobs to GEFS (NOAA-EMC#2292) Adds the wave post jobs for gridded and points to GEFS. Boundary point jobs are added even though the current GEFS buoy file does not contain any (tested by manually subbing in the GFS buoy file). Resolves NOAA-EMC#827 commit 842adf3 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Mon Feb 12 12:50:08 2024 -0500 Added additional test cases to the pr list in Jenkins (NOAA-EMC#2306) C48mx500_3DVarAOWCDA, C96C48_hybatmDA, and C96_atmsnowDA Co-authored-by: terrance.mcguinness <terrance.mcguinness@noaa.gov> commit bb4ca65 Author: CatherineThomas-NOAA <59020064+CatherineThomas-NOAA@users.noreply.github.com> Date: Mon Feb 12 14:50:41 2024 +0000 Redo v16.3 config.base changes for DA increments (NOAA-EMC#2304) Include the additional hydrometeors to the INCREMENTS_TO_ZERO and INCVARS_ZERO_STRAT variables in config.base that were modified in v16.3. Resolves: NOAA-EMC#2303 commit 061992b Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Sat Feb 10 01:33:36 2024 -0500 Fix Jenkins success reporting (NOAA-EMC#2302) Moving the post section back outside of main Run Experiments stage. This allows the system to correctly report the **Success** status until after all tests pass. _Had originally moved them in attempts to solve "Not an SCM GitHub Job" issue and cause the reporting to misbehave._ Also ran through Jenkins linter and updated some messaging that was incorrectly reporting system build type. commit 28ccf78 Merge: b972f66 54daa31 Author: David Huber <david.huber@noaa.gov> Date: Fri Feb 9 14:00:43 2024 -0600 Merge remote-tracking branch 'emc/develop' into ss160 commit b972f66 Author: David Huber <david.huber@noaa.gov> Date: Fri Feb 9 10:47:00 2024 -0600 Fix SS versions for CI modules. commit 4b01d8e Author: David Huber <david.huber@noaa.gov> Date: Fri Feb 9 10:44:30 2024 -0600 Revert Hercules modules to SS/1.5.1. commit 54daa31 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Feb 8 15:48:38 2024 -0500 Jenkins Declartive Pipeline for CI with gfs/gefs multibuilds (NOAA-EMC#2246) Adding top level Jenkins file for CI tests running on Jenkins Controller: - Declarative Multi-branch Pipeline (has enhanced restart capabilities on a per section bases) - Starts Pipeline from Label PR same as BASH system (for now) - Progress and restarts can me managed with CAC Login at [EPIC OAR Jenkins](https://jenkins.epic.oarcloud.noaa.gov) - Has logic for multi **gfs/gefs** system builds (arguments based on a configuration file `ci/casts/yamls/build.yaml`) - Any number of **systems** may be added by manual adding an ele- ment to the matrix in the Jenkinsfile - _It may be possible to dynamic add matrix values with a specialty plug-in_ - Currently only runs on **Orion** and **Hera** using `mterry` account Resolves NOAA-EMC#2119 Resolves NOAA-EMC#2118 commit 43429e2 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Feb 8 15:30:28 2024 -0500 Enable AO WCDA test (NOAA-EMC#1963) This PR: - adds GSI + SOCA C48 5-deg ocean 3DVar test (courtesy @guillaumevernieres) - adds a toggle to optionally disable ocnanalvrfy job. commit 2d08d01 Merge: 4745d4a f563528 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Feb 8 07:24:54 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit f563528 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Feb 7 15:09:12 2024 -0500 Update JGLOBAL_FORECAST for octal error (NOAA-EMC#2295) Add "10#" to ENSMEM value > 0 check to handle octal errors. commit 4745d4a Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Wed Feb 7 08:45:49 2024 -0700 Removed jlogfile references. commit 5894ca2 Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Wed Feb 7 08:32:16 2024 -0700 Removed dummy variable passed to perl scripts. commit dae884a Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Wed Feb 7 08:29:49 2024 -0700 Removed jlogfile and postmsg references within gempak scripts. commit 801058f Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Feb 7 00:41:59 2024 -0700 Consolidate `npe_node_max` (NOAA-EMC#2289) - The environment variable `npe_node_max` is removed from all files beneath `global-workflow/env`; - The environment variable `npe_node_max` is removed from `parm/config/gefs/config.ufs` and `parm/config/gfs/config.ufs`; - The environment variable `npe_node_max` is maintained only within `parm/config/gefs/config.resources` and `parm/config/gfs/config.resources`. Resolves NOAA-EMC#2133 commit b0325e0 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Feb 7 00:40:20 2024 -0700 Removes files module loading file no longer used by the GW (NOAA-EMC#2281) Removes `module-setup.csh.inc` and `module-setup.sh.inc`. The module `ush/module-setup.sh` is updated such that it now sources `ush/detect_machine.sh` to determine which supported platform the global-workflow is being execute on. Resolves NOAA-EMC#2130 commit 1ccc989 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Feb 5 14:16:07 2024 -0500 Remove EnKF forecast groups (NOAA-EMC#2280) Removes the grouping of EnKF forecasts so each job only runs one forecast. Member and MEMDIR are now set at the workflow manager (rocoto) level. This change makes much of the system simpler (especially dependencies) and allows the elimination of the separate efcs scripts. Metatask names of updated jobs have been updated to make them a little less opaque by using the same name name as its constituent tasks (e.g. the forecast metatask is named `enkgdasfcst`, not `enkfgdasefcs`). Metatasks that weren't updated retain the same names as before for now. Resolves NOAA-EMC#2254 commit 9f3383f Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Mon Feb 5 12:15:13 2024 -0700 Updated detect_machine.sh using that from UFS WM. (NOAA-EMC#2252) Updates `ush/detect_machine.sh` to match the UFS weather-model `tests/detect_machine.sh` prepared by @BrianCurtis-NOAA Resolves NOAA-EMC#2228 commit 7d68b0b Author: CatherineThomas-NOAA <59020064+CatherineThomas-NOAA@users.noreply.github.com> Date: Sun Feb 4 22:02:41 2024 +0000 Update global_cycle for fractional grid (NOAA-EMC#2262) The hash for ufs_utils is updated to include the changes for fractional grid support within global_cycle. This commit also removes the hack to skip global_cycle in cycling mode with v17 physics. Resolves: NOAA-EMC#1775 Refs: ufs-community/UFS_UTILS#815 Refs: ufs-community/UFS_UTILS#891 commit ed592a6 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Sat Feb 3 02:55:14 2024 -0500 Retire cycle-specific FHMAX_GFS variables (NOAA-EMC#2278) This PR retires the `FHMAX_GFS_${cyc}` variables that allowed users to specify different gfs forecast lengths for each cycle. This function is no longer supported in global-workflow. The `FHMAX_GFS_*` variables will be removed and will no longer be checked to set the final `FHMAX_GFS` variable. The same forecast length will be set for every cycle. This PR also includes a small fix to add new post parm files into the `.gitignore` file. This was intended to be included in a different PR but that PR is on hold for further testing so it is being included here to get it into `develop` sooner. Resolves NOAA-EMC#2218 commit 977e2d6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Fri Feb 2 07:49:09 2024 -0700 New GDASApp hash. (NOAA-EMC#2285) commit b5f2bd9 Merge: 4d66742 0400e1f Author: David Huber <david.huber@noaa.gov> Date: Tue Jan 30 13:55:00 2024 -0600 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 0400e1f Author: David Huber <david.huber@noaa.gov> Date: Tue Jan 30 09:57:11 2024 -0600 Fix gfs_utils Orion spack-stack env path. commit 6bbe823 Author: DWesl <22566757+DWesl@users.noreply.github.com> Date: Mon Jan 29 21:15:30 2024 -0500 Use seq to generate the list of times, instead of a bash for-loop (NOAA-EMC#2264) I'm running a year-long forecast, which means I get a large portion of the log file dedicated to these loops. `seq ${START} ${STEP} ${STOP}` will generate a sequence going from START to STOP by STEP, including STOP if relevant. That seems to be the purpose of these loops. It will by default separate the list with newlines, but `seq -s ' ' ${START} ${STEP} ${STOP}` will separate them with spaces instead, more closely mimicing the previous behavior. I would like this to be two lines in the log, rather than a few hundred, and this may also be faster, though probably more for reasons of fewer writes to disk than because bash isn't designed for arithmetic. commit d5bee38 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Jan 29 14:35:02 2024 -0500 Correct typos in GFS config.resources (NOAA-EMC#2267) This PR corrects some typos in `parm/config/gfs/config.resources` that were introduced in PR NOAA-EMC#2216. The esfc job was failing in tests on WCOSS2 due to insufficient memory. This lead to discovering the other typos. The esfc job completes without error after its memory is set back to `80GB` from the incorrect `8GB`. Resolves NOAA-EMC#2266 commit 81557be Author: David Huber <david.huber@noaa.gov> Date: Mon Jan 29 12:13:31 2024 -0600 Update monitor hash to noaa-emc with SS/1.6.0 support. commit 2238dd6 Author: DavidHuber <david.huber@noaa.gov> Date: Mon Jan 29 13:21:30 2024 +0000 Update Orion, Hercules, S4 modulefiles. commit 6ffd94f Author: DavidHuber <david.huber@noaa.gov> Date: Fri Jan 26 16:01:23 2024 +0000 Update GDAS hash to include SS/1.6.0 support. commit be11f85 Merge: 56b9680 04e0772 Author: DavidHuber <david.huber@noaa.gov> Date: Fri Jan 26 15:34:24 2024 +0000 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 8ff3448 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jan 26 10:12:18 2024 -0500 Add a yaml for snow DA testing. (NOAA-EMC#2199) - adds a new test yaml C96_atmsnowDA.yaml for 3DVar atmosphere with GSI and Land (Snow) DA with JEDI - moves a few yamls from platforms/ to yamls/ - adds ability to overwrite a previously created experiment as an addition to user input. --------- Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> commit 04e0772 Author: David Huber <david.huber@noaa.gov> Date: Fri Jan 26 07:16:25 2024 -0600 Update ufs_utils hash for spack-stack/1.6.0 support. commit 3d44ff3 Author: Barry Baker <bbakernoaa@users.noreply.github.com> Date: Thu Jan 25 14:33:27 2024 -0500 GOCART ExtData biogenic climatology fix (NOAA-EMC#2253) Updates the ExtData for biogenic emissions to be climatology rather than for current time. Fixes an issue which will crash by default for other years. commit 66f58b8 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Thu Jan 25 13:16:41 2024 -0500 Added missing container case in gfs/config.resources (NOAA-EMC#2258) fixes NOAA-EMC#2257 commit 553b4f2 Author: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com> Date: Thu Jan 25 13:00:45 2024 -0500 Fix post parm links (NOAA-EMC#2243) Change symbolic links under parm/post with the latest version of develop branch from UPP repository and enable MERRA2 aerosol fields. Resolves NOAA-EMC#2259 commit 4d66742 Merge: 6c05803 afa09e3 Author: David Huber <david.huber@noaa.gov> Date: Thu Jan 25 07:49:08 2024 -0600 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 6c05803 Author: David Huber <david.huber@noaa.gov> Date: Thu Jan 25 07:48:42 2024 -0600 Fix wgrib2/gfs_utils on Hercules. commit ee6f536 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Jan 25 07:43:13 2024 -0500 Update GFS version to v16.3.13 in index.rst (NOAA-EMC#2256) GFSv16.3.13 WAFS update was implemented Refs NOAA-EMC#2013 commit 2445d44 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Thu Jan 25 06:17:11 2024 -0500 Simplify and extend load_ufsda_modules to Hercules (NOAA-EMC#2245) GDASApp jobs do not run on Hercules because `ush/load_ufsda_modules.sh` does not include logic to load the appropriate GDASApp modules on Hercules. This PR extends `load_ufsda_modules.sh` functionality to Hercules, thereby enabling GDASApp jobs to run on Hercules. Resolves NOAA-EMC#2244 commit 56b9680 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Jan 24 19:47:34 2024 +0000 Update hashes (revert WCOSS2 modules). commit afa09e3 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Jan 24 18:59:40 2024 +0000 New (cleaner history) gdas hash. commit a9eaec2 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Jan 24 18:52:27 2024 +0000 Update gdasapp to include ss/1.6.0 support. commit 5ef8eb2 Merge: 4c46354 e400068 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Jan 24 17:08:54 2024 +0000 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 4c46354 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Jan 24 17:05:12 2024 +0000 Reenable verif-global support commit f775755 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Jan 24 16:59:10 2024 +0000 Assign fcsthrs for awips_g2 job. commit e400068 Author: David Huber <david.huber@noaa.gov> Date: Mon Jan 22 15:01:07 2024 -0600 More gsi-addon path fixes. commit f663d47 Author: David Huber <david.huber@noaa.gov> Date: Mon Jan 22 14:41:59 2024 -0600 Fix gsi-addon paths for hercules, orion, and S4. commit e304bbe Author: DavidHuber <david.huber@noaa.gov> Date: Mon Jan 22 18:59:34 2024 +0000 Better optimize build jobs (more ufs jobs). commit ccc6e2d Author: DavidHuber <david.huber@noaa.gov> Date: Mon Jan 22 18:56:18 2024 +0000 Reenable verif-global. NOAA-EMC#2195 commit 3ef3411 Merge: 4365f63 f4d187f Author: DavidHuber <david.huber@noaa.gov> Date: Mon Jan 22 18:39:10 2024 +0000 Merge remote-tracking branch 'origin/develop' into ss160 commit 4365f63 Author: DavidHuber <david.huber@noaa.gov> Date: Mon Jan 22 18:37:25 2024 +0000 Corrected the SS env. name in the version files. NOAA-EMC#2195 commit f4d187f Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Mon Jan 22 12:28:28 2024 -0500 Converts obsproc to obsprep in prepoceanobs config file (NOAA-EMC#2236) Converts obsproc to obsprep in prepoceanobs config file as a compliment to mutually depended GDASApp PR NOAA-EMC/GDASApp#858 The motivations are explained in refs NOAA-EMC/GDASApp#857 commit 9a09d30 Author: DavidHuber <david.huber@noaa.gov> Date: Fri Jan 19 21:23:50 2024 +0000 Corrected gsi-addon-dev spelling. commit 21ff645 Author: DavidHuber <david.huber@noaa.gov> Date: Fri Jan 19 21:11:34 2024 +0000 Update modulefiles, submodules to spack-stack 1.6.0. NOAA-EMC#2195 commit d4c55d1 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Fri Jan 19 15:43:37 2024 -0500 Update typing hint for WCOSS version of python (NOAA-EMC#2238) The typing hint `typing.List` was deprecated with python 3.9 in favor of using the primitive `list[str]`, but the functional version of python on WCOSS2 is <3.9, causing `setup_xml.py` to fail there. This replaces `list[str]` as a typing hint with the deprecated form until the supported version on WCOSS2 is >=3.9. commit 4919287 Author: Barry Baker <bbakernoaa@users.noreply.github.com> Date: Thu Jan 18 22:31:27 2024 -0500 GOCART Emission updates for GEFSv13 and GDAS (NOAA-EMC#2201) This PR addresses several things needed for more recent simulations using GOCART2G as well as preparing for the GEFSv13 30 year run. The main updates are: - Update CEDS to use monthly emission files instead of daily. This will drastically reduce the number of files needed. No science change - Update biogenic MEGAN inputs to use a climatology rather than the offline biogenic previously used. This is needed to deal with simulations where the current dataset is not available. - Update volcanic SO4 emissions to use degassing emissions only. This is to support the need for more recent simulations where data is not available. commit 13d25cf Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Jan 18 22:29:43 2024 -0500 Add `POSTAMBLE_CMD` into preamble postamble (NOAA-EMC#2235) This PR adds the ability to run a command at the end of jobs via the preamble's postamble function. A new command can be set via `POSTAMBLE_CMD` and will be invoked at the end of jobs. Users can add the command to the top of an env file to have every job run it or it can be placed within a job if-block in the env file to run for just that job. Resolves NOAA-EMC#1145 commit 7759163 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Jan 18 01:13:49 2024 -0500 Add option to create WGNE atmosphere products (NOAA-EMC#2233) Adds option to create WGNE products for the atmosphere. Resolves NOAA-EMC#1951 Resolves NOAA-EMC#2226 commit d95ed85 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 17 18:04:56 2024 -0500 Use ufs.configure, model_configure, MOM_input, data_table, and ice_in templates from UFS-weather-model (NOAA-EMC#2051) This PR: - links `ufs.configure.*.IN`, `model_configure.IN`, `MOM_input_${OCNRES}.in`, `MOM6_data_table.IN`, and `ice_in.IN` from ufs-weather-model into the global-workflow `parm/ufs` directory - prepares local variables for use in the templates in the respective functions for FV3, MOM6, and CICE6 - uses `atparse.bash` to render these templates into fully formed namelists - Work was performed by @DeniseWorthen in the ufs-weather-model to templatize several variables that are hard-wired in the ufs-weather-model for CICE. See ufs-community/ufs-weather-model/NOAA-EMC#2010 commit 44a66dd Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed Jan 17 13:52:09 2024 -0500 Update gdas.cd hash to use gsibec tag 1.1.3 (NOAA-EMC#2231) (NOAA-EMC#2234) commit 9046d97 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jan 17 10:19:18 2024 -0500 Add basic atmos products for GEFS and refactor resources (NOAA-EMC#2216) * Add basic atmos products for GEFS Adds basic atmosphere products for GEFS members (no mean or spread). To facilitate the addition of GEFS parameter lists, the existing GFS lists are renamed. They are also relocated to `parm/products/` direc tory instead of `parm/post/`. GEFS v12 uses different parameter lists for different resolutions, but for this implementation, the 0p25 lists are used for all resolutions. However, to hedge against the final con- figuration, all of the GEFS parameter lists have been added to parm. Implementation of different parameter lists for each resolution will take additional refactoring of the atmos_products job, as it currently assumes all resolutions use the same lists. The new GEFS rocoto task is implented as two loops of metatasks (made possible by PR NOAA-EMC#2189). The member is set at the rocoto level, so the setting in `config.base` had to be updated to accept a pass-through. The generation of a forecast hour list is moved up to its own function in `rocoto.tasks`, separate from the post groups which are not used. This can be used as a model for future metatasks (or refactoring of old ones). `rocoto_viewer.py` does function with the nested metatasks, though only one level of folding is available and the metatask name is that of the lower metatask (though it encompasses the entire outer metatask). Additionally, the GEFS `config.resources` had diverged from the GFS version, which included not having a section for the atm products job. This led to the refactoring of the GFS `config.resources`, including switching to using a `case` statement instead of sequential `elif`. This refactored script was then copied over to GEFS, replacing the old one, with all jobs not currently implemented for GEFS removed (except wave post, whose inclusion is immenent). New blocks can be copied over from GFS as they are added. Resolves NOAA-EMC#823 commit fbba174 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Tue Jan 16 14:05:48 2024 -0500 Update GDASApp (gdas.cd) hash (NOAA-EMC#2225) GDASApp now uses gitsubmodules commit dddd837 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 16 12:17:19 2024 -0500 Fix ocean resolution for the S2SWA test (NOAA-EMC#2223) commit 83edaf1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jan 16 11:07:02 2024 -0500 Apply fixes to archiving jobs (NOAA-EMC#2221) Add checks for potentially missing log/data files and update log names for archiving. Missing sflux index files are also added to the products script. Resolves NOAA-EMC#2076 commit c590476 Author: Rahul Mahajan <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

12Jan24 global-workflow UFS: 29Jan24, 625ac02 FV3: 29Jan24, bd38c56 UPP: 07Nov23, 78f369b UFS_UTILS: 22Dev23, ce385ce update pointers for ufs_model and ufs_utils add GSL C3_MYNN xml suite Change dt_inner=75 for any configuration running aerosol-aware Thompson (ltaerosol=.true.) Squashed commit of the following: commit 25c026ef03a8d8c0db0b7368d2836f0b2e866eae Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Feb 29 20:35:11 2024 +0000 update ufs_model pointer commit a28617a951c46b765aa996bfe4d28b554ec4e0a4 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Feb 22 06:16:26 2024 +0000 removed unneeded gsl directories commit 6fb4f90e8572e98c977a1d2ab385f033111f3ea7 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Feb 22 06:08:13 2024 +0000 update ufs_utils.fd pointer commit 9264f0c09239d046c5cd862d807e9b82f51dc3bd Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Feb 21 19:33:26 2024 +0000 update .gitmodules file commit f8edfa966147506f2c207728039e3a736cb95415 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Feb 21 19:30:47 2024 +0000 update pointer to ufs_utils.fd commit 5e0d2ab02d58e6a7a40db55a149a93008b28aa8b Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Feb 21 19:25:52 2024 +0000 update pointer to ufs_model.fd commit ebc9e1d02987a1c6aa8cabedf2323642748fab3c Merge: e7a81511 50cb1e6f Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> 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 <kayee.wong@noaa.gov> Date: Thu Feb 15 20:30:34 2024 +0000 Add pygraf workflow. commit 38b726125d49cff6cae4c0e5fff2438fc33143c5 Author: kayee.wong <kayee.wong@noaa.gov> 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 <kayee.wong@noaa.gov> Date: Tue Feb 13 23:57:06 2024 +0000 more fix. commit 6f80ea2edc5444e275a79b371d02b6e98e963662 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 23:50:01 2024 +0000 more bug fix. commit 56e283f1f666a38a4a3b30e1528e96eeb5c622e7 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 23:40:02 2024 +0000 Minor bug fix. commit 2dcfed06ff6789eb77cf92e22b80f5475923fafc Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 23:19:03 2024 +0000 Update parameter for c3 case Add c3 and mynn template commit cc46b19ccc7cdb54878340eff79dda9e747abdf7 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 20:51:23 2024 +0000 Update INFO. Add c3 SDF in the build. commit a444ed48a23f24724853036e522b4437bf412c59 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 18:42:33 2024 +0000 Update to UFS 2024 Jan 29 version. commit 88595707c7521cdce37ae1cf78720a7827242b24 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 18:16:46 2024 +0000 Minor bug fix. commit baa0e9f10b132098d5134efaad712a51ebc26b83 Author: kayee.wong <kayee.wong@noaa.gov> 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 <kayee.wong@noaa.gov> 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 <kayee.wong@noaa.gov> 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 <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 (#2219) commit c041968e165c07da785376f1441374687b55d6cc 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 (#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 <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 (#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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <david.huber@noaa.gov> Date: Thu Jan 11 11:49:08 2024 -0600 Update orion module/version files for met/metplus #2123 commit 94c9937f0bff380b0ebd6acdcfd2509e1ae99389 Author: DavidHuber <david.huber@noaa.gov> 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 <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 a65e4c675f21dbe72198d263e85e894e62b41e13 Author: David Huber <david.huber@noaa.gov> Date: Thu Jan 11 11:34:19 2024 -0600 Initial update of version/module files #2123 commit 4cb580201af68c1c0e2ae19faf0727dcbbe43b4d 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 (#2212) Fix OpenMP over-allocation of resources running MPMD tasks Co-authored-by: Innocent Souopgui <isouopgui@redlineperf.com> commit b056b531faee6929687cb8a588ffafa1a66426fb Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> 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 <aerorahul@users.noreply.github.com> 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 <aerorahul@users.noreply.github.com> 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 <aerorahul@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <143837053+jderrico-noaa@users.noreply.github.com> 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 <janet.m.derrico@noaa.gov> Date: Thu Feb 1 20:00:52 2024 +0000 adding consistent [[ ]] for if statements commit 67b99668c82a5fd8c42479b9b1bfe8b0bad0be25 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Feb 1 19:37:47 2024 +0000 Updated HOMEgfs in GSL XML templates commit 4d3719c086e7907a6eeff03112042d392e0d8c5e Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Sat Jan 27 02:07:43 2024 +0000 Create GSL version of archive script commit 529d9f71f97b6e643e76a53bc9871901ae861faf Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Tue Jan 16 16:46:25 2024 +0000 Update link script for ufs_utils.fd commit 5b21b31900955013b4e8106d3ae906b9da93b361 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Jan 16 16:45:25 2024 +0000 Add GSL archive scripts for initial conditions commit abb88baf9dd536a3b2ea1e24eaa99cbfe85af799 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Thu Jan 11 23:34:36 2024 +0000 Add namelist parameter, nord_tr, for GSL suites commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Tue Jan 9 02:26:22 2024 +0000 Add experiment setup script for p8_ugwpv1 commit c5a3697d22fdbb02bb80ddffee2629dddc10c702 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Tue Jan 9 02:13:42 2024 +0000 Updated GSL-specific files under ufs_utils.fd_gsl commit 1b153fc95b93a16eb40b791be7322100fde4a3d4 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jan 2 10:30:33 2024 -0700 Stop Gempak pgrb2 spec from modifying $DATA (#2147) This PR addresses issue #1224. The following is accomplished: - Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time; - Shell linter exceptions are addressed accordingly; - The respective GEMPAK tasks is added to the Rocoto mesh. Resolves #1224 commit 31ad23527802f7d07171132cc620f7135c4d8cba Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jan 2 10:27:30 2024 -0700 Reorganize NPOESS scripts (#2166) This PR addresses issue #1226. The following is accomplished: - Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated; - Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh` are moved accordingly; this specifically applies to the environment variable `FHOUR`, `SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`; - The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level (if necessary); - Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however, this may not be necessary (see `TODO` note within draft PR. Resolves #1226 commit 22bd82fa93b49e5ce98eb3f69123956dd5018049 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Jan 2 11:55:03 2024 -0500 Orog fix file reorg and fix directory variable standardization (#2181) This PR makes updates to use the newly reorganized `orog/20231027` fix file version and standardizes the fix file directory variables. Changes: 1. Update UFS_UTILS hash to ce385ce 2. Update fix file version file to use new orog timestamp: `orog_ver=20231027` 3. Add ".mx$(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 <40322596+ADCollard@users.noreply.github.com> 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 <jessica.meixner@noaa.gov> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <bbakernoaa@users.noreply.github.com> 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 <aerorahul@users.noreply.github.com> commit e55a05980709288d902ad1bd894164bfa5a18a65 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> 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 <terrence.mcguinness@cox.net> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <terrence.mcguinness@cox.net> 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 <aerorahul@users.noreply.github.com> Date: Thu Dec 14 16:05:33 2023 -0500 Correct fbwind (#2161) commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a Author: Kate Friedman <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <cory.r.martin@noaa.gov> Date: Thu Dec 7 15:12:05 2023 -0500 Update GDAS hash to most recent stable versions (#2138) commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Dec 7 10:41:05 2023 -0700 Corrected typo in a gempak job gempakncdcupapgif . (#2137) commit 3483f550db1ae35a680de49f7485ce5a11902dd9 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Thu Dec 7 12:34:56 2023 -0500 Add support for FGAT and IAU for aerosol DA (#1940) commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> commit a29f751aed05312da3d80d396159bb5a906d6ce4 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Dec 6 13:45:56 2023 -0700 Adds GEMPAK and related jobs to rocoto task mesh (#2127) commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <terrence.mcguinness@cox.net> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <jiande.wang@noaa.gov> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Wed Nov 29 15:17:36 2023 -0500 Added variables to config.prepoceanobs (#2101) commit c2d78a61a224678fb804eed19f39d1f07408ae5f Author: Kate Friedman <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <jessica.meixner@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <48260754+WenMeng-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <aerorahul@users.noreply.github.com> Date: Wed Nov 15 16:44:03 2023 -0500 Fix missing _PREV in ocean restart file location (#2070) commit 255616d37505c785bdddd5d3e39e8399110b626e Author: mdtoyNOAA <73618848+mdtoyNOAA@users.noreply.github.com> 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 <guillaume.vernieres@noaa.gov> 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 <guoqing.ge@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <aerorahul@users.noreply.github.com> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <jiande.wang@noaa.gov> 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 <bbakernoaa@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <terrence.mcguinness@cox.net> 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 <guillaume.vernieres@noaa.gov> 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 <jiande.wang@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu Nov 2 16:09:59 2023 -0400 changed optional script name vars for ocean analysis (#2025) commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6 Author: Kate Friedman <kate.friedman@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Wed Nov 1 14:19:55 2023 -0400 Updates to prep ocean obs task (#1870) commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <terrence.mcguinness@cox.net> 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 <terrence.mcguinness@cox.net> Date: Tue Oct 31 13:57:02 2023 +0000 Allow CI case to exclude running on certain platforms (#2001) commit 7cc137116f1619bf1e5a12eaacb98d17da97c223 Author: Jeff Whitaker <jswhit@fastmail.fm> Date: Tue Oct 31 07:54:24 2023 -0600 Add initial C96/1 deg coupled model support (#1991) commit 7086ddc4bece6fb2a8c1c2e6090800d4293e410e Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> 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 <guillaume.vernieres@noaa.gov> 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 <108816337+AnilKumar-NOAA@users.noreply.github.com> 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 <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Thu Oct 26 23:44:27 2023 -0400 Update GDASApp hash (#1975) Update GDASApp hash…

12Jan24 global-workflow UFS: 29Jan24, 625ac02 FV3: 29Jan24, bd38c56 (GSL: 28Feb24 , a439cc7) UPP: 07Nov23, 78f369b UFS_UTILS: 22Dev23, ce385ce update pointers for ufs_model and ufs_utils add GSL C3_MYNN xml suite Squashed commit of the following: commit db6a85e0ce36cec28714a4c9d6e13565253cf7bb Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Tue Mar 19 19:33:28 2024 +0000 29Jan ufs_model.fd, 29Jan FV3 with C3 files commit de7b382c4b259d99d39e8857cbcee7efe64c1956 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Mon Mar 18 16:23:05 2024 +0000 update pointer for atmos_cubed_sphere to Feb 1 hash commit 0fc27835205aaf57bdba228b1769e0ac7b37712e Merge: b2c8ef81 db06f7c5 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Mar 14 00:17:24 2024 +0000 Merge branch 'gsl_ufs_dev' of https://github.com/NOAA-GSL/global-workflow into gsl_ufs_dev commit b2c8ef81229b5e9b8e7592cb12c2f3e8e3179d92 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Mar 13 23:51:45 2024 +0000 ccpp pointer updates to framework and physics commit 484a18df8c9022190c8900c80e40507a6771e314 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Mar 13 23:43:18 2024 +0000 ccpp pointer update in ufs_model.fd/FV3 commit db06f7c57d4cfc863352a4613c8260b0dffd9afe Merge: 579f90c1 2dbd12a6 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Wed Mar 13 15:55:48 2024 -0600 Merge pull request #43 from kayeekayee/gsl_ufs_dev update GSL C3_MYNN files and change dt_inner=75 commit 2dbd12a695c4349071ee8470e597540e71bc0292 Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Mar 13 03:48:51 2024 +0000 update GSL C3_MYNN files commit 579f90c1e0e2896710046c1885f68560ea435fa6 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Mar 7 19:20:46 2024 +0000 update ufs_model.fd submodule pointer commit 2f2622d68eb8444afde9c1ddad470cfee1b63b99 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Mar 7 19:15:23 2024 +0000 update ufs_model.fd submod pointer commit 706a0c52bb11af78e016014550ebd6847cc0ee19 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Mar 7 19:12:35 2024 +0000 update ufs_model.fd/FV3 path commit 352f188f095e19442ade1f3fd167ff2fed501cd2 Merge: 5a8edc76 96545dcb Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Mar 7 17:58:38 2024 +0000 update ufs model pointer commit 5a8edc766f2f4d3e12c692069d46c02fd766c354 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Mar 7 17:42:00 2024 +0000 update FV3 and UPP commit 96545dcb63e3f8f7dfc036961d818db15fa1a003 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Mar 6 10:05:39 2024 -0700 update pointer for ufs_model.fd commit 25c026ef03a8d8c0db0b7368d2836f0b2e866eae Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Feb 29 20:35:11 2024 +0000 update ufs_model pointer commit a28617a951c46b765aa996bfe4d28b554ec4e0a4 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Feb 22 06:16:26 2024 +0000 removed unneeded gsl directories commit 6fb4f90e8572e98c977a1d2ab385f033111f3ea7 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Feb 22 06:08:13 2024 +0000 update ufs_utils.fd pointer commit 9264f0c09239d046c5cd862d807e9b82f51dc3bd Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Feb 21 19:33:26 2024 +0000 update .gitmodules file commit f8edfa966147506f2c207728039e3a736cb95415 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Feb 21 19:30:47 2024 +0000 update pointer to ufs_utils.fd commit 5e0d2ab02d58e6a7a40db55a149a93008b28aa8b Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Feb 21 19:25:52 2024 +0000 update pointer to ufs_model.fd commit ebc9e1d02987a1c6aa8cabedf2323642748fab3c Merge: e7a81511 50cb1e6f Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> 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 <kayee.wong@noaa.gov> Date: Thu Feb 15 20:30:34 2024 +0000 Add pygraf workflow. commit 38b726125d49cff6cae4c0e5fff2438fc33143c5 Author: kayee.wong <kayee.wong@noaa.gov> 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 <kayee.wong@noaa.gov> Date: Tue Feb 13 23:57:06 2024 +0000 more fix. commit 6f80ea2edc5444e275a79b371d02b6e98e963662 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 23:50:01 2024 +0000 more bug fix. commit 56e283f1f666a38a4a3b30e1528e96eeb5c622e7 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 23:40:02 2024 +0000 Minor bug fix. commit 2dcfed06ff6789eb77cf92e22b80f5475923fafc Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 23:19:03 2024 +0000 Update parameter for c3 case Add c3 and mynn template commit cc46b19ccc7cdb54878340eff79dda9e747abdf7 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 20:51:23 2024 +0000 Update INFO. Add c3 SDF in the build. commit a444ed48a23f24724853036e522b4437bf412c59 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 18:42:33 2024 +0000 Update to UFS 2024 Jan 29 version. commit 88595707c7521cdce37ae1cf78720a7827242b24 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 18:16:46 2024 +0000 Minor bug fix. commit baa0e9f10b132098d5134efaad712a51ebc26b83 Author: kayee.wong <kayee.wong@noaa.gov> 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 <kayee.wong@noaa.gov> 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 <kayee.wong@noaa.gov> 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 <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 (#2219) commit c041968e165c07da785376f1441374687b55d6cc 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 (#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 <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 (#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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <david.huber@noaa.gov> Date: Thu Jan 11 11:49:08 2024 -0600 Update orion module/version files for met/metplus #2123 commit 94c9937f0bff380b0ebd6acdcfd2509e1ae99389 Author: DavidHuber <david.huber@noaa.gov> 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 <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 a65e4c675f21dbe72198d263e85e894e62b41e13 Author: David Huber <david.huber@noaa.gov> Date: Thu Jan 11 11:34:19 2024 -0600 Initial update of version/module files #2123 commit 4cb580201af68c1c0e2ae19faf0727dcbbe43b4d 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 (#2212) Fix OpenMP over-allocation of resources running MPMD tasks Co-authored-by: Innocent Souopgui <isouopgui@redlineperf.com> commit b056b531faee6929687cb8a588ffafa1a66426fb Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> 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 <aerorahul@users.noreply.github.com> 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 <aerorahul@users.noreply.github.com> 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 <aerorahul@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <143837053+jderrico-noaa@users.noreply.github.com> 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 <janet.m.derrico@noaa.gov> Date: Thu Feb 1 20:00:52 2024 +0000 adding consistent [[ ]] for if statements commit 67b99668c82a5fd8c42479b9b1bfe8b0bad0be25 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Feb 1 19:37:47 2024 +0000 Updated HOMEgfs in GSL XML templates commit 4d3719c086e7907a6eeff03112042d392e0d8c5e Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Sat Jan 27 02:07:43 2024 +0000 Create GSL version of archive script commit 529d9f71f97b6e643e76a53bc9871901ae861faf Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Tue Jan 16 16:46:25 2024 +0000 Update link script for ufs_utils.fd commit 5b21b31900955013b4e8106d3ae906b9da93b361 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Jan 16 16:45:25 2024 +0000 Add GSL archive scripts for initial conditions commit abb88baf9dd536a3b2ea1e24eaa99cbfe85af799 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Thu Jan 11 23:34:36 2024 +0000 Add namelist parameter, nord_tr, for GSL suites commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Tue Jan 9 02:26:22 2024 +0000 Add experiment setup script for p8_ugwpv1 commit c5a3697d22fdbb02bb80ddffee2629dddc10c702 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Tue Jan 9 02:13:42 2024 +0000 Updated GSL-specific files under ufs_utils.fd_gsl commit 1b153fc95b93a16eb40b791be7322100fde4a3d4 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jan 2 10:30:33 2024 -0700 Stop Gempak pgrb2 spec from modifying $DATA (#2147) This PR addresses issue #1224. The following is accomplished: - Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time; - Shell linter exceptions are addressed accordingly; - The respective GEMPAK tasks is added to the Rocoto mesh. Resolves #1224 commit 31ad23527802f7d07171132cc620f7135c4d8cba Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jan 2 10:27:30 2024 -0700 Reorganize NPOESS scripts (#2166) This PR addresses issue #1226. The following is accomplished: - Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated; - Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh` are moved accordingly; this specifically applies to the environment variable `FHOUR`, `SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`; - The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level (if necessary); - Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however, this may not be necessary (see `TODO` note within draft PR. Resolves #1226 commit 22bd82fa93b49e5ce98eb3f69123956dd5018049 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Jan 2 11:55:03 2024 -0500 Orog fix file reorg and fix directory variable standardization (#2181) This PR makes updates to use the newly reorganized `orog/20231027` fix file version and standardizes the fix file directory variables. Changes: 1. Update UFS_UTILS hash to ce385ce 2. Update fix file version file to use new orog timestamp: `orog_ver=20231027` 3. Add ".mx$(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 <40322596+ADCollard@users.noreply.github.com> 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 <jessica.meixner@noaa.gov> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <bbakernoaa@users.noreply.github.com> 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 <aerorahul@users.noreply.github.com> commit e55a05980709288d902ad1bd894164bfa5a18a65 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> 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 <terrence.mcguinness@cox.net> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <terrence.mcguinness@cox.net> 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 <aerorahul@users.noreply.github.com> Date: Thu Dec 14 16:05:33 2023 -0500 Correct fbwind (#2161) commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a Author: Kate Friedman <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <cory.r.martin@noaa.gov> Date: Thu Dec 7 15:12:05 2023 -0500 Update GDAS hash to most recent stable versions (#2138) commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Dec 7 10:41:05 2023 -0700 Corrected typo in a gempak job gempakncdcupapgif . (#2137) commit 3483f550db1ae35a680de49f7485ce5a11902dd9 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Thu Dec 7 12:34:56 2023 -0500 Add support for FGAT and IAU for aerosol DA (#1940) commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> commit a29f751aed05312da3d80d396159bb5a906d6ce4 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Dec 6 13:45:56 2023 -0700 Adds GEMPAK and related jobs to rocoto task mesh (#2127) commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <terrence.mcguinness@cox.net> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <jiande.wang@noaa.gov> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Wed Nov 29 15:17:36 2023 -0500 Added variables to config.prepoceanobs (#2101) commit c2d78a61a224678fb804eed19f39d1f07408ae5f Author: Kate Friedman <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <jessica.meixner@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <48260754+WenMeng-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <aerorahul@users.noreply.github.com> Date: Wed Nov 15 16:44:03 2023 -0500 Fix missing _PREV in ocean restart file location (#2070) commit 255616d37505c785bdddd5d3e39e8399110b626e Author: mdtoyNOAA <73618848+mdtoyNOAA@users.noreply.github.com> 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 <guillaume.vernieres@noaa.gov> 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 <guoqing.ge@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <aerorahul@users.noreply.github.com> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <jiande.wang@noaa.gov> 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 <bbakernoaa@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <terrence.mcguinness@cox.net> 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 <guillaume.vernieres@noaa.gov> 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 <jiande.wang@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu Nov 2 16:09:59 2023 -0400 changed optional script name vars for ocean analysis (#2025) commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6 Author: Kate Friedman <kate.friedman@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Wed Nov 1 14:19:55 2023 -0400 Updates to prep ocean obs task (#1870) commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> Date: Tu…

12Jan24 global-workflow UFS: 29Jan24, 625ac02 FV3: 29Jan24, bd38c56 (GSL: 28Feb24 , a439cc7) UPP: 07Nov23, 78f369b UFS_UTILS: 22Dev23, ce385ce update pointers for ufs_model and ufs_utils add GSL C3_MYNN xml suite Change dt_inner=75 for any configuration running aerosol-aware Thompson (ltaerosol=.true.) Squashed commit of the following: commit db6a85e0ce36cec28714a4c9d6e13565253cf7bb Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Tue Mar 19 19:33:28 2024 +0000 29Jan ufs_model.fd, 29Jan FV3 with C3 files commit de7b382c4b259d99d39e8857cbcee7efe64c1956 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Mon Mar 18 16:23:05 2024 +0000 update pointer for atmos_cubed_sphere to Feb 1 hash commit 0fc27835205aaf57bdba228b1769e0ac7b37712e Merge: b2c8ef81 db06f7c5 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Mar 14 00:17:24 2024 +0000 Merge branch 'gsl_ufs_dev' of https://github.com/NOAA-GSL/global-workflow into gsl_ufs_dev commit b2c8ef81229b5e9b8e7592cb12c2f3e8e3179d92 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Mar 13 23:51:45 2024 +0000 ccpp pointer updates to framework and physics commit 484a18df8c9022190c8900c80e40507a6771e314 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Mar 13 23:43:18 2024 +0000 ccpp pointer update in ufs_model.fd/FV3 commit db06f7c57d4cfc863352a4613c8260b0dffd9afe Merge: 579f90c1 2dbd12a6 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Wed Mar 13 15:55:48 2024 -0600 Merge pull request #43 from kayeekayee/gsl_ufs_dev update GSL C3_MYNN files and change dt_inner=75 commit 2dbd12a695c4349071ee8470e597540e71bc0292 Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Mar 13 03:48:51 2024 +0000 update GSL C3_MYNN files commit 579f90c1e0e2896710046c1885f68560ea435fa6 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Mar 7 19:20:46 2024 +0000 update ufs_model.fd submodule pointer commit 2f2622d68eb8444afde9c1ddad470cfee1b63b99 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Mar 7 19:15:23 2024 +0000 update ufs_model.fd submod pointer commit 706a0c52bb11af78e016014550ebd6847cc0ee19 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Mar 7 19:12:35 2024 +0000 update ufs_model.fd/FV3 path commit 352f188f095e19442ade1f3fd167ff2fed501cd2 Merge: 5a8edc76 96545dcb Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Mar 7 17:58:38 2024 +0000 update ufs model pointer commit 5a8edc766f2f4d3e12c692069d46c02fd766c354 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Mar 7 17:42:00 2024 +0000 update FV3 and UPP commit 96545dcb63e3f8f7dfc036961d818db15fa1a003 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Mar 6 10:05:39 2024 -0700 update pointer for ufs_model.fd commit 25c026ef03a8d8c0db0b7368d2836f0b2e866eae Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Feb 29 20:35:11 2024 +0000 update ufs_model pointer commit a28617a951c46b765aa996bfe4d28b554ec4e0a4 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Feb 22 06:16:26 2024 +0000 removed unneeded gsl directories commit 6fb4f90e8572e98c977a1d2ab385f033111f3ea7 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Thu Feb 22 06:08:13 2024 +0000 update ufs_utils.fd pointer commit 9264f0c09239d046c5cd862d807e9b82f51dc3bd Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Feb 21 19:33:26 2024 +0000 update .gitmodules file commit f8edfa966147506f2c207728039e3a736cb95415 Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Feb 21 19:30:47 2024 +0000 update pointer to ufs_utils.fd commit 5e0d2ab02d58e6a7a40db55a149a93008b28aa8b Author: jderrico-noaa <janet.m.derrico@noaa.gov> Date: Wed Feb 21 19:25:52 2024 +0000 update pointer to ufs_model.fd commit ebc9e1d02987a1c6aa8cabedf2323642748fab3c Merge: e7a81511 50cb1e6f Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> 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 <kayee.wong@noaa.gov> Date: Thu Feb 15 20:30:34 2024 +0000 Add pygraf workflow. commit 38b726125d49cff6cae4c0e5fff2438fc33143c5 Author: kayee.wong <kayee.wong@noaa.gov> 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 <kayee.wong@noaa.gov> Date: Tue Feb 13 23:57:06 2024 +0000 more fix. commit 6f80ea2edc5444e275a79b371d02b6e98e963662 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 23:50:01 2024 +0000 more bug fix. commit 56e283f1f666a38a4a3b30e1528e96eeb5c622e7 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 23:40:02 2024 +0000 Minor bug fix. commit 2dcfed06ff6789eb77cf92e22b80f5475923fafc Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 23:19:03 2024 +0000 Update parameter for c3 case Add c3 and mynn template commit cc46b19ccc7cdb54878340eff79dda9e747abdf7 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 20:51:23 2024 +0000 Update INFO. Add c3 SDF in the build. commit a444ed48a23f24724853036e522b4437bf412c59 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 18:42:33 2024 +0000 Update to UFS 2024 Jan 29 version. commit 88595707c7521cdce37ae1cf78720a7827242b24 Author: kayee.wong <kayee.wong@noaa.gov> Date: Tue Feb 13 18:16:46 2024 +0000 Minor bug fix. commit baa0e9f10b132098d5134efaad712a51ebc26b83 Author: kayee.wong <kayee.wong@noaa.gov> 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 <kayee.wong@noaa.gov> 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 <kayee.wong@noaa.gov> 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 <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 (#2219) commit c041968e165c07da785376f1441374687b55d6cc 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 (#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 <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 (#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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <david.huber@noaa.gov> Date: Thu Jan 11 11:49:08 2024 -0600 Update orion module/version files for met/metplus #2123 commit 94c9937f0bff380b0ebd6acdcfd2509e1ae99389 Author: DavidHuber <david.huber@noaa.gov> 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 <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 a65e4c675f21dbe72198d263e85e894e62b41e13 Author: David Huber <david.huber@noaa.gov> Date: Thu Jan 11 11:34:19 2024 -0600 Initial update of version/module files #2123 commit 4cb580201af68c1c0e2ae19faf0727dcbbe43b4d 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 (#2212) Fix OpenMP over-allocation of resources running MPMD tasks Co-authored-by: Innocent Souopgui <isouopgui@redlineperf.com> commit b056b531faee6929687cb8a588ffafa1a66426fb Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> 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 <aerorahul@users.noreply.github.com> 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 <aerorahul@users.noreply.github.com> 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 <aerorahul@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <143837053+jderrico-noaa@users.noreply.github.com> 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 <janet.m.derrico@noaa.gov> Date: Thu Feb 1 20:00:52 2024 +0000 adding consistent [[ ]] for if statements commit 67b99668c82a5fd8c42479b9b1bfe8b0bad0be25 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Thu Feb 1 19:37:47 2024 +0000 Updated HOMEgfs in GSL XML templates commit 4d3719c086e7907a6eeff03112042d392e0d8c5e Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Sat Jan 27 02:07:43 2024 +0000 Create GSL version of archive script commit 529d9f71f97b6e643e76a53bc9871901ae861faf Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Tue Jan 16 16:46:25 2024 +0000 Update link script for ufs_utils.fd commit 5b21b31900955013b4e8106d3ae906b9da93b361 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> Date: Tue Jan 16 16:45:25 2024 +0000 Add GSL archive scripts for initial conditions commit abb88baf9dd536a3b2ea1e24eaa99cbfe85af799 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Thu Jan 11 23:34:36 2024 +0000 Add namelist parameter, nord_tr, for GSL suites commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Tue Jan 9 02:26:22 2024 +0000 Add experiment setup script for p8_ugwpv1 commit c5a3697d22fdbb02bb80ddffee2629dddc10c702 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <Judy.K.Henderson@noaa.gov> Date: Tue Jan 9 02:13:42 2024 +0000 Updated GSL-specific files under ufs_utils.fd_gsl commit 1b153fc95b93a16eb40b791be7322100fde4a3d4 Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jan 2 10:30:33 2024 -0700 Stop Gempak pgrb2 spec from modifying $DATA (#2147) This PR addresses issue #1224. The following is accomplished: - Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time; - Shell linter exceptions are addressed accordingly; - The respective GEMPAK tasks is added to the Rocoto mesh. Resolves #1224 commit 31ad23527802f7d07171132cc620f7135c4d8cba Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jan 2 10:27:30 2024 -0700 Reorganize NPOESS scripts (#2166) This PR addresses issue #1226. The following is accomplished: - Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated; - Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh` are moved accordingly; this specifically applies to the environment variable `FHOUR`, `SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`; - The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level (if necessary); - Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however, this may not be necessary (see `TODO` note within draft PR. Resolves #1226 commit 22bd82fa93b49e5ce98eb3f69123956dd5018049 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Tue Jan 2 11:55:03 2024 -0500 Orog fix file reorg and fix directory variable standardization (#2181) This PR makes updates to use the newly reorganized `orog/20231027` fix file version and standardizes the fix file directory variables. Changes: 1. Update UFS_UTILS hash to ce385ce 2. Update fix file version file to use new orog timestamp: `orog_ver=20231027` 3. Add ".mx$(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 <40322596+ADCollard@users.noreply.github.com> 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 <jessica.meixner@noaa.gov> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <bbakernoaa@users.noreply.github.com> 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 <aerorahul@users.noreply.github.com> commit e55a05980709288d902ad1bd894164bfa5a18a65 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> 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 <terrence.mcguinness@cox.net> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <terrence.mcguinness@cox.net> 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 <aerorahul@users.noreply.github.com> Date: Thu Dec 14 16:05:33 2023 -0500 Correct fbwind (#2161) commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a Author: Kate Friedman <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <cory.r.martin@noaa.gov> Date: Thu Dec 7 15:12:05 2023 -0500 Update GDAS hash to most recent stable versions (#2138) commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Dec 7 10:41:05 2023 -0700 Corrected typo in a gempak job gempakncdcupapgif . (#2137) commit 3483f550db1ae35a680de49f7485ce5a11902dd9 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Thu Dec 7 12:34:56 2023 -0500 Add support for FGAT and IAU for aerosol DA (#1940) commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> commit a29f751aed05312da3d80d396159bb5a906d6ce4 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Dec 6 13:45:56 2023 -0700 Adds GEMPAK and related jobs to rocoto task mesh (#2127) commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <terrence.mcguinness@cox.net> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <jiande.wang@noaa.gov> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Wed Nov 29 15:17:36 2023 -0500 Added variables to config.prepoceanobs (#2101) commit c2d78a61a224678fb804eed19f39d1f07408ae5f Author: Kate Friedman <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <jessica.meixner@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <48260754+WenMeng-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <aerorahul@users.noreply.github.com> Date: Wed Nov 15 16:44:03 2023 -0500 Fix missing _PREV in ocean restart file location (#2070) commit 255616d37505c785bdddd5d3e39e8399110b626e Author: mdtoyNOAA <73618848+mdtoyNOAA@users.noreply.github.com> 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 <guillaume.vernieres@noaa.gov> 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 <guoqing.ge@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <kate.friedman@noaa.gov> 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 <aerorahul@users.noreply.github.com> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <kate.friedman@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <jiande.wang@noaa.gov> 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 <bbakernoaa@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> 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 <terrence.mcguinness@cox.net> 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 <guillaume.vernieres@noaa.gov> 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 <jiande.wang@noaa.gov> 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 <Walter.Kolczynski@noaa.gov> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu Nov 2 16:09:59 2023 -0400 changed optional script name vars for ocean analysis (#2025) commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6 Author: Kate Friedman <kate.friedman@noaa.gov> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Wed Nov 1 14:19:55 2023 -0400 Updates to prep ocean obs task (#1870) commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> 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 <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Oct 31 16:33:11 2023 -0400 Parallelize the build scripts (#1998) Optimized/parallelized build scripts. A few notes: 1) The default number of build jobs is 20, but one could argue for using 40. When researching this, I looked up what the SRW is compiling with. That system uses 40 cores, which seems a little excessive, but on testing the global workflow, the actual number of cores being used at any given time rarely exceeds 16 when running with 40 cores. This is because the builds tend to use multiple threads in the beginning when compiling low-level modules while the higher-level modules are more or less serial AND because the GDASApp takes several minutes to initialize all of its subrepositories by which time the smaller builds are complete. 2) I also updated checkout.sh so that all checkouts are simultaneous. The CPU load for `git submodule` is quite low, so running 16 instead of 8 jobs at once is not much more expensive. 3) To make this work, I had to add `-j` options to most of the build scripts. The only exception is build_upp, for which the build script within the UPP is hard coded to use 6 cores. 4) I fixed a few small bugs in the build scripts along the way. 5) Lastly, this reduce the total build time from ~2.5 hours for the entire system (including GDAS and GSI in the same build) to ~40 minutes when running with `-j 40`. Resolves #1978 commit 67c050c201f92e8…

AndrewEichmann-NOAA added 7 commits December 19, 2023 20:57

add COMOUT_OBS to marine obs prep

754fc29

Merge branch 'develop' into feature/marine-obsproc

1c406db

adding prepoceanobs to workflow

6e49d51

Merge branch 'develop' into feature/marine-obsproc

30cab3d

changes to use ocean obs prep in cycling and remove r2d2

4a5cd4e

coding norms correction

efab33f

coding norms correction

949e3cb

AndrewEichmann-NOAA marked this pull request as ready for review January 10, 2024 20:47

guillaumevernieres reviewed Jan 10, 2024

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guillaumevernieres requested review from aerorahul and WalterKolczynski-NOAA January 10, 2024 22:02

aerorahul requested changes Jan 10, 2024

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make OBSPROC_YAML and DMPDIR setup-determined

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guillaumevernieres approved these changes Jan 11, 2024

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bugfixes

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AndrewEichmann-NOAA requested a review from aerorahul January 12, 2024 13:23

aerorahul approved these changes Jan 12, 2024

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aerorahul merged commit 997f978 into NOAA-EMC:develop Jan 12, 2024
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Allow use of ocean obs prep in WCDA cycling and remove R2D2 #2215

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

AndrewEichmann-NOAA commented Jan 10, 2024

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

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

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AndrewEichmann-NOAA commented Jan 10, 2024

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