Use JCB for assembling JEDI YAML files for atmospheric GDAS #2477

danholdaway · 2024-04-09T20:25:43Z

Description

Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI Configuration Builder (JCB) tool so that YAMLs can be made more portable and invoke the observation chronicle mechanism.

Resolves #2476

Type of change

New feature (adds functionality)

Change characteristics

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

How has this been tested?

Tested on Hera (GDAS testing. Complete testing waiting on #2420)

Checklist

Any dependent changes have been merged and published (Move Atmospheric YAMLs to JCB repo GDASApp#1033)
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

* upstream/develop: Flip the build for GFS and GEFS with waves (NOAA-EMC#2462) Add new data sources used in GFS v16.3.12 (NOAA-EMC#2283) The soca fix path is needed in config.prepoceanobs (NOAA-EMC#2460) Turn off reducedgrid in the EnKF (NOAA-EMC#2456) Rename generate_com to declare_from_tmpl (NOAA-EMC#2453)

CoryMartin-NOAA

Looks good to me

aerorahul

I have mostly high level comments at this time concerning operational acceptance on some aspects of jcb. Happy to discuss offline.

aerorahul · 2024-04-10T15:07:12Z

sorc/link_workflow.sh

+packages=("wxflow" "jcb")
+for package in "${packages[@]}"; do
+    cd "${HOMEgfs}/ush/python" || exit 1
+    [[ -s "${package}" ]] && rm -f "${package}"
+    ${LINK} "${HOMEgfs}/sorc/${package}/src/${package}" .
+    cd "${HOMEgfs}/workflow" || exit 1
+    [[ -s "${package}" ]] && rm -f "${package}"
+    ${LINK} "${HOMEgfs}/sorc/${package}/src/${package}" .
+    cd "${HOMEgfs}/ci/scripts" || exit 1
+    [[ -s "${package}" ]] && rm -f "${package}"
+    ${LINK} "${HOMEgfs}/sorc/${package}/src/${package}" .
+done


I don't think jcb needs to be linked in workflow/ or ci/scripts/

That was a bit of a blind copy of what's done for wxflow so likely not needed. For my improved understanding, what is the purpose of linking wxflow to these directories?

At some point when wxflow will be made available as a module or in a virtual environment. When that happens, all the linking of wxflow will be removed then.
Since wxflow is still being developed for various purposes, a quick way around the issue to use the latest version , is to link it in the respective directories where it is called via an import.

aerorahul · 2024-04-10T17:40:21Z

.gitmodules

@@ -30,3 +30,7 @@
  path = sorc/upp.fd
  url = https://github.com/NOAA-EMC/UPP.git
  ignore = dirty
+[submodule "sorc/jcb"]
+  path = sorc/jcb
+  url = https://github.com/noaa-emc/jcb


Are the yaml's in the jcb repo under configuration/ used?
If so, we will need to think about how to move them to parm/ for operational acceptance.
Ideally, we would install jcb as a python package, and the yamls would be part of global-workflow/gdasapp.

I was tying to play around with submodules to see if jcb could not clone its submodules since in the context of global-workflow they are indeed not needed. But I was not successful. The submodule of jcb (jcb-gdas) is also a submodule of GDASapp and that would be where the configuration files that global-workflow uses actually comes in and gets linked to parm/. Perhaps we can brainstorm a better way of doing this so that jcb-gdas is not a submodule of jcb. It's like that primarily to facilitate easy testing of jcb in a standalone context but perhaps it could be done with pip dependency or some other way that I'm not thinking about.

jcb-algorithms repo has been established, moving the generic JEDI-algortithm YAMLs to the gdas parm. Now there should be no YAML files in non-parm directories that are used anywhere.

* upstream/develop: Update fbwind for COM refactor (NOAA-EMC#2479) Update parm files for atm product (NOAA-EMC#2486) Fix paths in prepocnobs task (NOAA-EMC#2459) Add oceanalecn to workflow generator (NOAA-EMC#2409) Add support for CADS IR cloud detection scheme in the GSI (NOAA-EMC#2478) Improve error messaging to resolve bugzilla (NOAA-EMC#2468) Check the DO_JEDISNOWDA condition before adding snow DA analysis to the list (NOAA-EMC#2471)

RussTreadon-NOAA · 2024-04-16T00:30:37Z

danholdaway:feature/use_jcb_atm references gdas.cd @ 040711d. This hash is not found in GDASApp. Is 040711d the correct GDASApp hash?

danholdaway · 2024-04-17T13:27:49Z

danholdaway:feature/use_jcb_atm references gdas.cd @ 040711d. This hash is not found in GDASApp. Is 040711d the correct GDASApp hash?

Thanks for finding that, I'll take a look.

* upstream/develop: Add rocoto `sh` tag, script to check netcdf file and apply this to check ocean output (NOAA-EMC#2484) Revert file name changes in off-line post (NOAA-EMC#2499) Add mean/spread for atmos grib2 (NOAA-EMC#2482) Upadte and tested CI Bash for WCOSS2 (NOAA-EMC#2481)

danholdaway · 2024-04-17T19:18:50Z

@RussTreadon-NOAA I think the hash issue is fixed now. For some reason after I was merging develop of GW into my branch then updating the submodules it would change the hash of gdas to something uncommitted and then push that hash to the branch of GW. Still getting used the submodule thing.

* upstream/develop: Add CCPP suite and FASTER option to UFS build (NOAA-EMC#2521) New "atmanlfv3inc" Rocoto job (NOAA-EMC#2420) Hotfix to disable STALLED in CI as an error (NOAA-EMC#2523) Add restart on failure capability for the forecast executable (NOAA-EMC#2510) Update parm/transfer list files to match vetted GFSv16 set (NOAA-EMC#2517) Update gdas_gsibec_ver to 20240416 (NOAA-EMC#2497) Adding more cycles to gempak script gfs_meta_sa2.sh (NOAA-EMC#2518) Update gsi_enkf.sh hash to 457510c (NOAA-EMC#2514) Enable using the FV3_global_nest_v1 CCPP suite (NOAA-EMC#2512) CI Refactoring and STALLED case detection (NOAA-EMC#2488) Add C768 and C1152 S2SW test cases (NOAA-EMC#2509) Fix paths for refactored prepocnobs task (NOAA-EMC#2504)

WalterKolczynski-NOAA · 2024-05-08T19:24:21Z

@danholdaway why did you remove labels?

danholdaway · 2024-05-08T19:41:50Z

Oops, sorry about that @WalterKolczynski-NOAA. I think I confused myself there. I thought they were the old labels and was trying to get it ready to be run again. But I guess the page needed refreshing.

danholdaway · 2024-05-08T19:42:25Z

Out of interest, can I apply the labels myself or does the bot only listen when the labels are applied by specific people?

WalterKolczynski-NOAA · 2024-05-08T19:53:57Z

Out of interest, can I apply the labels myself or does the bot only listen when the labels are applied by specific people?

The bot isn't that smart, but we ask that you don't.

danholdaway · 2024-05-08T20:19:03Z

@WalterKolczynski-NOAA, OK thank you. I will leave the labels alone!

emcbot · 2024-05-09T00:40:31Z

CI Passed Hera at
Built and ran in directory /scratch1/NCEPDEV/global/CI/2477

…l 19 UFS (c127601) Squashed commit of the following: commit d599fff4aedd41ae587dbe02226acb12ff48efc1 Author: HelinWei-NOAA <48133472+HelinWei-NOAA@users.noreply.github.com> Date: Mon Aug 5 05:31:31 2024 -0400 Change land surface for HR4 (#2787) Resets the default value of opt_diag to 2 corresponding to the land surface upgrades in ufs-weather-model for HR4. Resolves #2786 commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Aug 2 15:41:29 2024 -0400 Run METplus serially and correct the name of prod tasks (#2804) Adds 2 hot fixes: - METplus v9.1.3 has a bug in it that sometimes attempts to create multiple copies of the same directory when running in parallel, causing a Python error and downstream problems. This PR makes METplus run in serial mode, preventing such issues. - Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod) commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri Aug 2 15:03:45 2024 -0400 Update Java Agent launching script for Jenkins connections (#2762) Made updates to the Jenkins Launching Script for robustness and less ambiguous documentation: - Clearer distinction between required user token for the remote api and the systems token for launching - Added pre-checks: `gh` is authenticating, named compliant token and secret file exists - More robust Jason based parser of the remote api response for checking the state of the Node connection - For `cron` use a 5 minute pause and recheck was added before re-launching of the java agent - Added concise header documentation of requirements and purpose --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit b73b1fd203496db97f8067652659573a632bcc67 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Aug 2 07:59:06 2024 -0400 Fix erroneous cdump addition (#2803) commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Aug 1 20:26:13 2024 -0400 Update ocean post-processing triggers (#2784) This PR: - replaces `check_netcdf.sh` checker for ocean post-processing with with ocean output at the next forecast hour or finishing of the forecast job for ocean prod - removes no longer needed `ush/check_netcdf.sh` commit aa2af1ca8d59424a60a1730722bf528775d9e606 Author: GeorgeGayno-NOAA <52789452+GeorgeGayno-NOAA@users.noreply.github.com> Date: Thu Aug 1 16:46:10 2024 -0400 Update the gfs_utils repository hash (#2801) # Description Point to the latest hash of the gfs-utils repository, which contains the bug fix to gaussian_sfcanl. Resolves #2669. Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73 commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Aug 1 08:12:14 2024 -0400 Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791) Changes how METplus jobs run so that they run on the last GFS cycle for a given `PDY`. This is a departure from operations where the METplus jobs run on the 00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through `${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on `${PDY}18` for cycles 00-18. See https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details. commit 1cf8b448af562dbb7af198399c78c585977e81da Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 30 10:38:49 2024 -0400 Simplify resource-related variables, remove CDUMP where unneeded (#2727) This overhauls resource-related variables to use a common set of variables for each job. In the process, this also removed the use of CDUMP in most cases. Resolves #1299 #2693 commit 61875f25c9e971f82ae499b5b612d7f095deebd4 Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Mon Jul 29 14:40:03 2024 -0400 Remove f000 from atmos rocoto tasks for replay cases (#2778) The main purpose of this PR is to remove the f000 from atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater than `0`, it becomes necessary to have the first lead hour set to `OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and the minimum lead time for the ocean_prod rocoto task needs to be 6 (assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up possible by removing 0 from fhrs for atmosphere-related tasks in `gefs_tasks.py` when replaying. This PR also moves where f000 is being removed for the ocean_prod and ice_prod tasks. The if-block that performs this f000 removal has been moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`. --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit f156a7894d639f177e3e2588f98eec1f6f59aa68 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Jul 26 14:18:32 2024 -0500 HR4 GWD update (#2732) This update is a combination of the gravity wave drag (GWD) versions from the NOAA/GSL and NOAA/PSL commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Jul 25 14:26:52 2024 -0400 Temporarily disable METplus jobs (#2796) commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Wed Jul 24 15:00:35 2024 -0400 Refactoring of the marine B-matrix job (#2749) Refactor the functionality of B-matrix generation from the GDASApp Resolves #2743 commit 65a7ab75dc0e4baba06a02e11ed0455787056a68 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 23 08:35:48 2024 -0400 Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775) Removes the namespace-based construction of EnKF member COM directories in the enkf archive template. commit c45b9611f3e701b819bd33dc5af29033f060bb91 Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Tue Jul 23 00:33:16 2024 -0400 Add task to process reforecast variables to save on WCOSS2 (#2680) # Description This PR adds an optional task to the global-workflow to process a subset of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for the GEFSv13 reforecast. This task is designed to process GEFS variables so that specific reforecast product requirements are met. A new variable in `config.base` called `DO_EXTRACTVARS` enables this task, which is currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by default and is specifically a task designed to be executed for the GEFSv13 reforecast. Refs #1878 # Type of change - New feature (adds functionality) # Change characteristics - Is this a breaking change (a change in existing functionality)? NO - Does this change require a documentation update? NO # How has this been tested? This has been cloned and tested on WCOSS2. This will need to be tested on Hera and other platforms on which the reforecast may be running. # Checklist - [ ] Any dependent changes have been merged and published - [x] My code follows the style guidelines of this project - [x] I have performed a self-review of my own code - [ ] I have commented my code, particularly in hard-to-understand areas - [x] My changes generate no new warnings - [x] New and existing tests pass with my changes - [ ] I have made corresponding changes to the documentation if necessary --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 71dc33c6ca991c16ce743760d99feaaf60f2218a Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jul 22 14:51:53 2024 -0400 Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774) Fix metp* resources and check that they completed properly; add support for Orion Rocky 9 commit 56df67a90fe090c425199f1285e5aac722c398b1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jul 22 09:28:18 2024 -0400 Hotfix: Update jcb to avoid git-lfs files (#2782) Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to be cloned on Hera. This hotfix points to a non-authoritative branch of the GDASApp (https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and should be updated ASAP back to the authoritative repository. commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jul 16 09:44:00 2024 -0400 Address issues in creating XML for GFS forecast-only with app S2SWA (#2757) This bugfix PR: - fixes an issue where a user is unable to generate the XML for a GFS forecast-only experiment with APP=S2SWA Specifically, the changes are related to defining `aero_fcst_cdumps`. Following `setup_expt.py`, the user will have to set `AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in `config.base`. commit e0878dba0e53706a7f53429b61aee2936e2c21bf Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Jul 15 10:25:11 2024 -0400 Updated prepobs and fit2obs versions for Orion Rocky9 (#2758) Update prepobs to v1.0.2 and fit2obs to v1.1.2 These versions now support Orion Rocky9. Updates are included for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet. commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jul 11 17:48:47 2024 +0000 CI maintenance updates and adding CI Unit Tests (#2740) This PR has a few maintenance updates to the CI pipeline and adds a test directory with Unit Tests **Major Maintenance updates:** - Added try blocks with appropriate messaging to GitHub PR of failure for: - - **scm** checkout - - build fail (with error logs sent as gists) - - create experiment fails with `stderr` sent to GitHub PR messaging - Pre-stage FAILS from the above are now captured these fails allow FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state labels in GitHub - see image below) **Minor Maintenance updates:** - Fix for STALLED cases reviled from PR 2700 (just needed a lambda specifier) - Fixed path to experiment directory in PR message (had dropped EXPDIR in path) - Needed `latin-1` decoder in reading log files for publishing **Added python Unit Tests for CI functionality:** - Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI utility codes - Cashed the install of Rocoto in the GitHub Runners to greatly reduce stetup time for running the unit tests - Unit Tests Python scripts added - `test_rocostat.py`: rocoto_statcount() rocoto_summary() rocoto_stalled() - `test_setup.py`: setup_expt() test_setup_xml() - `test_create_experment`: test_create_experiment() - - Runs all PR cases that do not have ICs in the GItHub Runner - Reporting mechanism in the Actions tab for Python Unit Testing results - Test case data for STALLED and RUNNING stored on S3 and pulled using wget during runtime of tests commit 5ef4db74649b8be03402c17aa29c024e71699a7b Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu Jul 11 08:59:24 2024 -0400 Adds contents of constructor and initialize methods to marine LETKF class (#2635) Adds contents of constructor and initialize methods to marine LETKF class Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091 --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> commit 8998ec7b74123e953b97a93fa14cc78d471a1aee Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 9 08:31:57 2024 -0400 Fix GDAS group B restart archiving (#2735) Archives the GDAS restartb dataset at a 6-hour offset from restarta This allows cycled experiments to restart from the archives. The tabbing for the master archive templates was also added to improve readability. Resolves #2722 commit 3ca74771255727033b9dc043c652ac585178629c Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Tue Jul 9 08:28:54 2024 -0400 Add fcst dependency to ocnanalprep (#2728) Add previous cycle's `fcst` as a dependency to `ocnanalprep` This ensures that the availability of restart files to the latter. This addresses a seldomly-encountered race condition where `ocnanalprep` fails due to the lack of the files. commit 58fca1668aecd6fb1afd12a441256ad35900e075 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jul 5 15:02:23 2024 -0400 Update (partially) global-workflow for orion+rocky9 (#2741) This PR: - updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils, GFS-utils) to include recent update to their modulefiles for Orion+Rocky9 upgrade - updates the modulefiles in global-workflow to load modules from Orion+Rocky9 paths - updates modulefiles for `gwsetup` and `gwci` as well. - removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not installed. - adds `parm/config.gfs/config.resources.ORION` to address GSI performance degradation after Rocky 9 upgrade. This PR: - does not update the build for UPP. Standalone UPP is not available via ufs-weather-model as of #2729 - will need a follow-up update for `prepobs` and `fit2obs` updated locations when they are installed in `glopara` space on Orion. # Type of change - Maintenance (code refactor, clean-up, new CI test, etc.) # Change characteristics - Is this a breaking change (a change in existing functionality)? NO - Does this change require a documentation update? NO # How has this been tested? This PR is not sufficient for Orion. This PR must be tested on other platforms (Hera, WCOSS2) as this PR updates submodules. # Checklist - [ ] Any dependent changes have been merged and published - [ ] My code follows the style guidelines of this project - [ ] I have performed a self-review of my own code - [ ] I have commented my code, particularly in hard-to-understand areas - [ ] My changes generate no new warnings - [ ] New and existing tests pass with my changes - [ ] I have made corresponding changes to the documentation if necessary --------- Co-authored-by: Kate Friedman <kate.friedman@noaa.gov> commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jul 3 21:07:49 2024 -0400 Update ufs model hash to 20240625 (#2729) Updates UFS weather model hash to hash from 2024-06-24 which has orion porting updates + a few namelist updates. commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jul 3 11:32:40 2024 -0400 Hotfix for undefined CLUSTERS (#2748) Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses the native `dict` `get` method to prevent grabbing an unset entry. commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Wed Jul 3 09:56:08 2024 -0400 Update gempak job to run one fcst hour per task (#2671) This PR updates gempak jobs (gfs, gdas, and goes) from processing all forecast hours at once to one forecast hour at a time. This will reduce the job runtime to less than 5 min, so restart capability is not needed. Resolves #1250 Ref #2666 #2667 --------- Co-authored-by: Walter.Kolczynski <Walter.Kolczynski@noaa.gov> commit 8215ae654202186a4f753c3abe937b7b9b91a9c7 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jul 2 16:22:11 2024 -0400 Hotfix for clusters from #2701 (#2747) Fixes an issue created from #2701 that added `CLUSTERS` to the `gaea.yaml`. commit 11943e36ba12b3df49c51942da780698fab02d38 Author: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> Date: Tue Jul 2 12:58:10 2024 -0400 Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701) This PR sets up the ability on Gaea for auto generation of a clean xml file, i.e., an xml file that does not need any alterations before running rocoto. Refs #2572 Refs #2664 commit de8706702ead0630beb54d868f83aa2cb23f8f79 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon Jul 1 09:29:14 2024 -0400 Update for JCB policies and stage DA job files with Jinja2-templates (#2700) This PR updates the `gdas.cd` hash to bring in new JCB conventions. Resolves #2699 From #2654 This PR will move much of the staging code that take place in the python initialization subroutines of the variational and ensemble DA jobs into Jinja2-templated YAML files to be passed into the wxflow file handler. Much of the staging has already been done this way, but this PR simply expands that strategy. The old Python routines that were doing this staging are now removed. This is part of a broader refactoring of the pygfs tasking. wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a companion to this PR. Co-authored-by: danholdaway <danholdaway@users.noreply.github.com> Co-authored-by: DavidNew-NOAA <david.new@noaa.gov> Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Co-authored-by: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jun 28 14:56:19 2024 -0400 Revert PR 2681 (#2739) This PR: - reverts #2681 in part - keeps some changes for `RUN`. - is a hotfix - should be merged ASAP after consensus w/ @guillaumevernieres @CatherineThomas-NOAA @WalterKolczynski-NOAA commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed Jun 26 15:46:08 2024 -0400 updated Finalize in Jenkinsfile and added try block around scm checkout (#2692) We are updating the Jenkins Pipeline with a try block around checkout to capture errors for the user. Also cleaned up Finalize and added section to clean out workspace on success. commit 968568f682bac7564095440bdb7813abefd76821 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 26 13:27:19 2024 -0400 Activate snow DA test on WCOSS (#2720) Activate the snow DA test on WCOSS. commit 7706760bb8adbdf78cb640b02739023c886e7699 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jun 26 10:02:22 2024 -0400 Cleanup of stale RUNDIRS from an experiment (#2719) This PR: - removes stale temporary scratch run directories from `$DATAROOT/` every 3 days. - should help to scrub failed attempts. - removes an unused variable `RUNDIR` defined in `config.base` commit 8962991691b5f0857b813bddfd28aa1034d4bd2b Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jun 26 09:43:48 2024 -0400 Update logic for MOM6 number of layers/exception values (#2681) Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine how many layers and sets the exception value for MOM6 to be 1e-34 for all scenarios. Note, we will no longer have zeros in the ocean grib output and the DA will also run without issues. Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615 commit 12431f76bdce807067929415007592cffc8a2457 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Jun 26 07:42:35 2024 -0600 Update wave jobs to use COMIN/COMOUT (#2643) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow wave model and products tasks. Refs #2451 commit b902c0bac126c323a07186ad8881384b032b6fda Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jun 25 07:48:46 2024 -0400 Assign machine- and RUN-specific resources (#2672) Redefine resource variables based explicitly on RUN or CDUMP Additionally, machine-specific resources are moved out of config.resources and placed in respective config.resources.{machine} files. Resolves #177 #2672 commit 4e1b937b67ed220120e81925c4507f03b9b8965f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jun 24 10:50:52 2024 -0400 Add minimum software requirements (#2712) Adds a table to HPC documentation stating the minimum support versions commit f43a86276aaef91efa28faadc71a3cf50e749efe Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Jun 21 13:44:29 2024 -0400 Fix and simplify online archiving and reenable METplus jobs (#2687) This fixes the online archiving portion of the `*arch` and `*earc00` jobs, a prerequisite for running METplus. This also reenables METplus by default. The approach previously taken created `FileHandler` dictionaries at varying levels within the resulting yaml, which was not properly parsed by `exglobal_archive.py`. This approach creates a single `FileHandler` dictionary and is much less complicated overall. Resolves #2673 #2647 commit 8993b42cb91144c0ab0501dc7841ea8d675c4701 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 19 21:51:22 2024 -0400 Eliminate post groups (#2667) Eliminates the post groups used for upp and products jobs so that each task only processes one forecast hour. This is more efficient and greatly simplifies downstream dependencies that depend on a specific forecast hour. Resolves #2666 Refs #2642 commit 0b810c888239853fedd0e4584fe62536c6aaacdf Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 20:32:48 2024 -0600 Removes misleading "No such file or directory" syntax errors from output files (#2688) This PR addresses issue #1252. The following is accomplished: - Prior to removing files, the existence of a file is checked prior to attempting to remove; this is performed as noted [here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369); this PR only addresses the the `chgrp` issue. Refs #1252 --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 12:17:59 2024 -0600 Hotfix for bug in template names. (#2697) This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/` template. Resolves #2696 Refs #2451 commit 35d4d99eaac669721add9ddcc793153e5ab3b30a Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 08:06:53 2024 -0600 Update archive job to use COMIN/COMOUT (#2668) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow archive task. Refs #2451 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 47b3a581c8257fa24411fb400df8bb0e1e04972a Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Jun 17 22:55:38 2024 -0400 Turn on high-frequency output in extended test (#2679) Turns on high-frequency (hourly) output in the extended products test to exercise that aspect of the code. This test only runs on WCOSS. Also adds the hooks to optionally turn on the metplus jobs, but that is deferred as they are not currently working correctly. commit 38f2df9fb0c074b1f80d3c637080be79be693161 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jun 17 17:12:55 2024 +0000 Optimize wavepostpnt (#2657) Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs This is done by 1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by - performing operations on all files at once instead of looping over each file - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`) - combining `sed` and `grep` calls when possible - adding logic to `awk` calls instead of handling that logic in bash 2) minimizing as much as possible the amount of data on disk that has to be read in (e.g. limiting sed to read only the line numbers it needs) --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 5af325a6a4e0a14d180514a418603ca79fada487 Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Fri Jun 14 18:05:23 2024 -0400 Update GDASapp hash to move JCB into GDASapp (#2665) This PR moves JCB into GDASapp. The PR also bumps up the hash of GDASapp to what is in `feature/move_jcb`, which at time of writing is develop plus the absorption of JCB into GDASapp. Note that I also took the changes from https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the testing @RussTreadon-NOAA has done. commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b Author: Yaping Wang <49168260+ypwang19@users.noreply.github.com> Date: Fri Jun 14 10:18:17 2024 -0500 Add observation preparation job for aerosols DA to workflow (#2624) Add a prepaeroobs job to prepare aerosol obs files for DA. This job does quality control of the VIIRS aerosol raw observations and convert them to ioda format. Resolves #2623 --------- Co-authored-by: ypwang19 <yaping.wang@users.noreply.github.com> Co-authored-by: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Jun 14 11:04:41 2024 -0400 Remove ocean daily files (#2689) This PR removes the ocn_daily files that are produced by the ocean component. These files can be recreated by averaging data that exists in the 6 hour aveaged files if needed. Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675 Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by removing them and making this obsolete) commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jun 13 12:22:03 2024 -0400 Update Jenkinsfile needed a comma commit dc21eac6c3941d7f30803891d91d82f4cc1f8183 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jun 13 11:41:14 2024 -0400 Add Hercules-EMC to the Jenkins configurable parameter list (#2685) This quick-fix PR is to update the Jenkins Pipeline's configurable parameter list to include the **Hercules-EMC** node. This allows Jenkins users to restart Jobs in the controller when no updates have been made. commit ebacebfbe458634b8c80af6a735d6b6d01e4e406 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Thu Jun 13 11:20:24 2024 -0400 Update gdas.cd and gsi_utils hashes (#2641) This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea build for gsi_utils. Resolves #2640 commit 34155fb4767769600a1ff95f0a65e37081addc2a Author: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com> Date: Thu Jun 13 11:18:22 2024 -0400 Add ability to use GEFS replay ICs (#2559) The PR allows the use of ICs from PSL's replay analysis. These replay ICs will be used for GEFS reforecasting and SFS. Two main changes are associated with these updates: (1) replay ICs being valid at 3Z, and (2) the use of warm starts. Resolves #1838 --------- Co-authored-by: Jessica Meixner <Jessica.Meixner@noaa.gov> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Jun 12 19:25:42 2024 -0600 Replace `sleep` with `wait_for_file` (#2586) This PR addresses issue #2444. The following is accomplished: - All `sleep` statements are replaced with `wait_for_file` for the relevant scripts beneath `scripts` and `ush`; - Indentation and shell-norms are updated where applicable. Note: The WAFS scripts are not updated as per @aerorahul direction. Resolves #2444 --------- Co-authored-by: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 12 13:31:55 2024 -0400 Add COM template for JEDI obs (#2678) Adds a COM template to define a path to store obs processed for JEDI. This will allow UFSDA to stop writing to COM_OBS, which should be read-only as it belongs to obsproc in operations. No functional change yet. commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Wed Jun 12 09:06:23 2024 -0600 Link both global-nest fix files and non-nest ones at the same time (#2632) This PR enables linking both global-nest fix files and non-nest ones at the same time and users can run both nesting and non-nesting experiments at the same time without worries about what fix files to be linked. Resolves #2631 commit 61de004d4f9e9edf8a31bb173f2719b46451a36a Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jun 12 11:03:13 2024 -0400 Update ufs-weather-model (#2663) Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack allowing some temporary fixes to be reverted. * removes upp submodule * uses upp from the ufs-weather-model * restores the build and link that were hacked during the Hera Rocky 8 transition to allow for UPP submodule * Removes forecast directories in clean-up Resolves #2617 Resolves #2437 --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Wed Jun 12 01:15:37 2024 -0400 Add ability to process ocean/ice products specific to GEFS (#2561) This PR begins to add the capability to produce GEFSv13 ocean and ice products in the global-workflow according to stakeholder requirements. The following features are added. - An oceanice prod yaml file has been added to address the ocean and ice products specific to GEFSv13. - The rocoto dependencies and config.base for GEFS have also been modified to allow for 24-hour averaged ocean and ice output. - Various scripts have been modified to allow for ocean and ice output frequencies of 24 hours. - `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN` and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`. Refs #1878 commit 6691e7489650e0b738c176fbd096109288dc09b6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 11 21:15:07 2024 -0600 Update cleanup job to use COMIN/COMOUT (#2649) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow clean-up task. Refs #2451 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Jun 11 16:17:25 2024 -0400 Add overwrite to creat experiment in BASH CI (#2676) This is a quick hotfix to the CI BASH driver script adding `--overwrite` to create experiment script to avoid errors from restarting an experiment. commit e7909af8d9e1f34140388a3f8556d8e582c58fe5 Author: emilyhcliu <36091766+emilyhcliu@users.noreply.github.com> Date: Mon Jun 10 15:11:27 2024 -0400 Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py (#2645) This PR proposes updates for the following two scripts: 1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select CRTM cloud optical table based on cloud microphysical scheme indicated by `imp_physics' The default scheme in the GFS forecast model is Thompson scheme (imp_physics = 8). 2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in the script due to increased variables to interplate increments and calculate analysis in the netcdf_io routines in GSI-utils. Here is the related [PR #46 for GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46). --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 9caa51de8fb7be07d2e61775da01937d576964f6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Jun 6 22:15:23 2024 -0600 Update RDHPCS Hera resource for `eupd` task (#2636) As per @wx20jjung, the resource for the `eupd` task have been updated for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job fails. Resolves #2454 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Thu Jun 6 11:49:03 2024 -0400 Parameterize some things in config.atmanl and config.atmensanl (#2661) This PR adds some parameters in config.atmanl and config.atmensanl that can be altered with the defaults.yaml. The motivation is to make these files match those in the GDASApp JJOB tests (example: https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl), so we can just use the Global Workflow config.atmanl and config.atmensanl in the tests rather than custom ones in GDASApp that have to be separately updated every time the ones in the Global Workflow are updated. commit 54ea0b73a07921be5fbb07fe41e976888bd3e549 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Thu Jun 6 01:36:02 2024 -0400 Add links to the ocean insitu obs processing tools (#2644) Add links to the marine bufr to ioda converters for the marine insitu observations. - fixes https://github.com/NOAA-EMC/GDASApp/issues/1106 - waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135 commit 205d0c2b13e2d7755cec75bf8c978ab20d453862 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jun 5 17:31:30 2024 +0000 Update S4 point of contact in docs (#2660) Update the point of contact for global workflow issues on S4. commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed Jun 5 12:50:14 2024 -0400 Enable wcoss2 ufsda build and module load (#2620) This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2. Resolves #2602 Resolves #2579 commit 67b833e0c7bc390865d453588b4609a1a7ede981 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Tue Jun 4 13:33:43 2024 -0400 Update ufs-weather-model (#2646) Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6 This should resolve the issue and allow C768 runs on Hera and allow for CICE to run on WCOSS2 (due to library updates to allow linking). From what I can tell, all updates needed were done by @HenryWinterbottom-NOAA which were updates for CICE Fixes #2490 commit c44d0ac86cfdf78eb87492431bf6d825e8bae637 Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Tue Jun 4 10:29:49 2024 -0400 Update wmo parm files to fix WMO header (#2652) This PR updates wmo parm files to switch WMO header of precipitation type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to instantaneous. Resolves #2566 commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Tue Jun 4 13:55:33 2024 +0000 Add IAU to snow DA (and its test) (#2610) This PR enables IAU for the snow DA which is necessary for GFSv17. A snow analysis is created for the center of the window regardless, and an additional at the beginning of the window is added if IAU is on. The former is needed for UPP and the latter, to initialize the model. The increment is valid throughout the window for 3DVar, so the same increment is added to both forecasts. Additionally, the input file that goes into global_cycle has been updated to be the output of the JEDI snow analysis instead of the forecast (@jiaruidong2017 I recall discussing this, can you confirm this is right or am I mistaken) This PR also makes the CI test for snow DA (and aerosol DA) include IAU rather than without IAU,. --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit c92bf415060750127c9c05a62a1d2851c489551a Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Sat Jun 1 05:11:07 2024 +0000 Archiving cleanup (#2621) 1) Adds a lot of comments to the jinja templates for archiving 2) Rearranges the gdas and enkf templates to a more logical order 3) Fixes a couple of bugs in the enkf archiving of increments and analyses 4) Disables archiving for the half cycle 5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`, instead relying on `DO_FIT2OBS` 6) Updates wxflow to add the option to not allow undefined variables when parsing jinja templates and invokes this feature when running archives Resolves #2612 commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri May 31 04:57:08 2024 -0400 Switch to Rocky 9 built external packages on Hercules (#2608) The workflow was updated to use modules built on Rocky 9, but the external packages (like prepobs) were still pointing to the versions built on CentOS (Orion). This transitions to packages built on Rocky 9. Updating of the tracker package has been deferred until later. As such, the tracker jobs have been disabled by returning immediately if they are on Hercules. Since these jobs are small, resource-wise, it should not meaningfully impact turnover time. commit 4422550c01c9214a2b3b8890bdcc898123ee216a Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Thu May 30 08:05:23 2024 -0600 Add the capability to use slurm reservation nodes (#2627) Add the capability to use slurm reservation nodes Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE Resolves #2626 commit a54153fd9d26126206bc07a1da4e80f50c0c5910 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 29 23:24:07 2024 -0400 Update forecast job to use COMIN/COMOUT (#2622) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the forecast job. Refs #2451 --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit d69a8af95d492982b918670322ed5c41ab074335 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed May 29 21:29:03 2024 -0400 Update to add 1-deg global wave grid (#2619) This PR adds options to use a global 1 deg grid, intended for testing with the SFS application. Requires new fix file changes NOAA-EMC/global-workflow#2618 commit 0b4670ecf83b99b72835c8380573b2bca7cf5324 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed May 29 17:17:21 2024 -0400 Add C384mx025_3DVarAOWCDA yamls (#2625) Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder. commit 2e885d05c64b947f00a3cf055a1277fbfac195c9 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 29 13:00:51 2024 -0400 Script to keep Jenkins Agent persistent from cron (#2634) This "persistent" Java Agent launch script can be ran from a cron job: - Uses Jenkins Remote API to check the status of the Node connection using curl for a given machine. - If it is not connected a new agent is launched for that node. Resolves #2633 commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5 Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Tue May 28 17:17:11 2024 -0400 Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611) Based on users' feedback, this PR do the following: 1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF 2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD, and VOGRD) from "%g m below water surface" to "%g m below sea level" 3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m) Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31 Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Tue May 28 17:16:23 2024 -0400 Add atmensanlfv3inc job (#2592) This PR creates the atmensanlfv3inc job, the ensemble version of atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is #[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3). commit 50c2b8951b29a3c883a778becbf8582f9519eb48 Author: Anil Kumar <108816337+AnilKumar-NOAA@users.noreply.github.com> Date: Tue May 28 13:23:53 2024 -0400 Global-workflow (AR) Generic updates for Gaea C5 (#2515) - Port global-workflow’s build and run capability to Gaea-C5 - Building global-workflow on Gaea-C5 - Setting up experiments with global-workflow on Gaea-C5 --------- Co-authored-by: AnilKumar-NOAA <Anil.Kumar@gaea53.ncrc.gov> Co-authored-by: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> commit b6ca771a0c584cbfcbbf9be739765d5f3815df97 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 24 10:52:45 2024 -0400 Update STMP and PTMP settings in host file for Orion and Hercules (#2614) - Updating STMP and PTMP settings in host file for Orion and Hercules because they are cross mounted. - Also took the opportunity to finally update **SLURM_ACCOUNT** to **HPC_ACCOUT** in CI over rides. - Added a refactor of the `rocotostat.py` tool that is more pythonic and as a execute retry feature because the `rocotostat` utility on Orion has been failing sometimes. commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Tue May 21 23:50:50 2024 -0400 Sea-ice analysis insertion (#2584) Allows cycling and restarting CICE with the sea-ice analysis if the marine DA is switched on. Resolves #2568 Resolves NOAA-EMC/GDASApp#1103 commit 5369a1ff3a3969149fcf32810fad0e50216752b7 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue May 21 22:12:29 2024 +0000 Refactored archiving (#2491) This provides a new pygfs task, archive.py, that provides all of the tools necessary to archive data to the local (`ARCDIR`) and backup (`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to define the file to be archived or tarred to replace the `hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts and make it easier to add new data and explicitly handle optional and required files. For `ATARDIR` archiving, a master jinja template is provided for each `RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2, master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both `enkfgdas` and `enkfgfs` `RUN`s. These templates then include the appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on experiment, cycle, and coupled parameters. Each of these templates corresponds to a single tarball to populate and are tabbed 4 spaces so they are defined within the master `datasets` dictionary. Future developers should not have to make modifications to archive.py unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then only a single `elif` needs to be added to the configure method to specify the master `ATARDIR` template to archive (e.g. `master_gefs.yaml.j2`). If a new component is coming online that needs to be archived to `ATARDIR` (e.g. SNOW), then create a new template for each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`) and reference the template in the appropriate master templates, e.g. `master_gdas.yaml:` ```jinja {% if DO_SNOW %} {% include "gdassnow.yaml.j2" %} {% endif %} ``` A few other issues were addressed along the way: 1. Aerosols have been reenabled. Aerosol forecasts should only be performed during gdas cycles, but analyses can be performed for both gfs and gdas cycles. This was accomplished by setting separate `AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs. 2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`. This prevented restarts from being used for cice-enable experiments. This feature was not tested. 3. Create a temporary fix for the `wgrib` utility. For spack-stack 1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in existing installations. Once complete, this temporary fix should be removed. 4. The number of `earc` jobs has been reduced for lower resolution experiments. Both C48 and C96 experiments will now only have two earc jobs (one for the non-member files to archive and another for the member files). C192 will have up to 3 earc jobs (one non-member, one for members 1-40 and another for members 41-80, if needed). Resolves #2345 Resolves #2318 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 17 12:57:59 2024 -0400 Add remove RUNDIRS step in CI before creating experements (#2607) As had been done in Bash CI we need to remove the RUNDIR in Jenkins before a creating an experiment in the event that case had beem previously ran. commit bb930050b3cd51d28ecba6b231c8675f6d11856c Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu May 16 12:28:30 2024 -0400 Adds jjob and other necessities for marine LETKF task (#2564) Adds jjob, rocoto script, config file, and other necessities for new marine LETKF task. Partially addresses NOAA-EMC/GDASApp#1091 commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu May 16 12:12:06 2024 -0400 Updating CI Machine configs with redundant PTMP (#2605) Quick fix adding PTMP as STMP in Machine configs for CI for completeness commit ef340ff33a6f89adf70838206ba3fd56a953fa7a Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu May 16 11:37:30 2024 -0400 Fix race condition in CI between Orion and Hercules (#2604) Hotfix to solve race conditions in the CI system due to cross-mounted file systems between Orion and Hercules commit e8b17e27f719df280170dc3f5bd9f19917cefaf2 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 15 17:16:30 2024 -0400 Remove existing EXPDIRs and COMROTs when CI is re-run (#2601) Quick hotfix for having default for re-runing jobs to start clean with new EXPDIRs and COMROTs commit b5d113efb1970ede5cd1d3d4dff8d96320519c41 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 15 16:52:49 2024 -0400 Moving logic for skipping hosts in pr cases (#2573) This PR removes the logic of skipping hosts for pr cases from `create_experiment.py` and moves it to a test in the cron bash driver using a `parse_yaml.py` python tool. The Jenkins pipeline was not effected as it uses the `get_host_case_list.py` utility to form the cases on a per host bases. Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed May 15 13:13:30 2024 -0400 Update gsi_utils.fd hash (#2598) This PR updates the `gsi_utils.fd` hash to bring in updates which add safeguards to - `src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90` - `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90` The safeguards are described in GSI-utils PR [#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated issue. Resolves #2597 commit d5366c66bd67f89d118b18956fe230207cbf0aea Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 15 13:12:56 2024 -0400 Update CICE and MOM6 fix versions (#2600) This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions to the newer `20240416` timestamps, which includes updates and fixes to the `100` (1-deg) resolution files. Resolves #2480 Resolves #2483 Resolves #2595 commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon May 13 22:57:38 2024 +0000 Limit gfswavepostpnt to 40 PEs/node (#2588) This fixes the slow runtime of the gfswavepostpnt job on Hercules. The job is very I/O intensive and does not scale well to large nodes, so limit the number of jobs/node to 40. Resolves #2587 commit 4fb7c12c325702a47f27c802a5067efd33d0327c Author: Fanglin Yang <fanglin.yang@noaa.gov> Date: Mon May 13 16:37:51 2024 -0400 Update damping and time-step (#2575) Updates the model to use explicit Rayleigh damping for u/v and implicit damping to w. This improves model stability and allows for longer timesteps. Also unifies the GDAS and GFS to use the same damping. Results from a test at the C1152 resolution (coupled model) can be found at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/ Resolves #2574 Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Lisa Bengtsson <lbengtss@Orion-login-1.HPC.MsState.Edu> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 10 14:17:13 2024 -0400 Do not use BUILT_semphore to force rebuilds when re-run (#2593) Remove the placement of the `BUILT_semaphore` file after the build in the Jenkins Pipeline and force it to rebuild any changes after a PR is re-ran. commit 2346c6161f75ae02369cbf30f30c6150d3e12b66 Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com> Date: Thu May 9 21:17:06 2024 -0500 Migration to Rocky8 spack-stack installations on Jet (#2458) # Description Migrates Global Workflow to Rocky8 spack-stack installations on Jet. Jet has moved from CentOS7 to Rocky8. Resolves #2377 Refs NOAA-EMC/UPP#919 Refs NOAA-EMC/gfs-utils#60 Refs NOAA-EMC/GSI#732 Refs NOAA-EMC/GSI-Monitor#130 Refs NOAA-EMC/GSI-utils#33 commit c7b3973014480a20dd8e24edaeb83a9e9e68159f Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu May 9 11:36:58 2024 -0400 Updates for cold start half cycle, then continuing with IAU for WCDA (#2560) This PR allows us to run C384 S2S with IAU, but starting with the first half-cycle as a cold-start. This will be necessary for cycled testing as we build towards the full system for GFSv17. This updates the copying of the restarts for RUN=gdas for both ocean and ice copying what the atm model is doing. It also reduced the amount of restart files from 4 to 3. Other updates: * Add DOJEDI ocean triggers for archiving certain files update from: @CatherineThomas-NOAA * Adds COPY_FINAL_RESTARTS option to turn on/off copying the last restart file to COM. Defaults to off... * Defines model_start_date_current_cycle & model_start_date_next_cycle to help with knowing which IC to grab. Refs #2546 Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2 Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Wed May 8 20:52:48 2024 -0400 Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477) Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI Configuration Builder (JCB) tool so that YAMLs can be made more portable and invoke the observation chronicle mechanism. Resolves #2476 Co-authored-by: danholdaway <danholdaway@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 8 02:04:16 2024 -0400 Add CI test for products (#2567) Adds a new version of the atm3DVar test that runs the full forecast length and produces most of the secondary products. For now, this test will only run on WCOSS due to gempak failures on other machines as well as computational needs. On other machines, the original version will run (the original version will not run on WCOSS). AWIPS remains off for now in this extended test due to a bug involving tocgrib2 and the convective precip fields (see #2566). The new test runs for 4½ cycles and the full 384-hr forecast length to ensure all gempak scripts are exercised. Since the cycle throttle is 3 and the bulk of the time is in the free forecast, the cycles run mostly concurrently so it doesn't extend the total test time too much beyond that of a single 384-hr forecast. Fixes a bug in NPOESS that was introduced when the post filenames were reverted to the previous format for the GOES products until the final filenames are determined (#2499). Also removes the AWIPS g2 job from the rocoto mesh to complete the retirement of grib1 products. Resolves #2132 Resolves #2445 commit 9b6f8404ac4507d14adc404b77cfdf002b55e832 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue May 7 00:14:36 2024 -0400 Add task to prepare emissions for GEFS (#2562) This PR: - introduces a task to prepare emissions for a forecast into the GEFS application. - adds configuration, j-job, rocoto job, ex-script and the python class for this job - updates GEFS workflow to be able to generate the XML to call this job. - updates the `fcst` and `efcs` job dependencies in the GEFS application to depend on `prep_emissions` if aerosols are turned ON. - provides a placeholder for @bbakernoaa to work on the details for preparing emissions. Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 233c18815d2e8e6b344f161fd0c102a4fbdfb66d Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Mon May 6 18:11:35 2024 -0400 Single Executable for main GDAS JEDI applications (#2565) Changes that accompany GDAS PR (NOAA-EMC/GDASApp/pull/1075) that allows building of a single gdas executable, which should be more compliant with NCO requirements. Addresses https://github.com/NOAA-EMC/GDASApp/issues/1085 commit a005244bbfb2f1c525bca60d966f8095aa1acb8e Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Thu May 2 20:32:53 2024 -0600 Add nest capability (#2545) This PR adds the global nesting capability to the global workflow so that one can run a regional domain nested in a global run. Resolves #2544 Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit cb87daaced9fddd17f8370a1842d7e4ddab24e8f Author: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> Date: Thu May 2 15:30:53 2024 -0400 Update gfs_utils for Gaea (#2556) What: add build capability to the gfs_utils submod within the global workflow on Gaea Refs #2535 Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 707a1cc5124bcd8e006839a17f76ceb88f45f902 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed May 1 18:13:02 2024 -0600 Updated GEMPAK version and APRUN launcher. (#2555) This PR addresses issue #2248 and #2513. The following is accomplished: - Updates the parallel executable for GEMPAK applications; - Updates the GEMPAK version for RDHPCS Hera. Describe your changes. Focus on the *what* and *why*. The *how* will be evident from the changes. In particular, be sure to note any interface changes, such as command line syntax, that will need to be communicated to users. At the end of your description, please be sure to add the issue this PR solves using the word "Resolves". If there are any issues that are related but not yet resolved (including in other repos), you may use "Refs". Resolves #2248 Resolves #2513 Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> commit f151cbf394e998ca0fdae893ca174499468d0c85 Author: Travis Elless <113720457+TravisElless-NOAA@users.noreply.github.com> Date: Wed May 1 11:01:18 2024 -0400 Utilize scale-dependent localization for atmospheric analysis (#2542) The plan for GFSv17 is to use a scale-dependent localization for the atmospheric analysis. This PR adds the necessary parameters to allow this feature to be used by default. commit 53b6764392cb4c0f3b4506ccd3f8cba5c5d2c56e Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Apr 30 16:37:54 2024 -0400 Remove implicit symlink names (#2527) Lustre has a defect under Rocky 9 that results in symlink sometimes failing when the link name is not explicit. This updates all link creation to use explicit names. `config.base` is updated to turn off two monitor jobs on Hercules because the executables are not yet built there. This, combined with the previous change, should make workflow available for use on Hercules. Also removes the redundant utility names for NCP, NLN, etc. in the gdas scripts that are already defined in `config.base`. Resolves #2131 Resolves #2522 commit 762f040a2045db17cdacd9026df9c4b8fd520156 Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Mon Apr 29 22:26:28 2024 -0400 Fixes sea ice archiving (#2541) Removes/changes sea ice output files that are failing to be added to list for archiving, causing `gdasarch` to fail in WCDA cycling. Resolves https://github.com/NOAA-EMC/GDASApp/issues/1044 commit 2ecf4f86e0cbe59407ba2c4e105ee7292f1eda01 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon Apr 29 22:25:57 2024 -0400 Link ensemble analysis increment files to COMROOT for warm_start (#2553) Scripting is added to `setup_expt.py` to link ensemble analysis increment files to COMROOT for warm_start experiments. Resolves #2552 commit 3a7abe1d63c573006e0e656237f1220002c3f579 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Apr 30 02:25:28 2024 +0000 Launch Multiple Platforms to Jenkins with polling (#2548) When launching Jenkins CI Tests all requested RDHPCS machines can now be selected via the Ready label at once. This is all that is required sense polling also works now on the controller end. Killing the jobs still needs to be done directly on the Jenkins Controller. Do not try to update the CI process using Labels. It is for launching only. Jenkins will update the labels as the states change. NOTE: When a case fails the label will be update to a **Fail** for that system but will continue to report failures of subsequent cases until otherwise stopped in the Jenkins Controller directly. Do not update any labels to **Ready** until a push has been made to the repo of the PR, and The job has been completed or stopped directly on the controller first. You can do this at anytime without having to wait until the other machines are completed. Co-authored-by: tmcguinness <terry.mcguinness@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 4b96c1237c562b67650c2d2fa015984c95b228eb Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Sat Apr 27 19:03:26 2024 -0400 Turn C48mx500_3DVarAOWCDA back on (#2543) This PR turns the C48mx500_3DVarAOWCDA test back on. This required a few bugfixes in GDAS app which have now been merged. Resolves #2438 Resolves #2528 co-authors: @guillaumevernieres and @aerorahul who provided the bug fixes. commit 48489b4e7758e80660941279652431e49fdd3cfa Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Sat Apr 27 00:23:00 2024 -0600 Add option to link different orog/ugwd fix files for global nest (#2532) The global nest runs use a different set of tiles and need a different set of orog and ugwd fix files. The PR add an option to link correct fix files for global nest. Resolves #2530 Resolves #2529 commit 7911f12ef0213f487a0681b260e4c982c946c17c Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Fri Apr 26 16:20:44 2024 -0400 Retire AWIPS GRIB1 products (#2547) This PR retires AWIPS GRIB1 products by deleting the files that are responsible for it. This PR does not remove the awips_g2 tasks from rocoto task list. It will be addressed in a follow up PR by workflow developers Refs #2445 commit 93c853d464908a88222d5a6eeca686cd1a413c0e Author: James Jung <Jim.Jung@noaa.gov> Date: Fri Apr 26 13:16:47 2024 -0400 Add CADS use flexibility (#2540) The current design requires a script change to turn CADS on/off for specific instruments. The new design moves the on/off (true/false) flags to the config.anal file. Resolves #2538 commit 11bf141319ef2a29398742007a29d79bbf4439d5 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Apr 25 23:35:57 2024 +0000 Hot fix for bash CI on WCOSS2 (#2536) A couple of minor hotfixes need for bash CI to work on WCOSS2. PR tested in bash on WCOSS with these changes Co-authored-by: tmcguinness <terry.mcguinness@noaa.gov> commit f11bf3dc2bc062c070b901ce3aa808bd6b69a007 Author: Walter Kolczynski - NOAA <Walter…

- based on gsl_ufs_dev from KaYee's fork global-workflow: 07Aug24,37c53ac [dev_07Aug2024_37c53ac] UFS: 19Jul24, c127601 FV3: 19Jul24, 2527c11 UPP: 23Apr24, be0410e CCPP-PHYSICS: 19Jul24, 46df080 UFS_UTILS: 26Jun24, 3ef2e6b Squashed commit of the following: commit 70b557836379bb7e545fcc6642e28d66cfc17735 Merge: 5edbd123e 37c53ac69 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Wed Aug 7 11:02:24 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 7 08:11:21 2024 -0400 Revert MSU FIX_DIRs back to glopara (#2811) commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Aug 6 14:47:36 2024 -0400 Bugfix for updating label states in Jenkins (#2808) Quick bug fix for updating state labels in CI during finalize. (did not reference GitHub CLI executable correctly in the pipeline script) commit 8fee36f0307b0c08080e3a8fa8fa6703e7da5fce Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Aug 6 11:02:45 2024 -0400 Clean-up temporary rundirs - take 2. (#2753) This PR: - is a follow-up to a previous PR that aggressively pruned run directories. - removes run directories for the current cycle in the clean-up if the cycle is successful. If the cycle is not successful, cleanup is not called and all run directories for the cycle are safe from being purged. - also updates the PR template to list/query for any updates to submodules. --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: David Huber <david.huber@noaa.gov> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit d599fff4aedd41ae587dbe02226acb12ff48efc1 Author: HelinWei-NOAA <48133472+HelinWei-NOAA@users.noreply.github.com> Date: Mon Aug 5 05:31:31 2024 -0400 Change land surface for HR4 (#2787) Resets the default value of opt_diag to 2 corresponding to the land surface upgrades in ufs-weather-model for HR4. Resolves #2786 commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Aug 2 15:41:29 2024 -0400 Run METplus serially and correct the name of prod tasks (#2804) Adds 2 hot fixes: - METplus v9.1.3 has a bug in it that sometimes attempts to create multiple copies of the same directory when running in parallel, causing a Python error and downstream problems. This PR makes METplus run in serial mode, preventing such issues. - Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod) commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri Aug 2 15:03:45 2024 -0400 Update Java Agent launching script for Jenkins connections (#2762) Made updates to the Jenkins Launching Script for robustness and less ambiguous documentation: - Clearer distinction between required user token for the remote api and the systems token for launching - Added pre-checks: `gh` is authenticating, named compliant token and secret file exists - More robust Jason based parser of the remote api response for checking the state of the Node connection - For `cron` use a 5 minute pause and recheck was added before re-launching of the java agent - Added concise header documentation of requirements and purpose --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit b73b1fd203496db97f8067652659573a632bcc67 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Aug 2 07:59:06 2024 -0400 Fix erroneous cdump addition (#2803) commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Aug 1 20:26:13 2024 -0400 Update ocean post-processing triggers (#2784) This PR: - replaces `check_netcdf.sh` checker for ocean post-processing with with ocean output at the next forecast hour or finishing of the forecast job for ocean prod - removes no longer needed `ush/check_netcdf.sh` commit aa2af1ca8d59424a60a1730722bf528775d9e606 Author: GeorgeGayno-NOAA <52789452+GeorgeGayno-NOAA@users.noreply.github.com> Date: Thu Aug 1 16:46:10 2024 -0400 Update the gfs_utils repository hash (#2801) # Description Point to the latest hash of the gfs-utils repository, which contains the bug fix to gaussian_sfcanl. Resolves #2669. Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73 commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Aug 1 08:12:14 2024 -0400 Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791) Changes how METplus jobs run so that they run on the last GFS cycle for a given `PDY`. This is a departure from operations where the METplus jobs run on the 00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through `${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on `${PDY}18` for cycles 00-18. See https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details. commit 1cf8b448af562dbb7af198399c78c585977e81da Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 30 10:38:49 2024 -0400 Simplify resource-related variables, remove CDUMP where unneeded (#2727) This overhauls resource-related variables to use a common set of variables for each job. In the process, this also removed the use of CDUMP in most cases. Resolves #1299 #2693 commit 61875f25c9e971f82ae499b5b612d7f095deebd4 Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Mon Jul 29 14:40:03 2024 -0400 Remove f000 from atmos rocoto tasks for replay cases (#2778) The main purpose of this PR is to remove the f000 from atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater than `0`, it becomes necessary to have the first lead hour set to `OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and the minimum lead time for the ocean_prod rocoto task needs to be 6 (assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up possible by removing 0 from fhrs for atmosphere-related tasks in `gefs_tasks.py` when replaying. This PR also moves where f000 is being removed for the ocean_prod and ice_prod tasks. The if-block that performs this f000 removal has been moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`. --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit f156a7894d639f177e3e2588f98eec1f6f59aa68 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Jul 26 14:18:32 2024 -0500 HR4 GWD update (#2732) This update is a combination of the gravity wave drag (GWD) versions from the NOAA/GSL and NOAA/PSL commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Jul 25 14:26:52 2024 -0400 Temporarily disable METplus jobs (#2796) commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Wed Jul 24 15:00:35 2024 -0400 Refactoring of the marine B-matrix job (#2749) Refactor the functionality of B-matrix generation from the GDASApp Resolves #2743 commit 65a7ab75dc0e4baba06a02e11ed0455787056a68 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 23 08:35:48 2024 -0400 Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775) Removes the namespace-based construction of EnKF member COM directories in the enkf archive template. commit c45b9611f3e701b819bd33dc5af29033f060bb91 Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Tue Jul 23 00:33:16 2024 -0400 Add task to process reforecast variables to save on WCOSS2 (#2680) # Description This PR adds an optional task to the global-workflow to process a subset of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for the GEFSv13 reforecast. This task is designed to process GEFS variables so that specific reforecast product requirements are met. A new variable in `config.base` called `DO_EXTRACTVARS` enables this task, which is currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by default and is specifically a task designed to be executed for the GEFSv13 reforecast. Refs #1878 # Type of change - New feature (adds functionality) # Change characteristics - Is this a breaking change (a change in existing functionality)? NO - Does this change require a documentation update? NO # How has this been tested? This has been cloned and tested on WCOSS2. This will need to be tested on Hera and other platforms on which the reforecast may be running. # Checklist - [ ] Any dependent changes have been merged and published - [x] My code follows the style guidelines of this project - [x] I have performed a self-review of my own code - [ ] I have commented my code, particularly in hard-to-understand areas - [x] My changes generate no new warnings - [x] New and existing tests pass with my changes - [ ] I have made corresponding changes to the documentation if necessary --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 71dc33c6ca991c16ce743760d99feaaf60f2218a Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jul 22 14:51:53 2024 -0400 Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774) Fix metp* resources and check that they completed properly; add support for Orion Rocky 9 commit 56df67a90fe090c425199f1285e5aac722c398b1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jul 22 09:28:18 2024 -0400 Hotfix: Update jcb to avoid git-lfs files (#2782) Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to be cloned on Hera. This hotfix points to a non-authoritative branch of the GDASApp (https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and should be updated ASAP back to the authoritative repository. commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jul 16 09:44:00 2024 -0400 Address issues in creating XML for GFS forecast-only with app S2SWA (#2757) This bugfix PR: - fixes an issue where a user is unable to generate the XML for a GFS forecast-only experiment with APP=S2SWA Specifically, the changes are related to defining `aero_fcst_cdumps`. Following `setup_expt.py`, the user will have to set `AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in `config.base`. commit e0878dba0e53706a7f53429b61aee2936e2c21bf Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Jul 15 10:25:11 2024 -0400 Updated prepobs and fit2obs versions for Orion Rocky9 (#2758) Update prepobs to v1.0.2 and fit2obs to v1.1.2 These versions now support Orion Rocky9. Updates are included for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet. commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jul 11 17:48:47 2024 +0000 CI maintenance updates and adding CI Unit Tests (#2740) This PR has a few maintenance updates to the CI pipeline and adds a test directory with Unit Tests **Major Maintenance updates:** - Added try blocks with appropriate messaging to GitHub PR of failure for: - - **scm** checkout - - build fail (with error logs sent as gists) - - create experiment fails with `stderr` sent to GitHub PR messaging - Pre-stage FAILS from the above are now captured these fails allow FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state labels in GitHub - see image below) **Minor Maintenance updates:** - Fix for STALLED cases reviled from PR 2700 (just needed a lambda specifier) - Fixed path to experiment directory in PR message (had dropped EXPDIR in path) - Needed `latin-1` decoder in reading log files for publishing **Added python Unit Tests for CI functionality:** - Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI utility codes - Cashed the install of Rocoto in the GitHub Runners to greatly reduce stetup time for running the unit tests - Unit Tests Python scripts added - `test_rocostat.py`: rocoto_statcount() rocoto_summary() rocoto_stalled() - `test_setup.py`: setup_expt() test_setup_xml() - `test_create_experment`: test_create_experiment() - - Runs all PR cases that do not have ICs in the GItHub Runner - Reporting mechanism in the Actions tab for Python Unit Testing results - Test case data for STALLED and RUNNING stored on S3 and pulled using wget during runtime of tests commit 5ef4db74649b8be03402c17aa29c024e71699a7b Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu Jul 11 08:59:24 2024 -0400 Adds contents of constructor and initialize methods to marine LETKF class (#2635) Adds contents of constructor and initialize methods to marine LETKF class Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091 --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> commit 8998ec7b74123e953b97a93fa14cc78d471a1aee Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 9 08:31:57 2024 -0400 Fix GDAS group B restart archiving (#2735) Archives the GDAS restartb dataset at a 6-hour offset from restarta This allows cycled experiments to restart from the archives. The tabbing for the master archive templates was also added to improve readability. Resolves #2722 commit 3ca74771255727033b9dc043c652ac585178629c Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Tue Jul 9 08:28:54 2024 -0400 Add fcst dependency to ocnanalprep (#2728) Add previous cycle's `fcst` as a dependency to `ocnanalprep` This ensures that the availability of restart files to the latter. This addresses a seldomly-encountered race condition where `ocnanalprep` fails due to the lack of the files. commit 58fca1668aecd6fb1afd12a441256ad35900e075 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jul 5 15:02:23 2024 -0400 Update (partially) global-workflow for orion+rocky9 (#2741) This PR: - updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils, GFS-utils) to include recent update to their modulefiles for Orion+Rocky9 upgrade - updates the modulefiles in global-workflow to load modules from Orion+Rocky9 paths - updates modulefiles for `gwsetup` and `gwci` as well. - removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not installed. - adds `parm/config.gfs/config.resources.ORION` to address GSI performance degradation after Rocky 9 upgrade. This PR: - does not update the build for UPP. Standalone UPP is not available via ufs-weather-model as of #2729 - will need a follow-up update for `prepobs` and `fit2obs` updated locations when they are installed in `glopara` space on Orion. # Type of change - Maintenance (code refactor, clean-up, new CI test, etc.) # Change characteristics - Is this a breaking change (a change in existing functionality)? NO - Does this change require a documentation update? NO # How has this been tested? This PR is not sufficient for Orion. This PR must be tested on other platforms (Hera, WCOSS2) as this PR updates submodules. # Checklist - [ ] Any dependent changes have been merged and published - [ ] My code follows the style guidelines of this project - [ ] I have performed a self-review of my own code - [ ] I have commented my code, particularly in hard-to-understand areas - [ ] My changes generate no new warnings - [ ] New and existing tests pass with my changes - [ ] I have made corresponding changes to the documentation if necessary --------- Co-authored-by: Kate Friedman <kate.friedman@noaa.gov> commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jul 3 21:07:49 2024 -0400 Update ufs model hash to 20240625 (#2729) Updates UFS weather model hash to hash from 2024-06-24 which has orion porting updates + a few namelist updates. commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jul 3 11:32:40 2024 -0400 Hotfix for undefined CLUSTERS (#2748) Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses the native `dict` `get` method to prevent grabbing an unset entry. commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Wed Jul 3 09:56:08 2024 -0400 Update gempak job to run one fcst hour per task (#2671) This PR updates gempak jobs (gfs, gdas, and goes) from processing all forecast hours at once to one forecast hour at a time. This will reduce the job runtime to less than 5 min, so restart capability is not needed. Resolves #1250 Ref #2666 #2667 --------- Co-authored-by: Walter.Kolczynski <Walter.Kolczynski@noaa.gov> commit 8215ae654202186a4f753c3abe937b7b9b91a9c7 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jul 2 16:22:11 2024 -0400 Hotfix for clusters from #2701 (#2747) Fixes an issue created from #2701 that added `CLUSTERS` to the `gaea.yaml`. commit 11943e36ba12b3df49c51942da780698fab02d38 Author: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> Date: Tue Jul 2 12:58:10 2024 -0400 Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701) This PR sets up the ability on Gaea for auto generation of a clean xml file, i.e., an xml file that does not need any alterations before running rocoto. Refs #2572 Refs #2664 commit de8706702ead0630beb54d868f83aa2cb23f8f79 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon Jul 1 09:29:14 2024 -0400 Update for JCB policies and stage DA job files with Jinja2-templates (#2700) This PR updates the `gdas.cd` hash to bring in new JCB conventions. Resolves #2699 From #2654 This PR will move much of the staging code that take place in the python initialization subroutines of the variational and ensemble DA jobs into Jinja2-templated YAML files to be passed into the wxflow file handler. Much of the staging has already been done this way, but this PR simply expands that strategy. The old Python routines that were doing this staging are now removed. This is part of a broader refactoring of the pygfs tasking. wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a companion to this PR. Co-authored-by: danholdaway <danholdaway@users.noreply.github.com> Co-authored-by: DavidNew-NOAA <david.new@noaa.gov> Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Co-authored-by: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jun 28 14:56:19 2024 -0400 Revert PR 2681 (#2739) This PR: - reverts #2681 in part - keeps some changes for `RUN`. - is a hotfix - should be merged ASAP after consensus w/ @guillaumevernieres @CatherineThomas-NOAA @WalterKolczynski-NOAA commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed Jun 26 15:46:08 2024 -0400 updated Finalize in Jenkinsfile and added try block around scm checkout (#2692) We are updating the Jenkins Pipeline with a try block around checkout to capture errors for the user. Also cleaned up Finalize and added section to clean out workspace on success. commit 968568f682bac7564095440bdb7813abefd76821 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 26 13:27:19 2024 -0400 Activate snow DA test on WCOSS (#2720) Activate the snow DA test on WCOSS. commit 7706760bb8adbdf78cb640b02739023c886e7699 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jun 26 10:02:22 2024 -0400 Cleanup of stale RUNDIRS from an experiment (#2719) This PR: - removes stale temporary scratch run directories from `$DATAROOT/` every 3 days. - should help to scrub failed attempts. - removes an unused variable `RUNDIR` defined in `config.base` commit 8962991691b5f0857b813bddfd28aa1034d4bd2b Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jun 26 09:43:48 2024 -0400 Update logic for MOM6 number of layers/exception values (#2681) Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine how many layers and sets the exception value for MOM6 to be 1e-34 for all scenarios. Note, we will no longer have zeros in the ocean grib output and the DA will also run without issues. Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615 commit 12431f76bdce807067929415007592cffc8a2457 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Jun 26 07:42:35 2024 -0600 Update wave jobs to use COMIN/COMOUT (#2643) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow wave model and products tasks. Refs #2451 commit b902c0bac126c323a07186ad8881384b032b6fda Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jun 25 07:48:46 2024 -0400 Assign machine- and RUN-specific resources (#2672) Redefine resource variables based explicitly on RUN or CDUMP Additionally, machine-specific resources are moved out of config.resources and placed in respective config.resources.{machine} files. Resolves #177 #2672 commit 5edbd123e2878a07f5cce8e3c7ea6147f286633a Merge: 09333c01d 4e1b937b6 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Mon Jun 24 12:44:05 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit 4e1b937b67ed220120e81925c4507f03b9b8965f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jun 24 10:50:52 2024 -0400 Add minimum software requirements (#2712) Adds a table to HPC documentation stating the minimum support versions commit f43a86276aaef91efa28faadc71a3cf50e749efe Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Jun 21 13:44:29 2024 -0400 Fix and simplify online archiving and reenable METplus jobs (#2687) This fixes the online archiving portion of the `*arch` and `*earc00` jobs, a prerequisite for running METplus. This also reenables METplus by default. The approach previously taken created `FileHandler` dictionaries at varying levels within the resulting yaml, which was not properly parsed by `exglobal_archive.py`. This approach creates a single `FileHandler` dictionary and is much less complicated overall. Resolves #2673 #2647 commit 8993b42cb91144c0ab0501dc7841ea8d675c4701 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 19 21:51:22 2024 -0400 Eliminate post groups (#2667) Eliminates the post groups used for upp and products jobs so that each task only processes one forecast hour. This is more efficient and greatly simplifies downstream dependencies that depend on a specific forecast hour. Resolves #2666 Refs #2642 commit 0b810c888239853fedd0e4584fe62536c6aaacdf Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 20:32:48 2024 -0600 Removes misleading "No such file or directory" syntax errors from output files (#2688) This PR addresses issue #1252. The following is accomplished: - Prior to removing files, the existence of a file is checked prior to attempting to remove; this is performed as noted [here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369); this PR only addresses the the `chgrp` issue. Refs #1252 --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 12:17:59 2024 -0600 Hotfix for bug in template names. (#2697) This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/` template. Resolves #2696 Refs #2451 commit 35d4d99eaac669721add9ddcc793153e5ab3b30a Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 08:06:53 2024 -0600 Update archive job to use COMIN/COMOUT (#2668) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow archive task. Refs #2451 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 47b3a581c8257fa24411fb400df8bb0e1e04972a Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Jun 17 22:55:38 2024 -0400 Turn on high-frequency output in extended test (#2679) Turns on high-frequency (hourly) output in the extended products test to exercise that aspect of the code. This test only runs on WCOSS. Also adds the hooks to optionally turn on the metplus jobs, but that is deferred as they are not currently working correctly. commit 38f2df9fb0c074b1f80d3c637080be79be693161 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jun 17 17:12:55 2024 +0000 Optimize wavepostpnt (#2657) Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs This is done by 1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by - performing operations on all files at once instead of looping over each file - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`) - combining `sed` and `grep` calls when possible - adding logic to `awk` calls instead of handling that logic in bash 2) minimizing as much as possible the amount of data on disk that has to be read in (e.g. limiting sed to read only the line numbers it needs) --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 5af325a6a4e0a14d180514a418603ca79fada487 Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Fri Jun 14 18:05:23 2024 -0400 Update GDASapp hash to move JCB into GDASapp (#2665) This PR moves JCB into GDASapp. The PR also bumps up the hash of GDASapp to what is in `feature/move_jcb`, which at time of writing is develop plus the absorption of JCB into GDASapp. Note that I also took the changes from https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the testing @RussTreadon-NOAA has done. commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b Author: Yaping Wang <49168260+ypwang19@users.noreply.github.com> Date: Fri Jun 14 10:18:17 2024 -0500 Add observation preparation job for aerosols DA to workflow (#2624) Add a prepaeroobs job to prepare aerosol obs files for DA. This job does quality control of the VIIRS aerosol raw observations and convert them to ioda format. Resolves #2623 --------- Co-authored-by: ypwang19 <yaping.wang@users.noreply.github.com> Co-authored-by: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Jun 14 11:04:41 2024 -0400 Remove ocean daily files (#2689) This PR removes the ocn_daily files that are produced by the ocean component. These files can be recreated by averaging data that exists in the 6 hour aveaged files if needed. Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675 Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by removing them and making this obsolete) commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jun 13 12:22:03 2024 -0400 Update Jenkinsfile needed a comma commit dc21eac6c3941d7f30803891d91d82f4cc1f8183 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jun 13 11:41:14 2024 -0400 Add Hercules-EMC to the Jenkins configurable parameter list (#2685) This quick-fix PR is to update the Jenkins Pipeline's configurable parameter list to include the **Hercules-EMC** node. This allows Jenkins users to restart Jobs in the controller when no updates have been made. commit ebacebfbe458634b8c80af6a735d6b6d01e4e406 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Thu Jun 13 11:20:24 2024 -0400 Update gdas.cd and gsi_utils hashes (#2641) This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea build for gsi_utils. Resolves #2640 commit 34155fb4767769600a1ff95f0a65e37081addc2a Author: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com> Date: Thu Jun 13 11:18:22 2024 -0400 Add ability to use GEFS replay ICs (#2559) The PR allows the use of ICs from PSL's replay analysis. These replay ICs will be used for GEFS reforecasting and SFS. Two main changes are associated with these updates: (1) replay ICs being valid at 3Z, and (2) the use of warm starts. Resolves #1838 --------- Co-authored-by: Jessica Meixner <Jessica.Meixner@noaa.gov> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Jun 12 19:25:42 2024 -0600 Replace `sleep` with `wait_for_file` (#2586) This PR addresses issue #2444. The following is accomplished: - All `sleep` statements are replaced with `wait_for_file` for the relevant scripts beneath `scripts` and `ush`; - Indentation and shell-norms are updated where applicable. Note: The WAFS scripts are not updated as per @aerorahul direction. Resolves #2444 --------- Co-authored-by: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 12 13:31:55 2024 -0400 Add COM template for JEDI obs (#2678) Adds a COM template to define a path to store obs processed for JEDI. This will allow UFSDA to stop writing to COM_OBS, which should be read-only as it belongs to obsproc in operations. No functional change yet. commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Wed Jun 12 09:06:23 2024 -0600 Link both global-nest fix files and non-nest ones at the same time (#2632) This PR enables linking both global-nest fix files and non-nest ones at the same time and users can run both nesting and non-nesting experiments at the same time without worries about what fix files to be linked. Resolves #2631 commit 61de004d4f9e9edf8a31bb173f2719b46451a36a Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jun 12 11:03:13 2024 -0400 Update ufs-weather-model (#2663) Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack allowing some temporary fixes to be reverted. * removes upp submodule * uses upp from the ufs-weather-model * restores the build and link that were hacked during the Hera Rocky 8 transition to allow for UPP submodule * Removes forecast directories in clean-up Resolves #2617 Resolves #2437 --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Wed Jun 12 01:15:37 2024 -0400 Add ability to process ocean/ice products specific to GEFS (#2561) This PR begins to add the capability to produce GEFSv13 ocean and ice products in the global-workflow according to stakeholder requirements. The following features are added. - An oceanice prod yaml file has been added to address the ocean and ice products specific to GEFSv13. - The rocoto dependencies and config.base for GEFS have also been modified to allow for 24-hour averaged ocean and ice output. - Various scripts have been modified to allow for ocean and ice output frequencies of 24 hours. - `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN` and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`. Refs #1878 commit 6691e7489650e0b738c176fbd096109288dc09b6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 11 21:15:07 2024 -0600 Update cleanup job to use COMIN/COMOUT (#2649) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow clean-up task. Refs #2451 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Jun 11 16:17:25 2024 -0400 Add overwrite to creat experiment in BASH CI (#2676) This is a quick hotfix to the CI BASH driver script adding `--overwrite` to create experiment script to avoid errors from restarting an experiment. commit e7909af8d9e1f34140388a3f8556d8e582c58fe5 Author: emilyhcliu <36091766+emilyhcliu@users.noreply.github.com> Date: Mon Jun 10 15:11:27 2024 -0400 Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py (#2645) This PR proposes updates for the following two scripts: 1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select CRTM cloud optical table based on cloud microphysical scheme indicated by `imp_physics' The default scheme in the GFS forecast model is Thompson scheme (imp_physics = 8). 2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in the script due to increased variables to interplate increments and calculate analysis in the netcdf_io routines in GSI-utils. Here is the related [PR #46 for GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46). --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 9caa51de8fb7be07d2e61775da01937d576964f6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Jun 6 22:15:23 2024 -0600 Update RDHPCS Hera resource for `eupd` task (#2636) As per @wx20jjung, the resource for the `eupd` task have been updated for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job fails. Resolves #2454 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Thu Jun 6 11:49:03 2024 -0400 Parameterize some things in config.atmanl and config.atmensanl (#2661) This PR adds some parameters in config.atmanl and config.atmensanl that can be altered with the defaults.yaml. The motivation is to make these files match those in the GDASApp JJOB tests (example: https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl), so we can just use the Global Workflow config.atmanl and config.atmensanl in the tests rather than custom ones in GDASApp that have to be separately updated every time the ones in the Global Workflow are updated. commit 54ea0b73a07921be5fbb07fe41e976888bd3e549 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Thu Jun 6 01:36:02 2024 -0400 Add links to the ocean insitu obs processing tools (#2644) Add links to the marine bufr to ioda converters for the marine insitu observations. - fixes https://github.com/NOAA-EMC/GDASApp/issues/1106 - waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135 commit 205d0c2b13e2d7755cec75bf8c978ab20d453862 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jun 5 17:31:30 2024 +0000 Update S4 point of contact in docs (#2660) Update the point of contact for global workflow issues on S4. commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed Jun 5 12:50:14 2024 -0400 Enable wcoss2 ufsda build and module load (#2620) This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2. Resolves #2602 Resolves #2579 commit 67b833e0c7bc390865d453588b4609a1a7ede981 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Tue Jun 4 13:33:43 2024 -0400 Update ufs-weather-model (#2646) Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6 This should resolve the issue and allow C768 runs on Hera and allow for CICE to run on WCOSS2 (due to library updates to allow linking). From what I can tell, all updates needed were done by @HenryWinterbottom-NOAA which were updates for CICE Fixes #2490 commit c44d0ac86cfdf78eb87492431bf6d825e8bae637 Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Tue Jun 4 10:29:49 2024 -0400 Update wmo parm files to fix WMO header (#2652) This PR updates wmo parm files to switch WMO header of precipitation type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to instantaneous. Resolves #2566 commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Tue Jun 4 13:55:33 2024 +0000 Add IAU to snow DA (and its test) (#2610) This PR enables IAU for the snow DA which is necessary for GFSv17. A snow analysis is created for the center of the window regardless, and an additional at the beginning of the window is added if IAU is on. The former is needed for UPP and the latter, to initialize the model. The increment is valid throughout the window for 3DVar, so the same increment is added to both forecasts. Additionally, the input file that goes into global_cycle has been updated to be the output of the JEDI snow analysis instead of the forecast (@jiaruidong2017 I recall discussing this, can you confirm this is right or am I mistaken) This PR also makes the CI test for snow DA (and aerosol DA) include IAU rather than without IAU,. --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit c92bf415060750127c9c05a62a1d2851c489551a Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Sat Jun 1 05:11:07 2024 +0000 Archiving cleanup (#2621) 1) Adds a lot of comments to the jinja templates for archiving 2) Rearranges the gdas and enkf templates to a more logical order 3) Fixes a couple of bugs in the enkf archiving of increments and analyses 4) Disables archiving for the half cycle 5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`, instead relying on `DO_FIT2OBS` 6) Updates wxflow to add the option to not allow undefined variables when parsing jinja templates and invokes this feature when running archives Resolves #2612 commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri May 31 04:57:08 2024 -0400 Switch to Rocky 9 built external packages on Hercules (#2608) The workflow was updated to use modules built on Rocky 9, but the external packages (like prepobs) were still pointing to the versions built on CentOS (Orion). This transitions to packages built on Rocky 9. Updating of the tracker package has been deferred until later. As such, the tracker jobs have been disabled by returning immediately if they are on Hercules. Since these jobs are small, resource-wise, it should not meaningfully impact turnover time. commit 4422550c01c9214a2b3b8890bdcc898123ee216a Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Thu May 30 08:05:23 2024 -0600 Add the capability to use slurm reservation nodes (#2627) Add the capability to use slurm reservation nodes Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE Resolves #2626 commit a54153fd9d26126206bc07a1da4e80f50c0c5910 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 29 23:24:07 2024 -0400 Update forecast job to use COMIN/COMOUT (#2622) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the forecast job. Refs #2451 --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit d69a8af95d492982b918670322ed5c41ab074335 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed May 29 21:29:03 2024 -0400 Update to add 1-deg global wave grid (#2619) This PR adds options to use a global 1 deg grid, intended for testing with the SFS application. Requires new fix file changes NOAA-EMC/global-workflow#2618 commit 0b4670ecf83b99b72835c8380573b2bca7cf5324 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed May 29 17:17:21 2024 -0400 Add C384mx025_3DVarAOWCDA yamls (#2625) Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder. commit 2e885d05c64b947f00a3cf055a1277fbfac195c9 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 29 13:00:51 2024 -0400 Script to keep Jenkins Agent persistent from cron (#2634) This "persistent" Java Agent launch script can be ran from a cron job: - Uses Jenkins Remote API to check the status of the Node connection using curl for a given machine. - If it is not connected a new agent is launched for that node. Resolves #2633 commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5 Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Tue May 28 17:17:11 2024 -0400 Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611) Based on users' feedback, this PR do the following: 1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF 2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD, and VOGRD) from "%g m below water surface" to "%g m below sea level" 3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m) Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31 Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Tue May 28 17:16:23 2024 -0400 Add atmensanlfv3inc job (#2592) This PR creates the atmensanlfv3inc job, the ensemble version of atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is #[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3). commit 50c2b8951b29a3c883a778becbf8582f9519eb48 Author: Anil Kumar <108816337+AnilKumar-NOAA@users.noreply.github.com> Date: Tue May 28 13:23:53 2024 -0400 Global-workflow (AR) Generic updates for Gaea C5 (#2515) - Port global-workflow’s build and run capability to Gaea-C5 - Building global-workflow on Gaea-C5 - Setting up experiments with global-workflow on Gaea-C5 --------- Co-authored-by: AnilKumar-NOAA <Anil.Kumar@gaea53.ncrc.gov> Co-authored-by: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> commit b6ca771a0c584cbfcbbf9be739765d5f3815df97 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 24 10:52:45 2024 -0400 Update STMP and PTMP settings in host file for Orion and Hercules (#2614) - Updating STMP and PTMP settings in host file for Orion and Hercules because they are cross mounted. - Also took the opportunity to finally update **SLURM_ACCOUNT** to **HPC_ACCOUT** in CI over rides. - Added a refactor of the `rocotostat.py` tool that is more pythonic and as a execute retry feature because the `rocotostat` utility on Orion has been failing sometimes. commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Tue May 21 23:50:50 2024 -0400 Sea-ice analysis insertion (#2584) Allows cycling and restarting CICE with the sea-ice analysis if the marine DA is switched on. Resolves #2568 Resolves NOAA-EMC/GDASApp#1103 commit 5369a1ff3a3969149fcf32810fad0e50216752b7 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue May 21 22:12:29 2024 +0000 Refactored archiving (#2491) This provides a new pygfs task, archive.py, that provides all of the tools necessary to archive data to the local (`ARCDIR`) and backup (`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to define the file to be archived or tarred to replace the `hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts and make it easier to add new data and explicitly handle optional and required files. For `ATARDIR` archiving, a master jinja template is provided for each `RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2, master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both `enkfgdas` and `enkfgfs` `RUN`s. These templates then include the appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on experiment, cycle, and coupled parameters. Each of these templates corresponds to a single tarball to populate and are tabbed 4 spaces so they are defined within the master `datasets` dictionary. Future developers should not have to make modifications to archive.py unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then only a single `elif` needs to be added to the configure method to specify the master `ATARDIR` template to archive (e.g. `master_gefs.yaml.j2`). If a new component is coming online that needs to be archived to `ATARDIR` (e.g. SNOW), then create a new template for each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`) and reference the template in the appropriate master templates, e.g. `master_gdas.yaml:` ```jinja {% if DO_SNOW %} {% include "gdassnow.yaml.j2" %} {% endif %} ``` A few other issues were addressed along the way: 1. Aerosols have been reenabled. Aerosol forecasts should only be performed during gdas cycles, but analyses can be performed for both gfs and gdas cycles. This was accomplished by setting separate `AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs. 2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`. This prevented restarts from being used for cice-enable experiments. This feature was not tested. 3. Create a temporary fix for the `wgrib` utility. For spack-stack 1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in existing installations. Once complete, this temporary fix should be removed. 4. The number of `earc` jobs has been reduced for lower resolution experiments. Both C48 and C96 experiments will now only have two earc jobs (one for the non-member files to archive and another for the member files). C192 will have up to 3 earc jobs (one non-member, one for members 1-40 and another for members 41-80, if needed). Resolves #2345 Resolves #2318 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 17 12:57:59 2024 -0400 Add remove RUNDIRS step in CI before creating experements (#2607) As had been done in Bash CI we need to remove the RUNDIR in Jenkins before a creating an experiment in the event that case had beem previously ran. commit 09333c01dbafddb2d2fe7e181b479af3cc6d3621 Merge: f7e9f4489 bb930050b Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Thu May 16 14:33:19 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit bb930050b3cd51d28ecba6b231c8675f6d11856c Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu May 16 12:28:30 2024 -0400 Adds jjob and other necessities for marine LETKF task (#2564) Adds jjob, rocoto script, config file, and other necessities for new marine LETKF task. Partially addresses NOAA-EMC/GDASApp#1091 commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu May 16 12:12:06 2024 -0400 Updating CI Machine configs with redundant PTMP (#2605) Quick fix adding PTMP as STMP in Machine configs for CI for completeness commit ef340ff33a6f89adf70838206ba3fd56a953fa7a Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu May 16 11:37:30 2024 -0400 Fix race condition in CI between Orion and Hercules (#2604) Hotfix to solve race conditions in the CI system due to cross-mounted file systems between Orion and Hercules commit e8b17e27f719df280170dc3f5bd9f19917cefaf2 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 15 17:16:30 2024 -0400 Remove existing EXPDIRs and COMROTs when CI is re-run (#2601) Quick hotfix for having default for re-runing jobs to start clean with new EXPDIRs and COMROTs commit b5d113efb1970ede5cd1d3d4dff8d96320519c41 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 15 16:52:49 2024 -0400 Moving logic for skipping hosts in pr cases (#2573) This PR removes the logic of skipping hosts for pr cases from `create_experiment.py` and moves it to a test in the cron bash driver using a `parse_yaml.py` python tool. The Jenkins pipeline was not effected as it uses the `get_host_case_list.py` utility to form the cases on a per host bases. Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed May 15 13:13:30 2024 -0400 Update gsi_utils.fd hash (#2598) This PR updates the `gsi_utils.fd` hash to bring in updates which add safeguards to - `src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90` - `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90` The safeguards are described in GSI-utils PR [#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated issue. Resolves #2597 commit d5366c66bd67f89d118b18956fe230207cbf0aea Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 15 13:12:56 2024 -0400 Update CICE and MOM6 fix versions (#2600) This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions to the newer `20240416` timestamps, which includes updates and fixes to the `100` (1-deg) resolution files. Resolves #2480 Resolves #2483 Resolves #2595 commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon May 13 22:57:38 2024 +0000 Limit gfswavepostpnt to 40 PEs/node (#2588) This fixes the slow runtime of the gfswavepostpnt job on Hercules. The job is very I/O intensive and does not scale well to large nodes, so limit the number of jobs/node to 40. Resolves #2587 commit 4fb7c12c325702a47f27c802a5067efd33d0327c Author: Fanglin Yang <fanglin.yang@noaa.gov> Date: Mon May 13 16:37:51 2024 -0400 Update damping and time-step (#2575) Updates the model to use explicit Rayleigh damping for u/v and implicit damping to w. This improves model stability and allows for longer timesteps. Also unifies the GDAS and GFS to use the same damping. Results from a test at the C1152 resolution (coupled model) can be found at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/ Resolves #2574 Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Lisa Bengtsson <lbengtss@Orion-login-1.HPC.MsState.Edu> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 10 14:17:13 2024 -0400 Do not use BUILT_semphore to force rebuilds when re-run (#2593) Remove the placement of the `BUILT_semaphore` file after the build in the Jenkins Pipeline and force it to rebuild any changes after a PR is re-ran. commit 2346c6161f75ae02369cbf30f30c6150d3e12b66 Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com> Date: Thu May 9 21:17:06 2024 -0500 Migration to Rocky8 spack-stack installations on Jet (#2458) # Description Migrates Global Workflow to Rocky8 spack-stack installations on Jet. Jet has moved from CentOS7 to Rocky8. Resolves #2377 Refs NOAA-EMC/UPP#919 Refs NOAA-EMC/gfs-utils#60 Refs NOAA-EMC/GSI#732 Refs NOAA-EMC/GSI-Monitor#130 Refs NOAA-EMC/GSI-utils#33 commit c7b3973014480a20dd8e24edaeb83a9e9e68159f Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu May 9 11:36:58 2024 -0400 Updates for cold start half cycle, then continuing with IAU for WCDA (#2560) This PR allows us to run C384 S2S with IAU, but starting with the first half-cycle as a cold-start. This will be necessary for cycled testing as we build towards the full system for GFSv17. This updates the copying of the restarts for RUN=gdas for both ocean and ice copying what the atm model is doing. It also reduced the amount of restart files from 4 to 3. Other updates: * Add DOJEDI ocean triggers for archiving certain files update from: @CatherineThomas-NOAA * Adds COPY_FINAL_RESTARTS option to turn on/off copying the last restart file to COM. Defaults to off... * Defines model_start_date_current_cycle & model_start_date_next_cycle to help with knowing which IC to grab. Refs #2546 Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2 Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Wed May 8 20:52:48 2024 -0400 Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477) Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI Configuration Builder (JCB) tool so that YAMLs can be made more portable and invoke the observation chronicle mechanism. Resolves #2476 Co-authored-by: danholdaway <danholdaway@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 8 02:04:16 2024 -0400 Add CI test for products (#2567) Adds a new version of the atm3DVar test that runs the full forecast length and produces most of the secondary products. For now, this test will only run on WCOSS due to gempak failures on other machines as well as computational needs. On other machines, the original version will run (the original version will not run on WCOSS). AWIPS remains off for now in this extended test due to a bug involving tocgrib2 and the convective precip fields (see #2566). The new test runs for 4½ cycles and the full 384-hr forecast length to ensure all gempak scripts are exercised. Since the cycle throttle is 3 and the bulk of the time is in the free forecast, the cycles run mostly concurrently so it doesn't extend the total test time too much beyond that of a single 384-hr forecast. Fixes a bug in NPOESS that was introduced when the post filenames were reverted to the previous format for the GOES products until the final filenames are determined (#2499). Also removes the AWIPS g2 job from the rocoto mesh to complete the retirement of grib1 products. Resolves #2132 Resolves #2445 commit 9b6f8404ac4507d14adc404b77cfdf002b55e832 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue May 7 00:14:36 2024 -0400 Add task to prepare emissions for GEFS (#2562) This PR: - introduces a task to prepare emissions for a forecast into the GEFS application. - adds configuration, j-job, rocoto job, ex-script and the python class for this job - updates GEFS workflow to be able to generate the XML to call this job. - updates the `fcst` and `efcs` job dependencies in the GEFS application to depend on `prep_emissions` if aerosols are turned ON. - provides a placeholder for @bbakernoaa to work on the details for preparing emissions. Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 233c18815d2e8e6b344f161fd0c102a4fbdfb66d Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Mon May 6 18:11:35 2024 -0400 Single Executable for main GDAS JEDI applications (#2565) Changes that accompany GDAS PR (NOAA-EMC/GDASApp/pull/1075) that allows building of a single gdas executable, which should be more compliant with NCO requirements. Addresses https://github.com/NOAA-EMC/GDASApp/issues/1085 commit a005244bbfb2f1c525bca60d966f8095aa1acb8e Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Thu May 2 20:32:53 2024 -0600 Add nest capability (#2545) This PR adds the global nesting capability to the global workflow so that one can run a regional domain nested in a global run. Resolves #2544 Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit cb87daaced9fddd17f8370a1842d7e4ddab24e8f Author: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> Date: Thu May 2 15:30:53 2024 -0400 Update gfs_utils for Gaea (#2556) What: add build capability to the gfs_utils submod within the global workflow on Gaea Refs #2535 Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 707a1cc5124bcd8e006839a17f76ceb88f45f902 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed May 1 18:13:02 2024 -0600 Updated GEMPAK version and APRUN launcher. (#2555) This PR addresses issue #2248 and #2513. The following is accomplished: - Updates the parallel executable for GEMPAK applications; - Updates the GEMPAK version for RDHPCS Hera. Describe your changes. Focus on the *what* and *why*. The *how* will be evident from the changes. In particular, be sure to note any interface changes, such as command line syntax, that will need to be communicated to users. At the end of your description, please be sure to add the issue this PR solves using the word "Resolves". If there are any issues that are related but not yet resolved (including in other repos), you may use "Refs". Resolves #2248 Resolves #2513 Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> commit f151cbf394e998ca0fdae893ca174499468d0c85 Author: Travis Elless <113720457+TravisElless-NOAA@users.noreply.github.com> Date: Wed May 1 11:01:18 2024 -0400 Utilize scale-dependent localization for atmospheric analysis (#2542) The plan for GFSv17 is to use a scale-dependent localization for the atmospheric analysis. This PR adds the necessary parameters to allow this feature to be used by default. commit 53b6764392cb4c0f3b4506ccd3f8cba5c5d2c56e Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Apr 30 16:37:54 2024 -0400 Remove implicit symlink names (#2527) Lustre has a defect under Rocky 9 that results in symlink sometimes failing when the link name is not explicit. This updates all link creation to use explicit names. `config.base` is updated to turn off two monitor jobs on Hercules because the executables are not yet built there. This, combined with the previous change, should make workflow available for use on Hercules. Also removes the redundant utility names for NCP, NLN, etc. in the gdas scripts that are already defined in `config.base`. Resolves #2131 Resolves #2522 commit f7e9f4489fc0b10830f621fdf149e8e3149d6a51 Merge: 67a4810c4 762f040a2 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Tue Apr 30 12:24:48 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit 762f040a2045db17cdacd9026df9c4b8fd520156 Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Mon Apr 29 22:26:28 2024 -0400 Fixes sea ice archiving (#2541) Removes/changes sea ice output files that are failing to be added to list for archiving, causing `gdasarch` to fail in WCDA cycling. Resolves https://github.com/NOAA-EMC/GDASApp/issues/1044 commit 2ecf4f86e0cbe59407ba2c4e105ee7292f1eda01 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon Apr 29 22:25:57 2024 -0400 Link ensemble analysis increment files to COMROOT for warm_start (#2553) Scripting is added to `setup_expt.py` to link ensemble analysis increment files to COMROOT for warm_start experiments. Resolves #2552 commit 3a7abe1d63c573006e0e656237f1220002c3f579 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Apr 30 02:25:28 2024 +0000 Launch Multiple Platforms to Jenkins with polling (#2548) When launching Jenkins CI Tests all requested RDHPCS machines can now be selected via the Ready label at once. This is all that is required sense polling also works now on the controller end. Killing the jobs still needs to be done directly on the Jenkins Controller. Do not try to update the CI process using Labels. It is for launching only. Jenkins will update the labels as the states change. NOTE: When a case fails the label will be update to a **Fail** for that system but will continue to report failures of subsequent cases until otherwise stopped in the Jenkins Controller directly. Do not update any labels to …

- based on gsl_ufs_dev from KaYee's fork global-workflow: 07Aug24,37c53ac [develop_07Aug2024_37c53ac] UFS: 19Jul24, c127601 FV3: 19Jul24, 2527c11 UPP: 23Apr24, be0410e CCPP-PHYSICS: 19Jul24, 46df080 UFS_UTILS: 26Jun24, 3ef2e6b Squashed commit of the following: commit 70b557836379bb7e545fcc6642e28d66cfc17735 Merge: 5edbd123e 37c53ac69 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Wed Aug 7 11:02:24 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 7 08:11:21 2024 -0400 Revert MSU FIX_DIRs back to glopara (#2811) commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Aug 6 14:47:36 2024 -0400 Bugfix for updating label states in Jenkins (#2808) Quick bug fix for updating state labels in CI during finalize. (did not reference GitHub CLI executable correctly in the pipeline script) commit 8fee36f0307b0c08080e3a8fa8fa6703e7da5fce Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Aug 6 11:02:45 2024 -0400 Clean-up temporary rundirs - take 2. (#2753) This PR: - is a follow-up to a previous PR that aggressively pruned run directories. - removes run directories for the current cycle in the clean-up if the cycle is successful. If the cycle is not successful, cleanup is not called and all run directories for the cycle are safe from being purged. - also updates the PR template to list/query for any updates to submodules. --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: David Huber <david.huber@noaa.gov> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit d599fff4aedd41ae587dbe02226acb12ff48efc1 Author: HelinWei-NOAA <48133472+HelinWei-NOAA@users.noreply.github.com> Date: Mon Aug 5 05:31:31 2024 -0400 Change land surface for HR4 (#2787) Resets the default value of opt_diag to 2 corresponding to the land surface upgrades in ufs-weather-model for HR4. Resolves #2786 commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Aug 2 15:41:29 2024 -0400 Run METplus serially and correct the name of prod tasks (#2804) Adds 2 hot fixes: - METplus v9.1.3 has a bug in it that sometimes attempts to create multiple copies of the same directory when running in parallel, causing a Python error and downstream problems. This PR makes METplus run in serial mode, preventing such issues. - Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod) commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri Aug 2 15:03:45 2024 -0400 Update Java Agent launching script for Jenkins connections (#2762) Made updates to the Jenkins Launching Script for robustness and less ambiguous documentation: - Clearer distinction between required user token for the remote api and the systems token for launching - Added pre-checks: `gh` is authenticating, named compliant token and secret file exists - More robust Jason based parser of the remote api response for checking the state of the Node connection - For `cron` use a 5 minute pause and recheck was added before re-launching of the java agent - Added concise header documentation of requirements and purpose --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit b73b1fd203496db97f8067652659573a632bcc67 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Aug 2 07:59:06 2024 -0400 Fix erroneous cdump addition (#2803) commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Aug 1 20:26:13 2024 -0400 Update ocean post-processing triggers (#2784) This PR: - replaces `check_netcdf.sh` checker for ocean post-processing with with ocean output at the next forecast hour or finishing of the forecast job for ocean prod - removes no longer needed `ush/check_netcdf.sh` commit aa2af1ca8d59424a60a1730722bf528775d9e606 Author: GeorgeGayno-NOAA <52789452+GeorgeGayno-NOAA@users.noreply.github.com> Date: Thu Aug 1 16:46:10 2024 -0400 Update the gfs_utils repository hash (#2801) # Description Point to the latest hash of the gfs-utils repository, which contains the bug fix to gaussian_sfcanl. Resolves #2669. Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73 commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Aug 1 08:12:14 2024 -0400 Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791) Changes how METplus jobs run so that they run on the last GFS cycle for a given `PDY`. This is a departure from operations where the METplus jobs run on the 00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through `${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on `${PDY}18` for cycles 00-18. See https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details. commit 1cf8b448af562dbb7af198399c78c585977e81da Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 30 10:38:49 2024 -0400 Simplify resource-related variables, remove CDUMP where unneeded (#2727) This overhauls resource-related variables to use a common set of variables for each job. In the process, this also removed the use of CDUMP in most cases. Resolves #1299 #2693 commit 61875f25c9e971f82ae499b5b612d7f095deebd4 Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Mon Jul 29 14:40:03 2024 -0400 Remove f000 from atmos rocoto tasks for replay cases (#2778) The main purpose of this PR is to remove the f000 from atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater than `0`, it becomes necessary to have the first lead hour set to `OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and the minimum lead time for the ocean_prod rocoto task needs to be 6 (assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up possible by removing 0 from fhrs for atmosphere-related tasks in `gefs_tasks.py` when replaying. This PR also moves where f000 is being removed for the ocean_prod and ice_prod tasks. The if-block that performs this f000 removal has been moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`. --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit f156a7894d639f177e3e2588f98eec1f6f59aa68 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Jul 26 14:18:32 2024 -0500 HR4 GWD update (#2732) This update is a combination of the gravity wave drag (GWD) versions from the NOAA/GSL and NOAA/PSL commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Jul 25 14:26:52 2024 -0400 Temporarily disable METplus jobs (#2796) commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Wed Jul 24 15:00:35 2024 -0400 Refactoring of the marine B-matrix job (#2749) Refactor the functionality of B-matrix generation from the GDASApp Resolves #2743 commit 65a7ab75dc0e4baba06a02e11ed0455787056a68 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 23 08:35:48 2024 -0400 Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775) Removes the namespace-based construction of EnKF member COM directories in the enkf archive template. commit c45b9611f3e701b819bd33dc5af29033f060bb91 Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Tue Jul 23 00:33:16 2024 -0400 Add task to process reforecast variables to save on WCOSS2 (#2680) # Description This PR adds an optional task to the global-workflow to process a subset of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for the GEFSv13 reforecast. This task is designed to process GEFS variables so that specific reforecast product requirements are met. A new variable in `config.base` called `DO_EXTRACTVARS` enables this task, which is currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by default and is specifically a task designed to be executed for the GEFSv13 reforecast. Refs #1878 # Type of change - New feature (adds functionality) # Change characteristics - Is this a breaking change (a change in existing functionality)? NO - Does this change require a documentation update? NO # How has this been tested? This has been cloned and tested on WCOSS2. This will need to be tested on Hera and other platforms on which the reforecast may be running. # Checklist - [ ] Any dependent changes have been merged and published - [x] My code follows the style guidelines of this project - [x] I have performed a self-review of my own code - [ ] I have commented my code, particularly in hard-to-understand areas - [x] My changes generate no new warnings - [x] New and existing tests pass with my changes - [ ] I have made corresponding changes to the documentation if necessary --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 71dc33c6ca991c16ce743760d99feaaf60f2218a Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jul 22 14:51:53 2024 -0400 Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774) Fix metp* resources and check that they completed properly; add support for Orion Rocky 9 commit 56df67a90fe090c425199f1285e5aac722c398b1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jul 22 09:28:18 2024 -0400 Hotfix: Update jcb to avoid git-lfs files (#2782) Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to be cloned on Hera. This hotfix points to a non-authoritative branch of the GDASApp (https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and should be updated ASAP back to the authoritative repository. commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jul 16 09:44:00 2024 -0400 Address issues in creating XML for GFS forecast-only with app S2SWA (#2757) This bugfix PR: - fixes an issue where a user is unable to generate the XML for a GFS forecast-only experiment with APP=S2SWA Specifically, the changes are related to defining `aero_fcst_cdumps`. Following `setup_expt.py`, the user will have to set `AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in `config.base`. commit e0878dba0e53706a7f53429b61aee2936e2c21bf Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Jul 15 10:25:11 2024 -0400 Updated prepobs and fit2obs versions for Orion Rocky9 (#2758) Update prepobs to v1.0.2 and fit2obs to v1.1.2 These versions now support Orion Rocky9. Updates are included for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet. commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jul 11 17:48:47 2024 +0000 CI maintenance updates and adding CI Unit Tests (#2740) This PR has a few maintenance updates to the CI pipeline and adds a test directory with Unit Tests **Major Maintenance updates:** - Added try blocks with appropriate messaging to GitHub PR of failure for: - - **scm** checkout - - build fail (with error logs sent as gists) - - create experiment fails with `stderr` sent to GitHub PR messaging - Pre-stage FAILS from the above are now captured these fails allow FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state labels in GitHub - see image below) **Minor Maintenance updates:** - Fix for STALLED cases reviled from PR 2700 (just needed a lambda specifier) - Fixed path to experiment directory in PR message (had dropped EXPDIR in path) - Needed `latin-1` decoder in reading log files for publishing **Added python Unit Tests for CI functionality:** - Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI utility codes - Cashed the install of Rocoto in the GitHub Runners to greatly reduce stetup time for running the unit tests - Unit Tests Python scripts added - `test_rocostat.py`: rocoto_statcount() rocoto_summary() rocoto_stalled() - `test_setup.py`: setup_expt() test_setup_xml() - `test_create_experment`: test_create_experiment() - - Runs all PR cases that do not have ICs in the GItHub Runner - Reporting mechanism in the Actions tab for Python Unit Testing results - Test case data for STALLED and RUNNING stored on S3 and pulled using wget during runtime of tests commit 5ef4db74649b8be03402c17aa29c024e71699a7b Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu Jul 11 08:59:24 2024 -0400 Adds contents of constructor and initialize methods to marine LETKF class (#2635) Adds contents of constructor and initialize methods to marine LETKF class Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091 --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> commit 8998ec7b74123e953b97a93fa14cc78d471a1aee Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 9 08:31:57 2024 -0400 Fix GDAS group B restart archiving (#2735) Archives the GDAS restartb dataset at a 6-hour offset from restarta This allows cycled experiments to restart from the archives. The tabbing for the master archive templates was also added to improve readability. Resolves #2722 commit 3ca74771255727033b9dc043c652ac585178629c Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Tue Jul 9 08:28:54 2024 -0400 Add fcst dependency to ocnanalprep (#2728) Add previous cycle's `fcst` as a dependency to `ocnanalprep` This ensures that the availability of restart files to the latter. This addresses a seldomly-encountered race condition where `ocnanalprep` fails due to the lack of the files. commit 58fca1668aecd6fb1afd12a441256ad35900e075 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jul 5 15:02:23 2024 -0400 Update (partially) global-workflow for orion+rocky9 (#2741) This PR: - updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils, GFS-utils) to include recent update to their modulefiles for Orion+Rocky9 upgrade - updates the modulefiles in global-workflow to load modules from Orion+Rocky9 paths - updates modulefiles for `gwsetup` and `gwci` as well. - removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not installed. - adds `parm/config.gfs/config.resources.ORION` to address GSI performance degradation after Rocky 9 upgrade. This PR: - does not update the build for UPP. Standalone UPP is not available via ufs-weather-model as of #2729 - will need a follow-up update for `prepobs` and `fit2obs` updated locations when they are installed in `glopara` space on Orion. # Type of change - Maintenance (code refactor, clean-up, new CI test, etc.) # Change characteristics - Is this a breaking change (a change in existing functionality)? NO - Does this change require a documentation update? NO # How has this been tested? This PR is not sufficient for Orion. This PR must be tested on other platforms (Hera, WCOSS2) as this PR updates submodules. # Checklist - [ ] Any dependent changes have been merged and published - [ ] My code follows the style guidelines of this project - [ ] I have performed a self-review of my own code - [ ] I have commented my code, particularly in hard-to-understand areas - [ ] My changes generate no new warnings - [ ] New and existing tests pass with my changes - [ ] I have made corresponding changes to the documentation if necessary --------- Co-authored-by: Kate Friedman <kate.friedman@noaa.gov> commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jul 3 21:07:49 2024 -0400 Update ufs model hash to 20240625 (#2729) Updates UFS weather model hash to hash from 2024-06-24 which has orion porting updates + a few namelist updates. commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jul 3 11:32:40 2024 -0400 Hotfix for undefined CLUSTERS (#2748) Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses the native `dict` `get` method to prevent grabbing an unset entry. commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Wed Jul 3 09:56:08 2024 -0400 Update gempak job to run one fcst hour per task (#2671) This PR updates gempak jobs (gfs, gdas, and goes) from processing all forecast hours at once to one forecast hour at a time. This will reduce the job runtime to less than 5 min, so restart capability is not needed. Resolves #1250 Ref #2666 #2667 --------- Co-authored-by: Walter.Kolczynski <Walter.Kolczynski@noaa.gov> commit 8215ae654202186a4f753c3abe937b7b9b91a9c7 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jul 2 16:22:11 2024 -0400 Hotfix for clusters from #2701 (#2747) Fixes an issue created from #2701 that added `CLUSTERS` to the `gaea.yaml`. commit 11943e36ba12b3df49c51942da780698fab02d38 Author: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> Date: Tue Jul 2 12:58:10 2024 -0400 Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701) This PR sets up the ability on Gaea for auto generation of a clean xml file, i.e., an xml file that does not need any alterations before running rocoto. Refs #2572 Refs #2664 commit de8706702ead0630beb54d868f83aa2cb23f8f79 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon Jul 1 09:29:14 2024 -0400 Update for JCB policies and stage DA job files with Jinja2-templates (#2700) This PR updates the `gdas.cd` hash to bring in new JCB conventions. Resolves #2699 From #2654 This PR will move much of the staging code that take place in the python initialization subroutines of the variational and ensemble DA jobs into Jinja2-templated YAML files to be passed into the wxflow file handler. Much of the staging has already been done this way, but this PR simply expands that strategy. The old Python routines that were doing this staging are now removed. This is part of a broader refactoring of the pygfs tasking. wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a companion to this PR. Co-authored-by: danholdaway <danholdaway@users.noreply.github.com> Co-authored-by: DavidNew-NOAA <david.new@noaa.gov> Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Co-authored-by: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jun 28 14:56:19 2024 -0400 Revert PR 2681 (#2739) This PR: - reverts #2681 in part - keeps some changes for `RUN`. - is a hotfix - should be merged ASAP after consensus w/ @guillaumevernieres @CatherineThomas-NOAA @WalterKolczynski-NOAA commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed Jun 26 15:46:08 2024 -0400 updated Finalize in Jenkinsfile and added try block around scm checkout (#2692) We are updating the Jenkins Pipeline with a try block around checkout to capture errors for the user. Also cleaned up Finalize and added section to clean out workspace on success. commit 968568f682bac7564095440bdb7813abefd76821 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 26 13:27:19 2024 -0400 Activate snow DA test on WCOSS (#2720) Activate the snow DA test on WCOSS. commit 7706760bb8adbdf78cb640b02739023c886e7699 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jun 26 10:02:22 2024 -0400 Cleanup of stale RUNDIRS from an experiment (#2719) This PR: - removes stale temporary scratch run directories from `$DATAROOT/` every 3 days. - should help to scrub failed attempts. - removes an unused variable `RUNDIR` defined in `config.base` commit 8962991691b5f0857b813bddfd28aa1034d4bd2b Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jun 26 09:43:48 2024 -0400 Update logic for MOM6 number of layers/exception values (#2681) Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine how many layers and sets the exception value for MOM6 to be 1e-34 for all scenarios. Note, we will no longer have zeros in the ocean grib output and the DA will also run without issues. Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615 commit 12431f76bdce807067929415007592cffc8a2457 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Jun 26 07:42:35 2024 -0600 Update wave jobs to use COMIN/COMOUT (#2643) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow wave model and products tasks. Refs #2451 commit b902c0bac126c323a07186ad8881384b032b6fda Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jun 25 07:48:46 2024 -0400 Assign machine- and RUN-specific resources (#2672) Redefine resource variables based explicitly on RUN or CDUMP Additionally, machine-specific resources are moved out of config.resources and placed in respective config.resources.{machine} files. Resolves #177 #2672 commit 5edbd123e2878a07f5cce8e3c7ea6147f286633a Merge: 09333c01d 4e1b937b6 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Mon Jun 24 12:44:05 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit 4e1b937b67ed220120e81925c4507f03b9b8965f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jun 24 10:50:52 2024 -0400 Add minimum software requirements (#2712) Adds a table to HPC documentation stating the minimum support versions commit f43a86276aaef91efa28faadc71a3cf50e749efe Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Jun 21 13:44:29 2024 -0400 Fix and simplify online archiving and reenable METplus jobs (#2687) This fixes the online archiving portion of the `*arch` and `*earc00` jobs, a prerequisite for running METplus. This also reenables METplus by default. The approach previously taken created `FileHandler` dictionaries at varying levels within the resulting yaml, which was not properly parsed by `exglobal_archive.py`. This approach creates a single `FileHandler` dictionary and is much less complicated overall. Resolves #2673 #2647 commit 8993b42cb91144c0ab0501dc7841ea8d675c4701 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 19 21:51:22 2024 -0400 Eliminate post groups (#2667) Eliminates the post groups used for upp and products jobs so that each task only processes one forecast hour. This is more efficient and greatly simplifies downstream dependencies that depend on a specific forecast hour. Resolves #2666 Refs #2642 commit 0b810c888239853fedd0e4584fe62536c6aaacdf Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 20:32:48 2024 -0600 Removes misleading "No such file or directory" syntax errors from output files (#2688) This PR addresses issue #1252. The following is accomplished: - Prior to removing files, the existence of a file is checked prior to attempting to remove; this is performed as noted [here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369); this PR only addresses the the `chgrp` issue. Refs #1252 --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 12:17:59 2024 -0600 Hotfix for bug in template names. (#2697) This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/` template. Resolves #2696 Refs #2451 commit 35d4d99eaac669721add9ddcc793153e5ab3b30a Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 08:06:53 2024 -0600 Update archive job to use COMIN/COMOUT (#2668) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow archive task. Refs #2451 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 47b3a581c8257fa24411fb400df8bb0e1e04972a Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Jun 17 22:55:38 2024 -0400 Turn on high-frequency output in extended test (#2679) Turns on high-frequency (hourly) output in the extended products test to exercise that aspect of the code. This test only runs on WCOSS. Also adds the hooks to optionally turn on the metplus jobs, but that is deferred as they are not currently working correctly. commit 38f2df9fb0c074b1f80d3c637080be79be693161 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jun 17 17:12:55 2024 +0000 Optimize wavepostpnt (#2657) Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs This is done by 1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by - performing operations on all files at once instead of looping over each file - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`) - combining `sed` and `grep` calls when possible - adding logic to `awk` calls instead of handling that logic in bash 2) minimizing as much as possible the amount of data on disk that has to be read in (e.g. limiting sed to read only the line numbers it needs) --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 5af325a6a4e0a14d180514a418603ca79fada487 Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Fri Jun 14 18:05:23 2024 -0400 Update GDASapp hash to move JCB into GDASapp (#2665) This PR moves JCB into GDASapp. The PR also bumps up the hash of GDASapp to what is in `feature/move_jcb`, which at time of writing is develop plus the absorption of JCB into GDASapp. Note that I also took the changes from https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the testing @RussTreadon-NOAA has done. commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b Author: Yaping Wang <49168260+ypwang19@users.noreply.github.com> Date: Fri Jun 14 10:18:17 2024 -0500 Add observation preparation job for aerosols DA to workflow (#2624) Add a prepaeroobs job to prepare aerosol obs files for DA. This job does quality control of the VIIRS aerosol raw observations and convert them to ioda format. Resolves #2623 --------- Co-authored-by: ypwang19 <yaping.wang@users.noreply.github.com> Co-authored-by: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Jun 14 11:04:41 2024 -0400 Remove ocean daily files (#2689) This PR removes the ocn_daily files that are produced by the ocean component. These files can be recreated by averaging data that exists in the 6 hour aveaged files if needed. Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675 Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by removing them and making this obsolete) commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jun 13 12:22:03 2024 -0400 Update Jenkinsfile needed a comma commit dc21eac6c3941d7f30803891d91d82f4cc1f8183 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jun 13 11:41:14 2024 -0400 Add Hercules-EMC to the Jenkins configurable parameter list (#2685) This quick-fix PR is to update the Jenkins Pipeline's configurable parameter list to include the **Hercules-EMC** node. This allows Jenkins users to restart Jobs in the controller when no updates have been made. commit ebacebfbe458634b8c80af6a735d6b6d01e4e406 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Thu Jun 13 11:20:24 2024 -0400 Update gdas.cd and gsi_utils hashes (#2641) This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea build for gsi_utils. Resolves #2640 commit 34155fb4767769600a1ff95f0a65e37081addc2a Author: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com> Date: Thu Jun 13 11:18:22 2024 -0400 Add ability to use GEFS replay ICs (#2559) The PR allows the use of ICs from PSL's replay analysis. These replay ICs will be used for GEFS reforecasting and SFS. Two main changes are associated with these updates: (1) replay ICs being valid at 3Z, and (2) the use of warm starts. Resolves #1838 --------- Co-authored-by: Jessica Meixner <Jessica.Meixner@noaa.gov> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Jun 12 19:25:42 2024 -0600 Replace `sleep` with `wait_for_file` (#2586) This PR addresses issue #2444. The following is accomplished: - All `sleep` statements are replaced with `wait_for_file` for the relevant scripts beneath `scripts` and `ush`; - Indentation and shell-norms are updated where applicable. Note: The WAFS scripts are not updated as per @aerorahul direction. Resolves #2444 --------- Co-authored-by: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 12 13:31:55 2024 -0400 Add COM template for JEDI obs (#2678) Adds a COM template to define a path to store obs processed for JEDI. This will allow UFSDA to stop writing to COM_OBS, which should be read-only as it belongs to obsproc in operations. No functional change yet. commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Wed Jun 12 09:06:23 2024 -0600 Link both global-nest fix files and non-nest ones at the same time (#2632) This PR enables linking both global-nest fix files and non-nest ones at the same time and users can run both nesting and non-nesting experiments at the same time without worries about what fix files to be linked. Resolves #2631 commit 61de004d4f9e9edf8a31bb173f2719b46451a36a Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jun 12 11:03:13 2024 -0400 Update ufs-weather-model (#2663) Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack allowing some temporary fixes to be reverted. * removes upp submodule * uses upp from the ufs-weather-model * restores the build and link that were hacked during the Hera Rocky 8 transition to allow for UPP submodule * Removes forecast directories in clean-up Resolves #2617 Resolves #2437 --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Wed Jun 12 01:15:37 2024 -0400 Add ability to process ocean/ice products specific to GEFS (#2561) This PR begins to add the capability to produce GEFSv13 ocean and ice products in the global-workflow according to stakeholder requirements. The following features are added. - An oceanice prod yaml file has been added to address the ocean and ice products specific to GEFSv13. - The rocoto dependencies and config.base for GEFS have also been modified to allow for 24-hour averaged ocean and ice output. - Various scripts have been modified to allow for ocean and ice output frequencies of 24 hours. - `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN` and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`. Refs #1878 commit 6691e7489650e0b738c176fbd096109288dc09b6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 11 21:15:07 2024 -0600 Update cleanup job to use COMIN/COMOUT (#2649) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow clean-up task. Refs #2451 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Jun 11 16:17:25 2024 -0400 Add overwrite to creat experiment in BASH CI (#2676) This is a quick hotfix to the CI BASH driver script adding `--overwrite` to create experiment script to avoid errors from restarting an experiment. commit e7909af8d9e1f34140388a3f8556d8e582c58fe5 Author: emilyhcliu <36091766+emilyhcliu@users.noreply.github.com> Date: Mon Jun 10 15:11:27 2024 -0400 Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py (#2645) This PR proposes updates for the following two scripts: 1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select CRTM cloud optical table based on cloud microphysical scheme indicated by `imp_physics' The default scheme in the GFS forecast model is Thompson scheme (imp_physics = 8). 2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in the script due to increased variables to interplate increments and calculate analysis in the netcdf_io routines in GSI-utils. Here is the related [PR #46 for GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46). --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 9caa51de8fb7be07d2e61775da01937d576964f6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Jun 6 22:15:23 2024 -0600 Update RDHPCS Hera resource for `eupd` task (#2636) As per @wx20jjung, the resource for the `eupd` task have been updated for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job fails. Resolves #2454 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Thu Jun 6 11:49:03 2024 -0400 Parameterize some things in config.atmanl and config.atmensanl (#2661) This PR adds some parameters in config.atmanl and config.atmensanl that can be altered with the defaults.yaml. The motivation is to make these files match those in the GDASApp JJOB tests (example: https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl), so we can just use the Global Workflow config.atmanl and config.atmensanl in the tests rather than custom ones in GDASApp that have to be separately updated every time the ones in the Global Workflow are updated. commit 54ea0b73a07921be5fbb07fe41e976888bd3e549 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Thu Jun 6 01:36:02 2024 -0400 Add links to the ocean insitu obs processing tools (#2644) Add links to the marine bufr to ioda converters for the marine insitu observations. - fixes https://github.com/NOAA-EMC/GDASApp/issues/1106 - waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135 commit 205d0c2b13e2d7755cec75bf8c978ab20d453862 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jun 5 17:31:30 2024 +0000 Update S4 point of contact in docs (#2660) Update the point of contact for global workflow issues on S4. commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed Jun 5 12:50:14 2024 -0400 Enable wcoss2 ufsda build and module load (#2620) This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2. Resolves #2602 Resolves #2579 commit 67b833e0c7bc390865d453588b4609a1a7ede981 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Tue Jun 4 13:33:43 2024 -0400 Update ufs-weather-model (#2646) Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6 This should resolve the issue and allow C768 runs on Hera and allow for CICE to run on WCOSS2 (due to library updates to allow linking). From what I can tell, all updates needed were done by @HenryWinterbottom-NOAA which were updates for CICE Fixes #2490 commit c44d0ac86cfdf78eb87492431bf6d825e8bae637 Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Tue Jun 4 10:29:49 2024 -0400 Update wmo parm files to fix WMO header (#2652) This PR updates wmo parm files to switch WMO header of precipitation type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to instantaneous. Resolves #2566 commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Tue Jun 4 13:55:33 2024 +0000 Add IAU to snow DA (and its test) (#2610) This PR enables IAU for the snow DA which is necessary for GFSv17. A snow analysis is created for the center of the window regardless, and an additional at the beginning of the window is added if IAU is on. The former is needed for UPP and the latter, to initialize the model. The increment is valid throughout the window for 3DVar, so the same increment is added to both forecasts. Additionally, the input file that goes into global_cycle has been updated to be the output of the JEDI snow analysis instead of the forecast (@jiaruidong2017 I recall discussing this, can you confirm this is right or am I mistaken) This PR also makes the CI test for snow DA (and aerosol DA) include IAU rather than without IAU,. --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit c92bf415060750127c9c05a62a1d2851c489551a Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Sat Jun 1 05:11:07 2024 +0000 Archiving cleanup (#2621) 1) Adds a lot of comments to the jinja templates for archiving 2) Rearranges the gdas and enkf templates to a more logical order 3) Fixes a couple of bugs in the enkf archiving of increments and analyses 4) Disables archiving for the half cycle 5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`, instead relying on `DO_FIT2OBS` 6) Updates wxflow to add the option to not allow undefined variables when parsing jinja templates and invokes this feature when running archives Resolves #2612 commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri May 31 04:57:08 2024 -0400 Switch to Rocky 9 built external packages on Hercules (#2608) The workflow was updated to use modules built on Rocky 9, but the external packages (like prepobs) were still pointing to the versions built on CentOS (Orion). This transitions to packages built on Rocky 9. Updating of the tracker package has been deferred until later. As such, the tracker jobs have been disabled by returning immediately if they are on Hercules. Since these jobs are small, resource-wise, it should not meaningfully impact turnover time. commit 4422550c01c9214a2b3b8890bdcc898123ee216a Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Thu May 30 08:05:23 2024 -0600 Add the capability to use slurm reservation nodes (#2627) Add the capability to use slurm reservation nodes Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE Resolves #2626 commit a54153fd9d26126206bc07a1da4e80f50c0c5910 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 29 23:24:07 2024 -0400 Update forecast job to use COMIN/COMOUT (#2622) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the forecast job. Refs #2451 --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit d69a8af95d492982b918670322ed5c41ab074335 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed May 29 21:29:03 2024 -0400 Update to add 1-deg global wave grid (#2619) This PR adds options to use a global 1 deg grid, intended for testing with the SFS application. Requires new fix file changes NOAA-EMC/global-workflow#2618 commit 0b4670ecf83b99b72835c8380573b2bca7cf5324 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed May 29 17:17:21 2024 -0400 Add C384mx025_3DVarAOWCDA yamls (#2625) Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder. commit 2e885d05c64b947f00a3cf055a1277fbfac195c9 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 29 13:00:51 2024 -0400 Script to keep Jenkins Agent persistent from cron (#2634) This "persistent" Java Agent launch script can be ran from a cron job: - Uses Jenkins Remote API to check the status of the Node connection using curl for a given machine. - If it is not connected a new agent is launched for that node. Resolves #2633 commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5 Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Tue May 28 17:17:11 2024 -0400 Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611) Based on users' feedback, this PR do the following: 1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF 2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD, and VOGRD) from "%g m below water surface" to "%g m below sea level" 3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m) Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31 Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Tue May 28 17:16:23 2024 -0400 Add atmensanlfv3inc job (#2592) This PR creates the atmensanlfv3inc job, the ensemble version of atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is #[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3). commit 50c2b8951b29a3c883a778becbf8582f9519eb48 Author: Anil Kumar <108816337+AnilKumar-NOAA@users.noreply.github.com> Date: Tue May 28 13:23:53 2024 -0400 Global-workflow (AR) Generic updates for Gaea C5 (#2515) - Port global-workflow’s build and run capability to Gaea-C5 - Building global-workflow on Gaea-C5 - Setting up experiments with global-workflow on Gaea-C5 --------- Co-authored-by: AnilKumar-NOAA <Anil.Kumar@gaea53.ncrc.gov> Co-authored-by: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> commit b6ca771a0c584cbfcbbf9be739765d5f3815df97 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 24 10:52:45 2024 -0400 Update STMP and PTMP settings in host file for Orion and Hercules (#2614) - Updating STMP and PTMP settings in host file for Orion and Hercules because they are cross mounted. - Also took the opportunity to finally update **SLURM_ACCOUNT** to **HPC_ACCOUT** in CI over rides. - Added a refactor of the `rocotostat.py` tool that is more pythonic and as a execute retry feature because the `rocotostat` utility on Orion has been failing sometimes. commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Tue May 21 23:50:50 2024 -0400 Sea-ice analysis insertion (#2584) Allows cycling and restarting CICE with the sea-ice analysis if the marine DA is switched on. Resolves #2568 Resolves NOAA-EMC/GDASApp#1103 commit 5369a1ff3a3969149fcf32810fad0e50216752b7 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue May 21 22:12:29 2024 +0000 Refactored archiving (#2491) This provides a new pygfs task, archive.py, that provides all of the tools necessary to archive data to the local (`ARCDIR`) and backup (`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to define the file to be archived or tarred to replace the `hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts and make it easier to add new data and explicitly handle optional and required files. For `ATARDIR` archiving, a master jinja template is provided for each `RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2, master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both `enkfgdas` and `enkfgfs` `RUN`s. These templates then include the appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on experiment, cycle, and coupled parameters. Each of these templates corresponds to a single tarball to populate and are tabbed 4 spaces so they are defined within the master `datasets` dictionary. Future developers should not have to make modifications to archive.py unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then only a single `elif` needs to be added to the configure method to specify the master `ATARDIR` template to archive (e.g. `master_gefs.yaml.j2`). If a new component is coming online that needs to be archived to `ATARDIR` (e.g. SNOW), then create a new template for each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`) and reference the template in the appropriate master templates, e.g. `master_gdas.yaml:` ```jinja {% if DO_SNOW %} {% include "gdassnow.yaml.j2" %} {% endif %} ``` A few other issues were addressed along the way: 1. Aerosols have been reenabled. Aerosol forecasts should only be performed during gdas cycles, but analyses can be performed for both gfs and gdas cycles. This was accomplished by setting separate `AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs. 2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`. This prevented restarts from being used for cice-enable experiments. This feature was not tested. 3. Create a temporary fix for the `wgrib` utility. For spack-stack 1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in existing installations. Once complete, this temporary fix should be removed. 4. The number of `earc` jobs has been reduced for lower resolution experiments. Both C48 and C96 experiments will now only have two earc jobs (one for the non-member files to archive and another for the member files). C192 will have up to 3 earc jobs (one non-member, one for members 1-40 and another for members 41-80, if needed). Resolves #2345 Resolves #2318 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 17 12:57:59 2024 -0400 Add remove RUNDIRS step in CI before creating experements (#2607) As had been done in Bash CI we need to remove the RUNDIR in Jenkins before a creating an experiment in the event that case had beem previously ran. commit 09333c01dbafddb2d2fe7e181b479af3cc6d3621 Merge: f7e9f4489 bb930050b Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Thu May 16 14:33:19 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit bb930050b3cd51d28ecba6b231c8675f6d11856c Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu May 16 12:28:30 2024 -0400 Adds jjob and other necessities for marine LETKF task (#2564) Adds jjob, rocoto script, config file, and other necessities for new marine LETKF task. Partially addresses NOAA-EMC/GDASApp#1091 commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu May 16 12:12:06 2024 -0400 Updating CI Machine configs with redundant PTMP (#2605) Quick fix adding PTMP as STMP in Machine configs for CI for completeness commit ef340ff33a6f89adf70838206ba3fd56a953fa7a Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu May 16 11:37:30 2024 -0400 Fix race condition in CI between Orion and Hercules (#2604) Hotfix to solve race conditions in the CI system due to cross-mounted file systems between Orion and Hercules commit e8b17e27f719df280170dc3f5bd9f19917cefaf2 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 15 17:16:30 2024 -0400 Remove existing EXPDIRs and COMROTs when CI is re-run (#2601) Quick hotfix for having default for re-runing jobs to start clean with new EXPDIRs and COMROTs commit b5d113efb1970ede5cd1d3d4dff8d96320519c41 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 15 16:52:49 2024 -0400 Moving logic for skipping hosts in pr cases (#2573) This PR removes the logic of skipping hosts for pr cases from `create_experiment.py` and moves it to a test in the cron bash driver using a `parse_yaml.py` python tool. The Jenkins pipeline was not effected as it uses the `get_host_case_list.py` utility to form the cases on a per host bases. Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed May 15 13:13:30 2024 -0400 Update gsi_utils.fd hash (#2598) This PR updates the `gsi_utils.fd` hash to bring in updates which add safeguards to - `src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90` - `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90` The safeguards are described in GSI-utils PR [#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated issue. Resolves #2597 commit d5366c66bd67f89d118b18956fe230207cbf0aea Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 15 13:12:56 2024 -0400 Update CICE and MOM6 fix versions (#2600) This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions to the newer `20240416` timestamps, which includes updates and fixes to the `100` (1-deg) resolution files. Resolves #2480 Resolves #2483 Resolves #2595 commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon May 13 22:57:38 2024 +0000 Limit gfswavepostpnt to 40 PEs/node (#2588) This fixes the slow runtime of the gfswavepostpnt job on Hercules. The job is very I/O intensive and does not scale well to large nodes, so limit the number of jobs/node to 40. Resolves #2587 commit 4fb7c12c325702a47f27c802a5067efd33d0327c Author: Fanglin Yang <fanglin.yang@noaa.gov> Date: Mon May 13 16:37:51 2024 -0400 Update damping and time-step (#2575) Updates the model to use explicit Rayleigh damping for u/v and implicit damping to w. This improves model stability and allows for longer timesteps. Also unifies the GDAS and GFS to use the same damping. Results from a test at the C1152 resolution (coupled model) can be found at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/ Resolves #2574 Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Lisa Bengtsson <lbengtss@Orion-login-1.HPC.MsState.Edu> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 10 14:17:13 2024 -0400 Do not use BUILT_semphore to force rebuilds when re-run (#2593) Remove the placement of the `BUILT_semaphore` file after the build in the Jenkins Pipeline and force it to rebuild any changes after a PR is re-ran. commit 2346c6161f75ae02369cbf30f30c6150d3e12b66 Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com> Date: Thu May 9 21:17:06 2024 -0500 Migration to Rocky8 spack-stack installations on Jet (#2458) # Description Migrates Global Workflow to Rocky8 spack-stack installations on Jet. Jet has moved from CentOS7 to Rocky8. Resolves #2377 Refs NOAA-EMC/UPP#919 Refs NOAA-EMC/gfs-utils#60 Refs NOAA-EMC/GSI#732 Refs NOAA-EMC/GSI-Monitor#130 Refs NOAA-EMC/GSI-utils#33 commit c7b3973014480a20dd8e24edaeb83a9e9e68159f Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu May 9 11:36:58 2024 -0400 Updates for cold start half cycle, then continuing with IAU for WCDA (#2560) This PR allows us to run C384 S2S with IAU, but starting with the first half-cycle as a cold-start. This will be necessary for cycled testing as we build towards the full system for GFSv17. This updates the copying of the restarts for RUN=gdas for both ocean and ice copying what the atm model is doing. It also reduced the amount of restart files from 4 to 3. Other updates: * Add DOJEDI ocean triggers for archiving certain files update from: @CatherineThomas-NOAA * Adds COPY_FINAL_RESTARTS option to turn on/off copying the last restart file to COM. Defaults to off... * Defines model_start_date_current_cycle & model_start_date_next_cycle to help with knowing which IC to grab. Refs #2546 Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2 Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Wed May 8 20:52:48 2024 -0400 Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477) Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI Configuration Builder (JCB) tool so that YAMLs can be made more portable and invoke the observation chronicle mechanism. Resolves #2476 Co-authored-by: danholdaway <danholdaway@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 8 02:04:16 2024 -0400 Add CI test for products (#2567) Adds a new version of the atm3DVar test that runs the full forecast length and produces most of the secondary products. For now, this test will only run on WCOSS due to gempak failures on other machines as well as computational needs. On other machines, the original version will run (the original version will not run on WCOSS). AWIPS remains off for now in this extended test due to a bug involving tocgrib2 and the convective precip fields (see #2566). The new test runs for 4½ cycles and the full 384-hr forecast length to ensure all gempak scripts are exercised. Since the cycle throttle is 3 and the bulk of the time is in the free forecast, the cycles run mostly concurrently so it doesn't extend the total test time too much beyond that of a single 384-hr forecast. Fixes a bug in NPOESS that was introduced when the post filenames were reverted to the previous format for the GOES products until the final filenames are determined (#2499). Also removes the AWIPS g2 job from the rocoto mesh to complete the retirement of grib1 products. Resolves #2132 Resolves #2445 commit 9b6f8404ac4507d14adc404b77cfdf002b55e832 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue May 7 00:14:36 2024 -0400 Add task to prepare emissions for GEFS (#2562) This PR: - introduces a task to prepare emissions for a forecast into the GEFS application. - adds configuration, j-job, rocoto job, ex-script and the python class for this job - updates GEFS workflow to be able to generate the XML to call this job. - updates the `fcst` and `efcs` job dependencies in the GEFS application to depend on `prep_emissions` if aerosols are turned ON. - provides a placeholder for @bbakernoaa to work on the details for preparing emissions. Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 233c18815d2e8e6b344f161fd0c102a4fbdfb66d Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Mon May 6 18:11:35 2024 -0400 Single Executable for main GDAS JEDI applications (#2565) Changes that accompany GDAS PR (NOAA-EMC/GDASApp/pull/1075) that allows building of a single gdas executable, which should be more compliant with NCO requirements. Addresses https://github.com/NOAA-EMC/GDASApp/issues/1085 commit a005244bbfb2f1c525bca60d966f8095aa1acb8e Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Thu May 2 20:32:53 2024 -0600 Add nest capability (#2545) This PR adds the global nesting capability to the global workflow so that one can run a regional domain nested in a global run. Resolves #2544 Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit cb87daaced9fddd17f8370a1842d7e4ddab24e8f Author: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> Date: Thu May 2 15:30:53 2024 -0400 Update gfs_utils for Gaea (#2556) What: add build capability to the gfs_utils submod within the global workflow on Gaea Refs #2535 Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 707a1cc5124bcd8e006839a17f76ceb88f45f902 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed May 1 18:13:02 2024 -0600 Updated GEMPAK version and APRUN launcher. (#2555) This PR addresses issue #2248 and #2513. The following is accomplished: - Updates the parallel executable for GEMPAK applications; - Updates the GEMPAK version for RDHPCS Hera. Describe your changes. Focus on the *what* and *why*. The *how* will be evident from the changes. In particular, be sure to note any interface changes, such as command line syntax, that will need to be communicated to users. At the end of your description, please be sure to add the issue this PR solves using the word "Resolves". If there are any issues that are related but not yet resolved (including in other repos), you may use "Refs". Resolves #2248 Resolves #2513 Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> commit f151cbf394e998ca0fdae893ca174499468d0c85 Author: Travis Elless <113720457+TravisElless-NOAA@users.noreply.github.com> Date: Wed May 1 11:01:18 2024 -0400 Utilize scale-dependent localization for atmospheric analysis (#2542) The plan for GFSv17 is to use a scale-dependent localization for the atmospheric analysis. This PR adds the necessary parameters to allow this feature to be used by default. commit 53b6764392cb4c0f3b4506ccd3f8cba5c5d2c56e Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Apr 30 16:37:54 2024 -0400 Remove implicit symlink names (#2527) Lustre has a defect under Rocky 9 that results in symlink sometimes failing when the link name is not explicit. This updates all link creation to use explicit names. `config.base` is updated to turn off two monitor jobs on Hercules because the executables are not yet built there. This, combined with the previous change, should make workflow available for use on Hercules. Also removes the redundant utility names for NCP, NLN, etc. in the gdas scripts that are already defined in `config.base`. Resolves #2131 Resolves #2522 commit f7e9f4489fc0b10830f621fdf149e8e3149d6a51 Merge: 67a4810c4 762f040a2 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Tue Apr 30 12:24:48 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit 762f040a2045db17cdacd9026df9c4b8fd520156 Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Mon Apr 29 22:26:28 2024 -0400 Fixes sea ice archiving (#2541) Removes/changes sea ice output files that are failing to be added to list for archiving, causing `gdasarch` to fail in WCDA cycling. Resolves https://github.com/NOAA-EMC/GDASApp/issues/1044 commit 2ecf4f86e0cbe59407ba2c4e105ee7292f1eda01 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon Apr 29 22:25:57 2024 -0400 Link ensemble analysis increment files to COMROOT for warm_start (#2553) Scripting is added to `setup_expt.py` to link ensemble analysis increment files to COMROOT for warm_start experiments. Resolves #2552 commit 3a7abe1d63c573006e0e656237f1220002c3f579 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Apr 30 02:25:28 2024 +0000 Launch Multiple Platforms to Jenkins with polling (#2548) When launching Jenkins CI Tests all requested RDHPCS machines can now be selected via the Ready label at once. This is all that is required sense polling also works now on the controller end. Killing the jobs still needs to be done directly on the Jenkins Controller. Do not try to update the CI process using Labels. It is for launching only. Jenkins will update the labels as the states change. NOTE: When a case fails the label will be update to a **Fail** for that system but will continue to report failures of subsequent cases until otherwise stopped in the Jenkins Controller directly. Do not update any labels…

Squashed commit of the following: commit 4e0a81f7acf5ccba5de8d3bdf7ab19cae80812cb Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 18:37:50 2024 +0000 Fix typos/links/dependancy. commit d5fdcbf8d6e987dbdfcd6b4da34d0934c8d82c3b Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 07:37:52 2024 +0000 Fixed missing config.base files. commit c6239f925369b20fd8488e8537969e2f4f9e7725 Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 06:53:47 2024 +0000 Update submodule hashs. commit 32bf790f67b818ff50a7f6b74388fb81ed175b3a Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 06:09:41 2024 +0000 Update develop branch, gsl_ufs_dev - based on gsl_ufs_dev from KaYee's fork global-workflow: 07Aug24,37c53ac [develop_07Aug2024_37c53ac] UFS: 19Jul24, c127601 FV3: 19Jul24, 2527c11 UPP: 23Apr24, be0410e CCPP-PHYSICS: 19Jul24, 46df080 UFS_UTILS: 26Jun24, 3ef2e6b Squashed commit of the following: commit 70b557836379bb7e545fcc6642e28d66cfc17735 Merge: 5edbd123e 37c53ac69 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Wed Aug 7 11:02:24 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 7 08:11:21 2024 -0400 Revert MSU FIX_DIRs back to glopara (#2811) commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Aug 6 14:47:36 2024 -0400 Bugfix for updating label states in Jenkins (#2808) Quick bug fix for updating state labels in CI during finalize. (did not reference GitHub CLI executable correctly in the pipeline script) commit 8fee36f0307b0c08080e3a8fa8fa6703e7da5fce Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Aug 6 11:02:45 2024 -0400 Clean-up temporary rundirs - take 2. (#2753) This PR: - is a follow-up to a previous PR that aggressively pruned run directories. - removes run directories for the current cycle in the clean-up if the cycle is successful. If the cycle is not successful, cleanup is not called and all run directories for the cycle are safe from being purged. - also updates the PR template to list/query for any updates to submodules. --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: David Huber <david.huber@noaa.gov> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit d599fff4aedd41ae587dbe02226acb12ff48efc1 Author: HelinWei-NOAA <48133472+HelinWei-NOAA@users.noreply.github.com> Date: Mon Aug 5 05:31:31 2024 -0400 Change land surface for HR4 (#2787) Resets the default value of opt_diag to 2 corresponding to the land surface upgrades in ufs-weather-model for HR4. Resolves #2786 commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Aug 2 15:41:29 2024 -0400 Run METplus serially and correct the name of prod tasks (#2804) Adds 2 hot fixes: - METplus v9.1.3 has a bug in it that sometimes attempts to create multiple copies of the same directory when running in parallel, causing a Python error and downstream problems. This PR makes METplus run in serial mode, preventing such issues. - Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod) commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri Aug 2 15:03:45 2024 -0400 Update Java Agent launching script for Jenkins connections (#2762) Made updates to the Jenkins Launching Script for robustness and less ambiguous documentation: - Clearer distinction between required user token for the remote api and the systems token for launching - Added pre-checks: `gh` is authenticating, named compliant token and secret file exists - More robust Jason based parser of the remote api response for checking the state of the Node connection - For `cron` use a 5 minute pause and recheck was added before re-launching of the java agent - Added concise header documentation of requirements and purpose --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit b73b1fd203496db97f8067652659573a632bcc67 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Aug 2 07:59:06 2024 -0400 Fix erroneous cdump addition (#2803) commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Aug 1 20:26:13 2024 -0400 Update ocean post-processing triggers (#2784) This PR: - replaces `check_netcdf.sh` checker for ocean post-processing with with ocean output at the next forecast hour or finishing of the forecast job for ocean prod - removes no longer needed `ush/check_netcdf.sh` commit aa2af1ca8d59424a60a1730722bf528775d9e606 Author: GeorgeGayno-NOAA <52789452+GeorgeGayno-NOAA@users.noreply.github.com> Date: Thu Aug 1 16:46:10 2024 -0400 Update the gfs_utils repository hash (#2801) # Description Point to the latest hash of the gfs-utils repository, which contains the bug fix to gaussian_sfcanl. Resolves #2669. Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73 commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Aug 1 08:12:14 2024 -0400 Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791) Changes how METplus jobs run so that they run on the last GFS cycle for a given `PDY`. This is a departure from operations where the METplus jobs run on the 00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through `${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on `${PDY}18` for cycles 00-18. See https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details. commit 1cf8b448af562dbb7af198399c78c585977e81da Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 30 10:38:49 2024 -0400 Simplify resource-related variables, remove CDUMP where unneeded (#2727) This overhauls resource-related variables to use a common set of variables for each job. In the process, this also removed the use of CDUMP in most cases. Resolves #1299 #2693 commit 61875f25c9e971f82ae499b5b612d7f095deebd4 Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Mon Jul 29 14:40:03 2024 -0400 Remove f000 from atmos rocoto tasks for replay cases (#2778) The main purpose of this PR is to remove the f000 from atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater than `0`, it becomes necessary to have the first lead hour set to `OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and the minimum lead time for the ocean_prod rocoto task needs to be 6 (assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up possible by removing 0 from fhrs for atmosphere-related tasks in `gefs_tasks.py` when replaying. This PR also moves where f000 is being removed for the ocean_prod and ice_prod tasks. The if-block that performs this f000 removal has been moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`. --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit f156a7894d639f177e3e2588f98eec1f6f59aa68 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Jul 26 14:18:32 2024 -0500 HR4 GWD update (#2732) This update is a combination of the gravity wave drag (GWD) versions from the NOAA/GSL and NOAA/PSL commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Jul 25 14:26:52 2024 -0400 Temporarily disable METplus jobs (#2796) commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Wed Jul 24 15:00:35 2024 -0400 Refactoring of the marine B-matrix job (#2749) Refactor the functionality of B-matrix generation from the GDASApp Resolves #2743 commit 65a7ab75dc0e4baba06a02e11ed0455787056a68 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 23 08:35:48 2024 -0400 Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775) Removes the namespace-based construction of EnKF member COM directories in the enkf archive template. commit c45b9611f3e701b819bd33dc5af29033f060bb91 Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Tue Jul 23 00:33:16 2024 -0400 Add task to process reforecast variables to save on WCOSS2 (#2680) # Description This PR adds an optional task to the global-workflow to process a subset of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for the GEFSv13 reforecast. This task is designed to process GEFS variables so that specific reforecast product requirements are met. A new variable in `config.base` called `DO_EXTRACTVARS` enables this task, which is currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by default and is specifically a task designed to be executed for the GEFSv13 reforecast. Refs #1878 # Type of change - New feature (adds functionality) # Change characteristics - Is this a breaking change (a change in existing functionality)? NO - Does this change require a documentation update? NO # How has this been tested? This has been cloned and tested on WCOSS2. This will need to be tested on Hera and other platforms on which the reforecast may be running. # Checklist - [ ] Any dependent changes have been merged and published - [x] My code follows the style guidelines of this project - [x] I have performed a self-review of my own code - [ ] I have commented my code, particularly in hard-to-understand areas - [x] My changes generate no new warnings - [x] New and existing tests pass with my changes - [ ] I have made corresponding changes to the documentation if necessary --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 71dc33c6ca991c16ce743760d99feaaf60f2218a Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jul 22 14:51:53 2024 -0400 Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774) Fix metp* resources and check that they completed properly; add support for Orion Rocky 9 commit 56df67a90fe090c425199f1285e5aac722c398b1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jul 22 09:28:18 2024 -0400 Hotfix: Update jcb to avoid git-lfs files (#2782) Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to be cloned on Hera. This hotfix points to a non-authoritative branch of the GDASApp (https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and should be updated ASAP back to the authoritative repository. commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jul 16 09:44:00 2024 -0400 Address issues in creating XML for GFS forecast-only with app S2SWA (#2757) This bugfix PR: - fixes an issue where a user is unable to generate the XML for a GFS forecast-only experiment with APP=S2SWA Specifically, the changes are related to defining `aero_fcst_cdumps`. Following `setup_expt.py`, the user will have to set `AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in `config.base`. commit e0878dba0e53706a7f53429b61aee2936e2c21bf Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Jul 15 10:25:11 2024 -0400 Updated prepobs and fit2obs versions for Orion Rocky9 (#2758) Update prepobs to v1.0.2 and fit2obs to v1.1.2 These versions now support Orion Rocky9. Updates are included for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet. commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jul 11 17:48:47 2024 +0000 CI maintenance updates and adding CI Unit Tests (#2740) This PR has a few maintenance updates to the CI pipeline and adds a test directory with Unit Tests **Major Maintenance updates:** - Added try blocks with appropriate messaging to GitHub PR of failure for: - - **scm** checkout - - build fail (with error logs sent as gists) - - create experiment fails with `stderr` sent to GitHub PR messaging - Pre-stage FAILS from the above are now captured these fails allow FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state labels in GitHub - see image below) **Minor Maintenance updates:** - Fix for STALLED cases reviled from PR 2700 (just needed a lambda specifier) - Fixed path to experiment directory in PR message (had dropped EXPDIR in path) - Needed `latin-1` decoder in reading log files for publishing **Added python Unit Tests for CI functionality:** - Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI utility codes - Cashed the install of Rocoto in the GitHub Runners to greatly reduce stetup time for running the unit tests - Unit Tests Python scripts added - `test_rocostat.py`: rocoto_statcount() rocoto_summary() rocoto_stalled() - `test_setup.py`: setup_expt() test_setup_xml() - `test_create_experment`: test_create_experiment() - - Runs all PR cases that do not have ICs in the GItHub Runner - Reporting mechanism in the Actions tab for Python Unit Testing results - Test case data for STALLED and RUNNING stored on S3 and pulled using wget during runtime of tests commit 5ef4db74649b8be03402c17aa29c024e71699a7b Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu Jul 11 08:59:24 2024 -0400 Adds contents of constructor and initialize methods to marine LETKF class (#2635) Adds contents of constructor and initialize methods to marine LETKF class Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091 --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> commit 8998ec7b74123e953b97a93fa14cc78d471a1aee Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 9 08:31:57 2024 -0400 Fix GDAS group B restart archiving (#2735) Archives the GDAS restartb dataset at a 6-hour offset from restarta This allows cycled experiments to restart from the archives. The tabbing for the master archive templates was also added to improve readability. Resolves #2722 commit 3ca74771255727033b9dc043c652ac585178629c Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Tue Jul 9 08:28:54 2024 -0400 Add fcst dependency to ocnanalprep (#2728) Add previous cycle's `fcst` as a dependency to `ocnanalprep` This ensures that the availability of restart files to the latter. This addresses a seldomly-encountered race condition where `ocnanalprep` fails due to the lack of the files. commit 58fca1668aecd6fb1afd12a441256ad35900e075 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jul 5 15:02:23 2024 -0400 Update (partially) global-workflow for orion+rocky9 (#2741) This PR: - updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils, GFS-utils) to include recent update to their modulefiles for Orion+Rocky9 upgrade - updates the modulefiles in global-workflow to load modules from Orion+Rocky9 paths - updates modulefiles for `gwsetup` and `gwci` as well. - removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not installed. - adds `parm/config.gfs/config.resources.ORION` to address GSI performance degradation after Rocky 9 upgrade. This PR: - does not update the build for UPP. Standalone UPP is not available via ufs-weather-model as of #2729 - will need a follow-up update for `prepobs` and `fit2obs` updated locations when they are installed in `glopara` space on Orion. # Type of change - Maintenance (code refactor, clean-up, new CI test, etc.) # Change characteristics - Is this a breaking change (a change in existing functionality)? NO - Does this change require a documentation update? NO # How has this been tested? This PR is not sufficient for Orion. This PR must be tested on other platforms (Hera, WCOSS2) as this PR updates submodules. # Checklist - [ ] Any dependent changes have been merged and published - [ ] My code follows the style guidelines of this project - [ ] I have performed a self-review of my own code - [ ] I have commented my code, particularly in hard-to-understand areas - [ ] My changes generate no new warnings - [ ] New and existing tests pass with my changes - [ ] I have made corresponding changes to the documentation if necessary --------- Co-authored-by: Kate Friedman <kate.friedman@noaa.gov> commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jul 3 21:07:49 2024 -0400 Update ufs model hash to 20240625 (#2729) Updates UFS weather model hash to hash from 2024-06-24 which has orion porting updates + a few namelist updates. commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jul 3 11:32:40 2024 -0400 Hotfix for undefined CLUSTERS (#2748) Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses the native `dict` `get` method to prevent grabbing an unset entry. commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Wed Jul 3 09:56:08 2024 -0400 Update gempak job to run one fcst hour per task (#2671) This PR updates gempak jobs (gfs, gdas, and goes) from processing all forecast hours at once to one forecast hour at a time. This will reduce the job runtime to less than 5 min, so restart capability is not needed. Resolves #1250 Ref #2666 #2667 --------- Co-authored-by: Walter.Kolczynski <Walter.Kolczynski@noaa.gov> commit 8215ae654202186a4f753c3abe937b7b9b91a9c7 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jul 2 16:22:11 2024 -0400 Hotfix for clusters from #2701 (#2747) Fixes an issue created from #2701 that added `CLUSTERS` to the `gaea.yaml`. commit 11943e36ba12b3df49c51942da780698fab02d38 Author: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> Date: Tue Jul 2 12:58:10 2024 -0400 Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701) This PR sets up the ability on Gaea for auto generation of a clean xml file, i.e., an xml file that does not need any alterations before running rocoto. Refs #2572 Refs #2664 commit de8706702ead0630beb54d868f83aa2cb23f8f79 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon Jul 1 09:29:14 2024 -0400 Update for JCB policies and stage DA job files with Jinja2-templates (#2700) This PR updates the `gdas.cd` hash to bring in new JCB conventions. Resolves #2699 From #2654 This PR will move much of the staging code that take place in the python initialization subroutines of the variational and ensemble DA jobs into Jinja2-templated YAML files to be passed into the wxflow file handler. Much of the staging has already been done this way, but this PR simply expands that strategy. The old Python routines that were doing this staging are now removed. This is part of a broader refactoring of the pygfs tasking. wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a companion to this PR. Co-authored-by: danholdaway <danholdaway@users.noreply.github.com> Co-authored-by: DavidNew-NOAA <david.new@noaa.gov> Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Co-authored-by: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jun 28 14:56:19 2024 -0400 Revert PR 2681 (#2739) This PR: - reverts #2681 in part - keeps some changes for `RUN`. - is a hotfix - should be merged ASAP after consensus w/ @guillaumevernieres @CatherineThomas-NOAA @WalterKolczynski-NOAA commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed Jun 26 15:46:08 2024 -0400 updated Finalize in Jenkinsfile and added try block around scm checkout (#2692) We are updating the Jenkins Pipeline with a try block around checkout to capture errors for the user. Also cleaned up Finalize and added section to clean out workspace on success. commit 968568f682bac7564095440bdb7813abefd76821 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 26 13:27:19 2024 -0400 Activate snow DA test on WCOSS (#2720) Activate the snow DA test on WCOSS. commit 7706760bb8adbdf78cb640b02739023c886e7699 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jun 26 10:02:22 2024 -0400 Cleanup of stale RUNDIRS from an experiment (#2719) This PR: - removes stale temporary scratch run directories from `$DATAROOT/` every 3 days. - should help to scrub failed attempts. - removes an unused variable `RUNDIR` defined in `config.base` commit 8962991691b5f0857b813bddfd28aa1034d4bd2b Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jun 26 09:43:48 2024 -0400 Update logic for MOM6 number of layers/exception values (#2681) Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine how many layers and sets the exception value for MOM6 to be 1e-34 for all scenarios. Note, we will no longer have zeros in the ocean grib output and the DA will also run without issues. Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615 commit 12431f76bdce807067929415007592cffc8a2457 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Jun 26 07:42:35 2024 -0600 Update wave jobs to use COMIN/COMOUT (#2643) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow wave model and products tasks. Refs #2451 commit b902c0bac126c323a07186ad8881384b032b6fda Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jun 25 07:48:46 2024 -0400 Assign machine- and RUN-specific resources (#2672) Redefine resource variables based explicitly on RUN or CDUMP Additionally, machine-specific resources are moved out of config.resources and placed in respective config.resources.{machine} files. Resolves #177 #2672 commit 5edbd123e2878a07f5cce8e3c7ea6147f286633a Merge: 09333c01d 4e1b937b6 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Mon Jun 24 12:44:05 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit 4e1b937b67ed220120e81925c4507f03b9b8965f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jun 24 10:50:52 2024 -0400 Add minimum software requirements (#2712) Adds a table to HPC documentation stating the minimum support versions commit f43a86276aaef91efa28faadc71a3cf50e749efe Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Jun 21 13:44:29 2024 -0400 Fix and simplify online archiving and reenable METplus jobs (#2687) This fixes the online archiving portion of the `*arch` and `*earc00` jobs, a prerequisite for running METplus. This also reenables METplus by default. The approach previously taken created `FileHandler` dictionaries at varying levels within the resulting yaml, which was not properly parsed by `exglobal_archive.py`. This approach creates a single `FileHandler` dictionary and is much less complicated overall. Resolves #2673 #2647 commit 8993b42cb91144c0ab0501dc7841ea8d675c4701 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 19 21:51:22 2024 -0400 Eliminate post groups (#2667) Eliminates the post groups used for upp and products jobs so that each task only processes one forecast hour. This is more efficient and greatly simplifies downstream dependencies that depend on a specific forecast hour. Resolves #2666 Refs #2642 commit 0b810c888239853fedd0e4584fe62536c6aaacdf Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 20:32:48 2024 -0600 Removes misleading "No such file or directory" syntax errors from output files (#2688) This PR addresses issue #1252. The following is accomplished: - Prior to removing files, the existence of a file is checked prior to attempting to remove; this is performed as noted [here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369); this PR only addresses the the `chgrp` issue. Refs #1252 --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 12:17:59 2024 -0600 Hotfix for bug in template names. (#2697) This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/` template. Resolves #2696 Refs #2451 commit 35d4d99eaac669721add9ddcc793153e5ab3b30a Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 08:06:53 2024 -0600 Update archive job to use COMIN/COMOUT (#2668) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow archive task. Refs #2451 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 47b3a581c8257fa24411fb400df8bb0e1e04972a Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Jun 17 22:55:38 2024 -0400 Turn on high-frequency output in extended test (#2679) Turns on high-frequency (hourly) output in the extended products test to exercise that aspect of the code. This test only runs on WCOSS. Also adds the hooks to optionally turn on the metplus jobs, but that is deferred as they are not currently working correctly. commit 38f2df9fb0c074b1f80d3c637080be79be693161 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jun 17 17:12:55 2024 +0000 Optimize wavepostpnt (#2657) Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs This is done by 1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by - performing operations on all files at once instead of looping over each file - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`) - combining `sed` and `grep` calls when possible - adding logic to `awk` calls instead of handling that logic in bash 2) minimizing as much as possible the amount of data on disk that has to be read in (e.g. limiting sed to read only the line numbers it needs) --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 5af325a6a4e0a14d180514a418603ca79fada487 Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Fri Jun 14 18:05:23 2024 -0400 Update GDASapp hash to move JCB into GDASapp (#2665) This PR moves JCB into GDASapp. The PR also bumps up the hash of GDASapp to what is in `feature/move_jcb`, which at time of writing is develop plus the absorption of JCB into GDASapp. Note that I also took the changes from https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the testing @RussTreadon-NOAA has done. commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b Author: Yaping Wang <49168260+ypwang19@users.noreply.github.com> Date: Fri Jun 14 10:18:17 2024 -0500 Add observation preparation job for aerosols DA to workflow (#2624) Add a prepaeroobs job to prepare aerosol obs files for DA. This job does quality control of the VIIRS aerosol raw observations and convert them to ioda format. Resolves #2623 --------- Co-authored-by: ypwang19 <yaping.wang@users.noreply.github.com> Co-authored-by: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Jun 14 11:04:41 2024 -0400 Remove ocean daily files (#2689) This PR removes the ocn_daily files that are produced by the ocean component. These files can be recreated by averaging data that exists in the 6 hour aveaged files if needed. Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675 Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by removing them and making this obsolete) commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jun 13 12:22:03 2024 -0400 Update Jenkinsfile needed a comma commit dc21eac6c3941d7f30803891d91d82f4cc1f8183 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jun 13 11:41:14 2024 -0400 Add Hercules-EMC to the Jenkins configurable parameter list (#2685) This quick-fix PR is to update the Jenkins Pipeline's configurable parameter list to include the **Hercules-EMC** node. This allows Jenkins users to restart Jobs in the controller when no updates have been made. commit ebacebfbe458634b8c80af6a735d6b6d01e4e406 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Thu Jun 13 11:20:24 2024 -0400 Update gdas.cd and gsi_utils hashes (#2641) This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea build for gsi_utils. Resolves #2640 commit 34155fb4767769600a1ff95f0a65e37081addc2a Author: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com> Date: Thu Jun 13 11:18:22 2024 -0400 Add ability to use GEFS replay ICs (#2559) The PR allows the use of ICs from PSL's replay analysis. These replay ICs will be used for GEFS reforecasting and SFS. Two main changes are associated with these updates: (1) replay ICs being valid at 3Z, and (2) the use of warm starts. Resolves #1838 --------- Co-authored-by: Jessica Meixner <Jessica.Meixner@noaa.gov> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Jun 12 19:25:42 2024 -0600 Replace `sleep` with `wait_for_file` (#2586) This PR addresses issue #2444. The following is accomplished: - All `sleep` statements are replaced with `wait_for_file` for the relevant scripts beneath `scripts` and `ush`; - Indentation and shell-norms are updated where applicable. Note: The WAFS scripts are not updated as per @aerorahul direction. Resolves #2444 --------- Co-authored-by: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 12 13:31:55 2024 -0400 Add COM template for JEDI obs (#2678) Adds a COM template to define a path to store obs processed for JEDI. This will allow UFSDA to stop writing to COM_OBS, which should be read-only as it belongs to obsproc in operations. No functional change yet. commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Wed Jun 12 09:06:23 2024 -0600 Link both global-nest fix files and non-nest ones at the same time (#2632) This PR enables linking both global-nest fix files and non-nest ones at the same time and users can run both nesting and non-nesting experiments at the same time without worries about what fix files to be linked. Resolves #2631 commit 61de004d4f9e9edf8a31bb173f2719b46451a36a Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jun 12 11:03:13 2024 -0400 Update ufs-weather-model (#2663) Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack allowing some temporary fixes to be reverted. * removes upp submodule * uses upp from the ufs-weather-model * restores the build and link that were hacked during the Hera Rocky 8 transition to allow for UPP submodule * Removes forecast directories in clean-up Resolves #2617 Resolves #2437 --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Wed Jun 12 01:15:37 2024 -0400 Add ability to process ocean/ice products specific to GEFS (#2561) This PR begins to add the capability to produce GEFSv13 ocean and ice products in the global-workflow according to stakeholder requirements. The following features are added. - An oceanice prod yaml file has been added to address the ocean and ice products specific to GEFSv13. - The rocoto dependencies and config.base for GEFS have also been modified to allow for 24-hour averaged ocean and ice output. - Various scripts have been modified to allow for ocean and ice output frequencies of 24 hours. - `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN` and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`. Refs #1878 commit 6691e7489650e0b738c176fbd096109288dc09b6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 11 21:15:07 2024 -0600 Update cleanup job to use COMIN/COMOUT (#2649) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow clean-up task. Refs #2451 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Jun 11 16:17:25 2024 -0400 Add overwrite to creat experiment in BASH CI (#2676) This is a quick hotfix to the CI BASH driver script adding `--overwrite` to create experiment script to avoid errors from restarting an experiment. commit e7909af8d9e1f34140388a3f8556d8e582c58fe5 Author: emilyhcliu <36091766+emilyhcliu@users.noreply.github.com> Date: Mon Jun 10 15:11:27 2024 -0400 Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py (#2645) This PR proposes updates for the following two scripts: 1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select CRTM cloud optical table based on cloud microphysical scheme indicated by `imp_physics' The default scheme in the GFS forecast model is Thompson scheme (imp_physics = 8). 2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in the script due to increased variables to interplate increments and calculate analysis in the netcdf_io routines in GSI-utils. Here is the related [PR #46 for GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46). --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 9caa51de8fb7be07d2e61775da01937d576964f6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Jun 6 22:15:23 2024 -0600 Update RDHPCS Hera resource for `eupd` task (#2636) As per @wx20jjung, the resource for the `eupd` task have been updated for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job fails. Resolves #2454 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Thu Jun 6 11:49:03 2024 -0400 Parameterize some things in config.atmanl and config.atmensanl (#2661) This PR adds some parameters in config.atmanl and config.atmensanl that can be altered with the defaults.yaml. The motivation is to make these files match those in the GDASApp JJOB tests (example: https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl), so we can just use the Global Workflow config.atmanl and config.atmensanl in the tests rather than custom ones in GDASApp that have to be separately updated every time the ones in the Global Workflow are updated. commit 54ea0b73a07921be5fbb07fe41e976888bd3e549 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Thu Jun 6 01:36:02 2024 -0400 Add links to the ocean insitu obs processing tools (#2644) Add links to the marine bufr to ioda converters for the marine insitu observations. - fixes https://github.com/NOAA-EMC/GDASApp/issues/1106 - waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135 commit 205d0c2b13e2d7755cec75bf8c978ab20d453862 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jun 5 17:31:30 2024 +0000 Update S4 point of contact in docs (#2660) Update the point of contact for global workflow issues on S4. commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed Jun 5 12:50:14 2024 -0400 Enable wcoss2 ufsda build and module load (#2620) This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2. Resolves #2602 Resolves #2579 commit 67b833e0c7bc390865d453588b4609a1a7ede981 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Tue Jun 4 13:33:43 2024 -0400 Update ufs-weather-model (#2646) Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6 This should resolve the issue and allow C768 runs on Hera and allow for CICE to run on WCOSS2 (due to library updates to allow linking). From what I can tell, all updates needed were done by @HenryWinterbottom-NOAA which were updates for CICE Fixes #2490 commit c44d0ac86cfdf78eb87492431bf6d825e8bae637 Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Tue Jun 4 10:29:49 2024 -0400 Update wmo parm files to fix WMO header (#2652) This PR updates wmo parm files to switch WMO header of precipitation type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to instantaneous. Resolves #2566 commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Tue Jun 4 13:55:33 2024 +0000 Add IAU to snow DA (and its test) (#2610) This PR enables IAU for the snow DA which is necessary for GFSv17. A snow analysis is created for the center of the window regardless, and an additional at the beginning of the window is added if IAU is on. The former is needed for UPP and the latter, to initialize the model. The increment is valid throughout the window for 3DVar, so the same increment is added to both forecasts. Additionally, the input file that goes into global_cycle has been updated to be the output of the JEDI snow analysis instead of the forecast (@jiaruidong2017 I recall discussing this, can you confirm this is right or am I mistaken) This PR also makes the CI test for snow DA (and aerosol DA) include IAU rather than without IAU,. --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit c92bf415060750127c9c05a62a1d2851c489551a Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Sat Jun 1 05:11:07 2024 +0000 Archiving cleanup (#2621) 1) Adds a lot of comments to the jinja templates for archiving 2) Rearranges the gdas and enkf templates to a more logical order 3) Fixes a couple of bugs in the enkf archiving of increments and analyses 4) Disables archiving for the half cycle 5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`, instead relying on `DO_FIT2OBS` 6) Updates wxflow to add the option to not allow undefined variables when parsing jinja templates and invokes this feature when running archives Resolves #2612 commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri May 31 04:57:08 2024 -0400 Switch to Rocky 9 built external packages on Hercules (#2608) The workflow was updated to use modules built on Rocky 9, but the external packages (like prepobs) were still pointing to the versions built on CentOS (Orion). This transitions to packages built on Rocky 9. Updating of the tracker package has been deferred until later. As such, the tracker jobs have been disabled by returning immediately if they are on Hercules. Since these jobs are small, resource-wise, it should not meaningfully impact turnover time. commit 4422550c01c9214a2b3b8890bdcc898123ee216a Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Thu May 30 08:05:23 2024 -0600 Add the capability to use slurm reservation nodes (#2627) Add the capability to use slurm reservation nodes Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE Resolves #2626 commit a54153fd9d26126206bc07a1da4e80f50c0c5910 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 29 23:24:07 2024 -0400 Update forecast job to use COMIN/COMOUT (#2622) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the forecast job. Refs #2451 --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit d69a8af95d492982b918670322ed5c41ab074335 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed May 29 21:29:03 2024 -0400 Update to add 1-deg global wave grid (#2619) This PR adds options to use a global 1 deg grid, intended for testing with the SFS application. Requires new fix file changes NOAA-EMC/global-workflow#2618 commit 0b4670ecf83b99b72835c8380573b2bca7cf5324 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed May 29 17:17:21 2024 -0400 Add C384mx025_3DVarAOWCDA yamls (#2625) Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder. commit 2e885d05c64b947f00a3cf055a1277fbfac195c9 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 29 13:00:51 2024 -0400 Script to keep Jenkins Agent persistent from cron (#2634) This "persistent" Java Agent launch script can be ran from a cron job: - Uses Jenkins Remote API to check the status of the Node connection using curl for a given machine. - If it is not connected a new agent is launched for that node. Resolves #2633 commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5 Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Tue May 28 17:17:11 2024 -0400 Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611) Based on users' feedback, this PR do the following: 1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF 2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD, and VOGRD) from "%g m below water surface" to "%g m below sea level" 3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m) Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31 Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Tue May 28 17:16:23 2024 -0400 Add atmensanlfv3inc job (#2592) This PR creates the atmensanlfv3inc job, the ensemble version of atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is #[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3). commit 50c2b8951b29a3c883a778becbf8582f9519eb48 Author: Anil Kumar <108816337+AnilKumar-NOAA@users.noreply.github.com> Date: Tue May 28 13:23:53 2024 -0400 Global-workflow (AR) Generic updates for Gaea C5 (#2515) - Port global-workflow’s build and run capability to Gaea-C5 - Building global-workflow on Gaea-C5 - Setting up experiments with global-workflow on Gaea-C5 --------- Co-authored-by: AnilKumar-NOAA <Anil.Kumar@gaea53.ncrc.gov> Co-authored-by: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> commit b6ca771a0c584cbfcbbf9be739765d5f3815df97 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 24 10:52:45 2024 -0400 Update STMP and PTMP settings in host file for Orion and Hercules (#2614) - Updating STMP and PTMP settings in host file for Orion and Hercules because they are cross mounted. - Also took the opportunity to finally update **SLURM_ACCOUNT** to **HPC_ACCOUT** in CI over rides. - Added a refactor of the `rocotostat.py` tool that is more pythonic and as a execute retry feature because the `rocotostat` utility on Orion has been failing sometimes. commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Tue May 21 23:50:50 2024 -0400 Sea-ice analysis insertion (#2584) Allows cycling and restarting CICE with the sea-ice analysis if the marine DA is switched on. Resolves #2568 Resolves NOAA-EMC/GDASApp#1103 commit 5369a1ff3a3969149fcf32810fad0e50216752b7 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue May 21 22:12:29 2024 +0000 Refactored archiving (#2491) This provides a new pygfs task, archive.py, that provides all of the tools necessary to archive data to the local (`ARCDIR`) and backup (`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to define the file to be archived or tarred to replace the `hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts and make it easier to add new data and explicitly handle optional and required files. For `ATARDIR` archiving, a master jinja template is provided for each `RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2, master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both `enkfgdas` and `enkfgfs` `RUN`s. These templates then include the appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on experiment, cycle, and coupled parameters. Each of these templates corresponds to a single tarball to populate and are tabbed 4 spaces so they are defined within the master `datasets` dictionary. Future developers should not have to make modifications to archive.py unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then only a single `elif` needs to be added to the configure method to specify the master `ATARDIR` template to archive (e.g. `master_gefs.yaml.j2`). If a new component is coming online that needs to be archived to `ATARDIR` (e.g. SNOW), then create a new template for each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`) and reference the template in the appropriate master templates, e.g. `master_gdas.yaml:` ```jinja {% if DO_SNOW %} {% include "gdassnow.yaml.j2" %} {% endif %} ``` A few other issues were addressed along the way: 1. Aerosols have been reenabled. Aerosol forecasts should only be performed during gdas cycles, but analyses can be performed for both gfs and gdas cycles. This was accomplished by setting separate `AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs. 2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`. This prevented restarts from being used for cice-enable experiments. This feature was not tested. 3. Create a temporary fix for the `wgrib` utility. For spack-stack 1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in existing installations. Once complete, this temporary fix should be removed. 4. The number of `earc` jobs has been reduced for lower resolution experiments. Both C48 and C96 experiments will now only have two earc jobs (one for the non-member files to archive and another for the member files). C192 will have up to 3 earc jobs (one non-member, one for members 1-40 and another for members 41-80, if needed). Resolves #2345 Resolves #2318 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 17 12:57:59 2024 -0400 Add remove RUNDIRS step in CI before creating experements (#2607) As had been done in Bash CI we need to remove the RUNDIR in Jenkins before a creating an experiment in the event that case had beem previously ran. commit 09333c01dbafddb2d2fe7e181b479af3cc6d3621 Merge: f7e9f4489 bb930050b Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Thu May 16 14:33:19 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit bb930050b3cd51d28ecba6b231c8675f6d11856c Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu May 16 12:28:30 2024 -0400 Adds jjob and other necessities for marine LETKF task (#2564) Adds jjob, rocoto script, config file, and other necessities for new marine LETKF task. Partially addresses NOAA-EMC/GDASApp#1091 commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu May 16 12:12:06 2024 -0400 Updating CI Machine configs with redundant PTMP (#2605) Quick fix adding PTMP as STMP in Machine configs for CI for completeness commit ef340ff33a6f89adf70838206ba3fd56a953fa7a Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu May 16 11:37:30 2024 -0400 Fix race condition in CI between Orion and Hercules (#2604) Hotfix to solve race conditions in the CI system due to cross-mounted file systems between Orion and Hercules commit e8b17e27f719df280170dc3f5bd9f19917cefaf2 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 15 17:16:30 2024 -0400 Remove existing EXPDIRs and COMROTs when CI is re-run (#2601) Quick hotfix for having default for re-runing jobs to start clean with new EXPDIRs and COMROTs commit b5d113efb1970ede5cd1d3d4dff8d96320519c41 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 15 16:52:49 2024 -0400 Moving logic for skipping hosts in pr cases (#2573) This PR removes the logic of skipping hosts for pr cases from `create_experiment.py` and moves it to a test in the cron bash driver using a `parse_yaml.py` python tool. The Jenkins pipeline was not effected as it uses the `get_host_case_list.py` utility to form the cases on a per host bases. Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed May 15 13:13:30 2024 -0400 Update gsi_utils.fd hash (#2598) This PR updates the `gsi_utils.fd` hash to bring in updates which add safeguards to - `src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90` - `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90` The safeguards are described in GSI-utils PR [#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated issue. Resolves #2597 commit d5366c66bd67f89d118b18956fe230207cbf0aea Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 15 13:12:56 2024 -0400 Update CICE and MOM6 fix versions (#2600) This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions to the newer `20240416` timestamps, which includes updates and fixes to the `100` (1-deg) resolution files. Resolves #2480 Resolves #2483 Resolves #2595 commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon May 13 22:57:38 2024 +0000 Limit gfswavepostpnt to 40 PEs/node (#2588) This fixes the slow runtime of the gfswavepostpnt job on Hercules. The job is very I/O intensive and does not scale well to large nodes, so limit the number of jobs/node to 40. Resolves #2587 commit 4fb7c12c325702a47f27c802a5067efd33d0327c Author: Fanglin Yang <fanglin.yang@noaa.gov> Date: Mon May 13 16:37:51 2024 -0400 Update damping and time-step (#2575) Updates the model to use explicit Rayleigh damping for u/v and implicit damping to w. This improves model stability and allows for longer timesteps. Also unifies the GDAS and GFS to use the same damping. Results from a test at the C1152 resolution (coupled model) can be found at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/ Resolves #2574 Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Lisa Bengtsson <lbengtss@Orion-login-1.HPC.MsState.Edu> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 10 14:17:13 2024 -0400 Do not use BUILT_semphore to force rebuilds when re-run (#2593) Remove the placement of the `BUILT_semaphore` file after the build in the Jenkins Pipeline and force it to rebuild any changes after a PR is re-ran. commit 2346c6161f75ae02369cbf30f30c6150d3e12b66 Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com> Date: Thu May 9 21:17:06 2024 -0500 Migration to Rocky8 spack-stack installations on Jet (#2458) # Description Migrates Global Workflow to Rocky8 spack-stack installations on Jet. Jet has moved from CentOS7 to Rocky8. Resolves #2377 Refs NOAA-EMC/UPP#919 Refs NOAA-EMC/gfs-utils#60 Refs NOAA-EMC/GSI#732 Refs NOAA-EMC/GSI-Monitor#130 Refs NOAA-EMC/GSI-utils#33 commit c7b3973014480a20dd8e24edaeb83a9e9e68159f Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu May 9 11:36:58 2024 -0400 Updates for cold start half cycle, then continuing with IAU for WCDA (#2560) This PR allows us to run C384 S2S with IAU, but starting with the first half-cycle as a cold-start. This will be necessary for cycled testing as we build towards the full system for GFSv17. This updates the copying of the restarts for RUN=gdas for both ocean and ice copying what the atm model is doing. It also reduced the amount of restart files from 4 to 3. Other updates: * Add DOJEDI ocean triggers for archiving certain files update from: @CatherineThomas-NOAA * Adds COPY_FINAL_RESTARTS option to turn on/off copying the last restart file to COM. Defaults to off... * Defines model_start_date_current_cycle & model_start_date_next_cycle to help with knowing which IC to grab. Refs #2546 Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2 Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Wed May 8 20:52:48 2024 -0400 Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477) Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI Configuration Builder (JCB) tool so that YAMLs can be made more portable and invoke the observation chronicle mechanism. Resolves #2476 Co-authored-by: danholdaway <danholdaway@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 8 02:04:16 2024 -0400 Add CI test for products (#2567) Adds a new version of the atm3DVar test that runs the full forecast length and produces most of the secondary products. For now, this test will only run on WCOSS due to gempak failures on other machines as well as computational needs. On other machines, the original version will run (the original version will not run on WCOSS). AWIPS remains off for now in this extended test due to a bug involving tocgrib2 and the convective precip fields (see #2566). The new test runs for 4½ cycles and the full 384-hr forecast length to ensure all gempak scripts are exercised. Since the cycle throttle is 3 and the bulk of the time is in the free forecast, the cycles run mostly concurrently so it doesn't extend the total test time too much beyond that of a single 384-hr forecast. Fixes a bug in NPOESS that was introduced when the post filenames were reverted to the previous format for the GOES products until the final filenames are determined (#2499). Also removes the AWIPS g2 job from the rocoto mesh to complete the retirement of grib1 products. Resolves #2132 Resolves #2445 commit 9b6f8404ac4507d14adc404b77cfdf002b55e832 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue May 7 00:14:36 2024 -0400 Add task to prepare emissions for GEFS (#2562) This PR: - introduces a task to prepare emissions for a forecast into the GEFS application. - adds configuration, j-job, rocoto job, ex-script and the python class for this job - updates GEFS workflow to be able to generate the XML to call this job. - updates the `fcst` and `efcs` job dependencies in the GEFS application to depend on `prep_emissions` if aerosols are turned ON. - provides a placeholder for @bbakernoaa to work on the details for preparing emissions. Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 233c18815d2e8e6b344f161fd0c102a4fbdfb66d Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Mon May 6 18:11:35 2024 -0400 Single Executable for main GDAS JEDI applications (#2565) Changes that accompany GDAS PR (NOAA-EMC/GDASApp/pull/1075) that allow…

Squashed commit of the following: commit 4e0a81f7acf5ccba5de8d3bdf7ab19cae80812cb Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 18:37:50 2024 +0000 Fix typos/links/dependancy. commit d5fdcbf8d6e987dbdfcd6b4da34d0934c8d82c3b Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 07:37:52 2024 +0000 Fixed missing config.base files. commit c6239f925369b20fd8488e8537969e2f4f9e7725 Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 06:53:47 2024 +0000 Update submodule hashs. commit 32bf790f67b818ff50a7f6b74388fb81ed175b3a Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 06:09:41 2024 +0000 Update develop branch, gsl_ufs_dev - based on gsl_ufs_dev from KaYee's fork global-workflow: 07Aug24,37c53ac [develop_07Aug2024_37c53ac] UFS: 19Jul24, c127601 FV3: 19Jul24, 2527c11 UPP: 23Apr24, be0410e CCPP-PHYSICS: 19Jul24, 46df080 UFS_UTILS: 26Jun24, 3ef2e6b Squashed commit of the following: commit 70b557836379bb7e545fcc6642e28d66cfc17735 Merge: 5edbd123e 37c53ac69 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Wed Aug 7 11:02:24 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 7 08:11:21 2024 -0400 Revert MSU FIX_DIRs back to glopara (#2811) commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Aug 6 14:47:36 2024 -0400 Bugfix for updating label states in Jenkins (#2808) Quick bug fix for updating state labels in CI during finalize. (did not reference GitHub CLI executable correctly in the pipeline script) commit 8fee36f0307b0c08080e3a8fa8fa6703e7da5fce Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Aug 6 11:02:45 2024 -0400 Clean-up temporary rundirs - take 2. (#2753) This PR: - is a follow-up to a previous PR that aggressively pruned run directories. - removes run directories for the current cycle in the clean-up if the cycle is successful. If the cycle is not successful, cleanup is not called and all run directories for the cycle are safe from being purged. - also updates the PR template to list/query for any updates to submodules. --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: David Huber <david.huber@noaa.gov> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit d599fff4aedd41ae587dbe02226acb12ff48efc1 Author: HelinWei-NOAA <48133472+HelinWei-NOAA@users.noreply.github.com> Date: Mon Aug 5 05:31:31 2024 -0400 Change land surface for HR4 (#2787) Resets the default value of opt_diag to 2 corresponding to the land surface upgrades in ufs-weather-model for HR4. Resolves #2786 commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Aug 2 15:41:29 2024 -0400 Run METplus serially and correct the name of prod tasks (#2804) Adds 2 hot fixes: - METplus v9.1.3 has a bug in it that sometimes attempts to create multiple copies of the same directory when running in parallel, causing a Python error and downstream problems. This PR makes METplus run in serial mode, preventing such issues. - Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod) commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri Aug 2 15:03:45 2024 -0400 Update Java Agent launching script for Jenkins connections (#2762) Made updates to the Jenkins Launching Script for robustness and less ambiguous documentation: - Clearer distinction between required user token for the remote api and the systems token for launching - Added pre-checks: `gh` is authenticating, named compliant token and secret file exists - More robust Jason based parser of the remote api response for checking the state of the Node connection - For `cron` use a 5 minute pause and recheck was added before re-launching of the java agent - Added concise header documentation of requirements and purpose --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit b73b1fd203496db97f8067652659573a632bcc67 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Aug 2 07:59:06 2024 -0400 Fix erroneous cdump addition (#2803) commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Aug 1 20:26:13 2024 -0400 Update ocean post-processing triggers (#2784) This PR: - replaces `check_netcdf.sh` checker for ocean post-processing with with ocean output at the next forecast hour or finishing of the forecast job for ocean prod - removes no longer needed `ush/check_netcdf.sh` commit aa2af1ca8d59424a60a1730722bf528775d9e606 Author: GeorgeGayno-NOAA <52789452+GeorgeGayno-NOAA@users.noreply.github.com> Date: Thu Aug 1 16:46:10 2024 -0400 Update the gfs_utils repository hash (#2801) # Description Point to the latest hash of the gfs-utils repository, which contains the bug fix to gaussian_sfcanl. Resolves #2669. Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73 commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Aug 1 08:12:14 2024 -0400 Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791) Changes how METplus jobs run so that they run on the last GFS cycle for a given `PDY`. This is a departure from operations where the METplus jobs run on the 00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through `${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on `${PDY}18` for cycles 00-18. See https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details. commit 1cf8b448af562dbb7af198399c78c585977e81da Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 30 10:38:49 2024 -0400 Simplify resource-related variables, remove CDUMP where unneeded (#2727) This overhauls resource-related variables to use a common set of variables for each job. In the process, this also removed the use of CDUMP in most cases. Resolves #1299 #2693 commit 61875f25c9e971f82ae499b5b612d7f095deebd4 Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Mon Jul 29 14:40:03 2024 -0400 Remove f000 from atmos rocoto tasks for replay cases (#2778) The main purpose of this PR is to remove the f000 from atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater than `0`, it becomes necessary to have the first lead hour set to `OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and the minimum lead time for the ocean_prod rocoto task needs to be 6 (assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up possible by removing 0 from fhrs for atmosphere-related tasks in `gefs_tasks.py` when replaying. This PR also moves where f000 is being removed for the ocean_prod and ice_prod tasks. The if-block that performs this f000 removal has been moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`. --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit f156a7894d639f177e3e2588f98eec1f6f59aa68 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Jul 26 14:18:32 2024 -0500 HR4 GWD update (#2732) This update is a combination of the gravity wave drag (GWD) versions from the NOAA/GSL and NOAA/PSL commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Jul 25 14:26:52 2024 -0400 Temporarily disable METplus jobs (#2796) commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Wed Jul 24 15:00:35 2024 -0400 Refactoring of the marine B-matrix job (#2749) Refactor the functionality of B-matrix generation from the GDASApp Resolves #2743 commit 65a7ab75dc0e4baba06a02e11ed0455787056a68 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 23 08:35:48 2024 -0400 Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775) Removes the namespace-based construction of EnKF member COM directories in the enkf archive template. commit c45b9611f3e701b819bd33dc5af29033f060bb91 Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Tue Jul 23 00:33:16 2024 -0400 Add task to process reforecast variables to save on WCOSS2 (#2680) # Description This PR adds an optional task to the global-workflow to process a subset of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for the GEFSv13 reforecast. This task is designed to process GEFS variables so that specific reforecast product requirements are met. A new variable in `config.base` called `DO_EXTRACTVARS` enables this task, which is currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by default and is specifically a task designed to be executed for the GEFSv13 reforecast. Refs #1878 # Type of change - New feature (adds functionality) # Change characteristics - Is this a breaking change (a change in existing functionality)? NO - Does this change require a documentation update? NO # How has this been tested? This has been cloned and tested on WCOSS2. This will need to be tested on Hera and other platforms on which the reforecast may be running. # Checklist - [ ] Any dependent changes have been merged and published - [x] My code follows the style guidelines of this project - [x] I have performed a self-review of my own code - [ ] I have commented my code, particularly in hard-to-understand areas - [x] My changes generate no new warnings - [x] New and existing tests pass with my changes - [ ] I have made corresponding changes to the documentation if necessary --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 71dc33c6ca991c16ce743760d99feaaf60f2218a Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jul 22 14:51:53 2024 -0400 Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774) Fix metp* resources and check that they completed properly; add support for Orion Rocky 9 commit 56df67a90fe090c425199f1285e5aac722c398b1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jul 22 09:28:18 2024 -0400 Hotfix: Update jcb to avoid git-lfs files (#2782) Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to be cloned on Hera. This hotfix points to a non-authoritative branch of the GDASApp (https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and should be updated ASAP back to the authoritative repository. commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jul 16 09:44:00 2024 -0400 Address issues in creating XML for GFS forecast-only with app S2SWA (#2757) This bugfix PR: - fixes an issue where a user is unable to generate the XML for a GFS forecast-only experiment with APP=S2SWA Specifically, the changes are related to defining `aero_fcst_cdumps`. Following `setup_expt.py`, the user will have to set `AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in `config.base`. commit e0878dba0e53706a7f53429b61aee2936e2c21bf Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Jul 15 10:25:11 2024 -0400 Updated prepobs and fit2obs versions for Orion Rocky9 (#2758) Update prepobs to v1.0.2 and fit2obs to v1.1.2 These versions now support Orion Rocky9. Updates are included for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet. commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jul 11 17:48:47 2024 +0000 CI maintenance updates and adding CI Unit Tests (#2740) This PR has a few maintenance updates to the CI pipeline and adds a test directory with Unit Tests **Major Maintenance updates:** - Added try blocks with appropriate messaging to GitHub PR of failure for: - - **scm** checkout - - build fail (with error logs sent as gists) - - create experiment fails with `stderr` sent to GitHub PR messaging - Pre-stage FAILS from the above are now captured these fails allow FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state labels in GitHub - see image below) **Minor Maintenance updates:** - Fix for STALLED cases reviled from PR 2700 (just needed a lambda specifier) - Fixed path to experiment directory in PR message (had dropped EXPDIR in path) - Needed `latin-1` decoder in reading log files for publishing **Added python Unit Tests for CI functionality:** - Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI utility codes - Cashed the install of Rocoto in the GitHub Runners to greatly reduce stetup time for running the unit tests - Unit Tests Python scripts added - `test_rocostat.py`: rocoto_statcount() rocoto_summary() rocoto_stalled() - `test_setup.py`: setup_expt() test_setup_xml() - `test_create_experment`: test_create_experiment() - - Runs all PR cases that do not have ICs in the GItHub Runner - Reporting mechanism in the Actions tab for Python Unit Testing results - Test case data for STALLED and RUNNING stored on S3 and pulled using wget during runtime of tests commit 5ef4db74649b8be03402c17aa29c024e71699a7b Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu Jul 11 08:59:24 2024 -0400 Adds contents of constructor and initialize methods to marine LETKF class (#2635) Adds contents of constructor and initialize methods to marine LETKF class Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091 --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> commit 8998ec7b74123e953b97a93fa14cc78d471a1aee Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 9 08:31:57 2024 -0400 Fix GDAS group B restart archiving (#2735) Archives the GDAS restartb dataset at a 6-hour offset from restarta This allows cycled experiments to restart from the archives. The tabbing for the master archive templates was also added to improve readability. Resolves #2722 commit 3ca74771255727033b9dc043c652ac585178629c Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Tue Jul 9 08:28:54 2024 -0400 Add fcst dependency to ocnanalprep (#2728) Add previous cycle's `fcst` as a dependency to `ocnanalprep` This ensures that the availability of restart files to the latter. This addresses a seldomly-encountered race condition where `ocnanalprep` fails due to the lack of the files. commit 58fca1668aecd6fb1afd12a441256ad35900e075 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jul 5 15:02:23 2024 -0400 Update (partially) global-workflow for orion+rocky9 (#2741) This PR: - updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils, GFS-utils) to include recent update to their modulefiles for Orion+Rocky9 upgrade - updates the modulefiles in global-workflow to load modules from Orion+Rocky9 paths - updates modulefiles for `gwsetup` and `gwci` as well. - removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not installed. - adds `parm/config.gfs/config.resources.ORION` to address GSI performance degradation after Rocky 9 upgrade. This PR: - does not update the build for UPP. Standalone UPP is not available via ufs-weather-model as of #2729 - will need a follow-up update for `prepobs` and `fit2obs` updated locations when they are installed in `glopara` space on Orion. # Type of change - Maintenance (code refactor, clean-up, new CI test, etc.) # Change characteristics - Is this a breaking change (a change in existing functionality)? NO - Does this change require a documentation update? NO # How has this been tested? This PR is not sufficient for Orion. This PR must be tested on other platforms (Hera, WCOSS2) as this PR updates submodules. # Checklist - [ ] Any dependent changes have been merged and published - [ ] My code follows the style guidelines of this project - [ ] I have performed a self-review of my own code - [ ] I have commented my code, particularly in hard-to-understand areas - [ ] My changes generate no new warnings - [ ] New and existing tests pass with my changes - [ ] I have made corresponding changes to the documentation if necessary --------- Co-authored-by: Kate Friedman <kate.friedman@noaa.gov> commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jul 3 21:07:49 2024 -0400 Update ufs model hash to 20240625 (#2729) Updates UFS weather model hash to hash from 2024-06-24 which has orion porting updates + a few namelist updates. commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jul 3 11:32:40 2024 -0400 Hotfix for undefined CLUSTERS (#2748) Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses the native `dict` `get` method to prevent grabbing an unset entry. commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Wed Jul 3 09:56:08 2024 -0400 Update gempak job to run one fcst hour per task (#2671) This PR updates gempak jobs (gfs, gdas, and goes) from processing all forecast hours at once to one forecast hour at a time. This will reduce the job runtime to less than 5 min, so restart capability is not needed. Resolves #1250 Ref #2666 #2667 --------- Co-authored-by: Walter.Kolczynski <Walter.Kolczynski@noaa.gov> commit 8215ae654202186a4f753c3abe937b7b9b91a9c7 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jul 2 16:22:11 2024 -0400 Hotfix for clusters from #2701 (#2747) Fixes an issue created from #2701 that added `CLUSTERS` to the `gaea.yaml`. commit 11943e36ba12b3df49c51942da780698fab02d38 Author: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> Date: Tue Jul 2 12:58:10 2024 -0400 Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701) This PR sets up the ability on Gaea for auto generation of a clean xml file, i.e., an xml file that does not need any alterations before running rocoto. Refs #2572 Refs #2664 commit de8706702ead0630beb54d868f83aa2cb23f8f79 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon Jul 1 09:29:14 2024 -0400 Update for JCB policies and stage DA job files with Jinja2-templates (#2700) This PR updates the `gdas.cd` hash to bring in new JCB conventions. Resolves #2699 From #2654 This PR will move much of the staging code that take place in the python initialization subroutines of the variational and ensemble DA jobs into Jinja2-templated YAML files to be passed into the wxflow file handler. Much of the staging has already been done this way, but this PR simply expands that strategy. The old Python routines that were doing this staging are now removed. This is part of a broader refactoring of the pygfs tasking. wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a companion to this PR. Co-authored-by: danholdaway <danholdaway@users.noreply.github.com> Co-authored-by: DavidNew-NOAA <david.new@noaa.gov> Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Co-authored-by: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jun 28 14:56:19 2024 -0400 Revert PR 2681 (#2739) This PR: - reverts #2681 in part - keeps some changes for `RUN`. - is a hotfix - should be merged ASAP after consensus w/ @guillaumevernieres @CatherineThomas-NOAA @WalterKolczynski-NOAA commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed Jun 26 15:46:08 2024 -0400 updated Finalize in Jenkinsfile and added try block around scm checkout (#2692) We are updating the Jenkins Pipeline with a try block around checkout to capture errors for the user. Also cleaned up Finalize and added section to clean out workspace on success. commit 968568f682bac7564095440bdb7813abefd76821 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 26 13:27:19 2024 -0400 Activate snow DA test on WCOSS (#2720) Activate the snow DA test on WCOSS. commit 7706760bb8adbdf78cb640b02739023c886e7699 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jun 26 10:02:22 2024 -0400 Cleanup of stale RUNDIRS from an experiment (#2719) This PR: - removes stale temporary scratch run directories from `$DATAROOT/` every 3 days. - should help to scrub failed attempts. - removes an unused variable `RUNDIR` defined in `config.base` commit 8962991691b5f0857b813bddfd28aa1034d4bd2b Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jun 26 09:43:48 2024 -0400 Update logic for MOM6 number of layers/exception values (#2681) Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine how many layers and sets the exception value for MOM6 to be 1e-34 for all scenarios. Note, we will no longer have zeros in the ocean grib output and the DA will also run without issues. Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615 commit 12431f76bdce807067929415007592cffc8a2457 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Jun 26 07:42:35 2024 -0600 Update wave jobs to use COMIN/COMOUT (#2643) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow wave model and products tasks. Refs #2451 commit b902c0bac126c323a07186ad8881384b032b6fda Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jun 25 07:48:46 2024 -0400 Assign machine- and RUN-specific resources (#2672) Redefine resource variables based explicitly on RUN or CDUMP Additionally, machine-specific resources are moved out of config.resources and placed in respective config.resources.{machine} files. Resolves #177 #2672 commit 5edbd123e2878a07f5cce8e3c7ea6147f286633a Merge: 09333c01d 4e1b937b6 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Mon Jun 24 12:44:05 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit 4e1b937b67ed220120e81925c4507f03b9b8965f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jun 24 10:50:52 2024 -0400 Add minimum software requirements (#2712) Adds a table to HPC documentation stating the minimum support versions commit f43a86276aaef91efa28faadc71a3cf50e749efe Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Jun 21 13:44:29 2024 -0400 Fix and simplify online archiving and reenable METplus jobs (#2687) This fixes the online archiving portion of the `*arch` and `*earc00` jobs, a prerequisite for running METplus. This also reenables METplus by default. The approach previously taken created `FileHandler` dictionaries at varying levels within the resulting yaml, which was not properly parsed by `exglobal_archive.py`. This approach creates a single `FileHandler` dictionary and is much less complicated overall. Resolves #2673 #2647 commit 8993b42cb91144c0ab0501dc7841ea8d675c4701 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 19 21:51:22 2024 -0400 Eliminate post groups (#2667) Eliminates the post groups used for upp and products jobs so that each task only processes one forecast hour. This is more efficient and greatly simplifies downstream dependencies that depend on a specific forecast hour. Resolves #2666 Refs #2642 commit 0b810c888239853fedd0e4584fe62536c6aaacdf Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 20:32:48 2024 -0600 Removes misleading "No such file or directory" syntax errors from output files (#2688) This PR addresses issue #1252. The following is accomplished: - Prior to removing files, the existence of a file is checked prior to attempting to remove; this is performed as noted [here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369); this PR only addresses the the `chgrp` issue. Refs #1252 --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 12:17:59 2024 -0600 Hotfix for bug in template names. (#2697) This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/` template. Resolves #2696 Refs #2451 commit 35d4d99eaac669721add9ddcc793153e5ab3b30a Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 08:06:53 2024 -0600 Update archive job to use COMIN/COMOUT (#2668) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow archive task. Refs #2451 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 47b3a581c8257fa24411fb400df8bb0e1e04972a Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Jun 17 22:55:38 2024 -0400 Turn on high-frequency output in extended test (#2679) Turns on high-frequency (hourly) output in the extended products test to exercise that aspect of the code. This test only runs on WCOSS. Also adds the hooks to optionally turn on the metplus jobs, but that is deferred as they are not currently working correctly. commit 38f2df9fb0c074b1f80d3c637080be79be693161 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jun 17 17:12:55 2024 +0000 Optimize wavepostpnt (#2657) Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs This is done by 1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by - performing operations on all files at once instead of looping over each file - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`) - combining `sed` and `grep` calls when possible - adding logic to `awk` calls instead of handling that logic in bash 2) minimizing as much as possible the amount of data on disk that has to be read in (e.g. limiting sed to read only the line numbers it needs) --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 5af325a6a4e0a14d180514a418603ca79fada487 Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Fri Jun 14 18:05:23 2024 -0400 Update GDASapp hash to move JCB into GDASapp (#2665) This PR moves JCB into GDASapp. The PR also bumps up the hash of GDASapp to what is in `feature/move_jcb`, which at time of writing is develop plus the absorption of JCB into GDASapp. Note that I also took the changes from https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the testing @RussTreadon-NOAA has done. commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b Author: Yaping Wang <49168260+ypwang19@users.noreply.github.com> Date: Fri Jun 14 10:18:17 2024 -0500 Add observation preparation job for aerosols DA to workflow (#2624) Add a prepaeroobs job to prepare aerosol obs files for DA. This job does quality control of the VIIRS aerosol raw observations and convert them to ioda format. Resolves #2623 --------- Co-authored-by: ypwang19 <yaping.wang@users.noreply.github.com> Co-authored-by: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Jun 14 11:04:41 2024 -0400 Remove ocean daily files (#2689) This PR removes the ocn_daily files that are produced by the ocean component. These files can be recreated by averaging data that exists in the 6 hour aveaged files if needed. Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675 Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by removing them and making this obsolete) commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jun 13 12:22:03 2024 -0400 Update Jenkinsfile needed a comma commit dc21eac6c3941d7f30803891d91d82f4cc1f8183 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jun 13 11:41:14 2024 -0400 Add Hercules-EMC to the Jenkins configurable parameter list (#2685) This quick-fix PR is to update the Jenkins Pipeline's configurable parameter list to include the **Hercules-EMC** node. This allows Jenkins users to restart Jobs in the controller when no updates have been made. commit ebacebfbe458634b8c80af6a735d6b6d01e4e406 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Thu Jun 13 11:20:24 2024 -0400 Update gdas.cd and gsi_utils hashes (#2641) This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea build for gsi_utils. Resolves #2640 commit 34155fb4767769600a1ff95f0a65e37081addc2a Author: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com> Date: Thu Jun 13 11:18:22 2024 -0400 Add ability to use GEFS replay ICs (#2559) The PR allows the use of ICs from PSL's replay analysis. These replay ICs will be used for GEFS reforecasting and SFS. Two main changes are associated with these updates: (1) replay ICs being valid at 3Z, and (2) the use of warm starts. Resolves #1838 --------- Co-authored-by: Jessica Meixner <Jessica.Meixner@noaa.gov> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Jun 12 19:25:42 2024 -0600 Replace `sleep` with `wait_for_file` (#2586) This PR addresses issue #2444. The following is accomplished: - All `sleep` statements are replaced with `wait_for_file` for the relevant scripts beneath `scripts` and `ush`; - Indentation and shell-norms are updated where applicable. Note: The WAFS scripts are not updated as per @aerorahul direction. Resolves #2444 --------- Co-authored-by: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 12 13:31:55 2024 -0400 Add COM template for JEDI obs (#2678) Adds a COM template to define a path to store obs processed for JEDI. This will allow UFSDA to stop writing to COM_OBS, which should be read-only as it belongs to obsproc in operations. No functional change yet. commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Wed Jun 12 09:06:23 2024 -0600 Link both global-nest fix files and non-nest ones at the same time (#2632) This PR enables linking both global-nest fix files and non-nest ones at the same time and users can run both nesting and non-nesting experiments at the same time without worries about what fix files to be linked. Resolves #2631 commit 61de004d4f9e9edf8a31bb173f2719b46451a36a Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jun 12 11:03:13 2024 -0400 Update ufs-weather-model (#2663) Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack allowing some temporary fixes to be reverted. * removes upp submodule * uses upp from the ufs-weather-model * restores the build and link that were hacked during the Hera Rocky 8 transition to allow for UPP submodule * Removes forecast directories in clean-up Resolves #2617 Resolves #2437 --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Wed Jun 12 01:15:37 2024 -0400 Add ability to process ocean/ice products specific to GEFS (#2561) This PR begins to add the capability to produce GEFSv13 ocean and ice products in the global-workflow according to stakeholder requirements. The following features are added. - An oceanice prod yaml file has been added to address the ocean and ice products specific to GEFSv13. - The rocoto dependencies and config.base for GEFS have also been modified to allow for 24-hour averaged ocean and ice output. - Various scripts have been modified to allow for ocean and ice output frequencies of 24 hours. - `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN` and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`. Refs #1878 commit 6691e7489650e0b738c176fbd096109288dc09b6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 11 21:15:07 2024 -0600 Update cleanup job to use COMIN/COMOUT (#2649) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow clean-up task. Refs #2451 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Jun 11 16:17:25 2024 -0400 Add overwrite to creat experiment in BASH CI (#2676) This is a quick hotfix to the CI BASH driver script adding `--overwrite` to create experiment script to avoid errors from restarting an experiment. commit e7909af8d9e1f34140388a3f8556d8e582c58fe5 Author: emilyhcliu <36091766+emilyhcliu@users.noreply.github.com> Date: Mon Jun 10 15:11:27 2024 -0400 Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py (#2645) This PR proposes updates for the following two scripts: 1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select CRTM cloud optical table based on cloud microphysical scheme indicated by `imp_physics' The default scheme in the GFS forecast model is Thompson scheme (imp_physics = 8). 2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in the script due to increased variables to interplate increments and calculate analysis in the netcdf_io routines in GSI-utils. Here is the related [PR #46 for GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46). --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 9caa51de8fb7be07d2e61775da01937d576964f6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Jun 6 22:15:23 2024 -0600 Update RDHPCS Hera resource for `eupd` task (#2636) As per @wx20jjung, the resource for the `eupd` task have been updated for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job fails. Resolves #2454 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Thu Jun 6 11:49:03 2024 -0400 Parameterize some things in config.atmanl and config.atmensanl (#2661) This PR adds some parameters in config.atmanl and config.atmensanl that can be altered with the defaults.yaml. The motivation is to make these files match those in the GDASApp JJOB tests (example: https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl), so we can just use the Global Workflow config.atmanl and config.atmensanl in the tests rather than custom ones in GDASApp that have to be separately updated every time the ones in the Global Workflow are updated. commit 54ea0b73a07921be5fbb07fe41e976888bd3e549 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Thu Jun 6 01:36:02 2024 -0400 Add links to the ocean insitu obs processing tools (#2644) Add links to the marine bufr to ioda converters for the marine insitu observations. - fixes https://github.com/NOAA-EMC/GDASApp/issues/1106 - waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135 commit 205d0c2b13e2d7755cec75bf8c978ab20d453862 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jun 5 17:31:30 2024 +0000 Update S4 point of contact in docs (#2660) Update the point of contact for global workflow issues on S4. commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed Jun 5 12:50:14 2024 -0400 Enable wcoss2 ufsda build and module load (#2620) This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2. Resolves #2602 Resolves #2579 commit 67b833e0c7bc390865d453588b4609a1a7ede981 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Tue Jun 4 13:33:43 2024 -0400 Update ufs-weather-model (#2646) Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6 This should resolve the issue and allow C768 runs on Hera and allow for CICE to run on WCOSS2 (due to library updates to allow linking). From what I can tell, all updates needed were done by @HenryWinterbottom-NOAA which were updates for CICE Fixes #2490 commit c44d0ac86cfdf78eb87492431bf6d825e8bae637 Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Tue Jun 4 10:29:49 2024 -0400 Update wmo parm files to fix WMO header (#2652) This PR updates wmo parm files to switch WMO header of precipitation type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to instantaneous. Resolves #2566 commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Tue Jun 4 13:55:33 2024 +0000 Add IAU to snow DA (and its test) (#2610) This PR enables IAU for the snow DA which is necessary for GFSv17. A snow analysis is created for the center of the window regardless, and an additional at the beginning of the window is added if IAU is on. The former is needed for UPP and the latter, to initialize the model. The increment is valid throughout the window for 3DVar, so the same increment is added to both forecasts. Additionally, the input file that goes into global_cycle has been updated to be the output of the JEDI snow analysis instead of the forecast (@jiaruidong2017 I recall discussing this, can you confirm this is right or am I mistaken) This PR also makes the CI test for snow DA (and aerosol DA) include IAU rather than without IAU,. --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit c92bf415060750127c9c05a62a1d2851c489551a Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Sat Jun 1 05:11:07 2024 +0000 Archiving cleanup (#2621) 1) Adds a lot of comments to the jinja templates for archiving 2) Rearranges the gdas and enkf templates to a more logical order 3) Fixes a couple of bugs in the enkf archiving of increments and analyses 4) Disables archiving for the half cycle 5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`, instead relying on `DO_FIT2OBS` 6) Updates wxflow to add the option to not allow undefined variables when parsing jinja templates and invokes this feature when running archives Resolves #2612 commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri May 31 04:57:08 2024 -0400 Switch to Rocky 9 built external packages on Hercules (#2608) The workflow was updated to use modules built on Rocky 9, but the external packages (like prepobs) were still pointing to the versions built on CentOS (Orion). This transitions to packages built on Rocky 9. Updating of the tracker package has been deferred until later. As such, the tracker jobs have been disabled by returning immediately if they are on Hercules. Since these jobs are small, resource-wise, it should not meaningfully impact turnover time. commit 4422550c01c9214a2b3b8890bdcc898123ee216a Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Thu May 30 08:05:23 2024 -0600 Add the capability to use slurm reservation nodes (#2627) Add the capability to use slurm reservation nodes Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE Resolves #2626 commit a54153fd9d26126206bc07a1da4e80f50c0c5910 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 29 23:24:07 2024 -0400 Update forecast job to use COMIN/COMOUT (#2622) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the forecast job. Refs #2451 --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit d69a8af95d492982b918670322ed5c41ab074335 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed May 29 21:29:03 2024 -0400 Update to add 1-deg global wave grid (#2619) This PR adds options to use a global 1 deg grid, intended for testing with the SFS application. Requires new fix file changes NOAA-EMC/global-workflow#2618 commit 0b4670ecf83b99b72835c8380573b2bca7cf5324 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed May 29 17:17:21 2024 -0400 Add C384mx025_3DVarAOWCDA yamls (#2625) Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder. commit 2e885d05c64b947f00a3cf055a1277fbfac195c9 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 29 13:00:51 2024 -0400 Script to keep Jenkins Agent persistent from cron (#2634) This "persistent" Java Agent launch script can be ran from a cron job: - Uses Jenkins Remote API to check the status of the Node connection using curl for a given machine. - If it is not connected a new agent is launched for that node. Resolves #2633 commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5 Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Tue May 28 17:17:11 2024 -0400 Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611) Based on users' feedback, this PR do the following: 1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF 2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD, and VOGRD) from "%g m below water surface" to "%g m below sea level" 3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m) Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31 Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Tue May 28 17:16:23 2024 -0400 Add atmensanlfv3inc job (#2592) This PR creates the atmensanlfv3inc job, the ensemble version of atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is #[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3). commit 50c2b8951b29a3c883a778becbf8582f9519eb48 Author: Anil Kumar <108816337+AnilKumar-NOAA@users.noreply.github.com> Date: Tue May 28 13:23:53 2024 -0400 Global-workflow (AR) Generic updates for Gaea C5 (#2515) - Port global-workflow’s build and run capability to Gaea-C5 - Building global-workflow on Gaea-C5 - Setting up experiments with global-workflow on Gaea-C5 --------- Co-authored-by: AnilKumar-NOAA <Anil.Kumar@gaea53.ncrc.gov> Co-authored-by: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> commit b6ca771a0c584cbfcbbf9be739765d5f3815df97 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 24 10:52:45 2024 -0400 Update STMP and PTMP settings in host file for Orion and Hercules (#2614) - Updating STMP and PTMP settings in host file for Orion and Hercules because they are cross mounted. - Also took the opportunity to finally update **SLURM_ACCOUNT** to **HPC_ACCOUT** in CI over rides. - Added a refactor of the `rocotostat.py` tool that is more pythonic and as a execute retry feature because the `rocotostat` utility on Orion has been failing sometimes. commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Tue May 21 23:50:50 2024 -0400 Sea-ice analysis insertion (#2584) Allows cycling and restarting CICE with the sea-ice analysis if the marine DA is switched on. Resolves #2568 Resolves NOAA-EMC/GDASApp#1103 commit 5369a1ff3a3969149fcf32810fad0e50216752b7 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue May 21 22:12:29 2024 +0000 Refactored archiving (#2491) This provides a new pygfs task, archive.py, that provides all of the tools necessary to archive data to the local (`ARCDIR`) and backup (`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to define the file to be archived or tarred to replace the `hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts and make it easier to add new data and explicitly handle optional and required files. For `ATARDIR` archiving, a master jinja template is provided for each `RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2, master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both `enkfgdas` and `enkfgfs` `RUN`s. These templates then include the appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on experiment, cycle, and coupled parameters. Each of these templates corresponds to a single tarball to populate and are tabbed 4 spaces so they are defined within the master `datasets` dictionary. Future developers should not have to make modifications to archive.py unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then only a single `elif` needs to be added to the configure method to specify the master `ATARDIR` template to archive (e.g. `master_gefs.yaml.j2`). If a new component is coming online that needs to be archived to `ATARDIR` (e.g. SNOW), then create a new template for each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`) and reference the template in the appropriate master templates, e.g. `master_gdas.yaml:` ```jinja {% if DO_SNOW %} {% include "gdassnow.yaml.j2" %} {% endif %} ``` A few other issues were addressed along the way: 1. Aerosols have been reenabled. Aerosol forecasts should only be performed during gdas cycles, but analyses can be performed for both gfs and gdas cycles. This was accomplished by setting separate `AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs. 2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`. This prevented restarts from being used for cice-enable experiments. This feature was not tested. 3. Create a temporary fix for the `wgrib` utility. For spack-stack 1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in existing installations. Once complete, this temporary fix should be removed. 4. The number of `earc` jobs has been reduced for lower resolution experiments. Both C48 and C96 experiments will now only have two earc jobs (one for the non-member files to archive and another for the member files). C192 will have up to 3 earc jobs (one non-member, one for members 1-40 and another for members 41-80, if needed). Resolves #2345 Resolves #2318 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 17 12:57:59 2024 -0400 Add remove RUNDIRS step in CI before creating experements (#2607) As had been done in Bash CI we need to remove the RUNDIR in Jenkins before a creating an experiment in the event that case had beem previously ran. commit 09333c01dbafddb2d2fe7e181b479af3cc6d3621 Merge: f7e9f4489 bb930050b Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Thu May 16 14:33:19 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit bb930050b3cd51d28ecba6b231c8675f6d11856c Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu May 16 12:28:30 2024 -0400 Adds jjob and other necessities for marine LETKF task (#2564) Adds jjob, rocoto script, config file, and other necessities for new marine LETKF task. Partially addresses NOAA-EMC/GDASApp#1091 commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu May 16 12:12:06 2024 -0400 Updating CI Machine configs with redundant PTMP (#2605) Quick fix adding PTMP as STMP in Machine configs for CI for completeness commit ef340ff33a6f89adf70838206ba3fd56a953fa7a Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu May 16 11:37:30 2024 -0400 Fix race condition in CI between Orion and Hercules (#2604) Hotfix to solve race conditions in the CI system due to cross-mounted file systems between Orion and Hercules commit e8b17e27f719df280170dc3f5bd9f19917cefaf2 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 15 17:16:30 2024 -0400 Remove existing EXPDIRs and COMROTs when CI is re-run (#2601) Quick hotfix for having default for re-runing jobs to start clean with new EXPDIRs and COMROTs commit b5d113efb1970ede5cd1d3d4dff8d96320519c41 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 15 16:52:49 2024 -0400 Moving logic for skipping hosts in pr cases (#2573) This PR removes the logic of skipping hosts for pr cases from `create_experiment.py` and moves it to a test in the cron bash driver using a `parse_yaml.py` python tool. The Jenkins pipeline was not effected as it uses the `get_host_case_list.py` utility to form the cases on a per host bases. Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed May 15 13:13:30 2024 -0400 Update gsi_utils.fd hash (#2598) This PR updates the `gsi_utils.fd` hash to bring in updates which add safeguards to - `src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90` - `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90` The safeguards are described in GSI-utils PR [#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated issue. Resolves #2597 commit d5366c66bd67f89d118b18956fe230207cbf0aea Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 15 13:12:56 2024 -0400 Update CICE and MOM6 fix versions (#2600) This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions to the newer `20240416` timestamps, which includes updates and fixes to the `100` (1-deg) resolution files. Resolves #2480 Resolves #2483 Resolves #2595 commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon May 13 22:57:38 2024 +0000 Limit gfswavepostpnt to 40 PEs/node (#2588) This fixes the slow runtime of the gfswavepostpnt job on Hercules. The job is very I/O intensive and does not scale well to large nodes, so limit the number of jobs/node to 40. Resolves #2587 commit 4fb7c12c325702a47f27c802a5067efd33d0327c Author: Fanglin Yang <fanglin.yang@noaa.gov> Date: Mon May 13 16:37:51 2024 -0400 Update damping and time-step (#2575) Updates the model to use explicit Rayleigh damping for u/v and implicit damping to w. This improves model stability and allows for longer timesteps. Also unifies the GDAS and GFS to use the same damping. Results from a test at the C1152 resolution (coupled model) can be found at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/ Resolves #2574 Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Lisa Bengtsson <lbengtss@Orion-login-1.HPC.MsState.Edu> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 10 14:17:13 2024 -0400 Do not use BUILT_semphore to force rebuilds when re-run (#2593) Remove the placement of the `BUILT_semaphore` file after the build in the Jenkins Pipeline and force it to rebuild any changes after a PR is re-ran. commit 2346c6161f75ae02369cbf30f30c6150d3e12b66 Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com> Date: Thu May 9 21:17:06 2024 -0500 Migration to Rocky8 spack-stack installations on Jet (#2458) # Description Migrates Global Workflow to Rocky8 spack-stack installations on Jet. Jet has moved from CentOS7 to Rocky8. Resolves #2377 Refs NOAA-EMC/UPP#919 Refs NOAA-EMC/gfs-utils#60 Refs NOAA-EMC/GSI#732 Refs NOAA-EMC/GSI-Monitor#130 Refs NOAA-EMC/GSI-utils#33 commit c7b3973014480a20dd8e24edaeb83a9e9e68159f Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu May 9 11:36:58 2024 -0400 Updates for cold start half cycle, then continuing with IAU for WCDA (#2560) This PR allows us to run C384 S2S with IAU, but starting with the first half-cycle as a cold-start. This will be necessary for cycled testing as we build towards the full system for GFSv17. This updates the copying of the restarts for RUN=gdas for both ocean and ice copying what the atm model is doing. It also reduced the amount of restart files from 4 to 3. Other updates: * Add DOJEDI ocean triggers for archiving certain files update from: @CatherineThomas-NOAA * Adds COPY_FINAL_RESTARTS option to turn on/off copying the last restart file to COM. Defaults to off... * Defines model_start_date_current_cycle & model_start_date_next_cycle to help with knowing which IC to grab. Refs #2546 Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2 Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Wed May 8 20:52:48 2024 -0400 Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477) Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI Configuration Builder (JCB) tool so that YAMLs can be made more portable and invoke the observation chronicle mechanism. Resolves #2476 Co-authored-by: danholdaway <danholdaway@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 8 02:04:16 2024 -0400 Add CI test for products (#2567) Adds a new version of the atm3DVar test that runs the full forecast length and produces most of the secondary products. For now, this test will only run on WCOSS due to gempak failures on other machines as well as computational needs. On other machines, the original version will run (the original version will not run on WCOSS). AWIPS remains off for now in this extended test due to a bug involving tocgrib2 and the convective precip fields (see #2566). The new test runs for 4½ cycles and the full 384-hr forecast length to ensure all gempak scripts are exercised. Since the cycle throttle is 3 and the bulk of the time is in the free forecast, the cycles run mostly concurrently so it doesn't extend the total test time too much beyond that of a single 384-hr forecast. Fixes a bug in NPOESS that was introduced when the post filenames were reverted to the previous format for the GOES products until the final filenames are determined (#2499). Also removes the AWIPS g2 job from the rocoto mesh to complete the retirement of grib1 products. Resolves #2132 Resolves #2445 commit 9b6f8404ac4507d14adc404b77cfdf002b55e832 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue May 7 00:14:36 2024 -0400 Add task to prepare emissions for GEFS (#2562) This PR: - introduces a task to prepare emissions for a forecast into the GEFS application. - adds configuration, j-job, rocoto job, ex-script and the python class for this job - updates GEFS workflow to be able to generate the XML to call this job. - updates the `fcst` and `efcs` job dependencies in the GEFS application to depend on `prep_emissions` if aerosols are turned ON. - provides a placeholder for @bbakernoaa to work on the details for preparing emissions. Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 233c18815d2e8e6b344f161fd0c102a4fbdfb66d Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Mon May 6 18:11:35 2024 -0400 Single Executable for main GDAS JEDI applications (#2565) Changes that accompany GDAS PR (NOAA-EMC/GDASApp/pull/1075) that a…

Squashed commit of the following: commit 4ad0d52a6fbb581a9804bd0bb627b7c52f338bad Author: kayee.wong <kayee.wong@noaa.gov> Date: Thu Sep 19 19:20:06 2024 +0000 For pygraf plotting. commit 1bfba70ed6aaa3eb47974006ed0c5cae653b8ce8 Author: kayee.wong <kayee.wong@noaa.gov> Date: Thu Sep 19 04:27:55 2024 +0000 Fixed gfsatmprod file name and gfsarch data type. commit 4e0a81f7acf5ccba5de8d3bdf7ab19cae80812cb Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 18:37:50 2024 +0000 Fix typos/links/dependancy. commit d5fdcbf8d6e987dbdfcd6b4da34d0934c8d82c3b Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 07:37:52 2024 +0000 Fixed missing config.base files. commit c6239f925369b20fd8488e8537969e2f4f9e7725 Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 06:53:47 2024 +0000 Update submodule hashs. commit 32bf790f67b818ff50a7f6b74388fb81ed175b3a Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 06:09:41 2024 +0000 Update develop branch, gsl_ufs_dev - based on gsl_ufs_dev from KaYee's fork global-workflow: 07Aug24,37c53ac [develop_07Aug2024_37c53ac] UFS: 19Jul24, c127601 FV3: 19Jul24, 2527c11 UPP: 23Apr24, be0410e CCPP-PHYSICS: 19Jul24, 46df080 UFS_UTILS: 26Jun24, 3ef2e6b Squashed commit of the following: commit 70b557836379bb7e545fcc6642e28d66cfc17735 Merge: 5edbd123e 37c53ac69 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Wed Aug 7 11:02:24 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 7 08:11:21 2024 -0400 Revert MSU FIX_DIRs back to glopara (#2811) commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Aug 6 14:47:36 2024 -0400 Bugfix for updating label states in Jenkins (#2808) Quick bug fix for updating state labels in CI during finalize. (did not reference GitHub CLI executable correctly in the pipeline script) commit 8fee36f0307b0c08080e3a8fa8fa6703e7da5fce Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Aug 6 11:02:45 2024 -0400 Clean-up temporary rundirs - take 2. (#2753) This PR: - is a follow-up to a previous PR that aggressively pruned run directories. - removes run directories for the current cycle in the clean-up if the cycle is successful. If the cycle is not successful, cleanup is not called and all run directories for the cycle are safe from being purged. - also updates the PR template to list/query for any updates to submodules. --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: David Huber <david.huber@noaa.gov> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit d599fff4aedd41ae587dbe02226acb12ff48efc1 Author: HelinWei-NOAA <48133472+HelinWei-NOAA@users.noreply.github.com> Date: Mon Aug 5 05:31:31 2024 -0400 Change land surface for HR4 (#2787) Resets the default value of opt_diag to 2 corresponding to the land surface upgrades in ufs-weather-model for HR4. Resolves #2786 commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Aug 2 15:41:29 2024 -0400 Run METplus serially and correct the name of prod tasks (#2804) Adds 2 hot fixes: - METplus v9.1.3 has a bug in it that sometimes attempts to create multiple copies of the same directory when running in parallel, causing a Python error and downstream problems. This PR makes METplus run in serial mode, preventing such issues. - Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod) commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri Aug 2 15:03:45 2024 -0400 Update Java Agent launching script for Jenkins connections (#2762) Made updates to the Jenkins Launching Script for robustness and less ambiguous documentation: - Clearer distinction between required user token for the remote api and the systems token for launching - Added pre-checks: `gh` is authenticating, named compliant token and secret file exists - More robust Jason based parser of the remote api response for checking the state of the Node connection - For `cron` use a 5 minute pause and recheck was added before re-launching of the java agent - Added concise header documentation of requirements and purpose --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit b73b1fd203496db97f8067652659573a632bcc67 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Aug 2 07:59:06 2024 -0400 Fix erroneous cdump addition (#2803) commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Aug 1 20:26:13 2024 -0400 Update ocean post-processing triggers (#2784) This PR: - replaces `check_netcdf.sh` checker for ocean post-processing with with ocean output at the next forecast hour or finishing of the forecast job for ocean prod - removes no longer needed `ush/check_netcdf.sh` commit aa2af1ca8d59424a60a1730722bf528775d9e606 Author: GeorgeGayno-NOAA <52789452+GeorgeGayno-NOAA@users.noreply.github.com> Date: Thu Aug 1 16:46:10 2024 -0400 Update the gfs_utils repository hash (#2801) # Description Point to the latest hash of the gfs-utils repository, which contains the bug fix to gaussian_sfcanl. Resolves #2669. Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73 commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Aug 1 08:12:14 2024 -0400 Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791) Changes how METplus jobs run so that they run on the last GFS cycle for a given `PDY`. This is a departure from operations where the METplus jobs run on the 00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through `${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on `${PDY}18` for cycles 00-18. See https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details. commit 1cf8b448af562dbb7af198399c78c585977e81da Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 30 10:38:49 2024 -0400 Simplify resource-related variables, remove CDUMP where unneeded (#2727) This overhauls resource-related variables to use a common set of variables for each job. In the process, this also removed the use of CDUMP in most cases. Resolves #1299 #2693 commit 61875f25c9e971f82ae499b5b612d7f095deebd4 Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Mon Jul 29 14:40:03 2024 -0400 Remove f000 from atmos rocoto tasks for replay cases (#2778) The main purpose of this PR is to remove the f000 from atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater than `0`, it becomes necessary to have the first lead hour set to `OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and the minimum lead time for the ocean_prod rocoto task needs to be 6 (assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up possible by removing 0 from fhrs for atmosphere-related tasks in `gefs_tasks.py` when replaying. This PR also moves where f000 is being removed for the ocean_prod and ice_prod tasks. The if-block that performs this f000 removal has been moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`. --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit f156a7894d639f177e3e2588f98eec1f6f59aa68 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Jul 26 14:18:32 2024 -0500 HR4 GWD update (#2732) This update is a combination of the gravity wave drag (GWD) versions from the NOAA/GSL and NOAA/PSL commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Jul 25 14:26:52 2024 -0400 Temporarily disable METplus jobs (#2796) commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Wed Jul 24 15:00:35 2024 -0400 Refactoring of the marine B-matrix job (#2749) Refactor the functionality of B-matrix generation from the GDASApp Resolves #2743 commit 65a7ab75dc0e4baba06a02e11ed0455787056a68 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 23 08:35:48 2024 -0400 Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775) Removes the namespace-based construction of EnKF member COM directories in the enkf archive template. commit c45b9611f3e701b819bd33dc5af29033f060bb91 Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Tue Jul 23 00:33:16 2024 -0400 Add task to process reforecast variables to save on WCOSS2 (#2680) # Description This PR adds an optional task to the global-workflow to process a subset of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for the GEFSv13 reforecast. This task is designed to process GEFS variables so that specific reforecast product requirements are met. A new variable in `config.base` called `DO_EXTRACTVARS` enables this task, which is currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by default and is specifically a task designed to be executed for the GEFSv13 reforecast. Refs #1878 # Type of change - New feature (adds functionality) # Change characteristics - Is this a breaking change (a change in existing functionality)? NO - Does this change require a documentation update? NO # How has this been tested? This has been cloned and tested on WCOSS2. This will need to be tested on Hera and other platforms on which the reforecast may be running. # Checklist - [ ] Any dependent changes have been merged and published - [x] My code follows the style guidelines of this project - [x] I have performed a self-review of my own code - [ ] I have commented my code, particularly in hard-to-understand areas - [x] My changes generate no new warnings - [x] New and existing tests pass with my changes - [ ] I have made corresponding changes to the documentation if necessary --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 71dc33c6ca991c16ce743760d99feaaf60f2218a Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jul 22 14:51:53 2024 -0400 Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774) Fix metp* resources and check that they completed properly; add support for Orion Rocky 9 commit 56df67a90fe090c425199f1285e5aac722c398b1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jul 22 09:28:18 2024 -0400 Hotfix: Update jcb to avoid git-lfs files (#2782) Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to be cloned on Hera. This hotfix points to a non-authoritative branch of the GDASApp (https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and should be updated ASAP back to the authoritative repository. commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jul 16 09:44:00 2024 -0400 Address issues in creating XML for GFS forecast-only with app S2SWA (#2757) This bugfix PR: - fixes an issue where a user is unable to generate the XML for a GFS forecast-only experiment with APP=S2SWA Specifically, the changes are related to defining `aero_fcst_cdumps`. Following `setup_expt.py`, the user will have to set `AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in `config.base`. commit e0878dba0e53706a7f53429b61aee2936e2c21bf Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Jul 15 10:25:11 2024 -0400 Updated prepobs and fit2obs versions for Orion Rocky9 (#2758) Update prepobs to v1.0.2 and fit2obs to v1.1.2 These versions now support Orion Rocky9. Updates are included for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet. commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jul 11 17:48:47 2024 +0000 CI maintenance updates and adding CI Unit Tests (#2740) This PR has a few maintenance updates to the CI pipeline and adds a test directory with Unit Tests **Major Maintenance updates:** - Added try blocks with appropriate messaging to GitHub PR of failure for: - - **scm** checkout - - build fail (with error logs sent as gists) - - create experiment fails with `stderr` sent to GitHub PR messaging - Pre-stage FAILS from the above are now captured these fails allow FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state labels in GitHub - see image below) **Minor Maintenance updates:** - Fix for STALLED cases reviled from PR 2700 (just needed a lambda specifier) - Fixed path to experiment directory in PR message (had dropped EXPDIR in path) - Needed `latin-1` decoder in reading log files for publishing **Added python Unit Tests for CI functionality:** - Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI utility codes - Cashed the install of Rocoto in the GitHub Runners to greatly reduce stetup time for running the unit tests - Unit Tests Python scripts added - `test_rocostat.py`: rocoto_statcount() rocoto_summary() rocoto_stalled() - `test_setup.py`: setup_expt() test_setup_xml() - `test_create_experment`: test_create_experiment() - - Runs all PR cases that do not have ICs in the GItHub Runner - Reporting mechanism in the Actions tab for Python Unit Testing results - Test case data for STALLED and RUNNING stored on S3 and pulled using wget during runtime of tests commit 5ef4db74649b8be03402c17aa29c024e71699a7b Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu Jul 11 08:59:24 2024 -0400 Adds contents of constructor and initialize methods to marine LETKF class (#2635) Adds contents of constructor and initialize methods to marine LETKF class Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091 --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> commit 8998ec7b74123e953b97a93fa14cc78d471a1aee Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 9 08:31:57 2024 -0400 Fix GDAS group B restart archiving (#2735) Archives the GDAS restartb dataset at a 6-hour offset from restarta This allows cycled experiments to restart from the archives. The tabbing for the master archive templates was also added to improve readability. Resolves #2722 commit 3ca74771255727033b9dc043c652ac585178629c Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Tue Jul 9 08:28:54 2024 -0400 Add fcst dependency to ocnanalprep (#2728) Add previous cycle's `fcst` as a dependency to `ocnanalprep` This ensures that the availability of restart files to the latter. This addresses a seldomly-encountered race condition where `ocnanalprep` fails due to the lack of the files. commit 58fca1668aecd6fb1afd12a441256ad35900e075 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jul 5 15:02:23 2024 -0400 Update (partially) global-workflow for orion+rocky9 (#2741) This PR: - updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils, GFS-utils) to include recent update to their modulefiles for Orion+Rocky9 upgrade - updates the modulefiles in global-workflow to load modules from Orion+Rocky9 paths - updates modulefiles for `gwsetup` and `gwci` as well. - removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not installed. - adds `parm/config.gfs/config.resources.ORION` to address GSI performance degradation after Rocky 9 upgrade. This PR: - does not update the build for UPP. Standalone UPP is not available via ufs-weather-model as of #2729 - will need a follow-up update for `prepobs` and `fit2obs` updated locations when they are installed in `glopara` space on Orion. # Type of change - Maintenance (code refactor, clean-up, new CI test, etc.) # Change characteristics - Is this a breaking change (a change in existing functionality)? NO - Does this change require a documentation update? NO # How has this been tested? This PR is not sufficient for Orion. This PR must be tested on other platforms (Hera, WCOSS2) as this PR updates submodules. # Checklist - [ ] Any dependent changes have been merged and published - [ ] My code follows the style guidelines of this project - [ ] I have performed a self-review of my own code - [ ] I have commented my code, particularly in hard-to-understand areas - [ ] My changes generate no new warnings - [ ] New and existing tests pass with my changes - [ ] I have made corresponding changes to the documentation if necessary --------- Co-authored-by: Kate Friedman <kate.friedman@noaa.gov> commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jul 3 21:07:49 2024 -0400 Update ufs model hash to 20240625 (#2729) Updates UFS weather model hash to hash from 2024-06-24 which has orion porting updates + a few namelist updates. commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jul 3 11:32:40 2024 -0400 Hotfix for undefined CLUSTERS (#2748) Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses the native `dict` `get` method to prevent grabbing an unset entry. commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Wed Jul 3 09:56:08 2024 -0400 Update gempak job to run one fcst hour per task (#2671) This PR updates gempak jobs (gfs, gdas, and goes) from processing all forecast hours at once to one forecast hour at a time. This will reduce the job runtime to less than 5 min, so restart capability is not needed. Resolves #1250 Ref #2666 #2667 --------- Co-authored-by: Walter.Kolczynski <Walter.Kolczynski@noaa.gov> commit 8215ae654202186a4f753c3abe937b7b9b91a9c7 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jul 2 16:22:11 2024 -0400 Hotfix for clusters from #2701 (#2747) Fixes an issue created from #2701 that added `CLUSTERS` to the `gaea.yaml`. commit 11943e36ba12b3df49c51942da780698fab02d38 Author: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> Date: Tue Jul 2 12:58:10 2024 -0400 Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701) This PR sets up the ability on Gaea for auto generation of a clean xml file, i.e., an xml file that does not need any alterations before running rocoto. Refs #2572 Refs #2664 commit de8706702ead0630beb54d868f83aa2cb23f8f79 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon Jul 1 09:29:14 2024 -0400 Update for JCB policies and stage DA job files with Jinja2-templates (#2700) This PR updates the `gdas.cd` hash to bring in new JCB conventions. Resolves #2699 From #2654 This PR will move much of the staging code that take place in the python initialization subroutines of the variational and ensemble DA jobs into Jinja2-templated YAML files to be passed into the wxflow file handler. Much of the staging has already been done this way, but this PR simply expands that strategy. The old Python routines that were doing this staging are now removed. This is part of a broader refactoring of the pygfs tasking. wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a companion to this PR. Co-authored-by: danholdaway <danholdaway@users.noreply.github.com> Co-authored-by: DavidNew-NOAA <david.new@noaa.gov> Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Co-authored-by: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jun 28 14:56:19 2024 -0400 Revert PR 2681 (#2739) This PR: - reverts #2681 in part - keeps some changes for `RUN`. - is a hotfix - should be merged ASAP after consensus w/ @guillaumevernieres @CatherineThomas-NOAA @WalterKolczynski-NOAA commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed Jun 26 15:46:08 2024 -0400 updated Finalize in Jenkinsfile and added try block around scm checkout (#2692) We are updating the Jenkins Pipeline with a try block around checkout to capture errors for the user. Also cleaned up Finalize and added section to clean out workspace on success. commit 968568f682bac7564095440bdb7813abefd76821 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 26 13:27:19 2024 -0400 Activate snow DA test on WCOSS (#2720) Activate the snow DA test on WCOSS. commit 7706760bb8adbdf78cb640b02739023c886e7699 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jun 26 10:02:22 2024 -0400 Cleanup of stale RUNDIRS from an experiment (#2719) This PR: - removes stale temporary scratch run directories from `$DATAROOT/` every 3 days. - should help to scrub failed attempts. - removes an unused variable `RUNDIR` defined in `config.base` commit 8962991691b5f0857b813bddfd28aa1034d4bd2b Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jun 26 09:43:48 2024 -0400 Update logic for MOM6 number of layers/exception values (#2681) Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine how many layers and sets the exception value for MOM6 to be 1e-34 for all scenarios. Note, we will no longer have zeros in the ocean grib output and the DA will also run without issues. Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615 commit 12431f76bdce807067929415007592cffc8a2457 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Jun 26 07:42:35 2024 -0600 Update wave jobs to use COMIN/COMOUT (#2643) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow wave model and products tasks. Refs #2451 commit b902c0bac126c323a07186ad8881384b032b6fda Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jun 25 07:48:46 2024 -0400 Assign machine- and RUN-specific resources (#2672) Redefine resource variables based explicitly on RUN or CDUMP Additionally, machine-specific resources are moved out of config.resources and placed in respective config.resources.{machine} files. Resolves #177 #2672 commit 5edbd123e2878a07f5cce8e3c7ea6147f286633a Merge: 09333c01d 4e1b937b6 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Mon Jun 24 12:44:05 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit 4e1b937b67ed220120e81925c4507f03b9b8965f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jun 24 10:50:52 2024 -0400 Add minimum software requirements (#2712) Adds a table to HPC documentation stating the minimum support versions commit f43a86276aaef91efa28faadc71a3cf50e749efe Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Jun 21 13:44:29 2024 -0400 Fix and simplify online archiving and reenable METplus jobs (#2687) This fixes the online archiving portion of the `*arch` and `*earc00` jobs, a prerequisite for running METplus. This also reenables METplus by default. The approach previously taken created `FileHandler` dictionaries at varying levels within the resulting yaml, which was not properly parsed by `exglobal_archive.py`. This approach creates a single `FileHandler` dictionary and is much less complicated overall. Resolves #2673 #2647 commit 8993b42cb91144c0ab0501dc7841ea8d675c4701 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 19 21:51:22 2024 -0400 Eliminate post groups (#2667) Eliminates the post groups used for upp and products jobs so that each task only processes one forecast hour. This is more efficient and greatly simplifies downstream dependencies that depend on a specific forecast hour. Resolves #2666 Refs #2642 commit 0b810c888239853fedd0e4584fe62536c6aaacdf Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 20:32:48 2024 -0600 Removes misleading "No such file or directory" syntax errors from output files (#2688) This PR addresses issue #1252. The following is accomplished: - Prior to removing files, the existence of a file is checked prior to attempting to remove; this is performed as noted [here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369); this PR only addresses the the `chgrp` issue. Refs #1252 --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 12:17:59 2024 -0600 Hotfix for bug in template names. (#2697) This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/` template. Resolves #2696 Refs #2451 commit 35d4d99eaac669721add9ddcc793153e5ab3b30a Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 08:06:53 2024 -0600 Update archive job to use COMIN/COMOUT (#2668) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow archive task. Refs #2451 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 47b3a581c8257fa24411fb400df8bb0e1e04972a Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Jun 17 22:55:38 2024 -0400 Turn on high-frequency output in extended test (#2679) Turns on high-frequency (hourly) output in the extended products test to exercise that aspect of the code. This test only runs on WCOSS. Also adds the hooks to optionally turn on the metplus jobs, but that is deferred as they are not currently working correctly. commit 38f2df9fb0c074b1f80d3c637080be79be693161 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jun 17 17:12:55 2024 +0000 Optimize wavepostpnt (#2657) Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs This is done by 1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by - performing operations on all files at once instead of looping over each file - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`) - combining `sed` and `grep` calls when possible - adding logic to `awk` calls instead of handling that logic in bash 2) minimizing as much as possible the amount of data on disk that has to be read in (e.g. limiting sed to read only the line numbers it needs) --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 5af325a6a4e0a14d180514a418603ca79fada487 Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Fri Jun 14 18:05:23 2024 -0400 Update GDASapp hash to move JCB into GDASapp (#2665) This PR moves JCB into GDASapp. The PR also bumps up the hash of GDASapp to what is in `feature/move_jcb`, which at time of writing is develop plus the absorption of JCB into GDASapp. Note that I also took the changes from https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the testing @RussTreadon-NOAA has done. commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b Author: Yaping Wang <49168260+ypwang19@users.noreply.github.com> Date: Fri Jun 14 10:18:17 2024 -0500 Add observation preparation job for aerosols DA to workflow (#2624) Add a prepaeroobs job to prepare aerosol obs files for DA. This job does quality control of the VIIRS aerosol raw observations and convert them to ioda format. Resolves #2623 --------- Co-authored-by: ypwang19 <yaping.wang@users.noreply.github.com> Co-authored-by: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Jun 14 11:04:41 2024 -0400 Remove ocean daily files (#2689) This PR removes the ocn_daily files that are produced by the ocean component. These files can be recreated by averaging data that exists in the 6 hour aveaged files if needed. Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675 Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by removing them and making this obsolete) commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jun 13 12:22:03 2024 -0400 Update Jenkinsfile needed a comma commit dc21eac6c3941d7f30803891d91d82f4cc1f8183 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jun 13 11:41:14 2024 -0400 Add Hercules-EMC to the Jenkins configurable parameter list (#2685) This quick-fix PR is to update the Jenkins Pipeline's configurable parameter list to include the **Hercules-EMC** node. This allows Jenkins users to restart Jobs in the controller when no updates have been made. commit ebacebfbe458634b8c80af6a735d6b6d01e4e406 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Thu Jun 13 11:20:24 2024 -0400 Update gdas.cd and gsi_utils hashes (#2641) This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea build for gsi_utils. Resolves #2640 commit 34155fb4767769600a1ff95f0a65e37081addc2a Author: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com> Date: Thu Jun 13 11:18:22 2024 -0400 Add ability to use GEFS replay ICs (#2559) The PR allows the use of ICs from PSL's replay analysis. These replay ICs will be used for GEFS reforecasting and SFS. Two main changes are associated with these updates: (1) replay ICs being valid at 3Z, and (2) the use of warm starts. Resolves #1838 --------- Co-authored-by: Jessica Meixner <Jessica.Meixner@noaa.gov> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Jun 12 19:25:42 2024 -0600 Replace `sleep` with `wait_for_file` (#2586) This PR addresses issue #2444. The following is accomplished: - All `sleep` statements are replaced with `wait_for_file` for the relevant scripts beneath `scripts` and `ush`; - Indentation and shell-norms are updated where applicable. Note: The WAFS scripts are not updated as per @aerorahul direction. Resolves #2444 --------- Co-authored-by: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 12 13:31:55 2024 -0400 Add COM template for JEDI obs (#2678) Adds a COM template to define a path to store obs processed for JEDI. This will allow UFSDA to stop writing to COM_OBS, which should be read-only as it belongs to obsproc in operations. No functional change yet. commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Wed Jun 12 09:06:23 2024 -0600 Link both global-nest fix files and non-nest ones at the same time (#2632) This PR enables linking both global-nest fix files and non-nest ones at the same time and users can run both nesting and non-nesting experiments at the same time without worries about what fix files to be linked. Resolves #2631 commit 61de004d4f9e9edf8a31bb173f2719b46451a36a Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jun 12 11:03:13 2024 -0400 Update ufs-weather-model (#2663) Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack allowing some temporary fixes to be reverted. * removes upp submodule * uses upp from the ufs-weather-model * restores the build and link that were hacked during the Hera Rocky 8 transition to allow for UPP submodule * Removes forecast directories in clean-up Resolves #2617 Resolves #2437 --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Wed Jun 12 01:15:37 2024 -0400 Add ability to process ocean/ice products specific to GEFS (#2561) This PR begins to add the capability to produce GEFSv13 ocean and ice products in the global-workflow according to stakeholder requirements. The following features are added. - An oceanice prod yaml file has been added to address the ocean and ice products specific to GEFSv13. - The rocoto dependencies and config.base for GEFS have also been modified to allow for 24-hour averaged ocean and ice output. - Various scripts have been modified to allow for ocean and ice output frequencies of 24 hours. - `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN` and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`. Refs #1878 commit 6691e7489650e0b738c176fbd096109288dc09b6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 11 21:15:07 2024 -0600 Update cleanup job to use COMIN/COMOUT (#2649) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow clean-up task. Refs #2451 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Jun 11 16:17:25 2024 -0400 Add overwrite to creat experiment in BASH CI (#2676) This is a quick hotfix to the CI BASH driver script adding `--overwrite` to create experiment script to avoid errors from restarting an experiment. commit e7909af8d9e1f34140388a3f8556d8e582c58fe5 Author: emilyhcliu <36091766+emilyhcliu@users.noreply.github.com> Date: Mon Jun 10 15:11:27 2024 -0400 Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py (#2645) This PR proposes updates for the following two scripts: 1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select CRTM cloud optical table based on cloud microphysical scheme indicated by `imp_physics' The default scheme in the GFS forecast model is Thompson scheme (imp_physics = 8). 2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in the script due to increased variables to interplate increments and calculate analysis in the netcdf_io routines in GSI-utils. Here is the related [PR #46 for GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46). --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 9caa51de8fb7be07d2e61775da01937d576964f6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Jun 6 22:15:23 2024 -0600 Update RDHPCS Hera resource for `eupd` task (#2636) As per @wx20jjung, the resource for the `eupd` task have been updated for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job fails. Resolves #2454 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Thu Jun 6 11:49:03 2024 -0400 Parameterize some things in config.atmanl and config.atmensanl (#2661) This PR adds some parameters in config.atmanl and config.atmensanl that can be altered with the defaults.yaml. The motivation is to make these files match those in the GDASApp JJOB tests (example: https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl), so we can just use the Global Workflow config.atmanl and config.atmensanl in the tests rather than custom ones in GDASApp that have to be separately updated every time the ones in the Global Workflow are updated. commit 54ea0b73a07921be5fbb07fe41e976888bd3e549 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Thu Jun 6 01:36:02 2024 -0400 Add links to the ocean insitu obs processing tools (#2644) Add links to the marine bufr to ioda converters for the marine insitu observations. - fixes https://github.com/NOAA-EMC/GDASApp/issues/1106 - waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135 commit 205d0c2b13e2d7755cec75bf8c978ab20d453862 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jun 5 17:31:30 2024 +0000 Update S4 point of contact in docs (#2660) Update the point of contact for global workflow issues on S4. commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed Jun 5 12:50:14 2024 -0400 Enable wcoss2 ufsda build and module load (#2620) This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2. Resolves #2602 Resolves #2579 commit 67b833e0c7bc390865d453588b4609a1a7ede981 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Tue Jun 4 13:33:43 2024 -0400 Update ufs-weather-model (#2646) Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6 This should resolve the issue and allow C768 runs on Hera and allow for CICE to run on WCOSS2 (due to library updates to allow linking). From what I can tell, all updates needed were done by @HenryWinterbottom-NOAA which were updates for CICE Fixes #2490 commit c44d0ac86cfdf78eb87492431bf6d825e8bae637 Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Tue Jun 4 10:29:49 2024 -0400 Update wmo parm files to fix WMO header (#2652) This PR updates wmo parm files to switch WMO header of precipitation type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to instantaneous. Resolves #2566 commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Tue Jun 4 13:55:33 2024 +0000 Add IAU to snow DA (and its test) (#2610) This PR enables IAU for the snow DA which is necessary for GFSv17. A snow analysis is created for the center of the window regardless, and an additional at the beginning of the window is added if IAU is on. The former is needed for UPP and the latter, to initialize the model. The increment is valid throughout the window for 3DVar, so the same increment is added to both forecasts. Additionally, the input file that goes into global_cycle has been updated to be the output of the JEDI snow analysis instead of the forecast (@jiaruidong2017 I recall discussing this, can you confirm this is right or am I mistaken) This PR also makes the CI test for snow DA (and aerosol DA) include IAU rather than without IAU,. --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit c92bf415060750127c9c05a62a1d2851c489551a Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Sat Jun 1 05:11:07 2024 +0000 Archiving cleanup (#2621) 1) Adds a lot of comments to the jinja templates for archiving 2) Rearranges the gdas and enkf templates to a more logical order 3) Fixes a couple of bugs in the enkf archiving of increments and analyses 4) Disables archiving for the half cycle 5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`, instead relying on `DO_FIT2OBS` 6) Updates wxflow to add the option to not allow undefined variables when parsing jinja templates and invokes this feature when running archives Resolves #2612 commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri May 31 04:57:08 2024 -0400 Switch to Rocky 9 built external packages on Hercules (#2608) The workflow was updated to use modules built on Rocky 9, but the external packages (like prepobs) were still pointing to the versions built on CentOS (Orion). This transitions to packages built on Rocky 9. Updating of the tracker package has been deferred until later. As such, the tracker jobs have been disabled by returning immediately if they are on Hercules. Since these jobs are small, resource-wise, it should not meaningfully impact turnover time. commit 4422550c01c9214a2b3b8890bdcc898123ee216a Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Thu May 30 08:05:23 2024 -0600 Add the capability to use slurm reservation nodes (#2627) Add the capability to use slurm reservation nodes Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE Resolves #2626 commit a54153fd9d26126206bc07a1da4e80f50c0c5910 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 29 23:24:07 2024 -0400 Update forecast job to use COMIN/COMOUT (#2622) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the forecast job. Refs #2451 --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit d69a8af95d492982b918670322ed5c41ab074335 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed May 29 21:29:03 2024 -0400 Update to add 1-deg global wave grid (#2619) This PR adds options to use a global 1 deg grid, intended for testing with the SFS application. Requires new fix file changes NOAA-EMC/global-workflow#2618 commit 0b4670ecf83b99b72835c8380573b2bca7cf5324 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed May 29 17:17:21 2024 -0400 Add C384mx025_3DVarAOWCDA yamls (#2625) Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder. commit 2e885d05c64b947f00a3cf055a1277fbfac195c9 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 29 13:00:51 2024 -0400 Script to keep Jenkins Agent persistent from cron (#2634) This "persistent" Java Agent launch script can be ran from a cron job: - Uses Jenkins Remote API to check the status of the Node connection using curl for a given machine. - If it is not connected a new agent is launched for that node. Resolves #2633 commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5 Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Tue May 28 17:17:11 2024 -0400 Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611) Based on users' feedback, this PR do the following: 1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF 2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD, and VOGRD) from "%g m below water surface" to "%g m below sea level" 3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m) Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31 Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Tue May 28 17:16:23 2024 -0400 Add atmensanlfv3inc job (#2592) This PR creates the atmensanlfv3inc job, the ensemble version of atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is #[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3). commit 50c2b8951b29a3c883a778becbf8582f9519eb48 Author: Anil Kumar <108816337+AnilKumar-NOAA@users.noreply.github.com> Date: Tue May 28 13:23:53 2024 -0400 Global-workflow (AR) Generic updates for Gaea C5 (#2515) - Port global-workflow’s build and run capability to Gaea-C5 - Building global-workflow on Gaea-C5 - Setting up experiments with global-workflow on Gaea-C5 --------- Co-authored-by: AnilKumar-NOAA <Anil.Kumar@gaea53.ncrc.gov> Co-authored-by: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> commit b6ca771a0c584cbfcbbf9be739765d5f3815df97 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 24 10:52:45 2024 -0400 Update STMP and PTMP settings in host file for Orion and Hercules (#2614) - Updating STMP and PTMP settings in host file for Orion and Hercules because they are cross mounted. - Also took the opportunity to finally update **SLURM_ACCOUNT** to **HPC_ACCOUT** in CI over rides. - Added a refactor of the `rocotostat.py` tool that is more pythonic and as a execute retry feature because the `rocotostat` utility on Orion has been failing sometimes. commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Tue May 21 23:50:50 2024 -0400 Sea-ice analysis insertion (#2584) Allows cycling and restarting CICE with the sea-ice analysis if the marine DA is switched on. Resolves #2568 Resolves NOAA-EMC/GDASApp#1103 commit 5369a1ff3a3969149fcf32810fad0e50216752b7 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue May 21 22:12:29 2024 +0000 Refactored archiving (#2491) This provides a new pygfs task, archive.py, that provides all of the tools necessary to archive data to the local (`ARCDIR`) and backup (`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to define the file to be archived or tarred to replace the `hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts and make it easier to add new data and explicitly handle optional and required files. For `ATARDIR` archiving, a master jinja template is provided for each `RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2, master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both `enkfgdas` and `enkfgfs` `RUN`s. These templates then include the appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on experiment, cycle, and coupled parameters. Each of these templates corresponds to a single tarball to populate and are tabbed 4 spaces so they are defined within the master `datasets` dictionary. Future developers should not have to make modifications to archive.py unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then only a single `elif` needs to be added to the configure method to specify the master `ATARDIR` template to archive (e.g. `master_gefs.yaml.j2`). If a new component is coming online that needs to be archived to `ATARDIR` (e.g. SNOW), then create a new template for each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`) and reference the template in the appropriate master templates, e.g. `master_gdas.yaml:` ```jinja {% if DO_SNOW %} {% include "gdassnow.yaml.j2" %} {% endif %} ``` A few other issues were addressed along the way: 1. Aerosols have been reenabled. Aerosol forecasts should only be performed during gdas cycles, but analyses can be performed for both gfs and gdas cycles. This was accomplished by setting separate `AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs. 2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`. This prevented restarts from being used for cice-enable experiments. This feature was not tested. 3. Create a temporary fix for the `wgrib` utility. For spack-stack 1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in existing installations. Once complete, this temporary fix should be removed. 4. The number of `earc` jobs has been reduced for lower resolution experiments. Both C48 and C96 experiments will now only have two earc jobs (one for the non-member files to archive and another for the member files). C192 will have up to 3 earc jobs (one non-member, one for members 1-40 and another for members 41-80, if needed). Resolves #2345 Resolves #2318 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 17 12:57:59 2024 -0400 Add remove RUNDIRS step in CI before creating experements (#2607) As had been done in Bash CI we need to remove the RUNDIR in Jenkins before a creating an experiment in the event that case had beem previously ran. commit 09333c01dbafddb2d2fe7e181b479af3cc6d3621 Merge: f7e9f4489 bb930050b Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Thu May 16 14:33:19 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit bb930050b3cd51d28ecba6b231c8675f6d11856c Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu May 16 12:28:30 2024 -0400 Adds jjob and other necessities for marine LETKF task (#2564) Adds jjob, rocoto script, config file, and other necessities for new marine LETKF task. Partially addresses NOAA-EMC/GDASApp#1091 commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu May 16 12:12:06 2024 -0400 Updating CI Machine configs with redundant PTMP (#2605) Quick fix adding PTMP as STMP in Machine configs for CI for completeness commit ef340ff33a6f89adf70838206ba3fd56a953fa7a Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu May 16 11:37:30 2024 -0400 Fix race condition in CI between Orion and Hercules (#2604) Hotfix to solve race conditions in the CI system due to cross-mounted file systems between Orion and Hercules commit e8b17e27f719df280170dc3f5bd9f19917cefaf2 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 15 17:16:30 2024 -0400 Remove existing EXPDIRs and COMROTs when CI is re-run (#2601) Quick hotfix for having default for re-runing jobs to start clean with new EXPDIRs and COMROTs commit b5d113efb1970ede5cd1d3d4dff8d96320519c41 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 15 16:52:49 2024 -0400 Moving logic for skipping hosts in pr cases (#2573) This PR removes the logic of skipping hosts for pr cases from `create_experiment.py` and moves it to a test in the cron bash driver using a `parse_yaml.py` python tool. The Jenkins pipeline was not effected as it uses the `get_host_case_list.py` utility to form the cases on a per host bases. Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed May 15 13:13:30 2024 -0400 Update gsi_utils.fd hash (#2598) This PR updates the `gsi_utils.fd` hash to bring in updates which add safeguards to - `src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90` - `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90` The safeguards are described in GSI-utils PR [#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated issue. Resolves #2597 commit d5366c66bd67f89d118b18956fe230207cbf0aea Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 15 13:12:56 2024 -0400 Update CICE and MOM6 fix versions (#2600) This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions to the newer `20240416` timestamps, which includes updates and fixes to the `100` (1-deg) resolution files. Resolves #2480 Resolves #2483 Resolves #2595 commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon May 13 22:57:38 2024 +0000 Limit gfswavepostpnt to 40 PEs/node (#2588) This fixes the slow runtime of the gfswavepostpnt job on Hercules. The job is very I/O intensive and does not scale well to large nodes, so limit the number of jobs/node to 40. Resolves #2587 commit 4fb7c12c325702a47f27c802a5067efd33d0327c Author: Fanglin Yang <fanglin.yang@noaa.gov> Date: Mon May 13 16:37:51 2024 -0400 Update damping and time-step (#2575) Updates the model to use explicit Rayleigh damping for u/v and implicit damping to w. This improves model stability and allows for longer timesteps. Also unifies the GDAS and GFS to use the same damping. Results from a test at the C1152 resolution (coupled model) can be found at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/ Resolves #2574 Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Lisa Bengtsson <lbengtss@Orion-login-1.HPC.MsState.Edu> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 10 14:17:13 2024 -0400 Do not use BUILT_semphore to force rebuilds when re-run (#2593) Remove the placement of the `BUILT_semaphore` file after the build in the Jenkins Pipeline and force it to rebuild any changes after a PR is re-ran. commit 2346c6161f75ae02369cbf30f30c6150d3e12b66 Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com> Date: Thu May 9 21:17:06 2024 -0500 Migration to Rocky8 spack-stack installations on Jet (#2458) # Description Migrates Global Workflow to Rocky8 spack-stack installations on Jet. Jet has moved from CentOS7 to Rocky8. Resolves #2377 Refs NOAA-EMC/UPP#919 Refs NOAA-EMC/gfs-utils#60 Refs NOAA-EMC/GSI#732 Refs NOAA-EMC/GSI-Monitor#130 Refs NOAA-EMC/GSI-utils#33 commit c7b3973014480a20dd8e24edaeb83a9e9e68159f Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu May 9 11:36:58 2024 -0400 Updates for cold start half cycle, then continuing with IAU for WCDA (#2560) This PR allows us to run C384 S2S with IAU, but starting with the first half-cycle as a cold-start. This will be necessary for cycled testing as we build towards the full system for GFSv17. This updates the copying of the restarts for RUN=gdas for both ocean and ice copying what the atm model is doing. It also reduced the amount of restart files from 4 to 3. Other updates: * Add DOJEDI ocean triggers for archiving certain files update from: @CatherineThomas-NOAA * Adds COPY_FINAL_RESTARTS option to turn on/off copying the last restart file to COM. Defaults to off... * Defines model_start_date_current_cycle & model_start_date_next_cycle to help with knowing which IC to grab. Refs #2546 Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2 Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Wed May 8 20:52:48 2024 -0400 Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477) Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI Configuration Builder (JCB) tool so that YAMLs can be made more portable and invoke the observation chronicle mechanism. Resolves #2476 Co-authored-by: danholdaway <danholdaway@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 8 02:04:16 2024 -0400 Add CI test for products (#2567) Adds a new version of the atm3DVar test that runs the full forecast length and produces most of the secondary products. For now, this test will only run on WCOSS due to gempak failures on other machines as well as computational needs. On other machines, the original version will run (the original version will not run on WCOSS). AWIPS remains off for now in this extended test due to a bug involving tocgrib2 and the convective precip fields (see #2566). The new test runs for 4½ cycles and the full 384-hr forecast length to ensure all gempak scripts are exercised. Since the cycle throttle is 3 and the bulk of the time is in the free forecast, the cycles run mostly concurrently so it doesn't extend the total test time too much beyond that of a single 384-hr forecast. Fixes a bug in NPOESS that was introduced when the post filenames were reverted to the previous format for the GOES products until the final filenames are determined (#2499). Also removes the AWIPS g2 job from the rocoto mesh to complete the retirement of grib1 products. Resolves #2132 Resolves #2445 commit 9b6f8404ac4507d14adc404b77cfdf002b55e832 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue May 7 00:14:36 2024 -0400 Add task to prepare emissions for GEFS (#2562) This PR: - introduces a task to prepare emissions for a forecast into the GEFS application. - adds configuration, j-job, rocoto job, ex-script and the python class for this job - updates GEFS workflow to be able to generate the XML to call this job. - updates the `fcst` and `efcs` job dependencies in the GEFS application to depend on `prep_emissions` if aerosols are turned ON. - provides a placeholder for @bbakernoaa to work on the details for preparing emissions. Co-authored-by: Walter Kolczynski - NOAA <Walt…

* Added alpha_fd coefficient for Beljaars TOFD in GSL drag bug fix Update INFO * Update develop branch, gsl_ufs_dev Squashed commit of the following: commit 4ad0d52a6fbb581a9804bd0bb627b7c52f338bad Author: kayee.wong <kayee.wong@noaa.gov> Date: Thu Sep 19 19:20:06 2024 +0000 For pygraf plotting. commit 1bfba70ed6aaa3eb47974006ed0c5cae653b8ce8 Author: kayee.wong <kayee.wong@noaa.gov> Date: Thu Sep 19 04:27:55 2024 +0000 Fixed gfsatmprod file name and gfsarch data type. commit 4e0a81f7acf5ccba5de8d3bdf7ab19cae80812cb Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 18:37:50 2024 +0000 Fix typos/links/dependancy. commit d5fdcbf8d6e987dbdfcd6b4da34d0934c8d82c3b Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 07:37:52 2024 +0000 Fixed missing config.base files. commit c6239f925369b20fd8488e8537969e2f4f9e7725 Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 06:53:47 2024 +0000 Update submodule hashs. commit 32bf790f67b818ff50a7f6b74388fb81ed175b3a Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 06:09:41 2024 +0000 Update develop branch, gsl_ufs_dev - based on gsl_ufs_dev from KaYee's fork global-workflow: 07Aug24,37c53ac [develop_07Aug2024_37c53ac] UFS: 19Jul24, c127601 FV3: 19Jul24, 2527c11 UPP: 23Apr24, be0410e CCPP-PHYSICS: 19Jul24, 46df080 UFS_UTILS: 26Jun24, 3ef2e6b Squashed commit of the following: commit 70b557836379bb7e545fcc6642e28d66cfc17735 Merge: 5edbd123e 37c53ac69 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Wed Aug 7 11:02:24 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 7 08:11:21 2024 -0400 Revert MSU FIX_DIRs back to glopara (#2811) commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Aug 6 14:47:36 2024 -0400 Bugfix for updating label states in Jenkins (#2808) Quick bug fix for updating state labels in CI during finalize. (did not reference GitHub CLI executable correctly in the pipeline script) commit 8fee36f0307b0c08080e3a8fa8fa6703e7da5fce Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Aug 6 11:02:45 2024 -0400 Clean-up temporary rundirs - take 2. (#2753) This PR: - is a follow-up to a previous PR that aggressively pruned run directories. - removes run directories for the current cycle in the clean-up if the cycle is successful. If the cycle is not successful, cleanup is not called and all run directories for the cycle are safe from being purged. - also updates the PR template to list/query for any updates to submodules. --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: David Huber <david.huber@noaa.gov> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit d599fff4aedd41ae587dbe02226acb12ff48efc1 Author: HelinWei-NOAA <48133472+HelinWei-NOAA@users.noreply.github.com> Date: Mon Aug 5 05:31:31 2024 -0400 Change land surface for HR4 (#2787) Resets the default value of opt_diag to 2 corresponding to the land surface upgrades in ufs-weather-model for HR4. Resolves #2786 commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Aug 2 15:41:29 2024 -0400 Run METplus serially and correct the name of prod tasks (#2804) Adds 2 hot fixes: - METplus v9.1.3 has a bug in it that sometimes attempts to create multiple copies of the same directory when running in parallel, causing a Python error and downstream problems. This PR makes METplus run in serial mode, preventing such issues. - Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod) commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri Aug 2 15:03:45 2024 -0400 Update Java Agent launching script for Jenkins connections (#2762) Made updates to the Jenkins Launching Script for robustness and less ambiguous documentation: - Clearer distinction between required user token for the remote api and the systems token for launching - Added pre-checks: `gh` is authenticating, named compliant token and secret file exists - More robust Jason based parser of the remote api response for checking the state of the Node connection - For `cron` use a 5 minute pause and recheck was added before re-launching of the java agent - Added concise header documentation of requirements and purpose --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit b73b1fd203496db97f8067652659573a632bcc67 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Aug 2 07:59:06 2024 -0400 Fix erroneous cdump addition (#2803) commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Aug 1 20:26:13 2024 -0400 Update ocean post-processing triggers (#2784) This PR: - replaces `check_netcdf.sh` checker for ocean post-processing with with ocean output at the next forecast hour or finishing of the forecast job for ocean prod - removes no longer needed `ush/check_netcdf.sh` commit aa2af1ca8d59424a60a1730722bf528775d9e606 Author: GeorgeGayno-NOAA <52789452+GeorgeGayno-NOAA@users.noreply.github.com> Date: Thu Aug 1 16:46:10 2024 -0400 Update the gfs_utils repository hash (#2801) # Description Point to the latest hash of the gfs-utils repository, which contains the bug fix to gaussian_sfcanl. Resolves #2669. Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73 commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Aug 1 08:12:14 2024 -0400 Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791) Changes how METplus jobs run so that they run on the last GFS cycle for a given `PDY`. This is a departure from operations where the METplus jobs run on the 00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through `${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on `${PDY}18` for cycles 00-18. See https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details. commit 1cf8b448af562dbb7af198399c78c585977e81da Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 30 10:38:49 2024 -0400 Simplify resource-related variables, remove CDUMP where unneeded (#2727) This overhauls resource-related variables to use a common set of variables for each job. In the process, this also removed the use of CDUMP in most cases. Resolves #1299 #2693 commit 61875f25c9e971f82ae499b5b612d7f095deebd4 Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Mon Jul 29 14:40:03 2024 -0400 Remove f000 from atmos rocoto tasks for replay cases (#2778) The main purpose of this PR is to remove the f000 from atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater than `0`, it becomes necessary to have the first lead hour set to `OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and the minimum lead time for the ocean_prod rocoto task needs to be 6 (assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up possible by removing 0 from fhrs for atmosphere-related tasks in `gefs_tasks.py` when replaying. This PR also moves where f000 is being removed for the ocean_prod and ice_prod tasks. The if-block that performs this f000 removal has been moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`. --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit f156a7894d639f177e3e2588f98eec1f6f59aa68 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Jul 26 14:18:32 2024 -0500 HR4 GWD update (#2732) This update is a combination of the gravity wave drag (GWD) versions from the NOAA/GSL and NOAA/PSL commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Jul 25 14:26:52 2024 -0400 Temporarily disable METplus jobs (#2796) commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Wed Jul 24 15:00:35 2024 -0400 Refactoring of the marine B-matrix job (#2749) Refactor the functionality of B-matrix generation from the GDASApp Resolves #2743 commit 65a7ab75dc0e4baba06a02e11ed0455787056a68 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 23 08:35:48 2024 -0400 Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775) Removes the namespace-based construction of EnKF member COM directories in the enkf archive template. commit c45b9611f3e701b819bd33dc5af29033f060bb91 Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Tue Jul 23 00:33:16 2024 -0400 Add task to process reforecast variables to save on WCOSS2 (#2680) # Description This PR adds an optional task to the global-workflow to process a subset of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for the GEFSv13 reforecast. This task is designed to process GEFS variables so that specific reforecast product requirements are met. A new variable in `config.base` called `DO_EXTRACTVARS` enables this task, which is currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by default and is specifically a task designed to be executed for the GEFSv13 reforecast. Refs #1878 # Type of change - New feature (adds functionality) # Change characteristics - Is this a breaking change (a change in existing functionality)? NO - Does this change require a documentation update? NO # How has this been tested? This has been cloned and tested on WCOSS2. This will need to be tested on Hera and other platforms on which the reforecast may be running. # Checklist - [ ] Any dependent changes have been merged and published - [x] My code follows the style guidelines of this project - [x] I have performed a self-review of my own code - [ ] I have commented my code, particularly in hard-to-understand areas - [x] My changes generate no new warnings - [x] New and existing tests pass with my changes - [ ] I have made corresponding changes to the documentation if necessary --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 71dc33c6ca991c16ce743760d99feaaf60f2218a Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jul 22 14:51:53 2024 -0400 Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774) Fix metp* resources and check that they completed properly; add support for Orion Rocky 9 commit 56df67a90fe090c425199f1285e5aac722c398b1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jul 22 09:28:18 2024 -0400 Hotfix: Update jcb to avoid git-lfs files (#2782) Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to be cloned on Hera. This hotfix points to a non-authoritative branch of the GDASApp (https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and should be updated ASAP back to the authoritative repository. commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jul 16 09:44:00 2024 -0400 Address issues in creating XML for GFS forecast-only with app S2SWA (#2757) This bugfix PR: - fixes an issue where a user is unable to generate the XML for a GFS forecast-only experiment with APP=S2SWA Specifically, the changes are related to defining `aero_fcst_cdumps`. Following `setup_expt.py`, the user will have to set `AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in `config.base`. commit e0878dba0e53706a7f53429b61aee2936e2c21bf Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Jul 15 10:25:11 2024 -0400 Updated prepobs and fit2obs versions for Orion Rocky9 (#2758) Update prepobs to v1.0.2 and fit2obs to v1.1.2 These versions now support Orion Rocky9. Updates are included for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet. commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jul 11 17:48:47 2024 +0000 CI maintenance updates and adding CI Unit Tests (#2740) This PR has a few maintenance updates to the CI pipeline and adds a test directory with Unit Tests **Major Maintenance updates:** - Added try blocks with appropriate messaging to GitHub PR of failure for: - - **scm** checkout - - build fail (with error logs sent as gists) - - create experiment fails with `stderr` sent to GitHub PR messaging - Pre-stage FAILS from the above are now captured these fails allow FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state labels in GitHub - see image below) **Minor Maintenance updates:** - Fix for STALLED cases reviled from PR 2700 (just needed a lambda specifier) - Fixed path to experiment directory in PR message (had dropped EXPDIR in path) - Needed `latin-1` decoder in reading log files for publishing **Added python Unit Tests for CI functionality:** - Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI utility codes - Cashed the install of Rocoto in the GitHub Runners to greatly reduce stetup time for running the unit tests - Unit Tests Python scripts added - `test_rocostat.py`: rocoto_statcount() rocoto_summary() rocoto_stalled() - `test_setup.py`: setup_expt() test_setup_xml() - `test_create_experment`: test_create_experiment() - - Runs all PR cases that do not have ICs in the GItHub Runner - Reporting mechanism in the Actions tab for Python Unit Testing results - Test case data for STALLED and RUNNING stored on S3 and pulled using wget during runtime of tests commit 5ef4db74649b8be03402c17aa29c024e71699a7b Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu Jul 11 08:59:24 2024 -0400 Adds contents of constructor and initialize methods to marine LETKF class (#2635) Adds contents of constructor and initialize methods to marine LETKF class Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091 --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> commit 8998ec7b74123e953b97a93fa14cc78d471a1aee Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 9 08:31:57 2024 -0400 Fix GDAS group B restart archiving (#2735) Archives the GDAS restartb dataset at a 6-hour offset from restarta This allows cycled experiments to restart from the archives. The tabbing for the master archive templates was also added to improve readability. Resolves #2722 commit 3ca74771255727033b9dc043c652ac585178629c Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Tue Jul 9 08:28:54 2024 -0400 Add fcst dependency to ocnanalprep (#2728) Add previous cycle's `fcst` as a dependency to `ocnanalprep` This ensures that the availability of restart files to the latter. This addresses a seldomly-encountered race condition where `ocnanalprep` fails due to the lack of the files. commit 58fca1668aecd6fb1afd12a441256ad35900e075 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jul 5 15:02:23 2024 -0400 Update (partially) global-workflow for orion+rocky9 (#2741) This PR: - updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils, GFS-utils) to include recent update to their modulefiles for Orion+Rocky9 upgrade - updates the modulefiles in global-workflow to load modules from Orion+Rocky9 paths - updates modulefiles for `gwsetup` and `gwci` as well. - removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not installed. - adds `parm/config.gfs/config.resources.ORION` to address GSI performance degradation after Rocky 9 upgrade. This PR: - does not update the build for UPP. Standalone UPP is not available via ufs-weather-model as of #2729 - will need a follow-up update for `prepobs` and `fit2obs` updated locations when they are installed in `glopara` space on Orion. # Type of change - Maintenance (code refactor, clean-up, new CI test, etc.) # Change characteristics - Is this a breaking change (a change in existing functionality)? NO - Does this change require a documentation update? NO # How has this been tested? This PR is not sufficient for Orion. This PR must be tested on other platforms (Hera, WCOSS2) as this PR updates submodules. # Checklist - [ ] Any dependent changes have been merged and published - [ ] My code follows the style guidelines of this project - [ ] I have performed a self-review of my own code - [ ] I have commented my code, particularly in hard-to-understand areas - [ ] My changes generate no new warnings - [ ] New and existing tests pass with my changes - [ ] I have made corresponding changes to the documentation if necessary --------- Co-authored-by: Kate Friedman <kate.friedman@noaa.gov> commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jul 3 21:07:49 2024 -0400 Update ufs model hash to 20240625 (#2729) Updates UFS weather model hash to hash from 2024-06-24 which has orion porting updates + a few namelist updates. commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jul 3 11:32:40 2024 -0400 Hotfix for undefined CLUSTERS (#2748) Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses the native `dict` `get` method to prevent grabbing an unset entry. commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Wed Jul 3 09:56:08 2024 -0400 Update gempak job to run one fcst hour per task (#2671) This PR updates gempak jobs (gfs, gdas, and goes) from processing all forecast hours at once to one forecast hour at a time. This will reduce the job runtime to less than 5 min, so restart capability is not needed. Resolves #1250 Ref #2666 #2667 --------- Co-authored-by: Walter.Kolczynski <Walter.Kolczynski@noaa.gov> commit 8215ae654202186a4f753c3abe937b7b9b91a9c7 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jul 2 16:22:11 2024 -0400 Hotfix for clusters from #2701 (#2747) Fixes an issue created from #2701 that added `CLUSTERS` to the `gaea.yaml`. commit 11943e36ba12b3df49c51942da780698fab02d38 Author: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> Date: Tue Jul 2 12:58:10 2024 -0400 Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701) This PR sets up the ability on Gaea for auto generation of a clean xml file, i.e., an xml file that does not need any alterations before running rocoto. Refs #2572 Refs #2664 commit de8706702ead0630beb54d868f83aa2cb23f8f79 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon Jul 1 09:29:14 2024 -0400 Update for JCB policies and stage DA job files with Jinja2-templates (#2700) This PR updates the `gdas.cd` hash to bring in new JCB conventions. Resolves #2699 From #2654 This PR will move much of the staging code that take place in the python initialization subroutines of the variational and ensemble DA jobs into Jinja2-templated YAML files to be passed into the wxflow file handler. Much of the staging has already been done this way, but this PR simply expands that strategy. The old Python routines that were doing this staging are now removed. This is part of a broader refactoring of the pygfs tasking. wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a companion to this PR. Co-authored-by: danholdaway <danholdaway@users.noreply.github.com> Co-authored-by: DavidNew-NOAA <david.new@noaa.gov> Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Co-authored-by: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jun 28 14:56:19 2024 -0400 Revert PR 2681 (#2739) This PR: - reverts #2681 in part - keeps some changes for `RUN`. - is a hotfix - should be merged ASAP after consensus w/ @guillaumevernieres @CatherineThomas-NOAA @WalterKolczynski-NOAA commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed Jun 26 15:46:08 2024 -0400 updated Finalize in Jenkinsfile and added try block around scm checkout (#2692) We are updating the Jenkins Pipeline with a try block around checkout to capture errors for the user. Also cleaned up Finalize and added section to clean out workspace on success. commit 968568f682bac7564095440bdb7813abefd76821 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 26 13:27:19 2024 -0400 Activate snow DA test on WCOSS (#2720) Activate the snow DA test on WCOSS. commit 7706760bb8adbdf78cb640b02739023c886e7699 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jun 26 10:02:22 2024 -0400 Cleanup of stale RUNDIRS from an experiment (#2719) This PR: - removes stale temporary scratch run directories from `$DATAROOT/` every 3 days. - should help to scrub failed attempts. - removes an unused variable `RUNDIR` defined in `config.base` commit 8962991691b5f0857b813bddfd28aa1034d4bd2b Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jun 26 09:43:48 2024 -0400 Update logic for MOM6 number of layers/exception values (#2681) Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine how many layers and sets the exception value for MOM6 to be 1e-34 for all scenarios. Note, we will no longer have zeros in the ocean grib output and the DA will also run without issues. Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615 commit 12431f76bdce807067929415007592cffc8a2457 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Jun 26 07:42:35 2024 -0600 Update wave jobs to use COMIN/COMOUT (#2643) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow wave model and products tasks. Refs #2451 commit b902c0bac126c323a07186ad8881384b032b6fda Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jun 25 07:48:46 2024 -0400 Assign machine- and RUN-specific resources (#2672) Redefine resource variables based explicitly on RUN or CDUMP Additionally, machine-specific resources are moved out of config.resources and placed in respective config.resources.{machine} files. Resolves #177 #2672 commit 5edbd123e2878a07f5cce8e3c7ea6147f286633a Merge: 09333c01d 4e1b937b6 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Mon Jun 24 12:44:05 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit 4e1b937b67ed220120e81925c4507f03b9b8965f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jun 24 10:50:52 2024 -0400 Add minimum software requirements (#2712) Adds a table to HPC documentation stating the minimum support versions commit f43a86276aaef91efa28faadc71a3cf50e749efe Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Jun 21 13:44:29 2024 -0400 Fix and simplify online archiving and reenable METplus jobs (#2687) This fixes the online archiving portion of the `*arch` and `*earc00` jobs, a prerequisite for running METplus. This also reenables METplus by default. The approach previously taken created `FileHandler` dictionaries at varying levels within the resulting yaml, which was not properly parsed by `exglobal_archive.py`. This approach creates a single `FileHandler` dictionary and is much less complicated overall. Resolves #2673 #2647 commit 8993b42cb91144c0ab0501dc7841ea8d675c4701 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 19 21:51:22 2024 -0400 Eliminate post groups (#2667) Eliminates the post groups used for upp and products jobs so that each task only processes one forecast hour. This is more efficient and greatly simplifies downstream dependencies that depend on a specific forecast hour. Resolves #2666 Refs #2642 commit 0b810c888239853fedd0e4584fe62536c6aaacdf Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 20:32:48 2024 -0600 Removes misleading "No such file or directory" syntax errors from output files (#2688) This PR addresses issue #1252. The following is accomplished: - Prior to removing files, the existence of a file is checked prior to attempting to remove; this is performed as noted [here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369); this PR only addresses the the `chgrp` issue. Refs #1252 --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 12:17:59 2024 -0600 Hotfix for bug in template names. (#2697) This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/` template. Resolves #2696 Refs #2451 commit 35d4d99eaac669721add9ddcc793153e5ab3b30a Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 08:06:53 2024 -0600 Update archive job to use COMIN/COMOUT (#2668) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow archive task. Refs #2451 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 47b3a581c8257fa24411fb400df8bb0e1e04972a Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Jun 17 22:55:38 2024 -0400 Turn on high-frequency output in extended test (#2679) Turns on high-frequency (hourly) output in the extended products test to exercise that aspect of the code. This test only runs on WCOSS. Also adds the hooks to optionally turn on the metplus jobs, but that is deferred as they are not currently working correctly. commit 38f2df9fb0c074b1f80d3c637080be79be693161 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jun 17 17:12:55 2024 +0000 Optimize wavepostpnt (#2657) Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs This is done by 1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by - performing operations on all files at once instead of looping over each file - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`) - combining `sed` and `grep` calls when possible - adding logic to `awk` calls instead of handling that logic in bash 2) minimizing as much as possible the amount of data on disk that has to be read in (e.g. limiting sed to read only the line numbers it needs) --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 5af325a6a4e0a14d180514a418603ca79fada487 Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Fri Jun 14 18:05:23 2024 -0400 Update GDASapp hash to move JCB into GDASapp (#2665) This PR moves JCB into GDASapp. The PR also bumps up the hash of GDASapp to what is in `feature/move_jcb`, which at time of writing is develop plus the absorption of JCB into GDASapp. Note that I also took the changes from https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the testing @RussTreadon-NOAA has done. commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b Author: Yaping Wang <49168260+ypwang19@users.noreply.github.com> Date: Fri Jun 14 10:18:17 2024 -0500 Add observation preparation job for aerosols DA to workflow (#2624) Add a prepaeroobs job to prepare aerosol obs files for DA. This job does quality control of the VIIRS aerosol raw observations and convert them to ioda format. Resolves #2623 --------- Co-authored-by: ypwang19 <yaping.wang@users.noreply.github.com> Co-authored-by: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Jun 14 11:04:41 2024 -0400 Remove ocean daily files (#2689) This PR removes the ocn_daily files that are produced by the ocean component. These files can be recreated by averaging data that exists in the 6 hour aveaged files if needed. Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675 Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by removing them and making this obsolete) commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jun 13 12:22:03 2024 -0400 Update Jenkinsfile needed a comma commit dc21eac6c3941d7f30803891d91d82f4cc1f8183 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jun 13 11:41:14 2024 -0400 Add Hercules-EMC to the Jenkins configurable parameter list (#2685) This quick-fix PR is to update the Jenkins Pipeline's configurable parameter list to include the **Hercules-EMC** node. This allows Jenkins users to restart Jobs in the controller when no updates have been made. commit ebacebfbe458634b8c80af6a735d6b6d01e4e406 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Thu Jun 13 11:20:24 2024 -0400 Update gdas.cd and gsi_utils hashes (#2641) This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea build for gsi_utils. Resolves #2640 commit 34155fb4767769600a1ff95f0a65e37081addc2a Author: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com> Date: Thu Jun 13 11:18:22 2024 -0400 Add ability to use GEFS replay ICs (#2559) The PR allows the use of ICs from PSL's replay analysis. These replay ICs will be used for GEFS reforecasting and SFS. Two main changes are associated with these updates: (1) replay ICs being valid at 3Z, and (2) the use of warm starts. Resolves #1838 --------- Co-authored-by: Jessica Meixner <Jessica.Meixner@noaa.gov> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Jun 12 19:25:42 2024 -0600 Replace `sleep` with `wait_for_file` (#2586) This PR addresses issue #2444. The following is accomplished: - All `sleep` statements are replaced with `wait_for_file` for the relevant scripts beneath `scripts` and `ush`; - Indentation and shell-norms are updated where applicable. Note: The WAFS scripts are not updated as per @aerorahul direction. Resolves #2444 --------- Co-authored-by: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 12 13:31:55 2024 -0400 Add COM template for JEDI obs (#2678) Adds a COM template to define a path to store obs processed for JEDI. This will allow UFSDA to stop writing to COM_OBS, which should be read-only as it belongs to obsproc in operations. No functional change yet. commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Wed Jun 12 09:06:23 2024 -0600 Link both global-nest fix files and non-nest ones at the same time (#2632) This PR enables linking both global-nest fix files and non-nest ones at the same time and users can run both nesting and non-nesting experiments at the same time without worries about what fix files to be linked. Resolves #2631 commit 61de004d4f9e9edf8a31bb173f2719b46451a36a Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jun 12 11:03:13 2024 -0400 Update ufs-weather-model (#2663) Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack allowing some temporary fixes to be reverted. * removes upp submodule * uses upp from the ufs-weather-model * restores the build and link that were hacked during the Hera Rocky 8 transition to allow for UPP submodule * Removes forecast directories in clean-up Resolves #2617 Resolves #2437 --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Wed Jun 12 01:15:37 2024 -0400 Add ability to process ocean/ice products specific to GEFS (#2561) This PR begins to add the capability to produce GEFSv13 ocean and ice products in the global-workflow according to stakeholder requirements. The following features are added. - An oceanice prod yaml file has been added to address the ocean and ice products specific to GEFSv13. - The rocoto dependencies and config.base for GEFS have also been modified to allow for 24-hour averaged ocean and ice output. - Various scripts have been modified to allow for ocean and ice output frequencies of 24 hours. - `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN` and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`. Refs #1878 commit 6691e7489650e0b738c176fbd096109288dc09b6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 11 21:15:07 2024 -0600 Update cleanup job to use COMIN/COMOUT (#2649) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow clean-up task. Refs #2451 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Jun 11 16:17:25 2024 -0400 Add overwrite to creat experiment in BASH CI (#2676) This is a quick hotfix to the CI BASH driver script adding `--overwrite` to create experiment script to avoid errors from restarting an experiment. commit e7909af8d9e1f34140388a3f8556d8e582c58fe5 Author: emilyhcliu <36091766+emilyhcliu@users.noreply.github.com> Date: Mon Jun 10 15:11:27 2024 -0400 Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py (#2645) This PR proposes updates for the following two scripts: 1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select CRTM cloud optical table based on cloud microphysical scheme indicated by `imp_physics' The default scheme in the GFS forecast model is Thompson scheme (imp_physics = 8). 2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in the script due to increased variables to interplate increments and calculate analysis in the netcdf_io routines in GSI-utils. Here is the related [PR #46 for GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46). --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 9caa51de8fb7be07d2e61775da01937d576964f6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Jun 6 22:15:23 2024 -0600 Update RDHPCS Hera resource for `eupd` task (#2636) As per @wx20jjung, the resource for the `eupd` task have been updated for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job fails. Resolves #2454 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Thu Jun 6 11:49:03 2024 -0400 Parameterize some things in config.atmanl and config.atmensanl (#2661) This PR adds some parameters in config.atmanl and config.atmensanl that can be altered with the defaults.yaml. The motivation is to make these files match those in the GDASApp JJOB tests (example: https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl), so we can just use the Global Workflow config.atmanl and config.atmensanl in the tests rather than custom ones in GDASApp that have to be separately updated every time the ones in the Global Workflow are updated. commit 54ea0b73a07921be5fbb07fe41e976888bd3e549 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Thu Jun 6 01:36:02 2024 -0400 Add links to the ocean insitu obs processing tools (#2644) Add links to the marine bufr to ioda converters for the marine insitu observations. - fixes https://github.com/NOAA-EMC/GDASApp/issues/1106 - waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135 commit 205d0c2b13e2d7755cec75bf8c978ab20d453862 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jun 5 17:31:30 2024 +0000 Update S4 point of contact in docs (#2660) Update the point of contact for global workflow issues on S4. commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed Jun 5 12:50:14 2024 -0400 Enable wcoss2 ufsda build and module load (#2620) This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2. Resolves #2602 Resolves #2579 commit 67b833e0c7bc390865d453588b4609a1a7ede981 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Tue Jun 4 13:33:43 2024 -0400 Update ufs-weather-model (#2646) Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6 This should resolve the issue and allow C768 runs on Hera and allow for CICE to run on WCOSS2 (due to library updates to allow linking). From what I can tell, all updates needed were done by @HenryWinterbottom-NOAA which were updates for CICE Fixes #2490 commit c44d0ac86cfdf78eb87492431bf6d825e8bae637 Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Tue Jun 4 10:29:49 2024 -0400 Update wmo parm files to fix WMO header (#2652) This PR updates wmo parm files to switch WMO header of precipitation type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to instantaneous. Resolves #2566 commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Tue Jun 4 13:55:33 2024 +0000 Add IAU to snow DA (and its test) (#2610) This PR enables IAU for the snow DA which is necessary for GFSv17. A snow analysis is created for the center of the window regardless, and an additional at the beginning of the window is added if IAU is on. The former is needed for UPP and the latter, to initialize the model. The increment is valid throughout the window for 3DVar, so the same increment is added to both forecasts. Additionally, the input file that goes into global_cycle has been updated to be the output of the JEDI snow analysis instead of the forecast (@jiaruidong2017 I recall discussing this, can you confirm this is right or am I mistaken) This PR also makes the CI test for snow DA (and aerosol DA) include IAU rather than without IAU,. --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit c92bf415060750127c9c05a62a1d2851c489551a Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Sat Jun 1 05:11:07 2024 +0000 Archiving cleanup (#2621) 1) Adds a lot of comments to the jinja templates for archiving 2) Rearranges the gdas and enkf templates to a more logical order 3) Fixes a couple of bugs in the enkf archiving of increments and analyses 4) Disables archiving for the half cycle 5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`, instead relying on `DO_FIT2OBS` 6) Updates wxflow to add the option to not allow undefined variables when parsing jinja templates and invokes this feature when running archives Resolves #2612 commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri May 31 04:57:08 2024 -0400 Switch to Rocky 9 built external packages on Hercules (#2608) The workflow was updated to use modules built on Rocky 9, but the external packages (like prepobs) were still pointing to the versions built on CentOS (Orion). This transitions to packages built on Rocky 9. Updating of the tracker package has been deferred until later. As such, the tracker jobs have been disabled by returning immediately if they are on Hercules. Since these jobs are small, resource-wise, it should not meaningfully impact turnover time. commit 4422550c01c9214a2b3b8890bdcc898123ee216a Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Thu May 30 08:05:23 2024 -0600 Add the capability to use slurm reservation nodes (#2627) Add the capability to use slurm reservation nodes Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE Resolves #2626 commit a54153fd9d26126206bc07a1da4e80f50c0c5910 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 29 23:24:07 2024 -0400 Update forecast job to use COMIN/COMOUT (#2622) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the forecast job. Refs #2451 --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit d69a8af95d492982b918670322ed5c41ab074335 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed May 29 21:29:03 2024 -0400 Update to add 1-deg global wave grid (#2619) This PR adds options to use a global 1 deg grid, intended for testing with the SFS application. Requires new fix file changes NOAA-EMC/global-workflow#2618 commit 0b4670ecf83b99b72835c8380573b2bca7cf5324 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed May 29 17:17:21 2024 -0400 Add C384mx025_3DVarAOWCDA yamls (#2625) Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder. commit 2e885d05c64b947f00a3cf055a1277fbfac195c9 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 29 13:00:51 2024 -0400 Script to keep Jenkins Agent persistent from cron (#2634) This "persistent" Java Agent launch script can be ran from a cron job: - Uses Jenkins Remote API to check the status of the Node connection using curl for a given machine. - If it is not connected a new agent is launched for that node. Resolves #2633 commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5 Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Tue May 28 17:17:11 2024 -0400 Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611) Based on users' feedback, this PR do the following: 1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF 2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD, and VOGRD) from "%g m below water surface" to "%g m below sea level" 3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m) Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31 Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Tue May 28 17:16:23 2024 -0400 Add atmensanlfv3inc job (#2592) This PR creates the atmensanlfv3inc job, the ensemble version of atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is #[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3). commit 50c2b8951b29a3c883a778becbf8582f9519eb48 Author: Anil Kumar <108816337+AnilKumar-NOAA@users.noreply.github.com> Date: Tue May 28 13:23:53 2024 -0400 Global-workflow (AR) Generic updates for Gaea C5 (#2515) - Port global-workflow’s build and run capability to Gaea-C5 - Building global-workflow on Gaea-C5 - Setting up experiments with global-workflow on Gaea-C5 --------- Co-authored-by: AnilKumar-NOAA <Anil.Kumar@gaea53.ncrc.gov> Co-authored-by: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> commit b6ca771a0c584cbfcbbf9be739765d5f3815df97 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 24 10:52:45 2024 -0400 Update STMP and PTMP settings in host file for Orion and Hercules (#2614) - Updating STMP and PTMP settings in host file for Orion and Hercules because they are cross mounted. - Also took the opportunity to finally update **SLURM_ACCOUNT** to **HPC_ACCOUT** in CI over rides. - Added a refactor of the `rocotostat.py` tool that is more pythonic and as a execute retry feature because the `rocotostat` utility on Orion has been failing sometimes. commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Tue May 21 23:50:50 2024 -0400 Sea-ice analysis insertion (#2584) Allows cycling and restarting CICE with the sea-ice analysis if the marine DA is switched on. Resolves #2568 Resolves NOAA-EMC/GDASApp#1103 commit 5369a1ff3a3969149fcf32810fad0e50216752b7 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue May 21 22:12:29 2024 +0000 Refactored archiving (#2491) This provides a new pygfs task, archive.py, that provides all of the tools necessary to archive data to the local (`ARCDIR`) and backup (`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to define the file to be archived or tarred to replace the `hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts and make it easier to add new data and explicitly handle optional and required files. For `ATARDIR` archiving, a master jinja template is provided for each `RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2, master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both `enkfgdas` and `enkfgfs` `RUN`s. These templates then include the appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on experiment, cycle, and coupled parameters. Each of these templates corresponds to a single tarball to populate and are tabbed 4 spaces so they are defined within the master `datasets` dictionary. Future developers should not have to make modifications to archive.py unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then only a single `elif` needs to be added to the configure method to specify the master `ATARDIR` template to archive (e.g. `master_gefs.yaml.j2`). If a new component is coming online that needs to be archived to `ATARDIR` (e.g. SNOW), then create a new template for each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`) and reference the template in the appropriate master templates, e.g. `master_gdas.yaml:` ```jinja {% if DO_SNOW %} {% include "gdassnow.yaml.j2" %} {% endif %} ``` A few other issues were addressed along the way: 1. Aerosols have been reenabled. Aerosol forecasts should only be performed during gdas cycles, but analyses can be performed for both gfs and gdas cycles. This was accomplished by setting separate `AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs. 2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`. This prevented restarts from being used for cice-enable experiments. This feature was not tested. 3. Create a temporary fix for the `wgrib` utility. For spack-stack 1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in existing installations. Once complete, this temporary fix should be removed. 4. The number of `earc` jobs has been reduced for lower resolution experiments. Both C48 and C96 experiments will now only have two earc jobs (one for the non-member files to archive and another for the member files). C192 will have up to 3 earc jobs (one non-member, one for members 1-40 and another for members 41-80, if needed). Resolves #2345 Resolves #2318 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 17 12:57:59 2024 -0400 Add remove RUNDIRS step in CI before creating experements (#2607) As had been done in Bash CI we need to remove the RUNDIR in Jenkins before a creating an experiment in the event that case had beem previously ran. commit 09333c01dbafddb2d2fe7e181b479af3cc6d3621 Merge: f7e9f4489 bb930050b Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Thu May 16 14:33:19 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit bb930050b3cd51d28ecba6b231c8675f6d11856c Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu May 16 12:28:30 2024 -0400 Adds jjob and other necessities for marine LETKF task (#2564) Adds jjob, rocoto script, config file, and other necessities for new marine LETKF task. Partially addresses NOAA-EMC/GDASApp#1091 commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu May 16 12:12:06 2024 -0400 Updating CI Machine configs with redundant PTMP (#2605) Quick fix adding PTMP as STMP in Machine configs for CI for completeness commit ef340ff33a6f89adf70838206ba3fd56a953fa7a Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu May 16 11:37:30 2024 -0400 Fix race condition in CI between Orion and Hercules (#2604) Hotfix to solve race conditions in the CI system due to cross-mounted file systems between Orion and Hercules commit e8b17e27f719df280170dc3f5bd9f19917cefaf2 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 15 17:16:30 2024 -0400 Remove existing EXPDIRs and COMROTs when CI is re-run (#2601) Quick hotfix for having default for re-runing jobs to start clean with new EXPDIRs and COMROTs commit b5d113efb1970ede5cd1d3d4dff8d96320519c41 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 15 16:52:49 2024 -0400 Moving logic for skipping hosts in pr cases (#2573) This PR removes the logic of skipping hosts for pr cases from `create_experiment.py` and moves it to a test in the cron bash driver using a `parse_yaml.py` python tool. The Jenkins pipeline was not effected as it uses the `get_host_case_list.py` utility to form the cases on a per host bases. Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed May 15 13:13:30 2024 -0400 Update gsi_utils.fd hash (#2598) This PR updates the `gsi_utils.fd` hash to bring in updates which add safeguards to - `src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90` - `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90` The safeguards are described in GSI-utils PR [#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated issue. Resolves #2597 commit d5366c66bd67f89d118b18956fe230207cbf0aea Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 15 13:12:56 2024 -0400 Update CICE and MOM6 fix versions (#2600) This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions to the newer `20240416` timestamps, which includes updates and fixes to the `100` (1-deg) resolution files. Resolves #2480 Resolves #2483 Resolves #2595 commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon May 13 22:57:38 2024 +0000 Limit gfswavepostpnt to 40 PEs/node (#2588) This fixes the slow runtime of the gfswavepostpnt job on Hercules. The job is very I/O intensive and does not scale well to large nodes, so limit the number of jobs/node to 40. Resolves #2587 commit 4fb7c12c325702a47f27c802a5067efd33d0327c Author: Fanglin Yang <fanglin.yang@noaa.gov> Date: Mon May 13 16:37:51 2024 -0400 Update damping and time-step (#2575) Updates the model to use explicit Rayleigh damping for u/v and implicit damping to w. This improves model stability and allows for longer timesteps. Also unifies the GDAS and GFS to use the same damping. Results from a test at the C1152 resolution (coupled model) can be found at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/ Resolves #2574 Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Lisa Bengtsson <lbengtss@Orion-login-1.HPC.MsState.Edu> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 10 14:17:13 2024 -0400 Do not use BUILT_semphore to force rebuilds when re-run (#2593) Remove the placement of the `BUILT_semaphore` file after the build in the Jenkins Pipeline and force it to rebuild any changes after a PR is re-ran. commit 2346c6161f75ae02369cbf30f30c6150d3e12b66 Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com> Date: Thu May 9 21:17:06 2024 -0500 Migration to Rocky8 spack-stack installations on Jet (#2458) # Description Migrates Global Workflow to Rocky8 spack-stack installations on Jet. Jet has moved from CentOS7 to Rocky8. Resolves #2377 Refs NOAA-EMC/UPP#919 Refs NOAA-EMC/gfs-utils#60 Refs NOAA-EMC/GSI#732 Refs NOAA-EMC/GSI-Monitor#130 Refs NOAA-EMC/GSI-utils#33 commit c7b3973014480a20dd8e24edaeb83a9e9e68159f Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu May 9 11:36:58 2024 -0400 Updates for cold start half cycle, then continuing with IAU for WCDA (#2560) This PR allows us to run C384 S2S with IAU, but starting with the first half-cycle as a cold-start. This will be necessary for cycled testing as we build towards the full system for GFSv17. This updates the copying of the restarts for RUN=gdas for both ocean and ice copying what the atm model is doing. It also reduced the amount of restart files from 4 to 3. Other updates: * Add DOJEDI ocean triggers for archiving certain files update from: @CatherineThomas-NOAA * Adds COPY_FINAL_RESTARTS option to turn on/off copying the last restart file to COM. Defaults to off... * Defines model_start_date_current_cycle & model_start_date_next_cycle to help with knowing which IC to grab. Refs #2546 Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2 Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Wed May 8 20:52:48 2024 -0400 Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477) Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI Configuration Builder (JCB) tool so that YAMLs can be made more portable and invoke the observation chronicle mechanism. Resolves #2476 Co-authored-by: danholdaway <danholdaway@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 8 02:04:16 2024 -0400 Add CI test for products (#2567) Adds a new version of the atm3DVar test that runs the full forecast length and produces most of the secondary products. For now, this test will only run on WCOSS due to gempak failures on other machines as well as computational needs. On other machines, the original version will run (the original version will not run on WCOSS). A…

* Update realtime branch, gsl_ufs_rt. Squashed commit of the following: commit 4e0a81f7acf5ccba5de8d3bdf7ab19cae80812cb Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 18:37:50 2024 +0000 Fix typos/links/dependancy. commit d5fdcbf8d6e987dbdfcd6b4da34d0934c8d82c3b Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 07:37:52 2024 +0000 Fixed missing config.base files. commit c6239f925369b20fd8488e8537969e2f4f9e7725 Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 06:53:47 2024 +0000 Update submodule hashs. commit 32bf790f67b818ff50a7f6b74388fb81ed175b3a Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 06:09:41 2024 +0000 Update develop branch, gsl_ufs_dev - based on gsl_ufs_dev from KaYee's fork global-workflow: 07Aug24,37c53ac [develop_07Aug2024_37c53ac] UFS: 19Jul24, c127601 FV3: 19Jul24, 2527c11 UPP: 23Apr24, be0410e CCPP-PHYSICS: 19Jul24, 46df080 UFS_UTILS: 26Jun24, 3ef2e6b Squashed commit of the following: commit 70b557836379bb7e545fcc6642e28d66cfc17735 Merge: 5edbd123e 37c53ac69 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Wed Aug 7 11:02:24 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 7 08:11:21 2024 -0400 Revert MSU FIX_DIRs back to glopara (#2811) commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Aug 6 14:47:36 2024 -0400 Bugfix for updating label states in Jenkins (#2808) Quick bug fix for updating state labels in CI during finalize. (did not reference GitHub CLI executable correctly in the pipeline script) commit 8fee36f0307b0c08080e3a8fa8fa6703e7da5fce Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Aug 6 11:02:45 2024 -0400 Clean-up temporary rundirs - take 2. (#2753) This PR: - is a follow-up to a previous PR that aggressively pruned run directories. - removes run directories for the current cycle in the clean-up if the cycle is successful. If the cycle is not successful, cleanup is not called and all run directories for the cycle are safe from being purged. - also updates the PR template to list/query for any updates to submodules. --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: David Huber <david.huber@noaa.gov> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit d599fff4aedd41ae587dbe02226acb12ff48efc1 Author: HelinWei-NOAA <48133472+HelinWei-NOAA@users.noreply.github.com> Date: Mon Aug 5 05:31:31 2024 -0400 Change land surface for HR4 (#2787) Resets the default value of opt_diag to 2 corresponding to the land surface upgrades in ufs-weather-model for HR4. Resolves #2786 commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Aug 2 15:41:29 2024 -0400 Run METplus serially and correct the name of prod tasks (#2804) Adds 2 hot fixes: - METplus v9.1.3 has a bug in it that sometimes attempts to create multiple copies of the same directory when running in parallel, causing a Python error and downstream problems. This PR makes METplus run in serial mode, preventing such issues. - Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod) commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri Aug 2 15:03:45 2024 -0400 Update Java Agent launching script for Jenkins connections (#2762) Made updates to the Jenkins Launching Script for robustness and less ambiguous documentation: - Clearer distinction between required user token for the remote api and the systems token for launching - Added pre-checks: `gh` is authenticating, named compliant token and secret file exists - More robust Jason based parser of the remote api response for checking the state of the Node connection - For `cron` use a 5 minute pause and recheck was added before re-launching of the java agent - Added concise header documentation of requirements and purpose --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit b73b1fd203496db97f8067652659573a632bcc67 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Aug 2 07:59:06 2024 -0400 Fix erroneous cdump addition (#2803) commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Aug 1 20:26:13 2024 -0400 Update ocean post-processing triggers (#2784) This PR: - replaces `check_netcdf.sh` checker for ocean post-processing with with ocean output at the next forecast hour or finishing of the forecast job for ocean prod - removes no longer needed `ush/check_netcdf.sh` commit aa2af1ca8d59424a60a1730722bf528775d9e606 Author: GeorgeGayno-NOAA <52789452+GeorgeGayno-NOAA@users.noreply.github.com> Date: Thu Aug 1 16:46:10 2024 -0400 Update the gfs_utils repository hash (#2801) # Description Point to the latest hash of the gfs-utils repository, which contains the bug fix to gaussian_sfcanl. Resolves #2669. Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73 commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Aug 1 08:12:14 2024 -0400 Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791) Changes how METplus jobs run so that they run on the last GFS cycle for a given `PDY`. This is a departure from operations where the METplus jobs run on the 00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through `${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on `${PDY}18` for cycles 00-18. See https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details. commit 1cf8b448af562dbb7af198399c78c585977e81da Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 30 10:38:49 2024 -0400 Simplify resource-related variables, remove CDUMP where unneeded (#2727) This overhauls resource-related variables to use a common set of variables for each job. In the process, this also removed the use of CDUMP in most cases. Resolves #1299 #2693 commit 61875f25c9e971f82ae499b5b612d7f095deebd4 Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Mon Jul 29 14:40:03 2024 -0400 Remove f000 from atmos rocoto tasks for replay cases (#2778) The main purpose of this PR is to remove the f000 from atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater than `0`, it becomes necessary to have the first lead hour set to `OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and the minimum lead time for the ocean_prod rocoto task needs to be 6 (assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up possible by removing 0 from fhrs for atmosphere-related tasks in `gefs_tasks.py` when replaying. This PR also moves where f000 is being removed for the ocean_prod and ice_prod tasks. The if-block that performs this f000 removal has been moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`. --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit f156a7894d639f177e3e2588f98eec1f6f59aa68 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Jul 26 14:18:32 2024 -0500 HR4 GWD update (#2732) This update is a combination of the gravity wave drag (GWD) versions from the NOAA/GSL and NOAA/PSL commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Jul 25 14:26:52 2024 -0400 Temporarily disable METplus jobs (#2796) commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Wed Jul 24 15:00:35 2024 -0400 Refactoring of the marine B-matrix job (#2749) Refactor the functionality of B-matrix generation from the GDASApp Resolves #2743 commit 65a7ab75dc0e4baba06a02e11ed0455787056a68 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 23 08:35:48 2024 -0400 Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775) Removes the namespace-based construction of EnKF member COM directories in the enkf archive template. commit c45b9611f3e701b819bd33dc5af29033f060bb91 Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Tue Jul 23 00:33:16 2024 -0400 Add task to process reforecast variables to save on WCOSS2 (#2680) # Description This PR adds an optional task to the global-workflow to process a subset of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for the GEFSv13 reforecast. This task is designed to process GEFS variables so that specific reforecast product requirements are met. A new variable in `config.base` called `DO_EXTRACTVARS` enables this task, which is currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by default and is specifically a task designed to be executed for the GEFSv13 reforecast. Refs #1878 # Type of change - New feature (adds functionality) # Change characteristics - Is this a breaking change (a change in existing functionality)? NO - Does this change require a documentation update? NO # How has this been tested? This has been cloned and tested on WCOSS2. This will need to be tested on Hera and other platforms on which the reforecast may be running. # Checklist - [ ] Any dependent changes have been merged and published - [x] My code follows the style guidelines of this project - [x] I have performed a self-review of my own code - [ ] I have commented my code, particularly in hard-to-understand areas - [x] My changes generate no new warnings - [x] New and existing tests pass with my changes - [ ] I have made corresponding changes to the documentation if necessary --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 71dc33c6ca991c16ce743760d99feaaf60f2218a Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jul 22 14:51:53 2024 -0400 Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774) Fix metp* resources and check that they completed properly; add support for Orion Rocky 9 commit 56df67a90fe090c425199f1285e5aac722c398b1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jul 22 09:28:18 2024 -0400 Hotfix: Update jcb to avoid git-lfs files (#2782) Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to be cloned on Hera. This hotfix points to a non-authoritative branch of the GDASApp (https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and should be updated ASAP back to the authoritative repository. commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jul 16 09:44:00 2024 -0400 Address issues in creating XML for GFS forecast-only with app S2SWA (#2757) This bugfix PR: - fixes an issue where a user is unable to generate the XML for a GFS forecast-only experiment with APP=S2SWA Specifically, the changes are related to defining `aero_fcst_cdumps`. Following `setup_expt.py`, the user will have to set `AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in `config.base`. commit e0878dba0e53706a7f53429b61aee2936e2c21bf Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Jul 15 10:25:11 2024 -0400 Updated prepobs and fit2obs versions for Orion Rocky9 (#2758) Update prepobs to v1.0.2 and fit2obs to v1.1.2 These versions now support Orion Rocky9. Updates are included for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet. commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jul 11 17:48:47 2024 +0000 CI maintenance updates and adding CI Unit Tests (#2740) This PR has a few maintenance updates to the CI pipeline and adds a test directory with Unit Tests **Major Maintenance updates:** - Added try blocks with appropriate messaging to GitHub PR of failure for: - - **scm** checkout - - build fail (with error logs sent as gists) - - create experiment fails with `stderr` sent to GitHub PR messaging - Pre-stage FAILS from the above are now captured these fails allow FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state labels in GitHub - see image below) **Minor Maintenance updates:** - Fix for STALLED cases reviled from PR 2700 (just needed a lambda specifier) - Fixed path to experiment directory in PR message (had dropped EXPDIR in path) - Needed `latin-1` decoder in reading log files for publishing **Added python Unit Tests for CI functionality:** - Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI utility codes - Cashed the install of Rocoto in the GitHub Runners to greatly reduce stetup time for running the unit tests - Unit Tests Python scripts added - `test_rocostat.py`: rocoto_statcount() rocoto_summary() rocoto_stalled() - `test_setup.py`: setup_expt() test_setup_xml() - `test_create_experment`: test_create_experiment() - - Runs all PR cases that do not have ICs in the GItHub Runner - Reporting mechanism in the Actions tab for Python Unit Testing results - Test case data for STALLED and RUNNING stored on S3 and pulled using wget during runtime of tests commit 5ef4db74649b8be03402c17aa29c024e71699a7b Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu Jul 11 08:59:24 2024 -0400 Adds contents of constructor and initialize methods to marine LETKF class (#2635) Adds contents of constructor and initialize methods to marine LETKF class Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091 --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> commit 8998ec7b74123e953b97a93fa14cc78d471a1aee Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 9 08:31:57 2024 -0400 Fix GDAS group B restart archiving (#2735) Archives the GDAS restartb dataset at a 6-hour offset from restarta This allows cycled experiments to restart from the archives. The tabbing for the master archive templates was also added to improve readability. Resolves #2722 commit 3ca74771255727033b9dc043c652ac585178629c Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Tue Jul 9 08:28:54 2024 -0400 Add fcst dependency to ocnanalprep (#2728) Add previous cycle's `fcst` as a dependency to `ocnanalprep` This ensures that the availability of restart files to the latter. This addresses a seldomly-encountered race condition where `ocnanalprep` fails due to the lack of the files. commit 58fca1668aecd6fb1afd12a441256ad35900e075 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jul 5 15:02:23 2024 -0400 Update (partially) global-workflow for orion+rocky9 (#2741) This PR: - updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils, GFS-utils) to include recent update to their modulefiles for Orion+Rocky9 upgrade - updates the modulefiles in global-workflow to load modules from Orion+Rocky9 paths - updates modulefiles for `gwsetup` and `gwci` as well. - removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not installed. - adds `parm/config.gfs/config.resources.ORION` to address GSI performance degradation after Rocky 9 upgrade. This PR: - does not update the build for UPP. Standalone UPP is not available via ufs-weather-model as of #2729 - will need a follow-up update for `prepobs` and `fit2obs` updated locations when they are installed in `glopara` space on Orion. # Type of change - Maintenance (code refactor, clean-up, new CI test, etc.) # Change characteristics - Is this a breaking change (a change in existing functionality)? NO - Does this change require a documentation update? NO # How has this been tested? This PR is not sufficient for Orion. This PR must be tested on other platforms (Hera, WCOSS2) as this PR updates submodules. # Checklist - [ ] Any dependent changes have been merged and published - [ ] My code follows the style guidelines of this project - [ ] I have performed a self-review of my own code - [ ] I have commented my code, particularly in hard-to-understand areas - [ ] My changes generate no new warnings - [ ] New and existing tests pass with my changes - [ ] I have made corresponding changes to the documentation if necessary --------- Co-authored-by: Kate Friedman <kate.friedman@noaa.gov> commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jul 3 21:07:49 2024 -0400 Update ufs model hash to 20240625 (#2729) Updates UFS weather model hash to hash from 2024-06-24 which has orion porting updates + a few namelist updates. commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jul 3 11:32:40 2024 -0400 Hotfix for undefined CLUSTERS (#2748) Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses the native `dict` `get` method to prevent grabbing an unset entry. commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Wed Jul 3 09:56:08 2024 -0400 Update gempak job to run one fcst hour per task (#2671) This PR updates gempak jobs (gfs, gdas, and goes) from processing all forecast hours at once to one forecast hour at a time. This will reduce the job runtime to less than 5 min, so restart capability is not needed. Resolves #1250 Ref #2666 #2667 --------- Co-authored-by: Walter.Kolczynski <Walter.Kolczynski@noaa.gov> commit 8215ae654202186a4f753c3abe937b7b9b91a9c7 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jul 2 16:22:11 2024 -0400 Hotfix for clusters from #2701 (#2747) Fixes an issue created from #2701 that added `CLUSTERS` to the `gaea.yaml`. commit 11943e36ba12b3df49c51942da780698fab02d38 Author: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> Date: Tue Jul 2 12:58:10 2024 -0400 Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701) This PR sets up the ability on Gaea for auto generation of a clean xml file, i.e., an xml file that does not need any alterations before running rocoto. Refs #2572 Refs #2664 commit de8706702ead0630beb54d868f83aa2cb23f8f79 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon Jul 1 09:29:14 2024 -0400 Update for JCB policies and stage DA job files with Jinja2-templates (#2700) This PR updates the `gdas.cd` hash to bring in new JCB conventions. Resolves #2699 From #2654 This PR will move much of the staging code that take place in the python initialization subroutines of the variational and ensemble DA jobs into Jinja2-templated YAML files to be passed into the wxflow file handler. Much of the staging has already been done this way, but this PR simply expands that strategy. The old Python routines that were doing this staging are now removed. This is part of a broader refactoring of the pygfs tasking. wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a companion to this PR. Co-authored-by: danholdaway <danholdaway@users.noreply.github.com> Co-authored-by: DavidNew-NOAA <david.new@noaa.gov> Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Co-authored-by: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jun 28 14:56:19 2024 -0400 Revert PR 2681 (#2739) This PR: - reverts #2681 in part - keeps some changes for `RUN`. - is a hotfix - should be merged ASAP after consensus w/ @guillaumevernieres @CatherineThomas-NOAA @WalterKolczynski-NOAA commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed Jun 26 15:46:08 2024 -0400 updated Finalize in Jenkinsfile and added try block around scm checkout (#2692) We are updating the Jenkins Pipeline with a try block around checkout to capture errors for the user. Also cleaned up Finalize and added section to clean out workspace on success. commit 968568f682bac7564095440bdb7813abefd76821 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 26 13:27:19 2024 -0400 Activate snow DA test on WCOSS (#2720) Activate the snow DA test on WCOSS. commit 7706760bb8adbdf78cb640b02739023c886e7699 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jun 26 10:02:22 2024 -0400 Cleanup of stale RUNDIRS from an experiment (#2719) This PR: - removes stale temporary scratch run directories from `$DATAROOT/` every 3 days. - should help to scrub failed attempts. - removes an unused variable `RUNDIR` defined in `config.base` commit 8962991691b5f0857b813bddfd28aa1034d4bd2b Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jun 26 09:43:48 2024 -0400 Update logic for MOM6 number of layers/exception values (#2681) Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine how many layers and sets the exception value for MOM6 to be 1e-34 for all scenarios. Note, we will no longer have zeros in the ocean grib output and the DA will also run without issues. Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615 commit 12431f76bdce807067929415007592cffc8a2457 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Jun 26 07:42:35 2024 -0600 Update wave jobs to use COMIN/COMOUT (#2643) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow wave model and products tasks. Refs #2451 commit b902c0bac126c323a07186ad8881384b032b6fda Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jun 25 07:48:46 2024 -0400 Assign machine- and RUN-specific resources (#2672) Redefine resource variables based explicitly on RUN or CDUMP Additionally, machine-specific resources are moved out of config.resources and placed in respective config.resources.{machine} files. Resolves #177 #2672 commit 5edbd123e2878a07f5cce8e3c7ea6147f286633a Merge: 09333c01d 4e1b937b6 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Mon Jun 24 12:44:05 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit 4e1b937b67ed220120e81925c4507f03b9b8965f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jun 24 10:50:52 2024 -0400 Add minimum software requirements (#2712) Adds a table to HPC documentation stating the minimum support versions commit f43a86276aaef91efa28faadc71a3cf50e749efe Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Jun 21 13:44:29 2024 -0400 Fix and simplify online archiving and reenable METplus jobs (#2687) This fixes the online archiving portion of the `*arch` and `*earc00` jobs, a prerequisite for running METplus. This also reenables METplus by default. The approach previously taken created `FileHandler` dictionaries at varying levels within the resulting yaml, which was not properly parsed by `exglobal_archive.py`. This approach creates a single `FileHandler` dictionary and is much less complicated overall. Resolves #2673 #2647 commit 8993b42cb91144c0ab0501dc7841ea8d675c4701 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 19 21:51:22 2024 -0400 Eliminate post groups (#2667) Eliminates the post groups used for upp and products jobs so that each task only processes one forecast hour. This is more efficient and greatly simplifies downstream dependencies that depend on a specific forecast hour. Resolves #2666 Refs #2642 commit 0b810c888239853fedd0e4584fe62536c6aaacdf Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 20:32:48 2024 -0600 Removes misleading "No such file or directory" syntax errors from output files (#2688) This PR addresses issue #1252. The following is accomplished: - Prior to removing files, the existence of a file is checked prior to attempting to remove; this is performed as noted [here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369); this PR only addresses the the `chgrp` issue. Refs #1252 --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 12:17:59 2024 -0600 Hotfix for bug in template names. (#2697) This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/` template. Resolves #2696 Refs #2451 commit 35d4d99eaac669721add9ddcc793153e5ab3b30a Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 08:06:53 2024 -0600 Update archive job to use COMIN/COMOUT (#2668) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow archive task. Refs #2451 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 47b3a581c8257fa24411fb400df8bb0e1e04972a Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Jun 17 22:55:38 2024 -0400 Turn on high-frequency output in extended test (#2679) Turns on high-frequency (hourly) output in the extended products test to exercise that aspect of the code. This test only runs on WCOSS. Also adds the hooks to optionally turn on the metplus jobs, but that is deferred as they are not currently working correctly. commit 38f2df9fb0c074b1f80d3c637080be79be693161 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jun 17 17:12:55 2024 +0000 Optimize wavepostpnt (#2657) Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs This is done by 1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by - performing operations on all files at once instead of looping over each file - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`) - combining `sed` and `grep` calls when possible - adding logic to `awk` calls instead of handling that logic in bash 2) minimizing as much as possible the amount of data on disk that has to be read in (e.g. limiting sed to read only the line numbers it needs) --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 5af325a6a4e0a14d180514a418603ca79fada487 Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Fri Jun 14 18:05:23 2024 -0400 Update GDASapp hash to move JCB into GDASapp (#2665) This PR moves JCB into GDASapp. The PR also bumps up the hash of GDASapp to what is in `feature/move_jcb`, which at time of writing is develop plus the absorption of JCB into GDASapp. Note that I also took the changes from https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the testing @RussTreadon-NOAA has done. commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b Author: Yaping Wang <49168260+ypwang19@users.noreply.github.com> Date: Fri Jun 14 10:18:17 2024 -0500 Add observation preparation job for aerosols DA to workflow (#2624) Add a prepaeroobs job to prepare aerosol obs files for DA. This job does quality control of the VIIRS aerosol raw observations and convert them to ioda format. Resolves #2623 --------- Co-authored-by: ypwang19 <yaping.wang@users.noreply.github.com> Co-authored-by: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Jun 14 11:04:41 2024 -0400 Remove ocean daily files (#2689) This PR removes the ocn_daily files that are produced by the ocean component. These files can be recreated by averaging data that exists in the 6 hour aveaged files if needed. Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675 Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by removing them and making this obsolete) commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jun 13 12:22:03 2024 -0400 Update Jenkinsfile needed a comma commit dc21eac6c3941d7f30803891d91d82f4cc1f8183 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jun 13 11:41:14 2024 -0400 Add Hercules-EMC to the Jenkins configurable parameter list (#2685) This quick-fix PR is to update the Jenkins Pipeline's configurable parameter list to include the **Hercules-EMC** node. This allows Jenkins users to restart Jobs in the controller when no updates have been made. commit ebacebfbe458634b8c80af6a735d6b6d01e4e406 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Thu Jun 13 11:20:24 2024 -0400 Update gdas.cd and gsi_utils hashes (#2641) This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea build for gsi_utils. Resolves #2640 commit 34155fb4767769600a1ff95f0a65e37081addc2a Author: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com> Date: Thu Jun 13 11:18:22 2024 -0400 Add ability to use GEFS replay ICs (#2559) The PR allows the use of ICs from PSL's replay analysis. These replay ICs will be used for GEFS reforecasting and SFS. Two main changes are associated with these updates: (1) replay ICs being valid at 3Z, and (2) the use of warm starts. Resolves #1838 --------- Co-authored-by: Jessica Meixner <Jessica.Meixner@noaa.gov> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Jun 12 19:25:42 2024 -0600 Replace `sleep` with `wait_for_file` (#2586) This PR addresses issue #2444. The following is accomplished: - All `sleep` statements are replaced with `wait_for_file` for the relevant scripts beneath `scripts` and `ush`; - Indentation and shell-norms are updated where applicable. Note: The WAFS scripts are not updated as per @aerorahul direction. Resolves #2444 --------- Co-authored-by: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 12 13:31:55 2024 -0400 Add COM template for JEDI obs (#2678) Adds a COM template to define a path to store obs processed for JEDI. This will allow UFSDA to stop writing to COM_OBS, which should be read-only as it belongs to obsproc in operations. No functional change yet. commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Wed Jun 12 09:06:23 2024 -0600 Link both global-nest fix files and non-nest ones at the same time (#2632) This PR enables linking both global-nest fix files and non-nest ones at the same time and users can run both nesting and non-nesting experiments at the same time without worries about what fix files to be linked. Resolves #2631 commit 61de004d4f9e9edf8a31bb173f2719b46451a36a Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jun 12 11:03:13 2024 -0400 Update ufs-weather-model (#2663) Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack allowing some temporary fixes to be reverted. * removes upp submodule * uses upp from the ufs-weather-model * restores the build and link that were hacked during the Hera Rocky 8 transition to allow for UPP submodule * Removes forecast directories in clean-up Resolves #2617 Resolves #2437 --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Wed Jun 12 01:15:37 2024 -0400 Add ability to process ocean/ice products specific to GEFS (#2561) This PR begins to add the capability to produce GEFSv13 ocean and ice products in the global-workflow according to stakeholder requirements. The following features are added. - An oceanice prod yaml file has been added to address the ocean and ice products specific to GEFSv13. - The rocoto dependencies and config.base for GEFS have also been modified to allow for 24-hour averaged ocean and ice output. - Various scripts have been modified to allow for ocean and ice output frequencies of 24 hours. - `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN` and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`. Refs #1878 commit 6691e7489650e0b738c176fbd096109288dc09b6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 11 21:15:07 2024 -0600 Update cleanup job to use COMIN/COMOUT (#2649) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow clean-up task. Refs #2451 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Jun 11 16:17:25 2024 -0400 Add overwrite to creat experiment in BASH CI (#2676) This is a quick hotfix to the CI BASH driver script adding `--overwrite` to create experiment script to avoid errors from restarting an experiment. commit e7909af8d9e1f34140388a3f8556d8e582c58fe5 Author: emilyhcliu <36091766+emilyhcliu@users.noreply.github.com> Date: Mon Jun 10 15:11:27 2024 -0400 Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py (#2645) This PR proposes updates for the following two scripts: 1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select CRTM cloud optical table based on cloud microphysical scheme indicated by `imp_physics' The default scheme in the GFS forecast model is Thompson scheme (imp_physics = 8). 2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in the script due to increased variables to interplate increments and calculate analysis in the netcdf_io routines in GSI-utils. Here is the related [PR #46 for GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46). --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 9caa51de8fb7be07d2e61775da01937d576964f6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Jun 6 22:15:23 2024 -0600 Update RDHPCS Hera resource for `eupd` task (#2636) As per @wx20jjung, the resource for the `eupd` task have been updated for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job fails. Resolves #2454 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Thu Jun 6 11:49:03 2024 -0400 Parameterize some things in config.atmanl and config.atmensanl (#2661) This PR adds some parameters in config.atmanl and config.atmensanl that can be altered with the defaults.yaml. The motivation is to make these files match those in the GDASApp JJOB tests (example: https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl), so we can just use the Global Workflow config.atmanl and config.atmensanl in the tests rather than custom ones in GDASApp that have to be separately updated every time the ones in the Global Workflow are updated. commit 54ea0b73a07921be5fbb07fe41e976888bd3e549 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Thu Jun 6 01:36:02 2024 -0400 Add links to the ocean insitu obs processing tools (#2644) Add links to the marine bufr to ioda converters for the marine insitu observations. - fixes https://github.com/NOAA-EMC/GDASApp/issues/1106 - waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135 commit 205d0c2b13e2d7755cec75bf8c978ab20d453862 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jun 5 17:31:30 2024 +0000 Update S4 point of contact in docs (#2660) Update the point of contact for global workflow issues on S4. commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed Jun 5 12:50:14 2024 -0400 Enable wcoss2 ufsda build and module load (#2620) This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2. Resolves #2602 Resolves #2579 commit 67b833e0c7bc390865d453588b4609a1a7ede981 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Tue Jun 4 13:33:43 2024 -0400 Update ufs-weather-model (#2646) Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6 This should resolve the issue and allow C768 runs on Hera and allow for CICE to run on WCOSS2 (due to library updates to allow linking). From what I can tell, all updates needed were done by @HenryWinterbottom-NOAA which were updates for CICE Fixes #2490 commit c44d0ac86cfdf78eb87492431bf6d825e8bae637 Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Tue Jun 4 10:29:49 2024 -0400 Update wmo parm files to fix WMO header (#2652) This PR updates wmo parm files to switch WMO header of precipitation type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to instantaneous. Resolves #2566 commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Tue Jun 4 13:55:33 2024 +0000 Add IAU to snow DA (and its test) (#2610) This PR enables IAU for the snow DA which is necessary for GFSv17. A snow analysis is created for the center of the window regardless, and an additional at the beginning of the window is added if IAU is on. The former is needed for UPP and the latter, to initialize the model. The increment is valid throughout the window for 3DVar, so the same increment is added to both forecasts. Additionally, the input file that goes into global_cycle has been updated to be the output of the JEDI snow analysis instead of the forecast (@jiaruidong2017 I recall discussing this, can you confirm this is right or am I mistaken) This PR also makes the CI test for snow DA (and aerosol DA) include IAU rather than without IAU,. --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit c92bf415060750127c9c05a62a1d2851c489551a Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Sat Jun 1 05:11:07 2024 +0000 Archiving cleanup (#2621) 1) Adds a lot of comments to the jinja templates for archiving 2) Rearranges the gdas and enkf templates to a more logical order 3) Fixes a couple of bugs in the enkf archiving of increments and analyses 4) Disables archiving for the half cycle 5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`, instead relying on `DO_FIT2OBS` 6) Updates wxflow to add the option to not allow undefined variables when parsing jinja templates and invokes this feature when running archives Resolves #2612 commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri May 31 04:57:08 2024 -0400 Switch to Rocky 9 built external packages on Hercules (#2608) The workflow was updated to use modules built on Rocky 9, but the external packages (like prepobs) were still pointing to the versions built on CentOS (Orion). This transitions to packages built on Rocky 9. Updating of the tracker package has been deferred until later. As such, the tracker jobs have been disabled by returning immediately if they are on Hercules. Since these jobs are small, resource-wise, it should not meaningfully impact turnover time. commit 4422550c01c9214a2b3b8890bdcc898123ee216a Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Thu May 30 08:05:23 2024 -0600 Add the capability to use slurm reservation nodes (#2627) Add the capability to use slurm reservation nodes Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE Resolves #2626 commit a54153fd9d26126206bc07a1da4e80f50c0c5910 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 29 23:24:07 2024 -0400 Update forecast job to use COMIN/COMOUT (#2622) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the forecast job. Refs #2451 --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit d69a8af95d492982b918670322ed5c41ab074335 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed May 29 21:29:03 2024 -0400 Update to add 1-deg global wave grid (#2619) This PR adds options to use a global 1 deg grid, intended for testing with the SFS application. Requires new fix file changes NOAA-EMC/global-workflow#2618 commit 0b4670ecf83b99b72835c8380573b2bca7cf5324 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed May 29 17:17:21 2024 -0400 Add C384mx025_3DVarAOWCDA yamls (#2625) Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder. commit 2e885d05c64b947f00a3cf055a1277fbfac195c9 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 29 13:00:51 2024 -0400 Script to keep Jenkins Agent persistent from cron (#2634) This "persistent" Java Agent launch script can be ran from a cron job: - Uses Jenkins Remote API to check the status of the Node connection using curl for a given machine. - If it is not connected a new agent is launched for that node. Resolves #2633 commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5 Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Tue May 28 17:17:11 2024 -0400 Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611) Based on users' feedback, this PR do the following: 1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF 2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD, and VOGRD) from "%g m below water surface" to "%g m below sea level" 3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m) Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31 Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Tue May 28 17:16:23 2024 -0400 Add atmensanlfv3inc job (#2592) This PR creates the atmensanlfv3inc job, the ensemble version of atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is #[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3). commit 50c2b8951b29a3c883a778becbf8582f9519eb48 Author: Anil Kumar <108816337+AnilKumar-NOAA@users.noreply.github.com> Date: Tue May 28 13:23:53 2024 -0400 Global-workflow (AR) Generic updates for Gaea C5 (#2515) - Port global-workflow’s build and run capability to Gaea-C5 - Building global-workflow on Gaea-C5 - Setting up experiments with global-workflow on Gaea-C5 --------- Co-authored-by: AnilKumar-NOAA <Anil.Kumar@gaea53.ncrc.gov> Co-authored-by: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> commit b6ca771a0c584cbfcbbf9be739765d5f3815df97 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 24 10:52:45 2024 -0400 Update STMP and PTMP settings in host file for Orion and Hercules (#2614) - Updating STMP and PTMP settings in host file for Orion and Hercules because they are cross mounted. - Also took the opportunity to finally update **SLURM_ACCOUNT** to **HPC_ACCOUT** in CI over rides. - Added a refactor of the `rocotostat.py` tool that is more pythonic and as a execute retry feature because the `rocotostat` utility on Orion has been failing sometimes. commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Tue May 21 23:50:50 2024 -0400 Sea-ice analysis insertion (#2584) Allows cycling and restarting CICE with the sea-ice analysis if the marine DA is switched on. Resolves #2568 Resolves NOAA-EMC/GDASApp#1103 commit 5369a1ff3a3969149fcf32810fad0e50216752b7 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue May 21 22:12:29 2024 +0000 Refactored archiving (#2491) This provides a new pygfs task, archive.py, that provides all of the tools necessary to archive data to the local (`ARCDIR`) and backup (`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to define the file to be archived or tarred to replace the `hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts and make it easier to add new data and explicitly handle optional and required files. For `ATARDIR` archiving, a master jinja template is provided for each `RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2, master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both `enkfgdas` and `enkfgfs` `RUN`s. These templates then include the appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on experiment, cycle, and coupled parameters. Each of these templates corresponds to a single tarball to populate and are tabbed 4 spaces so they are defined within the master `datasets` dictionary. Future developers should not have to make modifications to archive.py unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then only a single `elif` needs to be added to the configure method to specify the master `ATARDIR` template to archive (e.g. `master_gefs.yaml.j2`). If a new component is coming online that needs to be archived to `ATARDIR` (e.g. SNOW), then create a new template for each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`) and reference the template in the appropriate master templates, e.g. `master_gdas.yaml:` ```jinja {% if DO_SNOW %} {% include "gdassnow.yaml.j2" %} {% endif %} ``` A few other issues were addressed along the way: 1. Aerosols have been reenabled. Aerosol forecasts should only be performed during gdas cycles, but analyses can be performed for both gfs and gdas cycles. This was accomplished by setting separate `AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs. 2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`. This prevented restarts from being used for cice-enable experiments. This feature was not tested. 3. Create a temporary fix for the `wgrib` utility. For spack-stack 1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in existing installations. Once complete, this temporary fix should be removed. 4. The number of `earc` jobs has been reduced for lower resolution experiments. Both C48 and C96 experiments will now only have two earc jobs (one for the non-member files to archive and another for the member files). C192 will have up to 3 earc jobs (one non-member, one for members 1-40 and another for members 41-80, if needed). Resolves #2345 Resolves #2318 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 17 12:57:59 2024 -0400 Add remove RUNDIRS step in CI before creating experements (#2607) As had been done in Bash CI we need to remove the RUNDIR in Jenkins before a creating an experiment in the event that case had beem previously ran. commit 09333c01dbafddb2d2fe7e181b479af3cc6d3621 Merge: f7e9f4489 bb930050b Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Thu May 16 14:33:19 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit bb930050b3cd51d28ecba6b231c8675f6d11856c Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu May 16 12:28:30 2024 -0400 Adds jjob and other necessities for marine LETKF task (#2564) Adds jjob, rocoto script, config file, and other necessities for new marine LETKF task. Partially addresses NOAA-EMC/GDASApp#1091 commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu May 16 12:12:06 2024 -0400 Updating CI Machine configs with redundant PTMP (#2605) Quick fix adding PTMP as STMP in Machine configs for CI for completeness commit ef340ff33a6f89adf70838206ba3fd56a953fa7a Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu May 16 11:37:30 2024 -0400 Fix race condition in CI between Orion and Hercules (#2604) Hotfix to solve race conditions in the CI system due to cross-mounted file systems between Orion and Hercules commit e8b17e27f719df280170dc3f5bd9f19917cefaf2 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 15 17:16:30 2024 -0400 Remove existing EXPDIRs and COMROTs when CI is re-run (#2601) Quick hotfix for having default for re-runing jobs to start clean with new EXPDIRs and COMROTs commit b5d113efb1970ede5cd1d3d4dff8d96320519c41 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 15 16:52:49 2024 -0400 Moving logic for skipping hosts in pr cases (#2573) This PR removes the logic of skipping hosts for pr cases from `create_experiment.py` and moves it to a test in the cron bash driver using a `parse_yaml.py` python tool. The Jenkins pipeline was not effected as it uses the `get_host_case_list.py` utility to form the cases on a per host bases. Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed May 15 13:13:30 2024 -0400 Update gsi_utils.fd hash (#2598) This PR updates the `gsi_utils.fd` hash to bring in updates which add safeguards to - `src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90` - `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90` The safeguards are described in GSI-utils PR [#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated issue. Resolves #2597 commit d5366c66bd67f89d118b18956fe230207cbf0aea Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 15 13:12:56 2024 -0400 Update CICE and MOM6 fix versions (#2600) This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions to the newer `20240416` timestamps, which includes updates and fixes to the `100` (1-deg) resolution files. Resolves #2480 Resolves #2483 Resolves #2595 commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon May 13 22:57:38 2024 +0000 Limit gfswavepostpnt to 40 PEs/node (#2588) This fixes the slow runtime of the gfswavepostpnt job on Hercules. The job is very I/O intensive and does not scale well to large nodes, so limit the number of jobs/node to 40. Resolves #2587 commit 4fb7c12c325702a47f27c802a5067efd33d0327c Author: Fanglin Yang <fanglin.yang@noaa.gov> Date: Mon May 13 16:37:51 2024 -0400 Update damping and time-step (#2575) Updates the model to use explicit Rayleigh damping for u/v and implicit damping to w. This improves model stability and allows for longer timesteps. Also unifies the GDAS and GFS to use the same damping. Results from a test at the C1152 resolution (coupled model) can be found at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/ Resolves #2574 Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Lisa Bengtsson <lbengtss@Orion-login-1.HPC.MsState.Edu> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 10 14:17:13 2024 -0400 Do not use BUILT_semphore to force rebuilds when re-run (#2593) Remove the placement of the `BUILT_semaphore` file after the build in the Jenkins Pipeline and force it to rebuild any changes after a PR is re-ran. commit 2346c6161f75ae02369cbf30f30c6150d3e12b66 Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com> Date: Thu May 9 21:17:06 2024 -0500 Migration to Rocky8 spack-stack installations on Jet (#2458) # Description Migrates Global Workflow to Rocky8 spack-stack installations on Jet. Jet has moved from CentOS7 to Rocky8. Resolves #2377 Refs NOAA-EMC/UPP#919 Refs NOAA-EMC/gfs-utils#60 Refs NOAA-EMC/GSI#732 Refs NOAA-EMC/GSI-Monitor#130 Refs NOAA-EMC/GSI-utils#33 commit c7b3973014480a20dd8e24edaeb83a9e9e68159f Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu May 9 11:36:58 2024 -0400 Updates for cold start half cycle, then continuing with IAU for WCDA (#2560) This PR allows us to run C384 S2S with IAU, but starting with the first half-cycle as a cold-start. This will be necessary for cycled testing as we build towards the full system for GFSv17. This updates the copying of the restarts for RUN=gdas for both ocean and ice copying what the atm model is doing. It also reduced the amount of restart files from 4 to 3. Other updates: * Add DOJEDI ocean triggers for archiving certain files update from: @CatherineThomas-NOAA * Adds COPY_FINAL_RESTARTS option to turn on/off copying the last restart file to COM. Defaults to off... * Defines model_start_date_current_cycle & model_start_date_next_cycle to help with knowing which IC to grab. Refs #2546 Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2 Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Wed May 8 20:52:48 2024 -0400 Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477) Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI Configuration Builder (JCB) tool so that YAMLs can be made more portable and invoke the observation chronicle mechanism. Resolves #2476 Co-authored-by: danholdaway <danholdaway@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 8 02:04:16 2024 -0400 Add CI test for products (#2567) Adds a new version of the atm3DVar test that runs the full forecast length and produces most of the secondary products. For now, this test will only run on WCOSS due to gempak failures on other machines as well as computational needs. On other machines, the original version will run (the original version will not run on WCOSS). AWIPS remains off for now in this extended test due to a bug involving tocgrib2 and the convective precip fields (see #2566). The new test runs for 4½ cycles and the full 384-hr forecast length to ensure all gempak scripts are exercised. Since the cycle throttle is 3 and the bulk of the time is in the free forecast, the cycles run mostly concurrently so it doesn't extend the t…

* Update realtime branch, gsl_ufs_rtdev1. Squashed commit of the following: commit 4e0a81f7acf5ccba5de8d3bdf7ab19cae80812cb Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 18:37:50 2024 +0000 Fix typos/links/dependancy. commit d5fdcbf8d6e987dbdfcd6b4da34d0934c8d82c3b Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 07:37:52 2024 +0000 Fixed missing config.base files. commit c6239f925369b20fd8488e8537969e2f4f9e7725 Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 06:53:47 2024 +0000 Update submodule hashs. commit 32bf790f67b818ff50a7f6b74388fb81ed175b3a Author: kayee.wong <kayee.wong@noaa.gov> Date: Wed Sep 18 06:09:41 2024 +0000 Update develop branch, gsl_ufs_dev - based on gsl_ufs_dev from KaYee's fork global-workflow: 07Aug24,37c53ac [develop_07Aug2024_37c53ac] UFS: 19Jul24, c127601 FV3: 19Jul24, 2527c11 UPP: 23Apr24, be0410e CCPP-PHYSICS: 19Jul24, 46df080 UFS_UTILS: 26Jun24, 3ef2e6b Squashed commit of the following: commit 70b557836379bb7e545fcc6642e28d66cfc17735 Merge: 5edbd123e 37c53ac69 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Wed Aug 7 11:02:24 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Aug 7 08:11:21 2024 -0400 Revert MSU FIX_DIRs back to glopara (#2811) commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Aug 6 14:47:36 2024 -0400 Bugfix for updating label states in Jenkins (#2808) Quick bug fix for updating state labels in CI during finalize. (did not reference GitHub CLI executable correctly in the pipeline script) commit 8fee36f0307b0c08080e3a8fa8fa6703e7da5fce Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Aug 6 11:02:45 2024 -0400 Clean-up temporary rundirs - take 2. (#2753) This PR: - is a follow-up to a previous PR that aggressively pruned run directories. - removes run directories for the current cycle in the clean-up if the cycle is successful. If the cycle is not successful, cleanup is not called and all run directories for the cycle are safe from being purged. - also updates the PR template to list/query for any updates to submodules. --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: David Huber <david.huber@noaa.gov> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit d599fff4aedd41ae587dbe02226acb12ff48efc1 Author: HelinWei-NOAA <48133472+HelinWei-NOAA@users.noreply.github.com> Date: Mon Aug 5 05:31:31 2024 -0400 Change land surface for HR4 (#2787) Resets the default value of opt_diag to 2 corresponding to the land surface upgrades in ufs-weather-model for HR4. Resolves #2786 commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Aug 2 15:41:29 2024 -0400 Run METplus serially and correct the name of prod tasks (#2804) Adds 2 hot fixes: - METplus v9.1.3 has a bug in it that sometimes attempts to create multiple copies of the same directory when running in parallel, causing a Python error and downstream problems. This PR makes METplus run in serial mode, preventing such issues. - Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod) commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri Aug 2 15:03:45 2024 -0400 Update Java Agent launching script for Jenkins connections (#2762) Made updates to the Jenkins Launching Script for robustness and less ambiguous documentation: - Clearer distinction between required user token for the remote api and the systems token for launching - Added pre-checks: `gh` is authenticating, named compliant token and secret file exists - More robust Jason based parser of the remote api response for checking the state of the Node connection - For `cron` use a 5 minute pause and recheck was added before re-launching of the java agent - Added concise header documentation of requirements and purpose --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit b73b1fd203496db97f8067652659573a632bcc67 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri Aug 2 07:59:06 2024 -0400 Fix erroneous cdump addition (#2803) commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Aug 1 20:26:13 2024 -0400 Update ocean post-processing triggers (#2784) This PR: - replaces `check_netcdf.sh` checker for ocean post-processing with with ocean output at the next forecast hour or finishing of the forecast job for ocean prod - removes no longer needed `ush/check_netcdf.sh` commit aa2af1ca8d59424a60a1730722bf528775d9e606 Author: GeorgeGayno-NOAA <52789452+GeorgeGayno-NOAA@users.noreply.github.com> Date: Thu Aug 1 16:46:10 2024 -0400 Update the gfs_utils repository hash (#2801) # Description Point to the latest hash of the gfs-utils repository, which contains the bug fix to gaussian_sfcanl. Resolves #2669. Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73 commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Aug 1 08:12:14 2024 -0400 Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791) Changes how METplus jobs run so that they run on the last GFS cycle for a given `PDY`. This is a departure from operations where the METplus jobs run on the 00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through `${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on `${PDY}18` for cycles 00-18. See https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details. commit 1cf8b448af562dbb7af198399c78c585977e81da Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 30 10:38:49 2024 -0400 Simplify resource-related variables, remove CDUMP where unneeded (#2727) This overhauls resource-related variables to use a common set of variables for each job. In the process, this also removed the use of CDUMP in most cases. Resolves #1299 #2693 commit 61875f25c9e971f82ae499b5b612d7f095deebd4 Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Mon Jul 29 14:40:03 2024 -0400 Remove f000 from atmos rocoto tasks for replay cases (#2778) The main purpose of this PR is to remove the f000 from atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater than `0`, it becomes necessary to have the first lead hour set to `OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and the minimum lead time for the ocean_prod rocoto task needs to be 6 (assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up possible by removing 0 from fhrs for atmosphere-related tasks in `gefs_tasks.py` when replaying. This PR also moves where f000 is being removed for the ocean_prod and ice_prod tasks. The if-block that performs this f000 removal has been moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`. --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit f156a7894d639f177e3e2588f98eec1f6f59aa68 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Jul 26 14:18:32 2024 -0500 HR4 GWD update (#2732) This update is a combination of the gravity wave drag (GWD) versions from the NOAA/GSL and NOAA/PSL commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Thu Jul 25 14:26:52 2024 -0400 Temporarily disable METplus jobs (#2796) commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Wed Jul 24 15:00:35 2024 -0400 Refactoring of the marine B-matrix job (#2749) Refactor the functionality of B-matrix generation from the GDASApp Resolves #2743 commit 65a7ab75dc0e4baba06a02e11ed0455787056a68 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 23 08:35:48 2024 -0400 Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775) Removes the namespace-based construction of EnKF member COM directories in the enkf archive template. commit c45b9611f3e701b819bd33dc5af29033f060bb91 Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Tue Jul 23 00:33:16 2024 -0400 Add task to process reforecast variables to save on WCOSS2 (#2680) # Description This PR adds an optional task to the global-workflow to process a subset of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for the GEFSv13 reforecast. This task is designed to process GEFS variables so that specific reforecast product requirements are met. A new variable in `config.base` called `DO_EXTRACTVARS` enables this task, which is currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by default and is specifically a task designed to be executed for the GEFSv13 reforecast. Refs #1878 # Type of change - New feature (adds functionality) # Change characteristics - Is this a breaking change (a change in existing functionality)? NO - Does this change require a documentation update? NO # How has this been tested? This has been cloned and tested on WCOSS2. This will need to be tested on Hera and other platforms on which the reforecast may be running. # Checklist - [ ] Any dependent changes have been merged and published - [x] My code follows the style guidelines of this project - [x] I have performed a self-review of my own code - [ ] I have commented my code, particularly in hard-to-understand areas - [x] My changes generate no new warnings - [x] New and existing tests pass with my changes - [ ] I have made corresponding changes to the documentation if necessary --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 71dc33c6ca991c16ce743760d99feaaf60f2218a Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jul 22 14:51:53 2024 -0400 Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774) Fix metp* resources and check that they completed properly; add support for Orion Rocky 9 commit 56df67a90fe090c425199f1285e5aac722c398b1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jul 22 09:28:18 2024 -0400 Hotfix: Update jcb to avoid git-lfs files (#2782) Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to be cloned on Hera. This hotfix points to a non-authoritative branch of the GDASApp (https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and should be updated ASAP back to the authoritative repository. commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jul 16 09:44:00 2024 -0400 Address issues in creating XML for GFS forecast-only with app S2SWA (#2757) This bugfix PR: - fixes an issue where a user is unable to generate the XML for a GFS forecast-only experiment with APP=S2SWA Specifically, the changes are related to defining `aero_fcst_cdumps`. Following `setup_expt.py`, the user will have to set `AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in `config.base`. commit e0878dba0e53706a7f53429b61aee2936e2c21bf Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Jul 15 10:25:11 2024 -0400 Updated prepobs and fit2obs versions for Orion Rocky9 (#2758) Update prepobs to v1.0.2 and fit2obs to v1.1.2 These versions now support Orion Rocky9. Updates are included for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet. commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jul 11 17:48:47 2024 +0000 CI maintenance updates and adding CI Unit Tests (#2740) This PR has a few maintenance updates to the CI pipeline and adds a test directory with Unit Tests **Major Maintenance updates:** - Added try blocks with appropriate messaging to GitHub PR of failure for: - - **scm** checkout - - build fail (with error logs sent as gists) - - create experiment fails with `stderr` sent to GitHub PR messaging - Pre-stage FAILS from the above are now captured these fails allow FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state labels in GitHub - see image below) **Minor Maintenance updates:** - Fix for STALLED cases reviled from PR 2700 (just needed a lambda specifier) - Fixed path to experiment directory in PR message (had dropped EXPDIR in path) - Needed `latin-1` decoder in reading log files for publishing **Added python Unit Tests for CI functionality:** - Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI utility codes - Cashed the install of Rocoto in the GitHub Runners to greatly reduce stetup time for running the unit tests - Unit Tests Python scripts added - `test_rocostat.py`: rocoto_statcount() rocoto_summary() rocoto_stalled() - `test_setup.py`: setup_expt() test_setup_xml() - `test_create_experment`: test_create_experiment() - - Runs all PR cases that do not have ICs in the GItHub Runner - Reporting mechanism in the Actions tab for Python Unit Testing results - Test case data for STALLED and RUNNING stored on S3 and pulled using wget during runtime of tests commit 5ef4db74649b8be03402c17aa29c024e71699a7b Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu Jul 11 08:59:24 2024 -0400 Adds contents of constructor and initialize methods to marine LETKF class (#2635) Adds contents of constructor and initialize methods to marine LETKF class Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091 --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> commit 8998ec7b74123e953b97a93fa14cc78d471a1aee Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jul 9 08:31:57 2024 -0400 Fix GDAS group B restart archiving (#2735) Archives the GDAS restartb dataset at a 6-hour offset from restarta This allows cycled experiments to restart from the archives. The tabbing for the master archive templates was also added to improve readability. Resolves #2722 commit 3ca74771255727033b9dc043c652ac585178629c Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Tue Jul 9 08:28:54 2024 -0400 Add fcst dependency to ocnanalprep (#2728) Add previous cycle's `fcst` as a dependency to `ocnanalprep` This ensures that the availability of restart files to the latter. This addresses a seldomly-encountered race condition where `ocnanalprep` fails due to the lack of the files. commit 58fca1668aecd6fb1afd12a441256ad35900e075 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jul 5 15:02:23 2024 -0400 Update (partially) global-workflow for orion+rocky9 (#2741) This PR: - updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils, GFS-utils) to include recent update to their modulefiles for Orion+Rocky9 upgrade - updates the modulefiles in global-workflow to load modules from Orion+Rocky9 paths - updates modulefiles for `gwsetup` and `gwci` as well. - removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not installed. - adds `parm/config.gfs/config.resources.ORION` to address GSI performance degradation after Rocky 9 upgrade. This PR: - does not update the build for UPP. Standalone UPP is not available via ufs-weather-model as of #2729 - will need a follow-up update for `prepobs` and `fit2obs` updated locations when they are installed in `glopara` space on Orion. # Type of change - Maintenance (code refactor, clean-up, new CI test, etc.) # Change characteristics - Is this a breaking change (a change in existing functionality)? NO - Does this change require a documentation update? NO # How has this been tested? This PR is not sufficient for Orion. This PR must be tested on other platforms (Hera, WCOSS2) as this PR updates submodules. # Checklist - [ ] Any dependent changes have been merged and published - [ ] My code follows the style guidelines of this project - [ ] I have performed a self-review of my own code - [ ] I have commented my code, particularly in hard-to-understand areas - [ ] My changes generate no new warnings - [ ] New and existing tests pass with my changes - [ ] I have made corresponding changes to the documentation if necessary --------- Co-authored-by: Kate Friedman <kate.friedman@noaa.gov> commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jul 3 21:07:49 2024 -0400 Update ufs model hash to 20240625 (#2729) Updates UFS weather model hash to hash from 2024-06-24 which has orion porting updates + a few namelist updates. commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jul 3 11:32:40 2024 -0400 Hotfix for undefined CLUSTERS (#2748) Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses the native `dict` `get` method to prevent grabbing an unset entry. commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Wed Jul 3 09:56:08 2024 -0400 Update gempak job to run one fcst hour per task (#2671) This PR updates gempak jobs (gfs, gdas, and goes) from processing all forecast hours at once to one forecast hour at a time. This will reduce the job runtime to less than 5 min, so restart capability is not needed. Resolves #1250 Ref #2666 #2667 --------- Co-authored-by: Walter.Kolczynski <Walter.Kolczynski@noaa.gov> commit 8215ae654202186a4f753c3abe937b7b9b91a9c7 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jul 2 16:22:11 2024 -0400 Hotfix for clusters from #2701 (#2747) Fixes an issue created from #2701 that added `CLUSTERS` to the `gaea.yaml`. commit 11943e36ba12b3df49c51942da780698fab02d38 Author: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> Date: Tue Jul 2 12:58:10 2024 -0400 Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701) This PR sets up the ability on Gaea for auto generation of a clean xml file, i.e., an xml file that does not need any alterations before running rocoto. Refs #2572 Refs #2664 commit de8706702ead0630beb54d868f83aa2cb23f8f79 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon Jul 1 09:29:14 2024 -0400 Update for JCB policies and stage DA job files with Jinja2-templates (#2700) This PR updates the `gdas.cd` hash to bring in new JCB conventions. Resolves #2699 From #2654 This PR will move much of the staging code that take place in the python initialization subroutines of the variational and ensemble DA jobs into Jinja2-templated YAML files to be passed into the wxflow file handler. Much of the staging has already been done this way, but this PR simply expands that strategy. The old Python routines that were doing this staging are now removed. This is part of a broader refactoring of the pygfs tasking. wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a companion to this PR. Co-authored-by: danholdaway <danholdaway@users.noreply.github.com> Co-authored-by: DavidNew-NOAA <david.new@noaa.gov> Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Co-authored-by: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jun 28 14:56:19 2024 -0400 Revert PR 2681 (#2739) This PR: - reverts #2681 in part - keeps some changes for `RUN`. - is a hotfix - should be merged ASAP after consensus w/ @guillaumevernieres @CatherineThomas-NOAA @WalterKolczynski-NOAA commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed Jun 26 15:46:08 2024 -0400 updated Finalize in Jenkinsfile and added try block around scm checkout (#2692) We are updating the Jenkins Pipeline with a try block around checkout to capture errors for the user. Also cleaned up Finalize and added section to clean out workspace on success. commit 968568f682bac7564095440bdb7813abefd76821 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 26 13:27:19 2024 -0400 Activate snow DA test on WCOSS (#2720) Activate the snow DA test on WCOSS. commit 7706760bb8adbdf78cb640b02739023c886e7699 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jun 26 10:02:22 2024 -0400 Cleanup of stale RUNDIRS from an experiment (#2719) This PR: - removes stale temporary scratch run directories from `$DATAROOT/` every 3 days. - should help to scrub failed attempts. - removes an unused variable `RUNDIR` defined in `config.base` commit 8962991691b5f0857b813bddfd28aa1034d4bd2b Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jun 26 09:43:48 2024 -0400 Update logic for MOM6 number of layers/exception values (#2681) Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine how many layers and sets the exception value for MOM6 to be 1e-34 for all scenarios. Note, we will no longer have zeros in the ocean grib output and the DA will also run without issues. Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615 commit 12431f76bdce807067929415007592cffc8a2457 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Jun 26 07:42:35 2024 -0600 Update wave jobs to use COMIN/COMOUT (#2643) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow wave model and products tasks. Refs #2451 commit b902c0bac126c323a07186ad8881384b032b6fda Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jun 25 07:48:46 2024 -0400 Assign machine- and RUN-specific resources (#2672) Redefine resource variables based explicitly on RUN or CDUMP Additionally, machine-specific resources are moved out of config.resources and placed in respective config.resources.{machine} files. Resolves #177 #2672 commit 5edbd123e2878a07f5cce8e3c7ea6147f286633a Merge: 09333c01d 4e1b937b6 Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Mon Jun 24 12:44:05 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit 4e1b937b67ed220120e81925c4507f03b9b8965f Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jun 24 10:50:52 2024 -0400 Add minimum software requirements (#2712) Adds a table to HPC documentation stating the minimum support versions commit f43a86276aaef91efa28faadc71a3cf50e749efe Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Jun 21 13:44:29 2024 -0400 Fix and simplify online archiving and reenable METplus jobs (#2687) This fixes the online archiving portion of the `*arch` and `*earc00` jobs, a prerequisite for running METplus. This also reenables METplus by default. The approach previously taken created `FileHandler` dictionaries at varying levels within the resulting yaml, which was not properly parsed by `exglobal_archive.py`. This approach creates a single `FileHandler` dictionary and is much less complicated overall. Resolves #2673 #2647 commit 8993b42cb91144c0ab0501dc7841ea8d675c4701 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 19 21:51:22 2024 -0400 Eliminate post groups (#2667) Eliminates the post groups used for upp and products jobs so that each task only processes one forecast hour. This is more efficient and greatly simplifies downstream dependencies that depend on a specific forecast hour. Resolves #2666 Refs #2642 commit 0b810c888239853fedd0e4584fe62536c6aaacdf Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 20:32:48 2024 -0600 Removes misleading "No such file or directory" syntax errors from output files (#2688) This PR addresses issue #1252. The following is accomplished: - Prior to removing files, the existence of a file is checked prior to attempting to remove; this is performed as noted [here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369); this PR only addresses the the `chgrp` issue. Refs #1252 --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 12:17:59 2024 -0600 Hotfix for bug in template names. (#2697) This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/` template. Resolves #2696 Refs #2451 commit 35d4d99eaac669721add9ddcc793153e5ab3b30a Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 18 08:06:53 2024 -0600 Update archive job to use COMIN/COMOUT (#2668) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow archive task. Refs #2451 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 47b3a581c8257fa24411fb400df8bb0e1e04972a Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Jun 17 22:55:38 2024 -0400 Turn on high-frequency output in extended test (#2679) Turns on high-frequency (hourly) output in the extended products test to exercise that aspect of the code. This test only runs on WCOSS. Also adds the hooks to optionally turn on the metplus jobs, but that is deferred as they are not currently working correctly. commit 38f2df9fb0c074b1f80d3c637080be79be693161 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jun 17 17:12:55 2024 +0000 Optimize wavepostpnt (#2657) Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs This is done by 1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by - performing operations on all files at once instead of looping over each file - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`) - combining `sed` and `grep` calls when possible - adding logic to `awk` calls instead of handling that logic in bash 2) minimizing as much as possible the amount of data on disk that has to be read in (e.g. limiting sed to read only the line numbers it needs) --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 5af325a6a4e0a14d180514a418603ca79fada487 Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Fri Jun 14 18:05:23 2024 -0400 Update GDASapp hash to move JCB into GDASapp (#2665) This PR moves JCB into GDASapp. The PR also bumps up the hash of GDASapp to what is in `feature/move_jcb`, which at time of writing is develop plus the absorption of JCB into GDASapp. Note that I also took the changes from https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the testing @RussTreadon-NOAA has done. commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b Author: Yaping Wang <49168260+ypwang19@users.noreply.github.com> Date: Fri Jun 14 10:18:17 2024 -0500 Add observation preparation job for aerosols DA to workflow (#2624) Add a prepaeroobs job to prepare aerosol obs files for DA. This job does quality control of the VIIRS aerosol raw observations and convert them to ioda format. Resolves #2623 --------- Co-authored-by: ypwang19 <yaping.wang@users.noreply.github.com> Co-authored-by: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Jun 14 11:04:41 2024 -0400 Remove ocean daily files (#2689) This PR removes the ocn_daily files that are produced by the ocean component. These files can be recreated by averaging data that exists in the 6 hour aveaged files if needed. Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675 Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by removing them and making this obsolete) commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jun 13 12:22:03 2024 -0400 Update Jenkinsfile needed a comma commit dc21eac6c3941d7f30803891d91d82f4cc1f8183 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Jun 13 11:41:14 2024 -0400 Add Hercules-EMC to the Jenkins configurable parameter list (#2685) This quick-fix PR is to update the Jenkins Pipeline's configurable parameter list to include the **Hercules-EMC** node. This allows Jenkins users to restart Jobs in the controller when no updates have been made. commit ebacebfbe458634b8c80af6a735d6b6d01e4e406 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Thu Jun 13 11:20:24 2024 -0400 Update gdas.cd and gsi_utils hashes (#2641) This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea build for gsi_utils. Resolves #2640 commit 34155fb4767769600a1ff95f0a65e37081addc2a Author: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com> Date: Thu Jun 13 11:18:22 2024 -0400 Add ability to use GEFS replay ICs (#2559) The PR allows the use of ICs from PSL's replay analysis. These replay ICs will be used for GEFS reforecasting and SFS. Two main changes are associated with these updates: (1) replay ICs being valid at 3Z, and (2) the use of warm starts. Resolves #1838 --------- Co-authored-by: Jessica Meixner <Jessica.Meixner@noaa.gov> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Jun 12 19:25:42 2024 -0600 Replace `sleep` with `wait_for_file` (#2586) This PR addresses issue #2444. The following is accomplished: - All `sleep` statements are replaced with `wait_for_file` for the relevant scripts beneath `scripts` and `ush`; - Indentation and shell-norms are updated where applicable. Note: The WAFS scripts are not updated as per @aerorahul direction. Resolves #2444 --------- Co-authored-by: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jun 12 13:31:55 2024 -0400 Add COM template for JEDI obs (#2678) Adds a COM template to define a path to store obs processed for JEDI. This will allow UFSDA to stop writing to COM_OBS, which should be read-only as it belongs to obsproc in operations. No functional change yet. commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Wed Jun 12 09:06:23 2024 -0600 Link both global-nest fix files and non-nest ones at the same time (#2632) This PR enables linking both global-nest fix files and non-nest ones at the same time and users can run both nesting and non-nesting experiments at the same time without worries about what fix files to be linked. Resolves #2631 commit 61de004d4f9e9edf8a31bb173f2719b46451a36a Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Jun 12 11:03:13 2024 -0400 Update ufs-weather-model (#2663) Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack allowing some temporary fixes to be reverted. * removes upp submodule * uses upp from the ufs-weather-model * restores the build and link that were hacked during the Hera Rocky 8 transition to allow for UPP submodule * Removes forecast directories in clean-up Resolves #2617 Resolves #2437 --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com> Date: Wed Jun 12 01:15:37 2024 -0400 Add ability to process ocean/ice products specific to GEFS (#2561) This PR begins to add the capability to produce GEFSv13 ocean and ice products in the global-workflow according to stakeholder requirements. The following features are added. - An oceanice prod yaml file has been added to address the ocean and ice products specific to GEFSv13. - The rocoto dependencies and config.base for GEFS have also been modified to allow for 24-hour averaged ocean and ice output. - Various scripts have been modified to allow for ocean and ice output frequencies of 24 hours. - `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN` and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`. Refs #1878 commit 6691e7489650e0b738c176fbd096109288dc09b6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Jun 11 21:15:07 2024 -0600 Update cleanup job to use COMIN/COMOUT (#2649) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the global-workflow clean-up task. Refs #2451 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Jun 11 16:17:25 2024 -0400 Add overwrite to creat experiment in BASH CI (#2676) This is a quick hotfix to the CI BASH driver script adding `--overwrite` to create experiment script to avoid errors from restarting an experiment. commit e7909af8d9e1f34140388a3f8556d8e582c58fe5 Author: emilyhcliu <36091766+emilyhcliu@users.noreply.github.com> Date: Mon Jun 10 15:11:27 2024 -0400 Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py (#2645) This PR proposes updates for the following two scripts: 1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select CRTM cloud optical table based on cloud microphysical scheme indicated by `imp_physics' The default scheme in the GFS forecast model is Thompson scheme (imp_physics = 8). 2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in the script due to increased variables to interplate increments and calculate analysis in the netcdf_io routines in GSI-utils. Here is the related [PR #46 for GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46). --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 9caa51de8fb7be07d2e61775da01937d576964f6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Jun 6 22:15:23 2024 -0600 Update RDHPCS Hera resource for `eupd` task (#2636) As per @wx20jjung, the resource for the `eupd` task have been updated for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job fails. Resolves #2454 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Thu Jun 6 11:49:03 2024 -0400 Parameterize some things in config.atmanl and config.atmensanl (#2661) This PR adds some parameters in config.atmanl and config.atmensanl that can be altered with the defaults.yaml. The motivation is to make these files match those in the GDASApp JJOB tests (example: https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl), so we can just use the Global Workflow config.atmanl and config.atmensanl in the tests rather than custom ones in GDASApp that have to be separately updated every time the ones in the Global Workflow are updated. commit 54ea0b73a07921be5fbb07fe41e976888bd3e549 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Thu Jun 6 01:36:02 2024 -0400 Add links to the ocean insitu obs processing tools (#2644) Add links to the marine bufr to ioda converters for the marine insitu observations. - fixes https://github.com/NOAA-EMC/GDASApp/issues/1106 - waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135 commit 205d0c2b13e2d7755cec75bf8c978ab20d453862 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Wed Jun 5 17:31:30 2024 +0000 Update S4 point of contact in docs (#2660) Update the point of contact for global workflow issues on S4. commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed Jun 5 12:50:14 2024 -0400 Enable wcoss2 ufsda build and module load (#2620) This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2. Resolves #2602 Resolves #2579 commit 67b833e0c7bc390865d453588b4609a1a7ede981 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Tue Jun 4 13:33:43 2024 -0400 Update ufs-weather-model (#2646) Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6 This should resolve the issue and allow C768 runs on Hera and allow for CICE to run on WCOSS2 (due to library updates to allow linking). From what I can tell, all updates needed were done by @HenryWinterbottom-NOAA which were updates for CICE Fixes #2490 commit c44d0ac86cfdf78eb87492431bf6d825e8bae637 Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Tue Jun 4 10:29:49 2024 -0400 Update wmo parm files to fix WMO header (#2652) This PR updates wmo parm files to switch WMO header of precipitation type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to instantaneous. Resolves #2566 commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Tue Jun 4 13:55:33 2024 +0000 Add IAU to snow DA (and its test) (#2610) This PR enables IAU for the snow DA which is necessary for GFSv17. A snow analysis is created for the center of the window regardless, and an additional at the beginning of the window is added if IAU is on. The former is needed for UPP and the latter, to initialize the model. The increment is valid throughout the window for 3DVar, so the same increment is added to both forecasts. Additionally, the input file that goes into global_cycle has been updated to be the output of the JEDI snow analysis instead of the forecast (@jiaruidong2017 I recall discussing this, can you confirm this is right or am I mistaken) This PR also makes the CI test for snow DA (and aerosol DA) include IAU rather than without IAU,. --------- Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit c92bf415060750127c9c05a62a1d2851c489551a Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Sat Jun 1 05:11:07 2024 +0000 Archiving cleanup (#2621) 1) Adds a lot of comments to the jinja templates for archiving 2) Rearranges the gdas and enkf templates to a more logical order 3) Fixes a couple of bugs in the enkf archiving of increments and analyses 4) Disables archiving for the half cycle 5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`, instead relying on `DO_FIT2OBS` 6) Updates wxflow to add the option to not allow undefined variables when parsing jinja templates and invokes this feature when running archives Resolves #2612 commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Fri May 31 04:57:08 2024 -0400 Switch to Rocky 9 built external packages on Hercules (#2608) The workflow was updated to use modules built on Rocky 9, but the external packages (like prepobs) were still pointing to the versions built on CentOS (Orion). This transitions to packages built on Rocky 9. Updating of the tracker package has been deferred until later. As such, the tracker jobs have been disabled by returning immediately if they are on Hercules. Since these jobs are small, resource-wise, it should not meaningfully impact turnover time. commit 4422550c01c9214a2b3b8890bdcc898123ee216a Author: Guoqing Ge <guoqing.ge@noaa.gov> Date: Thu May 30 08:05:23 2024 -0600 Add the capability to use slurm reservation nodes (#2627) Add the capability to use slurm reservation nodes Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE Resolves #2626 commit a54153fd9d26126206bc07a1da4e80f50c0c5910 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 29 23:24:07 2024 -0400 Update forecast job to use COMIN/COMOUT (#2622) NCO has requested that each COM variable specify whether it is an input or an output. This completes that process for the forecast job. Refs #2451 --------- Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> commit d69a8af95d492982b918670322ed5c41ab074335 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed May 29 21:29:03 2024 -0400 Update to add 1-deg global wave grid (#2619) This PR adds options to use a global 1 deg grid, intended for testing with the SFS application. Requires new fix file changes NOAA-EMC/global-workflow#2618 commit 0b4670ecf83b99b72835c8380573b2bca7cf5324 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed May 29 17:17:21 2024 -0400 Add C384mx025_3DVarAOWCDA yamls (#2625) Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder. commit 2e885d05c64b947f00a3cf055a1277fbfac195c9 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 29 13:00:51 2024 -0400 Script to keep Jenkins Agent persistent from cron (#2634) This "persistent" Java Agent launch script can be ran from a cron job: - Uses Jenkins Remote API to check the status of the Node connection using curl for a given machine. - If it is not connected a new agent is launched for that node. Resolves #2633 commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5 Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com> Date: Tue May 28 17:17:11 2024 -0400 Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611) Based on users' feedback, this PR do the following: 1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF 2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD, and VOGRD) from "%g m below water surface" to "%g m below sea level" 3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m) Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31 Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Date: Tue May 28 17:16:23 2024 -0400 Add atmensanlfv3inc job (#2592) This PR creates the atmensanlfv3inc job, the ensemble version of atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is #[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3). commit 50c2b8951b29a3c883a778becbf8582f9519eb48 Author: Anil Kumar <108816337+AnilKumar-NOAA@users.noreply.github.com> Date: Tue May 28 13:23:53 2024 -0400 Global-workflow (AR) Generic updates for Gaea C5 (#2515) - Port global-workflow’s build and run capability to Gaea-C5 - Building global-workflow on Gaea-C5 - Setting up experiments with global-workflow on Gaea-C5 --------- Co-authored-by: AnilKumar-NOAA <Anil.Kumar@gaea53.ncrc.gov> Co-authored-by: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com> commit b6ca771a0c584cbfcbbf9be739765d5f3815df97 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 24 10:52:45 2024 -0400 Update STMP and PTMP settings in host file for Orion and Hercules (#2614) - Updating STMP and PTMP settings in host file for Orion and Hercules because they are cross mounted. - Also took the opportunity to finally update **SLURM_ACCOUNT** to **HPC_ACCOUT** in CI over rides. - Added a refactor of the `rocotostat.py` tool that is more pythonic and as a execute retry feature because the `rocotostat` utility on Orion has been failing sometimes. commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Tue May 21 23:50:50 2024 -0400 Sea-ice analysis insertion (#2584) Allows cycling and restarting CICE with the sea-ice analysis if the marine DA is switched on. Resolves #2568 Resolves NOAA-EMC/GDASApp#1103 commit 5369a1ff3a3969149fcf32810fad0e50216752b7 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue May 21 22:12:29 2024 +0000 Refactored archiving (#2491) This provides a new pygfs task, archive.py, that provides all of the tools necessary to archive data to the local (`ARCDIR`) and backup (`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to define the file to be archived or tarred to replace the `hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts and make it easier to add new data and explicitly handle optional and required files. For `ATARDIR` archiving, a master jinja template is provided for each `RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2, master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both `enkfgdas` and `enkfgfs` `RUN`s. These templates then include the appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on experiment, cycle, and coupled parameters. Each of these templates corresponds to a single tarball to populate and are tabbed 4 spaces so they are defined within the master `datasets` dictionary. Future developers should not have to make modifications to archive.py unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then only a single `elif` needs to be added to the configure method to specify the master `ATARDIR` template to archive (e.g. `master_gefs.yaml.j2`). If a new component is coming online that needs to be archived to `ATARDIR` (e.g. SNOW), then create a new template for each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`) and reference the template in the appropriate master templates, e.g. `master_gdas.yaml:` ```jinja {% if DO_SNOW %} {% include "gdassnow.yaml.j2" %} {% endif %} ``` A few other issues were addressed along the way: 1. Aerosols have been reenabled. Aerosol forecasts should only be performed during gdas cycles, but analyses can be performed for both gfs and gdas cycles. This was accomplished by setting separate `AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs. 2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`. This prevented restarts from being used for cice-enable experiments. This feature was not tested. 3. Create a temporary fix for the `wgrib` utility. For spack-stack 1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in existing installations. Once complete, this temporary fix should be removed. 4. The number of `earc` jobs has been reduced for lower resolution experiments. Both C48 and C96 experiments will now only have two earc jobs (one for the non-member files to archive and another for the member files). C192 will have up to 3 earc jobs (one non-member, one for members 1-40 and another for members 41-80, if needed). Resolves #2345 Resolves #2318 --------- Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 17 12:57:59 2024 -0400 Add remove RUNDIRS step in CI before creating experements (#2607) As had been done in Bash CI we need to remove the RUNDIR in Jenkins before a creating an experiment in the event that case had beem previously ran. commit 09333c01dbafddb2d2fe7e181b479af3cc6d3621 Merge: f7e9f4489 bb930050b Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com> Date: Thu May 16 14:33:19 2024 -0600 Merge branch 'NOAA-EMC:develop' into develop commit bb930050b3cd51d28ecba6b231c8675f6d11856c Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Thu May 16 12:28:30 2024 -0400 Adds jjob and other necessities for marine LETKF task (#2564) Adds jjob, rocoto script, config file, and other necessities for new marine LETKF task. Partially addresses NOAA-EMC/GDASApp#1091 commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu May 16 12:12:06 2024 -0400 Updating CI Machine configs with redundant PTMP (#2605) Quick fix adding PTMP as STMP in Machine configs for CI for completeness commit ef340ff33a6f89adf70838206ba3fd56a953fa7a Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu May 16 11:37:30 2024 -0400 Fix race condition in CI between Orion and Hercules (#2604) Hotfix to solve race conditions in the CI system due to cross-mounted file systems between Orion and Hercules commit e8b17e27f719df280170dc3f5bd9f19917cefaf2 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 15 17:16:30 2024 -0400 Remove existing EXPDIRs and COMROTs when CI is re-run (#2601) Quick hotfix for having default for re-runing jobs to start clean with new EXPDIRs and COMROTs commit b5d113efb1970ede5cd1d3d4dff8d96320519c41 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Wed May 15 16:52:49 2024 -0400 Moving logic for skipping hosts in pr cases (#2573) This PR removes the logic of skipping hosts for pr cases from `create_experiment.py` and moves it to a test in the cron bash driver using a `parse_yaml.py` python tool. The Jenkins pipeline was not effected as it uses the `get_host_case_list.py` utility to form the cases on a per host bases. Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed May 15 13:13:30 2024 -0400 Update gsi_utils.fd hash (#2598) This PR updates the `gsi_utils.fd` hash to bring in updates which add safeguards to - `src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90` - `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90` The safeguards are described in GSI-utils PR [#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated issue. Resolves #2597 commit d5366c66bd67f89d118b18956fe230207cbf0aea Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed May 15 13:12:56 2024 -0400 Update CICE and MOM6 fix versions (#2600) This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions to the newer `20240416` timestamps, which includes updates and fixes to the `100` (1-deg) resolution files. Resolves #2480 Resolves #2483 Resolves #2595 commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon May 13 22:57:38 2024 +0000 Limit gfswavepostpnt to 40 PEs/node (#2588) This fixes the slow runtime of the gfswavepostpnt job on Hercules. The job is very I/O intensive and does not scale well to large nodes, so limit the number of jobs/node to 40. Resolves #2587 commit 4fb7c12c325702a47f27c802a5067efd33d0327c Author: Fanglin Yang <fanglin.yang@noaa.gov> Date: Mon May 13 16:37:51 2024 -0400 Update damping and time-step (#2575) Updates the model to use explicit Rayleigh damping for u/v and implicit damping to w. This improves model stability and allows for longer timesteps. Also unifies the GDAS and GFS to use the same damping. Results from a test at the C1152 resolution (coupled model) can be found at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/ Resolves #2574 Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Co-authored-by: Lisa Bengtsson <lbengtss@Orion-login-1.HPC.MsState.Edu> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri May 10 14:17:13 2024 -0400 Do not use BUILT_semphore to force rebuilds when re-run (#2593) Remove the placement of the `BUILT_semaphore` file after the build in the Jenkins Pipeline and force it to rebuild any changes after a PR is re-ran. commit 2346c6161f75ae02369cbf30f30c6150d3e12b66 Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com> Date: Thu May 9 21:17:06 2024 -0500 Migration to Rocky8 spack-stack installations on Jet (#2458) # Description Migrates Global Workflow to Rocky8 spack-stack installations on Jet. Jet has moved from CentOS7 to Rocky8. Resolves #2377 Refs NOAA-EMC/UPP#919 Refs NOAA-EMC/gfs-utils#60 Refs NOAA-EMC/GSI#732 Refs NOAA-EMC/GSI-Monitor#130 Refs NOAA-EMC/GSI-utils#33 commit c7b3973014480a20dd8e24edaeb83a9e9e68159f Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Thu May 9 11:36:58 2024 -0400 Updates for cold start half cycle, then continuing with IAU for WCDA (#2560) This PR allows us to run C384 S2S with IAU, but starting with the first half-cycle as a cold-start. This will be necessary for cycled testing as we build towards the full system for GFSv17. This updates the copying of the restarts for RUN=gdas for both ocean and ice copying what the atm model is doing. It also reduced the amount of restart files from 4 to 3. Other updates: * Add DOJEDI ocean triggers for archiving certain files update from: @CatherineThomas-NOAA * Adds COPY_FINAL_RESTARTS option to turn on/off copying the last restart file to COM. Defaults to off... * Defines model_start_date_current_cycle & model_start_date_next_cycle to help with knowing which IC to grab. Refs #2546 Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2 Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com> Date: Wed May 8 20:52:48 2024 -0400 Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477) Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI Configuration Builder (JCB) tool so that YAMLs can be made more portable and invoke the observation chronicle mechanism. Resolves #2476 Co-authored-by: danholdaway <danholdaway@users.noreply.github.com> Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed May 8 02:04:16 2024 -0400 Add CI test for products (#2567) Adds a new version of the atm3DVar test that runs the full forecast length and produces most of the secondary products. For now, this test will only run on WCOSS due to gempak failures on other machines as well as computational needs. On other machines, the original version will run (the original version will not run on WCOSS). AWIPS remains off for now in this extended test due to a bug involving tocgrib2 and the convective precip fields (see #2566). The new test runs for 4½ cycles and the full 384-hr forecast length to ensure all gempak scripts are exercised. Since the cycle throttle is 3 and the bulk of the time is in the free forecast, the cycles run mostly concurrently so it doesn't exte…

danholdaway added 11 commits April 3, 2024 20:06

add some jcb things

32bd4ff

do not recurse inside jcb to avoid config files in sorc

1edba10

Use of JCB for gdas 3dvar

f8c4dea

remove left over prints

aef1289

unused import

8cc1422

refactor the way obs are decided

fccce33

remove rogue atm file

8e49292

remove unused import

08d51f3

letkf to jcb

a7d7b5d

towards letkf gdas tests working

9945964

danholdaway mentioned this pull request Apr 9, 2024

Move Atmospheric YAMLs to JCB repo NOAA-EMC/GDASApp#1033

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aerorahul requested a review from CoryMartin-NOAA April 10, 2024 15:06

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danholdaway added 6 commits April 15, 2024 18:34

update to jcb that has external algo YAMLs

1d50b11

keeping up with GDAS develop

5bd9b8d

clone jcb algo repo

c8dcffb

more updates for jcb algos

4c48dfb

gdas upgrade

2681b64

danholdaway added 2 commits April 17, 2024 19:13

reset gdas hash

324d8a7

RussTreadon-NOAA mentioned this pull request Apr 22, 2024

Update gdas_gsibec_ver to 20240416 #2497

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danholdaway added 2 commits April 23, 2024 17:20

update gdas hash

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WalterKolczynski-NOAA merged commit b405b7d into NOAA-EMC:develop May 9, 2024
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Update JEDI-T2O to work with JCB NOAA-EMC/JEDI-T2O#117

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Restore GDAS-validation functionality NOAA-EMC/JEDI-T2O#118

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Use JCB for assembling JEDI YAML files for atmospheric GDAS #2477

Use JCB for assembling JEDI YAML files for atmospheric GDAS #2477

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Use JCB for assembling JEDI YAML files for atmospheric GDAS #2477

Use JCB for assembling JEDI YAML files for atmospheric GDAS #2477

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