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Add flexibility for ocean/ice output time-steps #1629
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@JessicaMeixner-NOAA |
see https://github.com/NOAA-EMC/global-workflow/blob/develop/ush/forecast_postdet.sh#L773-L787 |
actually, global-workflow/ush/forecast_postdet.sh Line 758 in ae56219
CDATE is defined at the top as the current cycle and does not change.
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@jiandewang This file with midpoint date is then linked to COM with a valid datetime and midpoint datetime. I don't see why that is necessary and we will simplify this section in coming PRs. If the issue is to have a different averaging time for ocean, I think we can update the |
The frequency of the ocean output in GFSv17 is currently undecided, my understanding of the issue was found when we were trying to use 3 hourly atm output and 6 hourly ocean output, however, since |
@JessicaMeixner-NOAA |
Changes the output frequency from 3 to 6. While we may leave this setting as the default for development, it is required right now because the ocean frequency is hard-coded to 6 but links are created based on `$FHOUT_GFS`. Resolving NOAA-EMC#1629 should correct this limitation. Refs NOAA-EMC#1606 Refs NOAA-EMC#1629
When the prototype S2S was first added, we placed some settings in a `config.defaults.s2sw` file to avoid interference with existing settings. Now that we are moving towards v17 and run S2S regularly, it is time to merge these settings back into the other config files. The wave output frequency settings are updated to the coarser fre- quency as that is more suitable for development. The prior (ops) settings are noted as comments. There are a couple of settings that control ice fields within FV3. These are placed in `config.ice`, so when the ice model is on those settings are still used. Changes the output frequency from 3 to 6. While we may leave this setting as the default for development, it is required right now because the ocean frequency is hard-coded to 6 but links are created based on `$FHOUT_GFS`. Resolving #1629 should correct this limitation. "Gaussian" archive is updated to the former override values. Resolves #1606 Refs #1629
From @NeilBarton-NOAA -- we control the ice output frequency by the FHOUT variable here:
Note that the first lines "h" for hour corresponds to the "FHOUT" variable. |
global-workflow: 02Jan24, 9d901db UFS: 21Dec23, 991d652 UPP: 07Nov23, 78f369b Squashed commit of the following: commit 4e4e50803d95566e1c7967cf4cfa575391d77f25 Author: Judy.K.Henderson <[email protected]> Date: Fri Jan 12 00:44:59 2024 +0000 Change default HPSS_PROJECT to fim Change restart_interval_gfs to -1 so no files are written ro RERUN_RESTART directory commit 791d7a27c6b12f07d9c12ce491338e3da59eb1d8 Author: Judy.K.Henderson <[email protected]> Date: Thu Jan 11 23:34:36 2024 +0000 Add namelist parameter, nord_tr, for GSL suites commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5 Author: Judy.K.Henderson <[email protected]> Date: Thu Jan 11 23:31:22 2024 +0000 Add changes for running v17p8_mynn - new field table, field_table_thompson_aero_tke_progsigma - updated namelist parameters in config.fcst commit 982a1f02e3b880be43f4ae8a3f0ffbb34c056aea Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 9 02:26:22 2024 +0000 Add experiment setup script for p8_ugwpv1 commit c5a3697d22fdbb02bb80ddffee2629dddc10c702 Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 9 02:19:13 2024 +0000 Add memory report to srun command in env/HERA.env commit ece7e516ca65ec0240899e7d84321310a6887595 Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 9 02:13:42 2024 +0000 Updated GSL-specific files under ufs_utils.fd_gsl commit 1b153fc95b93a16eb40b791be7322100fde4a3d4 Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 9 01:52:56 2024 +0000 Create new branch, gsl_ufs_dev, from dev_02jan24_9d901db Add initial GSL modifications - changes to workflow files * GSL paths, projects, entities - new FV3_GFS_v17_p8_ugwpv1_mynn suite definition file (SDF) - updated namelist parameters in ush/parsing_namelists_FV3.sh - create new GSL directories: ufs_model.fd_gsl and ufs_utils.fd_gsl * new SDFs, add instantaneous flux variables to grib2 configuration files * add Thompson tracers to initial conditions - new sync script: rsync_gsl.sh - new job files: getic.sh, makeinit_link.sh - modify build_ufs.sh to include MYNN SDF commit 9d901dbbff4d41586580316bdc094d24760119e6 Author: Henry R. Winterbottom <[email protected]> Date: Tue Jan 2 10:30:33 2024 -0700 Stop Gempak pgrb2 spec from modifying $DATA (#2147) This PR addresses issue #1224. The following is accomplished: - Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time; - Shell linter exceptions are addressed accordingly; - The respective GEMPAK tasks is added to the Rocoto mesh. Resolves #1224 commit 31ad23527802f7d07171132cc620f7135c4d8cba Author: Henry R. Winterbottom <[email protected]> Date: Tue Jan 2 10:27:30 2024 -0700 Reorganize NPOESS scripts (#2166) This PR addresses issue #1226. The following is accomplished: - Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated; - Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh` are moved accordingly; this specifically applies to the environment variable `FHOUR`, `SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`; - The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level (if necessary); - Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however, this may not be necessary (see `TODO` note within draft PR. Resolves #1226 commit 22bd82fa93b49e5ce98eb3f69123956dd5018049 Author: Kate Friedman <[email protected]> Date: Tue Jan 2 11:55:03 2024 -0500 Orog fix file reorg and fix directory variable standardization (#2181) This PR makes updates to use the newly reorganized `orog/20231027` fix file version and standardizes the fix file directory variables. Changes: 1. Update UFS_UTILS hash to ce385ce 2. Update fix file version file to use new orog timestamp: `orog_ver=20231027` 3. Add ".mx$(OCNRES)" to `oro_data` filenames in scripts 4. Remove ".mx$(ocn_res)_frac" from the directory names for atmosphere resolutions under the `/orog` folder 5. Adds fix file directory variables to `config.base`, many of which are pulled up out of lower scripts; introduce `FIXcpl` 6. Renamed/replaced the following fix file directory variables: - `FV3JEDI_FIX` --> `FIXgdas` - `FIXfv3`, `FIX_orog` and `OROFIX` --> `FIXorog` - `FIX_ugwd` and `OROFIX_ugwd` --> `FIXugwd` - `FIX_am`, `FIXgsm`, `FIXSYND` --> `FIXam` - `FIX_lut` --> `FIXlut` - `FIX_aer` --> `FIXaer` - `FIX_SFC` --> `FIXsfc` - `FIX_DIR` --> `FIXgfs` - `RTMFIX` and `FIXCRTM` --> `CRTM_FIX` (is `CRTM_FIX` in crtm module, so not using `FIXcrtm`) 7. Correct the defaults for `FIXwave` in wave JJOB scripts 8. Update variable names in `*fixed_files.yaml` files, as well as update naming convention for `oro_data` files Resolves #1984 Resolves #1981 Resolves #2175 commit 03d03bf53b43914a55c384cb33eb06f6a9a443a6 Author: Andrew Collard <[email protected]> Date: Tue Jan 2 11:53:44 2024 -0500 Remove HIRS from GSI processing (#2183) With the update to CRTM 2.4.0.1, an issue with versioning of CRTM HIRS files has been exposed. This is documented in JCSDA/crtm#42. As HIRS radiances are no longer used in the GSI, these data should be removed from processing until a suitable update to CRTM is available. Resolves #2182 commit a3c50998d35525a39a66d5592fbf327ab3569e8b Author: Jessica Meixner <[email protected]> Date: Fri Dec 22 18:07:48 2023 -0500 Update ufs-weather-model version (#2186) * update model to latest version which includes needed bugfixes for HR3 commit 774c7302e618370ef578bec3ccabc70486d6da1b Author: David Huber <[email protected]> Date: Fri Dec 22 11:34:53 2023 -0500 Fix analysis post processing's handling of 0-padded negative integers (#2187) This screens for the analysis 'forecast' hour (-001) and handles the '-' and circumvents octal issues. commit d1251360325faf75af9df0608557fcd10202a883 Author: Barry Baker <[email protected]> Date: Thu Dec 21 11:23:48 2023 -0500 Fix for restoring cycling aerosols in fo-mode post COM refactor (#2179) - Update to COM reorg aerosol initialization job - Address bug in joining paths for data dependency in this job --------- Co-authored-by: Rahul Mahajan <[email protected]> commit e55a05980709288d902ad1bd894164bfa5a18a65 Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Dec 20 22:14:01 2023 -0500 Stop calling ufs-utils link script (#2172) The `link_workflow.sh` script was calling the ufs_utils version of the same. That step is only necessary if a user is going to run one of the stand-alone ufs-utils, which is rare. commit ef3e5ad7c63be1644c82333c95853c3caf2d8995 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Dec 19 22:02:55 2023 -0500 Fix handling of excluded hosts list (#2170) This PR fixes the issue with `create_experment.py` so that the yaml configuration file can have a string of list of strings when specifying the host name to exclude from the CI tests. commit ea74a5719efc8f0fe631c5ff93426a4299a614f3 Author: AndrewEichmann-NOAA <[email protected]> Date: Tue Dec 19 16:21:41 2023 -0500 Add COMOUT_OBS to marine obs prep (#2173) Adds `COMOUT_OBS` (defined from `COM_OBS_TMPL`) to marine obs prep task to properly handle marine obs prep files. Used to keep obs after IODA conversion, QC, and other prep. Towards resolving NOAA-EMC/GDASApp#815 commit c2500feace0bb7c04ce67a90dd3182120ee67b2e Author: David Huber <[email protected]> Date: Tue Dec 19 14:55:20 2023 -0500 Return failed status if a build fails. (#2171) If any of the builds fail, this makes build_all.sh return the sum of the error codes encountered. Fixes #2168 commit 76fdd81cd84ed812181996a102379d8d964ba27a Author: Kate Friedman <[email protected]> Date: Tue Dec 19 13:24:34 2023 -0500 Update index.rst for new GFSv16.3.12 in ops (#2169) Refs #2096 commit a81da33e8fe7541a36f68e7a4f14a384cadd36c8 Author: Kate Friedman <[email protected]> Date: Tue Dec 19 10:22:21 2023 -0500 Set place=shared for shared jobs on WCOSS2 (develop) (#2156) Set job as shared when not exclusive on WCOSS2 WCOSS2 defaults to exclusive when it is not specified as either exclusive (place=exclhost) or shared (place=shared). Now set shared when job should be shared. Refs #2135 commit 89aea972f7964dac3f515e8070d7c534812c5fb4 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Dec 15 16:31:06 2023 -0500 Update gfs-utils version for Hercules (#2163) An update of gfs-utils was misssing from the previous PR that added initial Hercules support (#2128). Also includes gfs-utils update for new marine post. commit 9505cb4abc6ca2643a8ab254d14ca2000747fa44 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Thu Dec 14 16:15:31 2023 -0500 CI Updates to support Hercules (#2155) If merged, this PR will update the CI scripts so they will run on Hercules for forecast only NOTE: This is a stop gap to issue #2131 until its block on #1588 is removed. Resolves #2154 commit c5ca82f04a2efae78389dec1c46b94ef4fb5bbe5 Author: Rahul Mahajan <[email protected]> Date: Thu Dec 14 16:05:33 2023 -0500 Correct fbwind (#2161) commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a Author: Kate Friedman <[email protected]> Date: Thu Dec 14 12:06:23 2023 -0500 Add MOS jobs to rocoto mesh (#2148) Create separate jobs for GFS MOS - extracted from now-retired vrfy job Refs #2068 commit bb6151aa50c27253cb9b8f0a6601ddd58526b8b3 Author: Walter Kolczynski - NOAA <[email protected]> Date: Thu Dec 14 05:38:29 2023 -0500 Replace checkout script with submodules (#2142) Replaces the checkout script with git submodules. This change brings workflow in line with other repos and git standards. Due to these changes, the build system is updated slightly. First, the options that were formerly used with `checkout.sh` to reduce unneeded builds (`-g` for GSI and `-u` for UFSDA) are moved to `build_all.sh` instead. This is needed since build all will not be able to key off directories existing or not to determine which com- ponents to build. Second, the partial build system is removed. It was rarely, if ever, used, and parts of it were already ignored with the previous changes to base builds off whether directories exist. The manage externals file is also removed since that is also not being used. Following these changes, clones/checkout will need to either be recursive, or `git submodule update` will need to be called separately to make sure components are properly checked out (non-exhaustive list): ``` ## Checkout develop (method 1) git clone --recursive https://github.com/NOAA-EMC/global-workflow destination ## Checkout develop (method 2) git clone --jobs 8 https://github.com/NOAA-EMC/global-workflow destination cd destination git submodule update --init --recursive --jobs 8 ## Checkout existing branch some_branch (method 1) git clone --recursive --jobs 8 -b some_branch https://github.com/NOAA-EMC/global-workflow destination ## Checkout existing branch some_branch (method 2) git clone https://github.com/NOAA-EMC/global-workflow destination cd destination git checkout --recurse-submodules some_branch ## Checkout existing branch some_branch (method 3) git clone https://github.com/NOAA-EMC/global-workflow destination cd destination git checkout some_branch git submodule update --init --recursive --jobs 8 ## Checkout new branch new_branch git clone https://github.com/NOAA-EMC/global-workflow destination cd destination git checkout -b new_branch git submodule update --init --recursive --jobs 8 ``` The git ignore list had to be updated to use explicit paths as the wildcard paths pick up the ones that are now submodules. UFS creates files during the build process that are not in its ignore list, so that sub- module ignores the "dirty" state to avoid confusing users running `git status`. CI and documentation are also updated to reflect the changes. Resolves #2141 commit 1332188ce2409e012ec127d44880e49732f7f379 Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Dec 13 09:32:57 2023 -0500 Enable radar reflectivity output (#2143) Turns on radar reflectivity output from FV3. This eliminates missing values appearing in the grib2 files. commit 24d898ec0ec0c7fcbda6966988f9a986f528ed14 Author: David Huber <[email protected]> Date: Wed Dec 13 09:32:24 2023 -0500 Fix Hercules hostname (#2150) * Allow lower or upper hostname on hercules. * Add Hercules to issue template. commit 2896bb8787698be28ad20f2298589e6e95eaf9fb Author: Kate Friedman <[email protected]> Date: Tue Dec 12 09:13:06 2023 -0500 Fix module load typo (#2145) Fix typo with loading the crtm module in the UPP hack for WCOSS2 Refs #2144 commit 29d34172a67d976f910e78158ff0337e1ef099ca Author: Cory Martin <[email protected]> Date: Thu Dec 7 15:12:05 2023 -0500 Update GDAS hash to most recent stable versions (#2138) commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102 Author: Henry R. Winterbottom <[email protected]> Date: Thu Dec 7 10:41:05 2023 -0700 Corrected typo in a gempak job gempakncdcupapgif . (#2137) commit 3483f550db1ae35a680de49f7485ce5a11902dd9 Author: Cory Martin <[email protected]> Date: Thu Dec 7 12:34:56 2023 -0500 Add support for FGAT and IAU for aerosol DA (#1940) commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9 Author: David Huber <[email protected]> Date: Thu Dec 7 12:33:46 2023 -0500 Enable forecast-only experiments on Hercules (#2128) This add forecast-only support for Hercules to the global workflow. Partially satisfies #1588. Co-authored-by: Walter Kolczynski - NOAA <[email protected]> commit a29f751aed05312da3d80d396159bb5a906d6ce4 Author: Henry R. Winterbottom <[email protected]> Date: Wed Dec 6 13:45:56 2023 -0700 Adds GEMPAK and related jobs to rocoto task mesh (#2127) commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082 Author: Rahul Mahajan <[email protected]> Date: Tue Dec 5 15:47:52 2023 -0500 Separate offline UPP from interpolated grib2 product generation (#2110) This PR: - Replaces the use of `JGLOBAL_ATMOS_POST` with `JGLOBAL_ATMOS_UPP` and `JGLOBAL_ATMOS_PRODUCTS`. - Introduces `JGLOBAL_ATMOS_PRODUCTS` that is responsible for creating grib2 products from the master file produced by UPP (inline from the model, or offline by running `JGLOBAL_ATMOS_UPP`). Rocoto job `atmos_products.sh`, ex-script `exglobal_atmos_products.sh` are also added along with a `config.atmos_products`. Updates are made to the relevant `env` files as well as `config.resources` to reflect the addition of this job. - reduces the number of cores needed appropriately for forecast products when there is no offline UPP necessary. - renames older `fv3gfs_dwn_nems.sh` to `interp_atmos_master.sh` and `inter_flux.sh` to `interp_atmos_sflux.sh` - removes `fv3gfs_downstream_nems.sh` as it is absorbed into `exglobal_atmos_products.sh` - removes no longer used scripts for `gfs_post.sh`, `gfs_transfer.sh` (DBN alerts are absorbed into `exglobal_atmos_products.sh`), `post.sh`, `JGLOBAL_ATMOS_POST`, `ex${RUN}_atmos_post.sh` scripts. - Rocoto workflow related scripts are updated to add `atmos_products` as a job. When `WRITE_DOPOST` is `.false.`, `upp.sh` job to run the UPP offline is also added. Dependencies have been appropriately applied. - removes `PGB1F` option that creates 1-degree grib1 products that are no longer needed in GFSv17. The hacks from (now deleted) `post.sh` had to be reinstated in `upp.sh` to load the modules from UPP instead of `load_fv3gfs_modules.sh`. commit 44186f594aaf5f8feea0eadd4c5c3b59de3a825e Author: Kate Friedman <[email protected]> Date: Tue Dec 5 12:28:08 2023 -0500 Update index.rst for new GFSv16.3.11 version (#2121) Refs #1356 commit e62a3a73cd22701962b7bf210fdfee37f37a5474 Author: Henry R. Winterbottom <[email protected]> Date: Tue Dec 5 09:08:12 2023 -0700 Splits AWIPS jobs into seperate tasks (#2094) This PR addresses issue #1228. The following is accomplished: - Separate rocoto jobs have been created beneath `jobs/rocoto/` -- `awips_20sh` and `awips_g2sh`; these jobs replace `awips.sh` which was calling multiple J-jobs within the respective `awips.sh` scripts; - New tasks has been added to `workflow/rocoto/tasks.py` for the new AWIPS scripts; - The `gfs_cycled` and `gfs_forecast_only` modules beneath `workflow/rocoto` have been updated accordingly. Resolves #1228 commit 04d97e9aa7ab84b9754ab670074cfb19d543aa26 Author: Kate Friedman <[email protected]> Date: Mon Dec 4 13:38:30 2023 -0500 Consolidate VMINMON and cleanup monitor scripts (#2088) This PR combines the GDAS and GFS versions of the VMINMON JJOB and ex-driver scripts into single GLOBAL/global versions. Additionally: * some further cleanup of the GSI-Monitor scripts is done; variable settings in ex-driver scripts are moved up to the JJOB level * the fix symlinks are consolidated into a new `fix/mon` subfolder (formerly `fix/gdas`) and copies of the gfs monitor fix files under `fix/products` are removed Resolves #1925 commit a286a11fdcbc31c8bc6d944890bc56294bc8caf6 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Mon Dec 4 17:48:44 2023 +0000 Robust CI Restarts (#2093) Improved CI robustness for reverting back to **CI-Ready** from any given state New Features: - Improved `scancel` routine (refactored into bash "subroutine") - Improved messaging (see below) when ever a user changes state - Any and all previous build scripts and running experiments are killed as a result of reset to **Ready** Resolves #2060 commit 73621e9b20b20f85e8b21e4c1e09ed1d80ecd46f Author: David Huber <[email protected]> Date: Sun Dec 3 11:19:19 2023 -0500 Upgrade to spack-stack/1.5.1 and Intel 2022 on non-production machines (#2084) Update module files to spack-stack/1.5.1 and compilers to Intel 2022+ on all non-production machines. commit 6d548b250688861eb20a7e0dc852a0e4ba9e64f4 Author: jiandewang <[email protected]> Date: Thu Nov 30 12:00:21 2023 -0500 Add variable tob in diag_table for ocean model output(#2105) commit c19810cce252fcdb25fd9960c05b08b5f8d8b1ad Author: AndrewEichmann-NOAA <[email protected]> Date: Wed Nov 29 15:17:36 2023 -0500 Added variables to config.prepoceanobs (#2101) commit c2d78a61a224678fb804eed19f39d1f07408ae5f Author: Kate Friedman <[email protected]> Date: Wed Nov 29 12:39:08 2023 -0500 Add missing cut to VDATE setting in JGFS_ATMOS_VERIFICATION (#2098) Refs #2097 commit c1c025f91ddac73aea595cc9fa4dd0bea80575fc Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Nov 29 17:15:10 2023 +0000 Add wave init to GEFS (#2089) Adds the wave init job to GEFS. Since the output would be the same for every member, the job is only run once for the control, then links are created in each of the member directories pointing to that copy. New ww3_multi and ww3_shell templates for GEFS are copied from the GFS versions. The GEFS restart frequency is changed to not be zero, and the comment about not setting it to zero is copied from the gfs config.base. The restart interval for the GEFS perturbed members is changed to equal that of the control. Also fixes a bug where `RUNwave` was not defined for ensemble forecasts, and another bug in the GEFS stage_ic dependency. Resolves #2017 commit 64a2470ce29b7d8d5cb85ebcb4048ff82958f64e Author: Kate Friedman <[email protected]> Date: Wed Nov 29 11:26:34 2023 -0500 Adjust permissions for jobs/JGFS_ATMOS_VERIFICATION (#2095) Add execute permissions (755) commit 964b77bc6de67291973c2c70598a1f8cb72501c5 Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Nov 28 18:45:51 2023 +0000 Make proper j-job for MET+ (#2090) Creates a proper j-job for the metp job, moving much of the material from the `jobs/rocoto` script there (some of it within `jjob_header`). Also updates the old `COMIN` variable for the COM refactor (although it does not appear used in the verify scripts currently). This is a partial step towards restoring/improving metp functionality and remains untested. Refs #1575 commit 8c11eeb8556619e8db4e0efb6394ce5a2c1aae0f Author: Henry R. Winterbottom <[email protected]> Date: Thu Nov 23 10:31:32 2023 -0700 Adds FBWINDS support to global-workflow (#2082) This PR addresses issue #1221. The following was accomplished: - A new Rocoto job is added; `jobs/rocoto/fbwinds.sh`; - `workflow/applications/gfs_cycled.py` is updated to include the `fbwinds` task; - `workflow/applications/gfs_forecast_only.py` is updated to include the `fbwinds` task; - A new function is added to `workflow/rocoto/gfs_tasks.py`, `fbwinds` is added as new GFS (only) task; - `workflow/rocoto/tasks.py` is updated to include the `fbwinds` task. Resolves #1221 commit 513db190d21f9ede0724a2cd5606372b1d7605de Author: Henry R. Winterbottom <[email protected]> Date: Tue Nov 21 22:52:58 2023 -0700 Adds NPOESS support to global-workflow (#2083) This PR addresses issue #1225. The following was accomplished: - A new Rocoto job is added; `jobs/rocoto/npoess.sh`; - `workflow/applications/gfs_cycled.py` is updated to include the `npoess` task; - `workflow/applications/gfs_forecast_only.py` is updated to include the `npoess` task; - A new function is added to `workflow/rocoto/gfs_tasks.py`, `npoess` is added as new GFS (only) task; - `workflow/rocoto/tasks.py` is updated to include the `npoess` task. Resolves #1225 commit 62d8e99e77ffe44784f4c61c3f2296c6d1a72413 Author: Kate Friedman <[email protected]> Date: Fri Nov 17 20:25:50 2023 -0500 Retire vrfy job (#2080) Retires the `vrfy` job from the global-workflow system. All associated scripts, configs, and references to the job are removed. Additionally, the switches listed in RTD were updated to reflect new ones added in other PRs for issue #235. Resolves #2069 Refs #235 commit ea386abf11ecbacef407388e8d57e71b30148a35 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Nov 17 23:59:46 2023 +0000 Enable different coupled settings for ensemble (#2030) Adds the ability to turn off some coupled components for the ensemble. To enable this, many settings are moved out of `config.fcst` and into `config.ufs` so they are calculated after any overrides of `DO_*` have been made. Some settings also had to be moved out of `config.base` for the same reason. A switch to turn on gocart is added to `config.ufs`, but unlike the other switches this one takes no arguments. The name of the ufs configure template used is converted from a partial file name to the full file name. Resolves #1692 commit fe792c0c9a1c46908cbd18c7e71eb836974cf1de Author: Kate Friedman <[email protected]> Date: Fri Nov 17 17:19:16 2023 -0500 Add --cpus-per-task to srun commands for Hera and Orion (#2077) This PR adds the `--cpus-per-task` flag to non-CFP `APRUN`/srun commands in the env files for Orion and Hera. This is needed as a result of an upgrade to SLURM on Orion that no longer exported the thread value to the environment. Issue #1996 was a hotfix to add this flag for the analysis job that was suddenly running slowly after the SLURM upgrade. A similar SLURM upgrade was done on Hera but the sysadmins there implemented a workaround so this issue did not appear there. This PR adds the `--cpus-per-task` flag for both machines...needed on Orion and as a safety measure on Hera. Also included in this PR is a fix to indentations in the `scripts/exglobal_diag.sh` script that was noticed during work for this PR. Timing differences were not observed for other jobs after adding this srun flag. Job timings were of a similar variation between control and test runs. Any potential additional speedup was not observed. The test runs also reproduced the control runs with `develop`. Resolves #2044 commit 42c943be305c297a56b104bb50727938c1ba688f Author: Kate Friedman <[email protected]> Date: Fri Nov 17 15:41:34 2023 -0500 Adjust modules in post.sh for WCOSS2 (#2079) On WCOSS2 the grib_util module is named a bit different and needs the libjpeg module loaded beforehand. commit cd4e6a1987e7fd71dff06766f540b5d32c8b648d Author: Jessica Meixner <[email protected]> Date: Fri Nov 17 11:49:32 2023 -0500 Update ufs-weather-model and remove upp hack (#2071) Updates the model to the most recent commit of ufs-weather-model. This should allow for the removal of the UPP hack that was added in PR #2042 This required changing nems.configure -> ufs.configure. Resolves #1942 commit 5a2d97e142aa4999b122fd5a130c63e59ea9f8e2 Author: Walter Kolczynski - NOAA <[email protected]> Date: Thu Nov 16 22:15:53 2023 +0000 Fix check for existence of preamble functions (#2066) A few of the setup scripts were checking for the existence of functions set by the preamble before calling them so they could also be used stand-alone. However, the `type` command returns `1` if the function name does not exist, which will cause the script to die is `set -e` is on. Now the `type` command fails over to an empty string. commit ed2ee7c2b1457b71b271a2c40f0dfa356e0f52f8 Author: WenMeng-NOAA <[email protected]> Date: Thu Nov 16 16:38:11 2023 -0500 Update UPP products for GFS v17 (#1973) Updates of generating GFS V17 UPP products to support HR3: - Update g2tmpl to 1.0.12 - Add changes to launch cfp on WCOSS2 to generate pgrb2/pgrb2b files - Changes for generating new products (MERRA2, six winter weather variables, 1km HLCY, SDEN) in pgrb2 files Resolves #1965 Resolves #1994 commit 635c4719e603538ce7cccf9ea6b31f3f84f20849 Author: Walter Kolczynski - NOAA <[email protected]> Date: Thu Nov 16 20:35:30 2023 +0000 Fix some rocoto dependencies (#2074) A few small errors/cleanup in the dependencies, mostly in fcst: A few small errors/cleanup have crept into the dependencies with recent changes, mostly in fcst: - Fixed the offset, as it would yield a string rocoto doesn't recognize when the interval was 24+ hrs - Removed the duplicate wave dependency. When `waveprep` is included, it depends on `waveinit` so there is no need to add a `waveinit` dependency. - Converted an interval in the archive job that was missed in #2039 Resolves #2075 commit d4c7508260975c6b94fc92fd085f39d4faf3f027 Author: Rahul Mahajan <[email protected]> Date: Wed Nov 15 16:44:03 2023 -0500 Fix missing _PREV in ocean restart file location (#2070) commit 255616d37505c785bdddd5d3e39e8399110b626e Author: mdtoyNOAA <[email protected]> Date: Wed Nov 15 12:02:09 2023 -0700 Update functionality for Prototype HR3 UGWP (#1987) This PR adds/modifies namelist options and activates new 'ccpp' suite definition files for the updated Unified Gravity Wave Physics (UGWP) in the ufs-weather- model recently updated for HR3. The changes to UGWP are the use of the GSL drag suite for orographic gravity wave drag (GWD) and blocking, as well as the new UGWP Version 1 non-stationary GWD. See ufs-community/ufs-weather-model#1923 for details. Resolves #1986 commit be9085e62aae147e3c74602e2f82a99b374fc783 Author: Guillaume Vernieres <[email protected]> Date: Wed Nov 15 13:48:58 2023 -0500 Save the required CICE history for the sea-ice DA (#2062) The hist_avg setting of CICE was changed to be an array. commit 85f1f5131ffd70061231304ea477bde0559eb67b Author: Guoqing Ge <[email protected]> Date: Wed Nov 15 11:47:21 2023 -0700 Use assim_freq to configure "offset" in dependencies (#2039) Use the assim_freq from config.base to configure "offset" in dependencies instead of hard-coding them. Resolves #2038 commit 4e3d82ba3a1fa7cdd4443bcd4cf83b2f8835137c Author: Kate Friedman <[email protected]> Date: Wed Nov 15 13:39:14 2023 -0500 Resolve ENKF archive script bugs (#2065) Fix two bugs in the exgdas_enkf_earc.sh script: 1) Replace ARCH_LIST with DATA to match changes done in PR #2000 and update path to generated archive list files. 2) Add status check and exit after script attempts to make tarball on HPSS. Refs #2064 commit 42d7f2f0c48fab898b764e09cfbbd7a9fabbae08 Author: Kate Friedman <[email protected]> Date: Tue Nov 14 17:54:29 2023 -0500 Separate tracker and genesis jobs from vrfy job (#2058) This PR creates new individual jobs for the tracker and genesis jobs that are being pulled out of the `vrfy` job (issue #235). The `tracker` and `genesis` jobs will be on by default while the `genesis_fsu` job will be off by default. This mimics the current settings in the `vrfy` job. No enhancements or upgrades are made to the jobs themselves in this PR, only to separate them from the `vrfy` job. However, one change compared to how they currently run in the `vrfy` job is to no longer run the `tracker` in the gdas suite. This mimics how the `ens_tracker` package is run in operations (gfs only). Changes in this PR: 1. Create rocoto job scripts for tracker/genesis jobs. 2. Create configs for tracker/genesis jobs, as well as `config.tropcy` for shared settings. 3. Add tracker/genesis jobs to `config.resources`; use resources from the ecf scripts for `ens_tracker` jobs in operations 4. Add tracker/genesis jobs to rocoto setup for both cycled and forecast-only modes. 5. Update arguments for `jjob_header.sh` script in tracker/genesis JJOB scripts to use specific job names and configs instead of vrfy. 6. Rename `tracker_ver` to `ens_tracker_ver` in version files to mimic variable within tracker package. 7. Rename and move tracker/genesis switches to `config.base`. 8. Remove tracker/genesis jobs from `vrfy` job (`jobs/rocoto/vrfy` and `config.vrfy`). 9. Reduce vrfy job resources to accommodate tasks having been removed. Refs #235 Resolves #1988 Resolves #2048 commit 0a0d6984e094d2a551d5d8331102142e7db13fc2 Author: Rahul Mahajan <[email protected]> Date: Tue Nov 14 14:08:26 2023 -0500 Enable warm starting of the model for forecast-only mode (#2031) This PR: - adds an option to warm|cold start the ufs-weather-model when setting up an experiment for GFS/GEFS - adds the capability to stage FV3 restarts when the atmosphere is warm started from FV3 restarts. This would be used in the GEFS free-forecast for part of the reforecast capability. - If a coupled model is warm started for the atmosphere, also check if mediator restarts are present. If so, stage mediator restarts to allow restarting the coupled model. Fixes #2016 commit 2cd6a589305a9ac9d3a9a0d2136e66e42f09d3bf Author: Henry R. Winterbottom <[email protected]> Date: Tue Nov 14 12:05:20 2023 -0700 Moves UFS WM configuration files to `COM_CONF` (#2054) The UFS weather-model (WM) files are place in the COM_CONF path rather than the respective component model COM history paths. Resolves #2015 commit 6f1693081662f241fafc930b1afc88125f7f5aff Author: Kate Friedman <[email protected]> Date: Tue Nov 14 11:15:02 2023 -0500 Refine fit2obs job in rocoto mesh (#2047) This PR adjusts the `fit2obs` job in the rocoto mesh to better define when it exists and how the archive job dependencies accommodate it not being in the first half cycle. Changes in PR: 1. Remove the `fit2obs` job from the first half cycle `cycledef`. 2. Adjust the archive job dependencies to now include the `fit2obs` job in the new logic check added in PR #1983. The `gdasarch` job in the first half cycle will check if `gdasfit2obs` is complete OR no prior cycle exists. Also cleaned up this new logic check block some to make it a tad simpler. 3. Also, fix the addition of the `fit2obs` config to the config list in setup scripts. Now tied to whether `fit2obs` job is on instead of always adding the config to the list. Resolves #2043 commit 5730a71fa5d311e49d9bb11528b500f27f33d69d Author: Henry R. Winterbottom <[email protected]> Date: Tue Nov 14 09:13:11 2023 -0700 Add `waveinit` and `waveprep` to half-cycle. (#2037) This PR addresses issue #1444. The `waveinit` and `waveprep` tasks have been added to the GDAS have cycle. The downstream dependencies for the respective GFS and GDAS forecast tasks have been removed. Resolves #1444 commit 28d2e93c3857de95b0309a089cd7dac736ccaded Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Nov 14 16:11:47 2023 +0000 Update wave IC source for C384 (#2055) The default wave grid for C384 has changed since P8, so a single wave IC on the new grid is available under a different IC name. commit 81dd2d9855091315611106a5afbdaeaa15e6e4ae Author: Walter Kolczynski - NOAA <[email protected]> Date: Thu Nov 9 17:19:57 2023 +0000 Fix analysis and post on Orion (#2046) Fixes a couple things to get workflow to work on Orion again: First, while #2042 allowed post to be built, the `upp.x` executable would fail due to a missing library. Now post jobs (temporarily) uses the UPP modules (plus others needed for runtime) instead of the normal workflow runtime module. This should actually fix #2041. This hack can likely be removed once we move to spack-stack. Second, the launcher command for the analysis jobs on Orion are updated to specify the number of CPUs per task. This was necessary as a recent slurm update on Orion discontinued reading that value from the scheduler. Other jobs will be handled later (see #2044). Additionally, a change is made to `module-setup.sh` that will eliminate the annoyance of `gw_setup.sh` breaking tab completion because undefined variable checking was turned on for the script but not back off. Resolves #1996 Resolves #2041 Refs #2044 commit 13d06ded4155cba2d08ef2a2cd553024c5abe29d Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Nov 8 18:25:47 2023 +0000 Hack UPP version (#2042) The stack UPP was using on Orion was recently deleted, leaving us unable to build the UFS verison of UPP there. UPP has an updated version using spack-stack that works, so the checkout script is modified to check out that version of UPP after UFS has been checked out. This temporary hack can be removed once we move to a UFS version that advances the UPP version to or beyond 78f369b. Resolves #2041 commit 20f6eceb8ff58f84174a27eb849c1d74566a3e03 Author: jiandewang <[email protected]> Date: Wed Nov 8 11:14:55 2023 -0500 Add basic C1152 settings (#2020) Adding C1152 setting in host.yaml, config.base and config.stage_ic so that can run C1152 S2SW. Resolves #2019 commit 5183c43bbbd07285869feacb49d8680afe85929a Author: Barry Baker <[email protected]> Date: Tue Nov 7 01:14:40 2023 -0500 Update UFS for dust fix and remove nitrates by default (#1989) This PR updates the `ufs-weather-model` to the latest hash that included the dust fix (PR #1922). Along with this I removed the nitrates by default in support of the GEFSv13 EP4 and EP5 experiments. Removed unneeded inputs that should help with speed improvements. commit 34a73cf2ed5afefc776d9cc73b6ebf439122a1bb Author: David Huber <[email protected]> Date: Mon Nov 6 14:00:51 2023 -0500 Reduce gdas builds to 8 #2029 (#2036) Reduce the default number of build jobs for the GDASApp to 8 from 16. This is needed for Orion as the build crashes during a linking step. Though not verified, it appears this may be caused by using too much memory with 16 builds. The issue disappears when using 8 build jobs. Resolves #2029 commit 75269e4bb9764b81589efc7d703825b80e74c8f5 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Mon Nov 6 17:34:47 2023 +0000 Streamline CI reporting to PRs (#2026) Cleaned up the logs for CI PRs sent to the GitHub Messages: - Eliminates redundant accumulative reporting - Reports on all created or skipped experiment instantiations in a single message - Gives one line report once for each experiment completion - Single final report completion of CI See some examples in forked [PR 195](https://github.com/TerrenceMcGuinness-NOAA/global-workflow/pull/195) Resolves #2007 commit 8d55126bb0b27c79c8bee7f72b014abd34950ff9 Author: Guillaume Vernieres <[email protected]> Date: Fri Nov 3 17:06:09 2023 -0400 Implement IAU Cycling Type with Marine Data Assimilation Enabled (#1944) Allows cycling in IAU mode with the S2S UFS model, soca and the GSI. Most of the work related to making IAU work was done by @JessicaMeixner-NOAA . Thanks @JessicaMeixner-NOAA ! Resolves #1943 Refs #1776 commit 2563806821d4ae3b57120bc61aa0575139a708f0 Author: jiandewang <[email protected]> Date: Fri Nov 3 11:49:37 2023 -0400 Add two ucx modules in load_ufswm_modules.sh to solve C768 and C1152 S2SW job hanging issue on WCOSS2 (#2021) commit cbdc09711a83493f363a737d1e3e46c48a09719d Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Nov 3 04:09:33 2023 +0000 Fix staging of MOM data (#2028) During the update to stage_ic, the copying of the additional res_N files for 0p25 was omitted. These are now properly copied. Resolves #2027 commit bd4c56d99c23c5c41f0bd5f8a980ef99ee160888 Author: AndrewEichmann-NOAA <[email protected]> Date: Thu Nov 2 16:09:59 2023 -0400 changed optional script name vars for ocean analysis (#2025) commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6 Author: Kate Friedman <[email protected]> Date: Thu Nov 2 16:01:18 2023 -0400 Create separate GSI monitor jobs and remove from vrfy job (#1983) This PR will move the GSI monitor tasks from the `vrfy` job into their own separate jobs in the rocoto mesh. This takes care of part of issue #235. Changes in this PR: 1. Create new individual GSI monitor jobs in the rocoto mesh to match how it is done in operations. The new jobs are: `gdasverfozn`, `gdasverfrad`, `gdasvminmon`, and `gfsvminmon`. The names correspond to the names in operations and the ecf script names. The jobs are only added to cycled mode, none of the jobs are run in forecast-only mode. 2. Updates to GSI monitor scripts: * Update `ush/jjob_header.sh` arguments in JJOB scripts to call new individual job names and configs. * Introduce `COM_*` variables and use of the `generate_com` utility. This results in the outputs landing in `COM` subfolders, like occurs in operations, instead of landing in the online archive. * Some variable cleanup in JJOB and ush scripts, includes cleaning up usage of `DATA` variable and its removal at the end of the jobs. * Add missing exit statements to `JGFS_ATMOS_VMINMON` and `JGDAS_ATMOS_VERFRAD`. 3. Create new rocoto job scripts for the new individual GSI monitor jobs. 4. Create new configs for the new individual GSI monitor jobs. 5. Add new individual GSI monitor jobs to resource configuration, using the same resources as in operations. 6. Move and rename GSI monitor job switches from `config.vrfy` to `config.base`. Also add switches to setup system. New switches to control each job being added to the rocoto mesh are: `DO_VERFOZN`, `DO_VERFRAD`, `DO_VMINMON` 7. Add GSI monitor job output to archival job and into resulting HPSS tarballs or local tarballs. This now matches what is done in operations. 8. Remove the GSI monitor tasks from the rocoto `vrfy` job and associated `config.vrfy`. Example output locations and files (not showing contents of oznmon/horiz or oznmon/time for brevity, see archival script for full list of output files): ``` kate.friedman@dlogin09:/lfs/h2/emc/ptmp/kate.friedman/comrot/testmonitor2> ll gdas.20211221/00/products/atmos/*mon gdas.20211221/00/products/atmos/minmon: total 112 -rw-r--r-- 1 kate.friedman emc 14030 Oct 25 15:00 2021122100.costs.txt -rw-r--r-- 1 kate.friedman emc 84932 Oct 25 15:00 2021122100.cost_terms.txt -rw-r--r-- 1 kate.friedman emc 808 Oct 25 15:00 2021122100.gnorms.ieee_d -rw-r--r-- 1 kate.friedman emc 808 Oct 25 15:00 2021122100.reduction.ieee_d -rw-r--r-- 1 kate.friedman emc 80 Oct 25 15:00 gnorm_data.txt gdas.20211221/00/products/atmos/oznmon: total 8 drwxr-sr-x 2 kate.friedman emc 4096 Oct 25 15:05 horiz drwxr-sr-x 2 kate.friedman emc 4096 Oct 25 15:05 time gdas.20211221/00/products/atmos/radmon: total 21036 -rw-r--r-- 1 kate.friedman emc 231 Oct 25 15:12 bad_diag.2021122100 -rw-r--r-- 1 kate.friedman emc 9035 Oct 25 15:12 bad_pen.2021122100 -rw-r--r-- 1 kate.friedman emc 1449 Oct 25 15:12 low_count.2021122100 -rw-r--r-- 1 kate.friedman emc 20523403 Oct 25 15:07 radmon_angle.tar.gz -rw-r--r-- 1 kate.friedman emc 217272 Oct 25 15:08 radmon_bcoef.tar.gz -rw-r--r-- 1 kate.friedman emc 502151 Oct 25 15:10 radmon_bcor.tar.gz -rw-r--r-- 1 kate.friedman emc 264480 Oct 25 15:12 radmon_time.tar.gz -rw-r--r-- 1 kate.friedman emc 684 Oct 25 15:12 warning.2021122100 kate.friedman@dlogin09:/lfs/h2/emc/ptmp/kate.friedman/comrot/testmonitor2> ll gfs.20211221/00/products/atmos/minmon/ total 88 -rw-r--r-- 1 kate.friedman emc 10530 Oct 25 14:55 2021122100.costs.txt -rw-r--r-- 1 kate.friedman emc 63882 Oct 25 14:55 2021122100.cost_terms.txt -rw-r--r-- 1 kate.friedman emc 808 Oct 25 14:55 2021122100.gnorms.ieee_d -rw-r--r-- 1 kate.friedman emc 608 Oct 25 14:55 2021122100.reduction.ieee_d -rw-r--r-- 1 kate.friedman emc 80 Oct 25 14:55 gnorm_data.txt ``` Lingering work and considerations: 1. Issue #1925 2. Consider not hardcoding the list of types in archival and perhaps tie it to something reliable or configurable (maybe into `config.verfozn`?): `subtyplist="gome_metop-b omi_aura ompslp_npp ompsnp_n20 ompsnp_npp ompstc8_n20 ompstc8_npp sbuv2_n19"` Resolves #1908 commit 31b05a99b77d0f6eaa8b116485a41a43867d20e1 Author: Henry R. Winterbottom <[email protected]> Date: Thu Nov 2 12:23:32 2023 -0600 Move analysis post to new stand-alone task (#1979) This PR addresses issue #1130. A new task `postanl.sh` has been added such that the `anl` post-processing is not it's own task within the Rocoto workflow. This change prevents the GDAS experiment from breaking due to failures caused by the `anl` not being available for the first cycle. Resolves #1130 commit 247cdf8c7e10e6c98f782799fc51c069b6474e70 Author: Henry R. Winterbottom <[email protected]> Date: Thu Nov 2 11:18:53 2023 -0600 Corrects missing local variable reference (#2023) Fixes missing `$` in variable reference in archive job. Resolves #2022 commit 241742b246da1794646b68e41c3d6fe00b95dd07 Author: AndrewEichmann-NOAA <[email protected]> Date: Wed Nov 1 14:19:55 2023 -0400 Updates to prep ocean obs task (#1870) commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd Author: Henry R. Winterbottom <[email protected]> Date: Wed Nov 1 12:09:33 2023 -0600 No longer write archive lists COM (#2000) Changes the respective `.txt` files used for the HPSS archive to the `DATA` path. Each defined text file has been updated to explicitly write to `DATA` rather than `COM` such that the files are deleted rather than being archived. Resolves #760 commit 517b92f9c20c9e44abba3183325e35a95a7334a5 Author: David Huber <[email protected]> Date: Tue Oct 31 16:33:11 2023 -0400 Parallelize the build scripts (#1998) Optimized/parallelized build scripts. A few notes: 1) The default number of build jobs is 20, but one could argue for using 40. When researching this, I looked up what the SRW is compiling with. That system uses 40 cores, which seems a little excessive, but on testing the global workflow, the actual number of cores being used at any given time rarely exceeds 16 when running with 40 cores. This is because the builds tend to use multiple threads in the beginning when compiling low-level modules while the higher-level modules are more or less serial AND because the GDASApp takes several minutes to initialize all of its subrepositories by which time the smaller builds are complete. 2) I also updated checkout.sh so that all checkouts are simultaneous. The CPU load for `git submodule` is quite low, so running 16 instead of 8 jobs at once is not much more expensive. 3) To make this work, I had to add `-j` options to most of the build scripts. The only exception is build_upp, for which the build script within the UPP is hard coded to use 6 cores. 4) I fixed a few small bugs in the build scripts along the way. 5) Lastly, this reduce the total build time from ~2.5 hours for the entire system (including GDAS and GSI in the same build) to ~40 minutes when running with `-j 40`. Resolves #1978 commit 67c050c201f92e855d09211e41a5f51ee1cb5230 Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Oct 31 19:00:47 2023 +0000 Add missing export for rCDUMP in stage_ic (#2009) rCDUMP is needed by the exscript but was never exported by the jjob. commit 872068cb5ea78b311f7a77e97ee1428ae027cb61 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Oct 31 14:37:55 2023 +0000 Add output error log to user for create_experiment.py on fail in CI (#1974) Small changes to driver CI bash scripts to recapture error log from `create_experment.py` logger Fixes #1939 commit b2e4a2e9d269842acbb1b37dd563ee5dee2adf0f Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Oct 31 13:57:02 2023 +0000 Allow CI case to exclude running on certain platforms (#2001) commit 7cc137116f1619bf1e5a12eaacb98d17da97c223 Author: Jeff Whitaker <[email protected]> Date: Tue Oct 31 07:54:24 2023 -0600 Add initial C96/1 deg coupled model support (#1991) commit 7086ddc4bece6fb2a8c1c2e6090800d4293e410e Author: AndrewEichmann-NOAA <[email protected]> Date: Mon Oct 30 19:58:43 2023 -0400 Add ocean analysis files to HPSS archiving task (#1985) This PR adds the files under `analysis/ocean` (except those in `bump` and `vrfy`) to the HPSS archiving job, in `gdasocean_analysis.tar`, which were previously not archived. Resolves NOAA-EMC/GDASApp/issues/693 commit eabc82ad30c118645c0e6e216162d823882a8139 Author: Guillaume Vernieres <[email protected]> Date: Mon Oct 30 10:31:27 2023 -0400 Make the early cycle work with the coupled UFS configured as S2S (#1954) commit aff6ca7ae559e424dae128d6cfd5da4a4e3049e7 Author: Anil Kumar <[email protected]> Date: Fri Oct 27 14:11:55 2023 -0400 GEFS Staging in exglobal_stage_ic (#1892) Adjusts source paths for forecast-only ICs in support of extension to ensembles. New paths omit the resolution (that is captured by the IC id name) and allow for a member level. Directories with the reorganized ICs have been added to the three tier-1 machines under glopara space. Building on this, also adds capability to stage GEFS ICs. Resolves #911 commit 77c1ff2bfa26b341b01f41e50ee0ecb31cc4f661 Author: RussTreadon-NOAA <[email protected]> Date: Thu Oct 26 23:44:27 2023 -0400 Update GDASApp hash (#1975) Update GDASApp hash to bring recent UFSDA development into g-w. Resolves #1972 commit 962368884991670d3a1ee1c5a065d5bce4b7561a Author: David Huber <[email protected]> Date: Thu Oct 26 16:10:23 2023 -0400 Test tarballs for rstprod before calling chgrp (#1967) Certain tarballs may or may not contain `rstprod` data. For instance, the first half cycle gdas and enkfgdas tarballs will not contain `rstprod`, while future cycles likely will. Also, some systems do not have `rstprod` on them. This will test the contents of the tarballs first before attempting to change the group to rstprod. Resolves #1460 commit c02e118c0ac5485109c9bd33472ff42db309cd9b Author: Jessica Meixner <[email protected]> Date: Thu Oct 26 15:05:05 2023 -0400 Update ufs model to version from 10-12-23 (#1933) This updates the ufs-weather-model to the commit hash from 10-12-23 from the HR2 tag. The diffs can be seen here: https://github.com/ufs-community/ufs-weather-model/compare/GFSv17.HR2...68050e58589a82ab509aaefaafdc2a6b90f34e48 Resolves #1811 commit 8556541daa79b0180fde48a58a8dcfb2f8c56ea5 Author: Rahul Mahajan <[email protected]> Date: Wed Oct 25 16:15:28 2023 -0400 Fix incorrect usage of CFP on WCOSS2 (#1977) commit 0b5cf9b67a8146d9d4815ea6545f7f2524120d83 Author: Kate Friedman <[email protected]> Date: Wed Oct 25 13:17:28 2023 -0400 Update GFS version in index.rst to v16.3.10 (#1976) Update the "State of operations" GFS version number to new v16.3.10 (Annual CO2 fix file update in operations). Refs #1924 commit e817f5dd38c26a88f76d90eb71124f1acbfc5a8f Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Oct 25 02:03:14 2023 +0000 Fix path for marine products (#1966) When PR #1823 was merged, the name of the marine product template was not updated in ocnpost, leading the products to be placed in the wrong location and missed by the archive job. Resolves #1902 commit 7cdfad4eaa7abe0769ff13396c54e6d93afebf8f Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Oct 24 22:19:46 2023 +0000 Build GDASapp for CI tests (#1964) * added -u to global checkout so CI test builds tests for GDASapps * Update check_ci.sh needed more quotes --------- Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]> commit c58deae0cf078d1ee093529064d74f60482aa3f4 Author: Henry R. Winterbottom <[email protected]> Date: Tue Oct 24 16:19:04 2023 -0600 Updates for NOAA CSP AWS global-workflow related file paths. (#1970) Co-authored-by: henrywinterbottom-wxdev <[email protected]> commit 1b00224e18842cd873eb1779be08f96687e49e1f Author: Kate Friedman <[email protected]> Date: Tue Oct 24 14:48:24 2023 -0400 Set SENDCOM=YES for tracker/genesis tasks (#1971) Set SENDCOM to YES in config.vrfy to get outputs copied back to COM. Will reevaluate the need for SENDCOM when moving the tracker/genesis jobs out of the vrfy job with issue #235 work. Refs #1947 commit e2c624d8904cd988394c73d0edb22fa593229d3f Author: RussTreadon-NOAA <[email protected]> Date: Tue Oct 24 13:32:52 2023 -0400 Refactor UFSDA ATM var and ens layout (#1945) commit 8940adddfe9d21189740e71487603fb2acee2336 Author: David Huber <[email protected]> Date: Tue Oct 24 11:02:29 2023 -0400 Optimize the checkout script (#1956) * Multithread the checkout script #1953 commit 4b5cd0bc435fc158258ca38c3d5f44add6b60469 Author: Rahul Mahajan <[email protected]> Date: Mon Oct 23 12:04:26 2023 -0400 Fix nth_eupd in gfs/config.resources. remove sections of jobs not run as part of gefs from gefs/config.resources (#1952) commit 08ce4f8d3ed8e07b4d488a80b5054c6206b04404 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Oct 20 16:14:53 2023 +0000 Fix enkfgfs cleanup dependency (#1941) When #1906 was merged, the dependency for enkf cycles was hard-coded to use the enkfgdas archive instead of depending on the `RUN`. commit 1a5d0b51642eb70f71e693355e86212d3607b7b3 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Oct 20 15:54:33 2023 +0000 Split clean-up into separate job (#1906) Moves the clean-up that was previously done in the archive jobs into their own separate job. The clean-up is also streamlined considerably by using only `COM_TOP` instead of going through every template. There is also additional streamlining/corrections in the function that does the actual removing. Some settings used by both jobs were elevated to `config.base`. Others only needed for cleanup were moved to the new config for that job. Also corrects a small error encountered when attempting to rerun an ensemble forecast. Resolves #583 Resolves #1872 commit 3de102c28daf9eb50ce65e0afe911f5a416ce861 Author: Rahul Mahajan <[email protected]> Date: Tue Oct 17 09:30:18 2023 -0400 Updates to CI to clarify HOMEgfs (#1931) * replace HOMEgfs_PR with HOMEgfs, and HOMEgfs with ROOT_DIR. ROOT_DIR is the location where the ci scripts live * update type to system in case yamls * move create_experiment.py to workflow/ * detect HOMEgfs in create_experiment.py based on location. update to use jinja templates in the cases * remove export of HOMEgfs from driver.sh commit bfea2594207a477ea00e3b7fef95c2d7befd492b Author: Henry R. Winterbottom <[email protected]> Date: Sun Oct 15 23:27:47 2023 -0600 Remove SENDCOM (#1929) This PR addresses issue #1501. All instances of `SENDCOM` gates have been removed. The workflow was inconsistent in its use of `SENDCOM` to gate movement of files to `COM` and have been removed based on NCO guidelines. Resolves #1501. commit 9a8911a0b30f0367d061facfb3b835480728081d Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Fri Oct 13 14:21:01 2023 +0000 update nth_eupd to 8 for Orion because of out of memmory errors (#1927) Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]> commit ea4dfa5800b5cb529478cc64d329f567393fa37d Author: Guillaume Vernieres <[email protected]> Date: Thu Oct 12 21:29:19 2023 -0400 Marine DA configuration updates (#1922) Minor updates the configuration related to running the marine DA and the coupled UFS. What's proposed in this PR: - Memory increased for the marine DA analysis step - The coupled UFS is (was?) running out of memory without the changes in `config.ufs`. - Updates to the IAU section of MOM_input to allow for a current increment. commit c2d112b40a926c9f33a653cfbb832cb811a60352 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Thu Oct 12 23:52:43 2023 +0000 Fix missing pipe in check_ci (#1926) Bugfix: left out pipe to word count` | wc -l` after updating: `num_platforms=$(ls ../platforms/config.* | wc -l)` to `num_platforms=$(find ../platforms -type f -name "config.*")` when it was flagged by the BASH linter. commit 51d93e15eb30382017aaf72813d34f7010f47948 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Oct 10 19:09:26 2023 +0000 Updated cron bash ci script to remove weekly CI test PR on success (#1915) This PR updates the check CI bash script in cron to remove the PR that is created by the weekly CI test driver when all the tests has passed on all the platforms. This is done by the script checking if all other labels for all the platforms for the PR that has currently been flagged to have run to a successful completion by the check ci bash script. commit 2d64b74a0b0407d01d6f657efa6af9637a131448 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Wed Oct 4 22:33:25 2023 +0000 CI driver_weekly bugfix deleting new branch if is already on repo (#1899) Bugfix and updates to weekly CI test that deletes the new modified branch if it is already on the repo but now also makes sure that the intermediary branch that creates the PR is coming from emcbot. commit e4a6c35ae020253f07921ca34a17f19e928b0b6c Author: Rahul Mahajan <[email protected]> Date: Wed Oct 4 09:42:12 2023 -0400 Fix typo in cice history filename commit d50938bc4f6705b722338bbea03f925614f953ed Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Oct 3 23:37:39 2023 -0400 Change metp dependency (#1900) MET+ jobs rely on files already having been placed in the local archive directory, but the job only depended on post, resulting in the job prematurely firing. The dependency is now updated to be on the archive job instead. Resolves #1756 commit 836642bb201cd2e5e205eda2ae4a28993623355d Author: Rahul Mahajan <[email protected]> Date: Tue Oct 3 14:45:57 2023 -0400 Use deterministic marine resolutions for ensemble (#1894) This PR determines the ensemble resolution for ocean, ice and waves based on the deterministic configuration as there is no dual-resolution capability requested for these model components. For cycled DA, if the deterministic uses a coupled model, the ensemble will also be a coupled model. This can be turned off manually via adding `DO_AERO_ENKF`, `DO_OCN_ENKF`, `DO_ICE_ENKF` and `DO_WAVE_ENKF` flags set in `config.base` or `config.efcs`. This is currently handled manually and will be automated when a requirement arises for this flexibility. Fixes #1730 commit 48ba775909870f0d27275128bd07ec134b92c356 Author: Kate Friedman <[email protected]> Date: Mon Oct 2 13:34:02 2023 -0400 Update vrfy.sh to only run MINMON in cycled mode (#1901) Update MINMON if-block in jobs/rocoto/vrfy.sh to only invoke this section when MODE is cycled. Refs #1076 commit e65162f3083c34b639854e3216e2355ff6fccc0b Author: RussTreadon-NOAA <[email protected]> Date: Fri Sep 29 19:18:07 2023 -0400 Update module loads to intel/2022 for jobs running gsi.x and enkf.x (#1882) This PR changes the module loads in g-w jobs `anal.sh`, `eobs.sh`, and `eupd.sh` to use machine specific modulefiles from `sorc/gsi_enkf.fd/modulefiles`. This is necessary because [NOAA-EMC/GSI#571](https://github.com/NOAA-EMC/GSI/pull/571) updated `gsi.x` and `enkf.x` builds to intel/2022 on NOAA RDHPCS machines. Resolves #1863 commit cd439d0bf2ae5fb57139fcb9983aa2755fdc9b2c Author: Rahul Mahajan <[email protected]> Date: Fri Sep 29 15:35:54 2023 -0400 Add coupled forecast-only tests for S2S and S2SW (#1895) This PR: - replaces the PR C48 S2S forecast-only test with a S2SW configuration - adds a weekly C384 S2SWA forecast-only test. The C384 S2SWA is a weekly test and will not be triggered/tested in this PR, but will be tested on Friday. See notes on Orion below in the testing section. @JessicaMeixner-NOAA kindly provided the details in https://github.com/NOAA-EMC/global-workflow/issues/1794#issuecomment-1740768751 commit 02787fe9ba9e5a6881e5ccf9a9e352545eeadb9d Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Fri Sep 29 18:03:23 2023 +0000 Ci rename platform scripts (#1896) Simply renaming the platform config files in ${HOMEgfs}/ci/platforms to config.${MACHINE} so wxflow can read them too in support of up and coming functional testing. commit bb5a58541d6514d16901dca240dfbbc810bd31c8 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Sep 29 13:28:39 2023 -0400 Merge S2S defaults config back into other configs (#1876) When the prototype S2S was first added, we placed some settings in a `config.defaults.s2sw` file to avoid interference with existing settings. Now that we are moving towards v17 and run S2S regularly, it is time to merge these settings back into the other config files. The wave output frequency settings are updated to the coarser fre- quency as that is more suitable for development. The prior (ops) settings are noted as comments. There are a couple of settings that control ice fields within FV3. These are placed in `config.ice`, so when the ice model is on those settings are still used. Changes the output frequency from 3 to 6. While we may leave this setting as the default for development, it is required right now because the ocean frequency is hard-coded to 6 but links are created based on `$FHOUT_GFS`. Resolving #1629 should correct this limitation. "Gaussian" archive is updated to the former override values. Resolves #1606 Refs #1629 commit 49dc315c1ef6c5f4952a06b0ba70c36e771f128e Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Sep 29 13:25:58 2023 -0400 Move product functions to separate script (#1891) PR #1822 converted some formerly stand-alone scripts and moved them inside one of the standard product scripts. However, `trim_rh.sh` is also used by gempak and AWIPS, so this change caused those jobs to start failing (they are not yet tested by CI). Those functions have now been moved into a separate product functions script that can be sourced by all the scripts that need the functions. A third similar script was also eliminated and converted into a function. Additionally fixes a base bug in AWIPS and updates some scripts to satisfy (or at least mostly satisfy) the linter. **AWIPS still failing when creating GRIB1 products.** That will be addressed in a future PR (and may need a subject-matter expert). Resolves #1890 commit 3e750d10be577106fb269a78e18765b8d2b8030d Author: Rahul Mahajan <[email protected]> Date: Thu Sep 28 16:21:52 2023 -0400 Fix a few bugs reported by devs (#1893) This PR fixes a few bugs that were reported by developers: - a namelist section is unclosed in `parsing_namelists_FV3.sh` - resolution is not being properly cut from `CASE` - date should be in UTC to properly go back and forth around DST dates. Resolves #1796 commit e886e8aef633389d65e23cc42456827e1db2a771 Author: Kate Friedman <[email protected]> Date: Tue Sep 26 13:01:17 2023 -0400 Fix wavepostbndpntbll data dependency (#1888) Update the data dependency path for the wavepostbndpntbll job to use the ATMOS/atmos subfolder instead of WAVE/wave for the atm.logf file it needs to fire off. Refs #1887 commit bb1e561c6a519b9b1cf3fb3ac724e2d240bc3b5b Author: Andy Tangborn <[email protected]> Date: Tue Sep 26 11:08:49 2023 -0400 Update aero analysis for new bump files and archive aero diags (#1886) This PR updates the global workflow so that it can handle the latest version of the JEDI aero staticb, and also archives the aerosol diagnostic files. commit 3d2b72ecd395585f650b2801b2ec3471bd938d63 Author: David Huber <[email protected]> Date: Tue …
Squashed commit of the following: commit 3c0c126a376af31866a93aef4cdd0b4145150c58 Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 16 17:32:25 2024 +0000 Add script for remapping 1/4 degree grib2 grids to other domains commit f217d4ed9a500e9a1bdcc17548729d972a1763ac Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 16 16:46:25 2024 +0000 Update link script for ufs_utils.fd commit 5b21b31900955013b4e8106d3ae906b9da93b361 Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 16 16:45:25 2024 +0000 Add GSL archive scripts for initial conditions commit abb88baf9dd536a3b2ea1e24eaa99cbfe85af799 Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 16 16:42:17 2024 +0000 Move configuration files for getic and init from jobs/rocoto to parm/config/gfs commit 45b235180719ab79d2514f0317207fbebfb8aedd Author: Judy.K.Henderson <[email protected]> Date: Sun Jan 14 03:21:15 2024 +0000 Add suite definition file for v17p8_ugwpv1_c3 to sorc/ufs_model.fd_gsl commit 147b1fce99254dcb602c333cc559feaa9a396e81 Author: Judy.K.Henderson <[email protected]> Date: Sun Jan 14 01:57:22 2024 +0000 Add getic and init tasks to workflow to create initial conditions in realtime commit 4e4e50803d95566e1c7967cf4cfa575391d77f25 Author: Judy.K.Henderson <[email protected]> Date: Fri Jan 12 00:44:59 2024 +0000 Change default HPSS_PROJECT to fim Change restart_interval_gfs to -1 so no files are written ro RERUN_RESTART directory commit 791d7a27c6b12f07d9c12ce491338e3da59eb1d8 Author: Judy.K.Henderson <[email protected]> Date: Thu Jan 11 23:34:36 2024 +0000 Add namelist parameter, nord_tr, for GSL suites commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5 Author: Judy.K.Henderson <[email protected]> Date: Thu Jan 11 23:31:22 2024 +0000 Add changes for running v17p8_mynn - new field table, field_table_thompson_aero_tke_progsigma - updated namelist parameters in config.fcst commit 982a1f02e3b880be43f4ae8a3f0ffbb34c056aea Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 9 02:26:22 2024 +0000 Add experiment setup script for p8_ugwpv1 commit c5a3697d22fdbb02bb80ddffee2629dddc10c702 Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 9 02:19:13 2024 +0000 Add memory report to srun command in env/HERA.env commit ece7e516ca65ec0240899e7d84321310a6887595 Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 9 02:13:42 2024 +0000 Updated GSL-specific files under ufs_utils.fd_gsl commit 1b153fc95b93a16eb40b791be7322100fde4a3d4 Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 9 01:52:56 2024 +0000 Create new branch, gsl_ufs_dev, from dev_02jan24_9d901db Add initial GSL modifications - changes to workflow files * GSL paths, projects, entities - new FV3_GFS_v17_p8_ugwpv1_mynn suite definition file (SDF) - updated namelist parameters in ush/parsing_namelists_FV3.sh - create new GSL directories: ufs_model.fd_gsl and ufs_utils.fd_gsl * new SDFs, add instantaneous flux variables to grib2 configuration files * add Thompson tracers to initial conditions - new sync script: rsync_gsl.sh - new job files: getic.sh, makeinit_link.sh - modify build_ufs.sh to include MYNN SDF commit 9d901dbbff4d41586580316bdc094d24760119e6 Author: Henry R. Winterbottom <[email protected]> Date: Tue Jan 2 10:30:33 2024 -0700 Stop Gempak pgrb2 spec from modifying $DATA (#2147) This PR addresses issue #1224. The following is accomplished: - Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time; - Shell linter exceptions are addressed accordingly; - The respective GEMPAK tasks is added to the Rocoto mesh. Resolves #1224 commit 31ad23527802f7d07171132cc620f7135c4d8cba Author: Henry R. Winterbottom <[email protected]> Date: Tue Jan 2 10:27:30 2024 -0700 Reorganize NPOESS scripts (#2166) This PR addresses issue #1226. The following is accomplished: - Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated; - Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh` are moved accordingly; this specifically applies to the environment variable `FHOUR`, `SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`; - The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level (if necessary); - Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however, this may not be necessary (see `TODO` note within draft PR. Resolves #1226 commit 22bd82fa93b49e5ce98eb3f69123956dd5018049 Author: Kate Friedman <[email protected]> Date: Tue Jan 2 11:55:03 2024 -0500 Orog fix file reorg and fix directory variable standardization (#2181) This PR makes updates to use the newly reorganized `orog/20231027` fix file version and standardizes the fix file directory variables. Changes: 1. Update UFS_UTILS hash to ce385ce 2. Update fix file version file to use new orog timestamp: `orog_ver=20231027` 3. Add ".mx$(OCNRES)" to `oro_data` filenames in scripts 4. Remove ".mx$(ocn_res)_frac" from the directory names for atmosphere resolutions under the `/orog` folder 5. Adds fix file directory variables to `config.base`, many of which are pulled up out of lower scripts; introduce `FIXcpl` 6. Renamed/replaced the following fix file directory variables: - `FV3JEDI_FIX` --> `FIXgdas` - `FIXfv3`, `FIX_orog` and `OROFIX` --> `FIXorog` - `FIX_ugwd` and `OROFIX_ugwd` --> `FIXugwd` - `FIX_am`, `FIXgsm`, `FIXSYND` --> `FIXam` - `FIX_lut` --> `FIXlut` - `FIX_aer` --> `FIXaer` - `FIX_SFC` --> `FIXsfc` - `FIX_DIR` --> `FIXgfs` - `RTMFIX` and `FIXCRTM` --> `CRTM_FIX` (is `CRTM_FIX` in crtm module, so not using `FIXcrtm`) 7. Correct the defaults for `FIXwave` in wave JJOB scripts 8. Update variable names in `*fixed_files.yaml` files, as well as update naming convention for `oro_data` files Resolves #1984 Resolves #1981 Resolves #2175 commit 03d03bf53b43914a55c384cb33eb06f6a9a443a6 Author: Andrew Collard <[email protected]> Date: Tue Jan 2 11:53:44 2024 -0500 Remove HIRS from GSI processing (#2183) With the update to CRTM 2.4.0.1, an issue with versioning of CRTM HIRS files has been exposed. This is documented in JCSDA/crtm#42. As HIRS radiances are no longer used in the GSI, these data should be removed from processing until a suitable update to CRTM is available. Resolves #2182 commit a3c50998d35525a39a66d5592fbf327ab3569e8b Author: Jessica Meixner <[email protected]> Date: Fri Dec 22 18:07:48 2023 -0500 Update ufs-weather-model version (#2186) * update model to latest version which includes needed bugfixes for HR3 commit 774c7302e618370ef578bec3ccabc70486d6da1b Author: David Huber <[email protected]> Date: Fri Dec 22 11:34:53 2023 -0500 Fix analysis post processing's handling of 0-padded negative integers (#2187) This screens for the analysis 'forecast' hour (-001) and handles the '-' and circumvents octal issues. commit d1251360325faf75af9df0608557fcd10202a883 Author: Barry Baker <[email protected]> Date: Thu Dec 21 11:23:48 2023 -0500 Fix for restoring cycling aerosols in fo-mode post COM refactor (#2179) - Update to COM reorg aerosol initialization job - Address bug in joining paths for data dependency in this job --------- Co-authored-by: Rahul Mahajan <[email protected]> commit e55a05980709288d902ad1bd894164bfa5a18a65 Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Dec 20 22:14:01 2023 -0500 Stop calling ufs-utils link script (#2172) The `link_workflow.sh` script was calling the ufs_utils version of the same. That step is only necessary if a user is going to run one of the stand-alone ufs-utils, which is rare. commit ef3e5ad7c63be1644c82333c95853c3caf2d8995 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Dec 19 22:02:55 2023 -0500 Fix handling of excluded hosts list (#2170) This PR fixes the issue with `create_experment.py` so that the yaml configuration file can have a string of list of strings when specifying the host name to exclude from the CI tests. commit ea74a5719efc8f0fe631c5ff93426a4299a614f3 Author: AndrewEichmann-NOAA <[email protected]> Date: Tue Dec 19 16:21:41 2023 -0500 Add COMOUT_OBS to marine obs prep (#2173) Adds `COMOUT_OBS` (defined from `COM_OBS_TMPL`) to marine obs prep task to properly handle marine obs prep files. Used to keep obs after IODA conversion, QC, and other prep. Towards resolving NOAA-EMC/GDASApp#815 commit c2500feace0bb7c04ce67a90dd3182120ee67b2e Author: David Huber <[email protected]> Date: Tue Dec 19 14:55:20 2023 -0500 Return failed status if a build fails. (#2171) If any of the builds fail, this makes build_all.sh return the sum of the error codes encountered. Fixes #2168 commit 76fdd81cd84ed812181996a102379d8d964ba27a Author: Kate Friedman <[email protected]> Date: Tue Dec 19 13:24:34 2023 -0500 Update index.rst for new GFSv16.3.12 in ops (#2169) Refs #2096 commit a81da33e8fe7541a36f68e7a4f14a384cadd36c8 Author: Kate Friedman <[email protected]> Date: Tue Dec 19 10:22:21 2023 -0500 Set place=shared for shared jobs on WCOSS2 (develop) (#2156) Set job as shared when not exclusive on WCOSS2 WCOSS2 defaults to exclusive when it is not specified as either exclusive (place=exclhost) or shared (place=shared). Now set shared when job should be shared. Refs #2135 commit 89aea972f7964dac3f515e8070d7c534812c5fb4 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Dec 15 16:31:06 2023 -0500 Update gfs-utils version for Hercules (#2163) An update of gfs-utils was misssing from the previous PR that added initial Hercules support (#2128). Also includes gfs-utils update for new marine post. commit 9505cb4abc6ca2643a8ab254d14ca2000747fa44 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Thu Dec 14 16:15:31 2023 -0500 CI Updates to support Hercules (#2155) If merged, this PR will update the CI scripts so they will run on Hercules for forecast only NOTE: This is a stop gap to issue #2131 until its block on #1588 is removed. Resolves #2154 commit c5ca82f04a2efae78389dec1c46b94ef4fb5bbe5 Author: Rahul Mahajan <[email protected]> Date: Thu Dec 14 16:05:33 2023 -0500 Correct fbwind (#2161) commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a Author: Kate Friedman <[email protected]> Date: Thu Dec 14 12:06:23 2023 -0500 Add MOS jobs to rocoto mesh (#2148) Create separate jobs for GFS MOS - extracted from now-retired vrfy job Refs #2068 commit bb6151aa50c27253cb9b8f0a6601ddd58526b8b3 Author: Walter Kolczynski - NOAA <[email protected]> Date: Thu Dec 14 05:38:29 2023 -0500 Replace checkout script with submodules (#2142) Replaces the checkout script with git submodules. This change brings workflow in line with other repos and git standards. Due to these changes, the build system is updated slightly. First, the options that were formerly used with `checkout.sh` to reduce unneeded builds (`-g` for GSI and `-u` for UFSDA) are moved to `build_all.sh` instead. This is needed since build all will not be able to key off directories existing or not to determine which com- ponents to build. Second, the partial build system is removed. It was rarely, if ever, used, and parts of it were already ignored with the previous changes to base builds off whether directories exist. The manage externals file is also removed since that is also not being used. Following these changes, clones/checkout will need to either be recursive, or `git submodule update` will need to be called separately to make sure components are properly checked out (non-exhaustive list): ``` ## Checkout develop (method 1) git clone --recursive https://github.com/NOAA-EMC/global-workflow destination ## Checkout develop (method 2) git clone --jobs 8 https://github.com/NOAA-EMC/global-workflow destination cd destination git submodule update --init --recursive --jobs 8 ## Checkout existing branch some_branch (method 1) git clone --recursive --jobs 8 -b some_branch https://github.com/NOAA-EMC/global-workflow destination ## Checkout existing branch some_branch (method 2) git clone https://github.com/NOAA-EMC/global-workflow destination cd destination git checkout --recurse-submodules some_branch ## Checkout existing branch some_branch (method 3) git clone https://github.com/NOAA-EMC/global-workflow destination cd destination git checkout some_branch git submodule update --init --recursive --jobs 8 ## Checkout new branch new_branch git clone https://github.com/NOAA-EMC/global-workflow destination cd destination git checkout -b new_branch git submodule update --init --recursive --jobs 8 ``` The git ignore list had to be updated to use explicit paths as the wildcard paths pick up the ones that are now submodules. UFS creates files during the build process that are not in its ignore list, so that sub- module ignores the "dirty" state to avoid confusing users running `git status`. CI and documentation are also updated to reflect the changes. Resolves #2141 commit 1332188ce2409e012ec127d44880e49732f7f379 Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Dec 13 09:32:57 2023 -0500 Enable radar reflectivity output (#2143) Turns on radar reflectivity output from FV3. This eliminates missing values appearing in the grib2 files. commit 24d898ec0ec0c7fcbda6966988f9a986f528ed14 Author: David Huber <[email protected]> Date: Wed Dec 13 09:32:24 2023 -0500 Fix Hercules hostname (#2150) * Allow lower or upper hostname on hercules. * Add Hercules to issue template. commit 2896bb8787698be28ad20f2298589e6e95eaf9fb Author: Kate Friedman <[email protected]> Date: Tue Dec 12 09:13:06 2023 -0500 Fix module load typo (#2145) Fix typo with loading the crtm module in the UPP hack for WCOSS2 Refs #2144 commit 29d34172a67d976f910e78158ff0337e1ef099ca Author: Cory Martin <[email protected]> Date: Thu Dec 7 15:12:05 2023 -0500 Update GDAS hash to most recent stable versions (#2138) commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102 Author: Henry R. Winterbottom <[email protected]> Date: Thu Dec 7 10:41:05 2023 -0700 Corrected typo in a gempak job gempakncdcupapgif . (#2137) commit 3483f550db1ae35a680de49f7485ce5a11902dd9 Author: Cory Martin <[email protected]> Date: Thu Dec 7 12:34:56 2023 -0500 Add support for FGAT and IAU for aerosol DA (#1940) commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9 Author: David Huber <[email protected]> Date: Thu Dec 7 12:33:46 2023 -0500 Enable forecast-only experiments on Hercules (#2128) This add forecast-only support for Hercules to the global workflow. Partially satisfies #1588. Co-authored-by: Walter Kolczynski - NOAA <[email protected]> commit a29f751aed05312da3d80d396159bb5a906d6ce4 Author: Henry R. Winterbottom <[email protected]> Date: Wed Dec 6 13:45:56 2023 -0700 Adds GEMPAK and related jobs to rocoto task mesh (#2127) commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082 Author: Rahul Mahajan <[email protected]> Date: Tue Dec 5 15:47:52 2023 -0500 Separate offline UPP from interpolated grib2 product generation (#2110) This PR: - Replaces the use of `JGLOBAL_ATMOS_POST` with `JGLOBAL_ATMOS_UPP` and `JGLOBAL_ATMOS_PRODUCTS`. - Introduces `JGLOBAL_ATMOS_PRODUCTS` that is responsible for creating grib2 products from the master file produced by UPP (inline from the model, or offline by running `JGLOBAL_ATMOS_UPP`). Rocoto job `atmos_products.sh`, ex-script `exglobal_atmos_products.sh` are also added along with a `config.atmos_products`. Updates are made to the relevant `env` files as well as `config.resources` to reflect the addition of this job. - reduces the number of cores needed appropriately for forecast products when there is no offline UPP necessary. - renames older `fv3gfs_dwn_nems.sh` to `interp_atmos_master.sh` and `inter_flux.sh` to `interp_atmos_sflux.sh` - removes `fv3gfs_downstream_nems.sh` as it is absorbed into `exglobal_atmos_products.sh` - removes no longer used scripts for `gfs_post.sh`, `gfs_transfer.sh` (DBN alerts are absorbed into `exglobal_atmos_products.sh`), `post.sh`, `JGLOBAL_ATMOS_POST`, `ex${RUN}_atmos_post.sh` scripts. - Rocoto workflow related scripts are updated to add `atmos_products` as a job. When `WRITE_DOPOST` is `.false.`, `upp.sh` job to run the UPP offline is also added. Dependencies have been appropriately applied. - removes `PGB1F` option that creates 1-degree grib1 products that are no longer needed in GFSv17. The hacks from (now deleted) `post.sh` had to be reinstated in `upp.sh` to load the modules from UPP instead of `load_fv3gfs_modules.sh`. commit 44186f594aaf5f8feea0eadd4c5c3b59de3a825e Author: Kate Friedman <[email protected]> Date: Tue Dec 5 12:28:08 2023 -0500 Update index.rst for new GFSv16.3.11 version (#2121) Refs #1356 commit e62a3a73cd22701962b7bf210fdfee37f37a5474 Author: Henry R. Winterbottom <[email protected]> Date: Tue Dec 5 09:08:12 2023 -0700 Splits AWIPS jobs into seperate tasks (#2094) This PR addresses issue #1228. The following is accomplished: - Separate rocoto jobs have been created beneath `jobs/rocoto/` -- `awips_20sh` and `awips_g2sh`; these jobs replace `awips.sh` which was calling multiple J-jobs within the respective `awips.sh` scripts; - New tasks has been added to `workflow/rocoto/tasks.py` for the new AWIPS scripts; - The `gfs_cycled` and `gfs_forecast_only` modules beneath `workflow/rocoto` have been updated accordingly. Resolves #1228 commit 04d97e9aa7ab84b9754ab670074cfb19d543aa26 Author: Kate Friedman <[email protected]> Date: Mon Dec 4 13:38:30 2023 -0500 Consolidate VMINMON and cleanup monitor scripts (#2088) This PR combines the GDAS and GFS versions of the VMINMON JJOB and ex-driver scripts into single GLOBAL/global versions. Additionally: * some further cleanup of the GSI-Monitor scripts is done; variable settings in ex-driver scripts are moved up to the JJOB level * the fix symlinks are consolidated into a new `fix/mon` subfolder (formerly `fix/gdas`) and copies of the gfs monitor fix files under `fix/products` are removed Resolves #1925 commit a286a11fdcbc31c8bc6d944890bc56294bc8caf6 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Mon Dec 4 17:48:44 2023 +0000 Robust CI Restarts (#2093) Improved CI robustness for reverting back to **CI-Ready** from any given state New Features: - Improved `scancel` routine (refactored into bash "subroutine") - Improved messaging (see below) when ever a user changes state - Any and all previous build scripts and running experiments are killed as a result of reset to **Ready** Resolves #2060 commit 73621e9b20b20f85e8b21e4c1e09ed1d80ecd46f Author: David Huber <[email protected]> Date: Sun Dec 3 11:19:19 2023 -0500 Upgrade to spack-stack/1.5.1 and Intel 2022 on non-production machines (#2084) Update module files to spack-stack/1.5.1 and compilers to Intel 2022+ on all non-production machines. commit 6d548b250688861eb20a7e0dc852a0e4ba9e64f4 Author: jiandewang <[email protected]> Date: Thu Nov 30 12:00:21 2023 -0500 Add variable tob in diag_table for ocean model output(#2105) commit c19810cce252fcdb25fd9960c05b08b5f8d8b1ad Author: AndrewEichmann-NOAA <[email protected]> Date: Wed Nov 29 15:17:36 2023 -0500 Added variables to config.prepoceanobs (#2101) commit c2d78a61a224678fb804eed19f39d1f07408ae5f Author: Kate Friedman <[email protected]> Date: Wed Nov 29 12:39:08 2023 -0500 Add missing cut to VDATE setting in JGFS_ATMOS_VERIFICATION (#2098) Refs #2097 commit c1c025f91ddac73aea595cc9fa4dd0bea80575fc Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Nov 29 17:15:10 2023 +0000 Add wave init to GEFS (#2089) Adds the wave init job to GEFS. Since the output would be the same for every member, the job is only run once for the control, then links are created in each of the member directories pointing to that copy. New ww3_multi and ww3_shell templates for GEFS are copied from the GFS versions. The GEFS restart frequency is changed to not be zero, and the comment about not setting it to zero is copied from the gfs config.base. The restart interval for the GEFS perturbed members is changed to equal that of the control. Also fixes a bug where `RUNwave` was not defined for ensemble forecasts, and another bug in the GEFS stage_ic dependency. Resolves #2017 commit 64a2470ce29b7d8d5cb85ebcb4048ff82958f64e Author: Kate Friedman <[email protected]> Date: Wed Nov 29 11:26:34 2023 -0500 Adjust permissions for jobs/JGFS_ATMOS_VERIFICATION (#2095) Add execute permissions (755) commit 964b77bc6de67291973c2c70598a1f8cb72501c5 Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Nov 28 18:45:51 2023 +0000 Make proper j-job for MET+ (#2090) Creates a proper j-job for the metp job, moving much of the material from the `jobs/rocoto` script there (some of it within `jjob_header`). Also updates the old `COMIN` variable for the COM refactor (although it does not appear used in the verify scripts currently). This is a partial step towards restoring/improving metp functionality and remains untested. Refs #1575 commit 8c11eeb8556619e8db4e0efb6394ce5a2c1aae0f Author: Henry R. Winterbottom <[email protected]> Date: Thu Nov 23 10:31:32 2023 -0700 Adds FBWINDS support to global-workflow (#2082) This PR addresses issue #1221. The following was accomplished: - A new Rocoto job is added; `jobs/rocoto/fbwinds.sh`; - `workflow/applications/gfs_cycled.py` is updated to include the `fbwinds` task; - `workflow/applications/gfs_forecast_only.py` is updated to include the `fbwinds` task; - A new function is added to `workflow/rocoto/gfs_tasks.py`, `fbwinds` is added as new GFS (only) task; - `workflow/rocoto/tasks.py` is updated to include the `fbwinds` task. Resolves #1221 commit 513db190d21f9ede0724a2cd5606372b1d7605de Author: Henry R. Winterbottom <[email protected]> Date: Tue Nov 21 22:52:58 2023 -0700 Adds NPOESS support to global-workflow (#2083) This PR addresses issue #1225. The following was accomplished: - A new Rocoto job is added; `jobs/rocoto/npoess.sh`; - `workflow/applications/gfs_cycled.py` is updated to include the `npoess` task; - `workflow/applications/gfs_forecast_only.py` is updated to include the `npoess` task; - A new function is added to `workflow/rocoto/gfs_tasks.py`, `npoess` is added as new GFS (only) task; - `workflow/rocoto/tasks.py` is updated to include the `npoess` task. Resolves #1225 commit 62d8e99e77ffe44784f4c61c3f2296c6d1a72413 Author: Kate Friedman <[email protected]> Date: Fri Nov 17 20:25:50 2023 -0500 Retire vrfy job (#2080) Retires the `vrfy` job from the global-workflow system. All associated scripts, configs, and references to the job are removed. Additionally, the switches listed in RTD were updated to reflect new ones added in other PRs for issue #235. Resolves #2069 Refs #235 commit ea386abf11ecbacef407388e8d57e71b30148a35 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Nov 17 23:59:46 2023 +0000 Enable different coupled settings for ensemble (#2030) Adds the ability to turn off some coupled components for the ensemble. To enable this, many settings are moved out of `config.fcst` and into `config.ufs` so they are calculated after any overrides of `DO_*` have been made. Some settings also had to be moved out of `config.base` for the same reason. A switch to turn on gocart is added to `config.ufs`, but unlike the other switches this one takes no arguments. The name of the ufs configure template used is converted from a partial file name to the full file name. Resolves #1692 commit fe792c0c9a1c46908cbd18c7e71eb836974cf1de Author: Kate Friedman <[email protected]> Date: Fri Nov 17 17:19:16 2023 -0500 Add --cpus-per-task to srun commands for Hera and Orion (#2077) This PR adds the `--cpus-per-task` flag to non-CFP `APRUN`/srun commands in the env files for Orion and Hera. This is needed as a result of an upgrade to SLURM on Orion that no longer exported the thread value to the environment. Issue #1996 was a hotfix to add this flag for the analysis job that was suddenly running slowly after the SLURM upgrade. A similar SLURM upgrade was done on Hera but the sysadmins there implemented a workaround so this issue did not appear there. This PR adds the `--cpus-per-task` flag for both machines...needed on Orion and as a safety measure on Hera. Also included in this PR is a fix to indentations in the `scripts/exglobal_diag.sh` script that was noticed during work for this PR. Timing differences were not observed for other jobs after adding this srun flag. Job timings were of a similar variation between control and test runs. Any potential additional speedup was not observed. The test runs also reproduced the control runs with `develop`. Resolves #2044 commit 42c943be305c297a56b104bb50727938c1ba688f Author: Kate Friedman <[email protected]> Date: Fri Nov 17 15:41:34 2023 -0500 Adjust modules in post.sh for WCOSS2 (#2079) On WCOSS2 the grib_util module is named a bit different and needs the libjpeg module loaded beforehand. commit cd4e6a1987e7fd71dff06766f540b5d32c8b648d Author: Jessica Meixner <[email protected]> Date: Fri Nov 17 11:49:32 2023 -0500 Update ufs-weather-model and remove upp hack (#2071) Updates the model to the most recent commit of ufs-weather-model. This should allow for the removal of the UPP hack that was added in PR #2042 This required changing nems.configure -> ufs.configure. Resolves #1942 commit 5a2d97e142aa4999b122fd5a130c63e59ea9f8e2 Author: Walter Kolczynski - NOAA <[email protected]> Date: Thu Nov 16 22:15:53 2023 +0000 Fix check for existence of preamble functions (#2066) A few of the setup scripts were checking for the existence of functions set by the preamble before calling them so they could also be used stand-alone. However, the `type` command returns `1` if the function name does not exist, which will cause the script to die is `set -e` is on. Now the `type` command fails over to an empty string. commit ed2ee7c2b1457b71b271a2c40f0dfa356e0f52f8 Author: WenMeng-NOAA <[email protected]> Date: Thu Nov 16 16:38:11 2023 -0500 Update UPP products for GFS v17 (#1973) Updates of generating GFS V17 UPP products to support HR3: - Update g2tmpl to 1.0.12 - Add changes to launch cfp on WCOSS2 to generate pgrb2/pgrb2b files - Changes for generating new products (MERRA2, six winter weather variables, 1km HLCY, SDEN) in pgrb2 files Resolves #1965 Resolves #1994 commit 635c4719e603538ce7cccf9ea6b31f3f84f20849 Author: Walter Kolczynski - NOAA <[email protected]> Date: Thu Nov 16 20:35:30 2023 +0000 Fix some rocoto dependencies (#2074) A few small errors/cleanup in the dependencies, mostly in fcst: A few small errors/cleanup have crept into the dependencies with recent changes, mostly in fcst: - Fixed the offset, as it would yield a string rocoto doesn't recognize when the interval was 24+ hrs - Removed the duplicate wave dependency. When `waveprep` is included, it depends on `waveinit` so there is no need to add a `waveinit` dependency. - Converted an interval in the archive job that was missed in #2039 Resolves #2075 commit d4c7508260975c6b94fc92fd085f39d4faf3f027 Author: Rahul Mahajan <[email protected]> Date: Wed Nov 15 16:44:03 2023 -0500 Fix missing _PREV in ocean restart file location (#2070) commit 255616d37505c785bdddd5d3e39e8399110b626e Author: mdtoyNOAA <[email protected]> Date: Wed Nov 15 12:02:09 2023 -0700 Update functionality for Prototype HR3 UGWP (#1987) This PR adds/modifies namelist options and activates new 'ccpp' suite definition files for the updated Unified Gravity Wave Physics (UGWP) in the ufs-weather- model recently updated for HR3. The changes to UGWP are the use of the GSL drag suite for orographic gravity wave drag (GWD) and blocking, as well as the new UGWP Version 1 non-stationary GWD. See ufs-community/ufs-weather-model#1923 for details. Resolves #1986 commit be9085e62aae147e3c74602e2f82a99b374fc783 Author: Guillaume Vernieres <[email protected]> Date: Wed Nov 15 13:48:58 2023 -0500 Save the required CICE history for the sea-ice DA (#2062) The hist_avg setting of CICE was changed to be an array. commit 85f1f5131ffd70061231304ea477bde0559eb67b Author: Guoqing Ge <[email protected]> Date: Wed Nov 15 11:47:21 2023 -0700 Use assim_freq to configure "offset" in dependencies (#2039) Use the assim_freq from config.base to configure "offset" in dependencies instead of hard-coding them. Resolves #2038 commit 4e3d82ba3a1fa7cdd4443bcd4cf83b2f8835137c Author: Kate Friedman <[email protected]> Date: Wed Nov 15 13:39:14 2023 -0500 Resolve ENKF archive script bugs (#2065) Fix two bugs in the exgdas_enkf_earc.sh script: 1) Replace ARCH_LIST with DATA to match changes done in PR #2000 and update path to generated archive list files. 2) Add status check and exit after script attempts to make tarball on HPSS. Refs #2064 commit 42d7f2f0c48fab898b764e09cfbbd7a9fabbae08 Author: Kate Friedman <[email protected]> Date: Tue Nov 14 17:54:29 2023 -0500 Separate tracker and genesis jobs from vrfy job (#2058) This PR creates new individual jobs for the tracker and genesis jobs that are being pulled out of the `vrfy` job (issue #235). The `tracker` and `genesis` jobs will be on by default while the `genesis_fsu` job will be off by default. This mimics the current settings in the `vrfy` job. No enhancements or upgrades are made to the jobs themselves in this PR, only to separate them from the `vrfy` job. However, one change compared to how they currently run in the `vrfy` job is to no longer run the `tracker` in the gdas suite. This mimics how the `ens_tracker` package is run in operations (gfs only). Changes in this PR: 1. Create rocoto job scripts for tracker/genesis jobs. 2. Create configs for tracker/genesis jobs, as well as `config.tropcy` for shared settings. 3. Add tracker/genesis jobs to `config.resources`; use resources from the ecf scripts for `ens_tracker` jobs in operations 4. Add tracker/genesis jobs to rocoto setup for both cycled and forecast-only modes. 5. Update arguments for `jjob_header.sh` script in tracker/genesis JJOB scripts to use specific job names and configs instead of vrfy. 6. Rename `tracker_ver` to `ens_tracker_ver` in version files to mimic variable within tracker package. 7. Rename and move tracker/genesis switches to `config.base`. 8. Remove tracker/genesis jobs from `vrfy` job (`jobs/rocoto/vrfy` and `config.vrfy`). 9. Reduce vrfy job resources to accommodate tasks having been removed. Refs #235 Resolves #1988 Resolves #2048 commit 0a0d6984e094d2a551d5d8331102142e7db13fc2 Author: Rahul Mahajan <[email protected]> Date: Tue Nov 14 14:08:26 2023 -0500 Enable warm starting of the model for forecast-only mode (#2031) This PR: - adds an option to warm|cold start the ufs-weather-model when setting up an experiment for GFS/GEFS - adds the capability to stage FV3 restarts when the atmosphere is warm started from FV3 restarts. This would be used in the GEFS free-forecast for part of the reforecast capability. - If a coupled model is warm started for the atmosphere, also check if mediator restarts are present. If so, stage mediator restarts to allow restarting the coupled model. Fixes #2016 commit 2cd6a589305a9ac9d3a9a0d2136e66e42f09d3bf Author: Henry R. Winterbottom <[email protected]> Date: Tue Nov 14 12:05:20 2023 -0700 Moves UFS WM configuration files to `COM_CONF` (#2054) The UFS weather-model (WM) files are place in the COM_CONF path rather than the respective component model COM history paths. Resolves #2015 commit 6f1693081662f241fafc930b1afc88125f7f5aff Author: Kate Friedman <[email protected]> Date: Tue Nov 14 11:15:02 2023 -0500 Refine fit2obs job in rocoto mesh (#2047) This PR adjusts the `fit2obs` job in the rocoto mesh to better define when it exists and how the archive job dependencies accommodate it not being in the first half cycle. Changes in PR: 1. Remove the `fit2obs` job from the first half cycle `cycledef`. 2. Adjust the archive job dependencies to now include the `fit2obs` job in the new logic check added in PR #1983. The `gdasarch` job in the first half cycle will check if `gdasfit2obs` is complete OR no prior cycle exists. Also cleaned up this new logic check block some to make it a tad simpler. 3. Also, fix the addition of the `fit2obs` config to the config list in setup scripts. Now tied to whether `fit2obs` job is on instead of always adding the config to the list. Resolves #2043 commit 5730a71fa5d311e49d9bb11528b500f27f33d69d Author: Henry R. Winterbottom <[email protected]> Date: Tue Nov 14 09:13:11 2023 -0700 Add `waveinit` and `waveprep` to half-cycle. (#2037) This PR addresses issue #1444. The `waveinit` and `waveprep` tasks have been added to the GDAS have cycle. The downstream dependencies for the respective GFS and GDAS forecast tasks have been removed. Resolves #1444 commit 28d2e93c3857de95b0309a089cd7dac736ccaded Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Nov 14 16:11:47 2023 +0000 Update wave IC source for C384 (#2055) The default wave grid for C384 has changed since P8, so a single wave IC on the new grid is available under a different IC name. commit 81dd2d9855091315611106a5afbdaeaa15e6e4ae Author: Walter Kolczynski - NOAA <[email protected]> Date: Thu Nov 9 17:19:57 2023 +0000 Fix analysis and post on Orion (#2046) Fixes a couple things to get workflow to work on Orion again: First, while #2042 allowed post to be built, the `upp.x` executable would fail due to a missing library. Now post jobs (temporarily) uses the UPP modules (plus others needed for runtime) instead of the normal workflow runtime module. This should actually fix #2041. This hack can likely be removed once we move to spack-stack. Second, the launcher command for the analysis jobs on Orion are updated to specify the number of CPUs per task. This was necessary as a recent slurm update on Orion discontinued reading that value from the scheduler. Other jobs will be handled later (see #2044). Additionally, a change is made to `module-setup.sh` that will eliminate the annoyance of `gw_setup.sh` breaking tab completion because undefined variable checking was turned on for the script but not back off. Resolves #1996 Resolves #2041 Refs #2044 commit 13d06ded4155cba2d08ef2a2cd553024c5abe29d Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Nov 8 18:25:47 2023 +0000 Hack UPP version (#2042) The stack UPP was using on Orion was recently deleted, leaving us unable to build the UFS verison of UPP there. UPP has an updated version using spack-stack that works, so the checkout script is modified to check out that version of UPP after UFS has been checked out. This temporary hack can be removed once we move to a UFS version that advances the UPP version to or beyond 78f369b. Resolves #2041 commit 20f6eceb8ff58f84174a27eb849c1d74566a3e03 Author: jiandewang <[email protected]> Date: Wed Nov 8 11:14:55 2023 -0500 Add basic C1152 settings (#2020) Adding C1152 setting in host.yaml, config.base and config.stage_ic so that can run C1152 S2SW. Resolves #2019 commit 5183c43bbbd07285869feacb49d8680afe85929a Author: Barry Baker <[email protected]> Date: Tue Nov 7 01:14:40 2023 -0500 Update UFS for dust fix and remove nitrates by default (#1989) This PR updates the `ufs-weather-model` to the latest hash that included the dust fix (PR #1922). Along with this I removed the nitrates by default in support of the GEFSv13 EP4 and EP5 experiments. Removed unneeded inputs that should help with speed improvements. commit 34a73cf2ed5afefc776d9cc73b6ebf439122a1bb Author: David Huber <[email protected]> Date: Mon Nov 6 14:00:51 2023 -0500 Reduce gdas builds to 8 #2029 (#2036) Reduce the default number of build jobs for the GDASApp to 8 from 16. This is needed for Orion as the build crashes during a linking step. Though not verified, it appears this may be caused by using too much memory with 16 builds. The issue disappears when using 8 build jobs. Resolves #2029 commit 75269e4bb9764b81589efc7d703825b80e74c8f5 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Mon Nov 6 17:34:47 2023 +0000 Streamline CI reporting to PRs (#2026) Cleaned up the logs for CI PRs sent to the GitHub Messages: - Eliminates redundant accumulative reporting - Reports on all created or skipped experiment instantiations in a single message - Gives one line report once for each experiment completion - Single final report completion of CI See some examples in forked [PR 195](https://github.com/TerrenceMcGuinness-NOAA/global-workflow/pull/195) Resolves #2007 commit 8d55126bb0b27c79c8bee7f72b014abd34950ff9 Author: Guillaume Vernieres <[email protected]> Date: Fri Nov 3 17:06:09 2023 -0400 Implement IAU Cycling Type with Marine Data Assimilation Enabled (#1944) Allows cycling in IAU mode with the S2S UFS model, soca and the GSI. Most of the work related to making IAU work was done by @JessicaMeixner-NOAA . Thanks @JessicaMeixner-NOAA ! Resolves #1943 Refs #1776 commit 2563806821d4ae3b57120bc61aa0575139a708f0 Author: jiandewang <[email protected]> Date: Fri Nov 3 11:49:37 2023 -0400 Add two ucx modules in load_ufswm_modules.sh to solve C768 and C1152 S2SW job hanging issue on WCOSS2 (#2021) commit cbdc09711a83493f363a737d1e3e46c48a09719d Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Nov 3 04:09:33 2023 +0000 Fix staging of MOM data (#2028) During the update to stage_ic, the copying of the additional res_N files for 0p25 was omitted. These are now properly copied. Resolves #2027 commit bd4c56d99c23c5c41f0bd5f8a980ef99ee160888 Author: AndrewEichmann-NOAA <[email protected]> Date: Thu Nov 2 16:09:59 2023 -0400 changed optional script name vars for ocean analysis (#2025) commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6 Author: Kate Friedman <[email protected]> Date: Thu Nov 2 16:01:18 2023 -0400 Create separate GSI monitor jobs and remove from vrfy job (#1983) This PR will move the GSI monitor tasks from the `vrfy` job into their own separate jobs in the rocoto mesh. This takes care of part of issue #235. Changes in this PR: 1. Create new individual GSI monitor jobs in the rocoto mesh to match how it is done in operations. The new jobs are: `gdasverfozn`, `gdasverfrad`, `gdasvminmon`, and `gfsvminmon`. The names correspond to the names in operations and the ecf script names. The jobs are only added to cycled mode, none of the jobs are run in forecast-only mode. 2. Updates to GSI monitor scripts: * Update `ush/jjob_header.sh` arguments in JJOB scripts to call new individual job names and configs. * Introduce `COM_*` variables and use of the `generate_com` utility. This results in the outputs landing in `COM` subfolders, like occurs in operations, instead of landing in the online archive. * Some variable cleanup in JJOB and ush scripts, includes cleaning up usage of `DATA` variable and its removal at the end of the jobs. * Add missing exit statements to `JGFS_ATMOS_VMINMON` and `JGDAS_ATMOS_VERFRAD`. 3. Create new rocoto job scripts for the new individual GSI monitor jobs. 4. Create new configs for the new individual GSI monitor jobs. 5. Add new individual GSI monitor jobs to resource configuration, using the same resources as in operations. 6. Move and rename GSI monitor job switches from `config.vrfy` to `config.base`. Also add switches to setup system. New switches to control each job being added to the rocoto mesh are: `DO_VERFOZN`, `DO_VERFRAD`, `DO_VMINMON` 7. Add GSI monitor job output to archival job and into resulting HPSS tarballs or local tarballs. This now matches what is done in operations. 8. Remove the GSI monitor tasks from the rocoto `vrfy` job and associated `config.vrfy`. Example output locations and files (not showing contents of oznmon/horiz or oznmon/time for brevity, see archival script for full list of output files): ``` kate.friedman@dlogin09:/lfs/h2/emc/ptmp/kate.friedman/comrot/testmonitor2> ll gdas.20211221/00/products/atmos/*mon gdas.20211221/00/products/atmos/minmon: total 112 -rw-r--r-- 1 kate.friedman emc 14030 Oct 25 15:00 2021122100.costs.txt -rw-r--r-- 1 kate.friedman emc 84932 Oct 25 15:00 2021122100.cost_terms.txt -rw-r--r-- 1 kate.friedman emc 808 Oct 25 15:00 2021122100.gnorms.ieee_d -rw-r--r-- 1 kate.friedman emc 808 Oct 25 15:00 2021122100.reduction.ieee_d -rw-r--r-- 1 kate.friedman emc 80 Oct 25 15:00 gnorm_data.txt gdas.20211221/00/products/atmos/oznmon: total 8 drwxr-sr-x 2 kate.friedman emc 4096 Oct 25 15:05 horiz drwxr-sr-x 2 kate.friedman emc 4096 Oct 25 15:05 time gdas.20211221/00/products/atmos/radmon: total 21036 -rw-r--r-- 1 kate.friedman emc 231 Oct 25 15:12 bad_diag.2021122100 -rw-r--r-- 1 kate.friedman emc 9035 Oct 25 15:12 bad_pen.2021122100 -rw-r--r-- 1 kate.friedman emc 1449 Oct 25 15:12 low_count.2021122100 -rw-r--r-- 1 kate.friedman emc 20523403 Oct 25 15:07 radmon_angle.tar.gz -rw-r--r-- 1 kate.friedman emc 217272 Oct 25 15:08 radmon_bcoef.tar.gz -rw-r--r-- 1 kate.friedman emc 502151 Oct 25 15:10 radmon_bcor.tar.gz -rw-r--r-- 1 kate.friedman emc 264480 Oct 25 15:12 radmon_time.tar.gz -rw-r--r-- 1 kate.friedman emc 684 Oct 25 15:12 warning.2021122100 kate.friedman@dlogin09:/lfs/h2/emc/ptmp/kate.friedman/comrot/testmonitor2> ll gfs.20211221/00/products/atmos/minmon/ total 88 -rw-r--r-- 1 kate.friedman emc 10530 Oct 25 14:55 2021122100.costs.txt -rw-r--r-- 1 kate.friedman emc 63882 Oct 25 14:55 2021122100.cost_terms.txt -rw-r--r-- 1 kate.friedman emc 808 Oct 25 14:55 2021122100.gnorms.ieee_d -rw-r--r-- 1 kate.friedman emc 608 Oct 25 14:55 2021122100.reduction.ieee_d -rw-r--r-- 1 kate.friedman emc 80 Oct 25 14:55 gnorm_data.txt ``` Lingering work and considerations: 1. Issue #1925 2. Consider not hardcoding the list of types in archival and perhaps tie it to something reliable or configurable (maybe into `config.verfozn`?): `subtyplist="gome_metop-b omi_aura ompslp_npp ompsnp_n20 ompsnp_npp ompstc8_n20 ompstc8_npp sbuv2_n19"` Resolves #1908 commit 31b05a99b77d0f6eaa8b116485a41a43867d20e1 Author: Henry R. Winterbottom <[email protected]> Date: Thu Nov 2 12:23:32 2023 -0600 Move analysis post to new stand-alone task (#1979) This PR addresses issue #1130. A new task `postanl.sh` has been added such that the `anl` post-processing is not it's own task within the Rocoto workflow. This change prevents the GDAS experiment from breaking due to failures caused by the `anl` not being available for the first cycle. Resolves #1130 commit 247cdf8c7e10e6c98f782799fc51c069b6474e70 Author: Henry R. Winterbottom <[email protected]> Date: Thu Nov 2 11:18:53 2023 -0600 Corrects missing local variable reference (#2023) Fixes missing `$` in variable reference in archive job. Resolves #2022 commit 241742b246da1794646b68e41c3d6fe00b95dd07 Author: AndrewEichmann-NOAA <[email protected]> Date: Wed Nov 1 14:19:55 2023 -0400 Updates to prep ocean obs task (#1870) commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd Author: Henry R. Winterbottom <[email protected]> Date: Wed Nov 1 12:09:33 2023 -0600 No longer write archive lists COM (#2000) Changes the respective `.txt` files used for the HPSS archive to the `DATA` path. Each defined text file has been updated to explicitly write to `DATA` rather than `COM` such that the files are deleted rather than being archived. Resolves #760 commit 517b92f9c20c9e44abba3183325e35a95a7334a5 Author: David Huber <[email protected]> Date: Tue Oct 31 16:33:11 2023 -0400 Parallelize the build scripts (#1998) Optimized/parallelized build scripts. A few notes: 1) The default number of build jobs is 20, but one could argue for using 40. When researching this, I looked up what the SRW is compiling with. That system uses 40 cores, which seems a little excessive, but on testing the global workflow, the actual number of cores being used at any given time rarely exceeds 16 when running with 40 cores. This is because the builds tend to use multiple threads in the beginning when compiling low-level modules while the higher-level modules are more or less serial AND because the GDASApp takes several minutes to initialize all of its subrepositories by which time the smaller builds are complete. 2) I also updated checkout.sh so that all checkouts are simultaneous. The CPU load for `git submodule` is quite low, so running 16 instead of 8 jobs at once is not much more expensive. 3) To make this work, I had to add `-j` options to most of the build scripts. The only exception is build_upp, for which the build script within the UPP is hard coded to use 6 cores. 4) I fixed a few small bugs in the build scripts along the way. 5) Lastly, this reduce the total build time from ~2.5 hours for the entire system (including GDAS and GSI in the same build) to ~40 minutes when running with `-j 40`. Resolves #1978 commit 67c050c201f92e855d09211e41a5f51ee1cb5230 Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Oct 31 19:00:47 2023 +0000 Add missing export for rCDUMP in stage_ic (#2009) rCDUMP is needed by the exscript but was never exported by the jjob. commit 872068cb5ea78b311f7a77e97ee1428ae027cb61 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Oct 31 14:37:55 2023 +0000 Add output error log to user for create_experiment.py on fail in CI (#1974) Small changes to driver CI bash scripts to recapture error log from `create_experment.py` logger Fixes #1939 commit b2e4a2e9d269842acbb1b37dd563ee5dee2adf0f Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Oct 31 13:57:02 2023 +0000 Allow CI case to exclude running on certain platforms (#2001) commit 7cc137116f1619bf1e5a12eaacb98d17da97c223 Author: Jeff Whitaker <[email protected]> Date: Tue Oct 31 07:54:24 2023 -0600 Add initial C96/1 deg coupled model support (#1991) commit 7086ddc4bece6fb2a8c1c2e6090800d4293e410e Author: AndrewEichmann-NOAA <[email protected]> Date: Mon Oct 30 19:58:43 2023 -0400 Add ocean analysis files to HPSS archiving task (#1985) This PR adds the files under `analysis/ocean` (except those in `bump` and `vrfy`) to the HPSS archiving job, in `gdasocean_analysis.tar`, which were previously not archived. Resolves NOAA-EMC/GDASApp/issues/693 commit eabc82ad30c118645c0e6e216162d823882a8139 Author: Guillaume Vernieres <[email protected]> Date: Mon Oct 30 10:31:27 2023 -0400 Make the early cycle work with the coupled UFS configured as S2S (#1954) commit aff6ca7ae559e424dae128d6cfd5da4a4e3049e7 Author: Anil Kumar <[email protected]> Date: Fri Oct 27 14:11:55 2023 -0400 GEFS Staging in exglobal_stage_ic (#1892) Adjusts source paths for forecast-only ICs in support of extension to ensembles. New paths omit the resolution (that is captured by the IC id name) and allow for a member level. Directories with the reorganized ICs have been added to the three tier-1 machines under glopara space. Building on this, also adds capability to stage GEFS ICs. Resolves #911 commit 77c1ff2bfa26b341b01f41e50ee0ecb31cc4f661 Author: RussTreadon-NOAA <[email protected]> Date: Thu Oct 26 23:44:27 2023 -0400 Update GDASApp hash (#1975) Update GDASApp hash to bring recent UFSDA development into g-w. Resolves #1972 commit 962368884991670d3a1ee1c5a065d5bce4b7561a Author: David Huber <[email protected]> Date: Thu Oct 26 16:10:23 2023 -0400 Test tarballs for rstprod before calling chgrp (#1967) Certain tarballs may or may not contain `rstprod` data. For instance, the first half cycle gdas and enkfgdas tarballs will not contain `rstprod`, while future cycles likely will. Also, some systems do not have `rstprod` on them. This will test the contents of the tarballs first before attempting to change the group to rstprod. Resolves #1460 commit c02e118c0ac5485109c9bd33472ff42db309cd9b Author: Jessica Meixner <[email protected]> Date: Thu Oct 26 15:05:05 2023 -0400 Update ufs model to version from 10-12-23 (#1933) This updates the ufs-weather-model to the commit hash from 10-12-23 from the HR2 tag. The diffs can be seen here: https://github.com/ufs-community/ufs-weather-model/compare/GFSv17.HR2...68050e58589a82ab509aaefaafdc2a6b90f34e48 Resolves #1811 commit 8556541daa79b0180fde48a58a8dcfb2f8c56ea5 Author: Rahul Mahajan <[email protected]> Date: Wed Oct 25 16:15:28 2023 -0400 Fix incorrect usage of CFP on WCOSS2 (#1977) commit 0b5cf9b67a8146d9d4815ea6545f7f2524120d83 Author: Kate Friedman <[email protected]> Date: Wed Oct 25 13:17:28 2023 -0400 Update GFS version in index.rst to v16.3.10 (#1976) Update the "State of operations" GFS version number to new v16.3.10 (Annual CO2 fix file update in operations). Refs #1924 commit e817f5dd38c26a88f76d90eb71124f1acbfc5a8f Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Oct 25 02:03:14 2023 +0000 Fix path for marine products (#1966) When PR #1823 was merged, the name of the marine product template was not updated in ocnpost, leading the products to be placed in the wrong location and missed by the archive job. Resolves #1902 commit 7cdfad4eaa7abe0769ff13396c54e6d93afebf8f Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Oct 24 22:19:46 2023 +0000 Build GDASapp for CI tests (#1964) * added -u to global checkout so CI test builds tests for GDASapps * Update check_ci.sh needed more quotes --------- Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]> commit c58deae0cf078d1ee093529064d74f60482aa3f4 Author: Henry R. Winterbottom <[email protected]> Date: Tue Oct 24 16:19:04 2023 -0600 Updates for NOAA CSP AWS global-workflow related file paths. (#1970) Co-authored-by: henrywinterbottom-wxdev <[email protected]> commit 1b00224e18842cd873eb1779be08f96687e49e1f Author: Kate Friedman <[email protected]> Date: Tue Oct 24 14:48:24 2023 -0400 Set SENDCOM=YES for tracker/genesis tasks (#1971) Set SENDCOM to YES in config.vrfy to get outputs copied back to COM. Will reevaluate the need for SENDCOM when moving the tracker/genesis jobs out of the vrfy job with issue #235 work. Refs #1947 commit e2c624d8904cd988394c73d0edb22fa593229d3f Author: RussTreadon-NOAA <[email protected]> Date: Tue Oct 24 13:32:52 2023 -0400 Refactor UFSDA ATM var and ens layout (#1945) commit 8940adddfe9d21189740e71487603fb2acee2336 Author: David Huber <[email protected]> Date: Tue Oct 24 11:02:29 2023 -0400 Optimize the checkout script (#1956) * Multithread the checkout script #1953 commit 4b5cd0bc435fc158258ca38c3d5f44add6b60469 Author: Rahul Mahajan <[email protected]> Date: Mon Oct 23 12:04:26 2023 -0400 Fix nth_eupd in gfs/config.resources. remove sections of jobs not run as part of gefs from gefs/config.resources (#1952) commit 08ce4f8d3ed8e07b4d488a80b5054c6206b04404 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Oct 20 16:14:53 2023 +0000 Fix enkfgfs cleanup dependency (#1941) When #1906 was merged, the dependency for enkf cycles was hard-coded to use the enkfgdas archive instead of depending on the `RUN`. commit 1a5d0b51642eb70f71e693355e86212d3607b7b3 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Oct 20 15:54:33 2023 +0000 Split clean-up into separate job (#1906) Moves the clean-up that was previously done in the archive jobs into their own separate job. The clean-up is also streamlined considerably by using only `COM_TOP` instead of going through every template. There is also additional streamlining/corrections in the function that does the actual removing. Some settings used by both jobs were elevated to `config.base`. Others only needed for cleanup were moved to the new config for that job. Also corrects a small error encountered when attempting to rerun an ensemble forecast. Resolves #583 Resolves #1872 commit 3de102c28daf9eb50ce65e0afe911f5a416ce861 Author: Rahul Mahajan <[email protected]> Date: Tue Oct 17 09:30:18 2023 -0400 Updates to CI to clarify HOMEgfs (#1931) * replace HOMEgfs_PR with HOMEgfs, and HOMEgfs with ROOT_DIR. ROOT_DIR is the location where the ci scripts live * update type to system in case yamls * move create_experiment.py to workflow/ * detect HOMEgfs in create_experiment.py based on location. update to use jinja templates in the cases * remove export of HOMEgfs from driver.sh commit bfea2594207a477ea00e3b7fef95c2d7befd492b Author: Henry R. Winterbottom <[email protected]> Date: Sun Oct 15 23:27:47 2023 -0600 Remove SENDCOM (#1929) This PR addresses issue #1501. All instances of `SENDCOM` gates have been removed. The workflow was inconsistent in its use of `SENDCOM` to gate movement of files to `COM` and have been removed based on NCO guidelines. Resolves #1501. commit 9a8911a0b30f0367d061facfb3b835480728081d Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Fri Oct 13 14:21:01 2023 +0000 update nth_eupd to 8 for Orion because of out of memmory errors (#1927) Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]> commit ea4dfa5800b5cb529478cc64d329f567393fa37d Author: Guillaume Vernieres <[email protected]> Date: Thu Oct 12 21:29:19 2023 -0400 Marine DA configuration updates (#1922) Minor updates the configuration related to running the marine DA and the coupled UFS. What's proposed in this PR: - Memory increased for the marine DA analysis step - The coupled UFS is (was?) running out of memory without the changes in `config.ufs`. - Updates to the IAU section of MOM_input to allow for a current increment. commit c2d112b40a926c9f33a653cfbb832cb811a60352 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Thu Oct 12 23:52:43 2023 +0000 Fix missing pipe in check_ci (#1926) Bugfix: left out pipe to word count` | wc -l` after updating: `num_platforms=$(ls ../platforms/config.* | wc -l)` to `num_platforms=$(find ../platforms -type f -name "config.*")` when it was flagged by the BASH linter. commit 51d93e15eb30382017aaf72813d34f7010f47948 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Oct 10 19:09:26 2023 +0000 Updated cron bash ci script to remove weekly CI test PR on success (#1915) This PR updates the check CI bash script in cron to remove the PR that is created by the weekly CI test driver when all the tests has passed on all the platforms. This is done by the script checking if all other labels for all the platforms for the PR that has currently been flagged to have run to a successful completion by the check ci bash script. commit 2d64b74a0b0407d01d6f657efa6af9637a131448 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Wed Oct 4 22:33:25 2023 +0000 CI driver_weekly bugfix deleting new branch if is already on repo (#1899) Bugfix and updates to weekly CI test that deletes the new modified branch if it is already on the repo but now also makes sure that the intermediary branch that creates the PR is coming from emcbot. commit e4a6c35ae020253f07921ca34a17f19e928b0b6c Author: Rahul Mahajan <[email protected]> Date: Wed Oct 4 09:42:12 2023 -0400 Fix typo in cice history filename commit d50938bc4f6705b722338bbea03f925614f953ed Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Oct 3 23:37:39 2023 -0400 Change metp dependency (#1900) MET+ jobs rely on files already having been placed in the local archive directory, but the job only depended on post, resulting in the job prematurely firing. The dependency is now updated to be on the archive job instead. Resolves #1756 commit 836642bb201cd2e5e205eda2ae4a28993623355d Author: Rahul Mahajan <[email protected]> Date: Tue Oct 3 14:45:57 2023 -0400 Use deterministic marine resolutions for ensemble (#1894) This PR determines the ensemble resolution for ocean, ice and waves based on the deterministic configuration as there is no dual-resolution capability requested for these model components. For cycled DA, if the deterministic uses a coupled model, the ensemble will also be a coupled model. This can be turned off manually via adding `DO_AERO_ENKF`, `DO_OCN_ENKF`, `DO_ICE_ENKF` and `DO_WAVE_ENKF` flags set in `config.base` or `config.efcs`. This is currently handled manually and will be automated when a requirement arises for this flexibility. Fixes #1730 commit 48ba775909870f0d27275128bd07ec134b92c356 Author: Kate Friedman <[email protected]> Date: Mon Oct 2 13:34:02 2023 -0400 Update vrfy.sh to only run MINMON in cycled mode (#1901) Update MINMON if-block in jobs/rocoto/vrfy.sh to only invoke this section when MODE is cycled. Refs #1076 commit e65162f3083c34b639854e3216e2355ff6fccc0b Author: RussTreadon-NOAA <[email protected]> Date: Fri Sep 29 19:18:07 2023 -0400 Update module loads to intel/2022 for jobs running gsi.x and enkf.x (#1882) This PR changes the module loads in g-w jobs `anal.sh`, `eobs.sh`, and `eupd.sh` to use machine specific modulefiles from `sorc/gsi_enkf.fd/modulefiles`. This is necessary because [NOAA-EMC/GSI#571](https://github.com/NOAA-EMC/GSI/pull/571) updated `gsi.x` and `enkf.x` builds to intel/2022 on NOAA RDHPCS machines. Resolves #1863 commit cd439d0bf2ae5fb57139fcb9983aa2755fdc9b2c Author: Rahul Mahajan <[email protected]> Date: Fri Sep 29 15:35:54 2023 -0400 Add coupled forecast-only tests for S2S and S2SW (#1895) This PR: - replaces the PR C48 S2S forecast-only test with a S2SW configuration - adds a weekly C384 S2SWA forecast-only test. The C384 S2SWA is a weekly test and will not be triggered/tested in this PR, but will be tested on Friday. See notes on Orion below in the testing section. @JessicaMeixner-NOAA kindly provided the details in https://github.com/NOAA-EMC/global-workflow/issues/1794#issuecomment-1740768751 commit 02787fe9ba9e5a6881e5ccf9a9e352545eeadb9d Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Fri Sep 29 18:03:23 2023 +0000 Ci rename platform scripts (#1896) Simply renaming the platform config files in ${HOMEgfs}/ci/platforms to config.${MACHINE} so wxflow can read them too in support of up and coming functional testing. commit bb5a58541d6514d16901dca240dfbbc810bd31c8 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Sep 29 13:28:39 2023 -0400 Merge S2S defaults config back into other configs (#1876) When the prototype S2S was first added, we placed some settings in a `config.defaults.s2sw` file to avoid interference with existing settings. Now that we are moving towards v17 and run S2S regularly, it is time to merge these settings back into the other config files. The wave output frequency settings are updated to the coarser fre- quency as that is more suitable for development. The prior (ops) settings are noted as comments. There are a couple of settings that control ice fields within FV3. These are placed in `config.ice`, so when the ice model is on those settings are still used. Changes the output frequency from 3 to 6. While we may leave this setting as the default for development, it is required right now because the ocean frequency is hard-coded to 6 but links are created based on `$FHOUT_GFS`. Resolving #1629 should correct this limitation. "Gaussian" archive is updated to the former override values. Resolves #1606 Refs #1629 commit 49dc315c1ef6c5f4952a06b0ba70c36e771f128e Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Sep 29 13:25:58 2023 -0400 Move product functions to separate script (#1891) PR #1822 converted some formerly stand-alone scripts and moved them inside one of the standard product scripts. However, `trim_rh.sh` is also used by gempak and AWIPS, so this change caused those jobs to start failing (they are not yet tested by CI). Those functions have now been moved into a separate product functions script that can be sourced by all the scripts that need the functions. A third similar script was also eliminated and converted into a function. Additionally fixes a base bug in AWIPS and updates some scripts to satisfy (or at least mostly satisfy) the linter. **AWIPS still failing when creating GRIB1 products.** That will be addressed in a future PR (and may need a subject-matter expert). Resolves #1890 commit 3e750d10be577106fb269a78e18765b8d2b8030d Author: Rahul Mahajan <[email protected]> Date: Thu Sep 28 16:21:52 2023 -0400 Fix a few bugs reported by devs (#1893) This PR fixes a …
@aerorahul I wanted to check in on this issue. @jiandewang ran some scout runs with what is now the develop branch with the unstructured grid in prep for HR3. We like to have 3 hourly output for atm model and that meant we manually made updates to run with 6 hours in the diag table with the updates in #2286 our previous work around no longer works. There's likely another simple work around that we can use to move forward, but before investigating that I thought I'd talk to you first about the longer term fix. |
So it looks like we could hard code FHOUT to 6 here: https://github.com/NOAA-EMC/global-workflow/blob/develop/ush/forecast_predet.sh#L250 but then the post jobs are still thinking it's 3 hours if we change FHOUT. So I'm looking for where that's set to see if that could also be temporarily hard coded to 6 for us to run HR3. -- I looked for your branches @aerorahul that you had pointed me to before but they no longer exist. |
This adds functionality to have ocean/ice output frequency be separate from the atm model. One time was created because there's an assumption in the post that these are the same. This could be further modified to remove this assumption. Refs #1629
I did not say that PR @2327 closed this issue because of GEFS, but in hindsight with @WalterKolczynski-NOAA updates I think we might be able to close this issue. @aerorahul thoughts? |
@JessicaMeixner-NOAA |
We meet the acceptance criteria. Closing! |
commit d1e8f33 Merge: e2d88dd 5166593 Author: kayee.wong <[email protected]> Date: Fri Mar 1 00:01:58 2024 +0000 Merge remote-tracking branch 'emcgw/develop' into develop remote: https://github.com/NOAA-EMC/global-workflow.git develop (Feb 29, commit 5166593) origin: https://github.com/kayeekayee/global-workflow.git gsl_ufs_dev (Feb 29,commit e0c3e4d) commit 5166593 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Thu Feb 29 20:14:41 2024 +0000 Move Jenkinsfile into ci subdirectory (NOAA-EMC#2355) Just moves the Jenkinsfile into the ci directory Co-authored-by: tmcguinness <[email protected]> commit b7af315 Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Feb 28 22:20:58 2024 +0000 Fix rocoto forecast hour determination for GEFS (NOAA-EMC#2351) The function that generates the list of forecast hours for rocoto was trying to use variables that are not defined for GEFS, causing workflow generation to fail. The function is updated to not try to load these variables before loading the ones actually used for GFS/ GEFS. Also turns GEFS CI test back on and adds an entry to stage C192 ICs (note: these have not been placed in the centralized location.) commit d3a4927 Author: Cory Martin <[email protected]> Date: Wed Feb 28 09:38:49 2024 -0500 Rename the land DA jobs to snow DA to better reflect what they are doing (NOAA-EMC#2330) This PR renames all of the land DA jobs to snow DA to better reflect that this is a JEDI-based snow analysis capability and not a more generic land surface analysis. commit 2693810 Author: Jessica Meixner <[email protected]> Date: Tue Feb 27 01:25:51 2024 -0500 Update ufs-waether-model hash (NOAA-EMC#2338) Routine update of ufs-weather-model hash. Other small updates: * removes comment referencing closed issue. * Updates the CICE diag frequency to once per day as recommend here: NOAA-EMC#1810 (comment) * Updated amount of time for C384 gdas forecast as it was running out of time * Removed unused variable wave_sys_ver commit 9608852 Author: RussTreadon-NOAA <[email protected]> Date: Mon Feb 26 14:10:01 2024 -0500 Update JEDI ATM to use .nc for obs and generalize x,y layout (NOAA-EMC#2336) # Description The changes in this PR are twofold 1. replace `.nc4` suffix for JEDI ATM observation related files with `.nc` 2. use templated variables to specify `{layout_x, layout_y}` for JEDI ATM variational and local ensemble apps The first change conforms with the Unidata recommendation that netCDF files end with the suffix `.nc`. The second change replaces hardwired JEDI ATM var and ens `{layout_x, layout_y}` in `config.resources` with a more flexible approach. Resolves NOAA-EMC#2335 commit c5c8466 Author: Kate Friedman <[email protected]> Date: Mon Feb 26 10:18:50 2024 -0500 Remove FIX* variables for fix subfolders (NOAA-EMC#2337) Remove `FIX*` variables for fix subfolders and replace them with the remaining `FIXgfs` variable and the subfolder name (e.g. `${FIXam}` -> `${FIXgfs}/am`). The UFS_UTILS and GDASApp repos were similarly updated. This PR includes a new UFS_UTILS hash. The updated GDASAPP hash was already committed within the spack-stack/1.6.0 PR NOAA-EMC#2239. Resolves NOAA-EMC#2184 commit 950c38a Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Fri Feb 23 21:15:46 2024 +0000 Fix several Jenkins issues (NOAA-EMC#2334) Jenkins Updates Resolving final kinks: - Removed all `git` shell commands and now exclusively use Software Control Manger (**scm**) plugin. - Add feature for skipping hosts per configuration specified in case yaml files. - Solved and tested false positive builds and experiments. - Tested archiving of task error log on case fail - First case fail quits pipeline and cancels all pending scheduled jobs - Duel build per yaml configuration arguments supported - All designated case files in PR directory pass on intended host (fully tested on Hera) Remaining updates: - Fist build fail short circuit when building sub-modules and archiving build error log. - Re-build/no-build built in logic for Replay and Rerunning previously failed experiments. commit c67393a Merge: 6f9afff 79d305e Author: David Huber <[email protected]> Date: Fri Feb 23 14:18:15 2024 +0000 Merge pull request NOAA-EMC#2239 from DavidHuber-NOAA/ss160 Update to spack-stack 1.6.0 Includes all submodules except the UFS, which will be updated at a later time. commit 79d305e Author: David Huber <[email protected]> Date: Thu Feb 22 14:53:57 2024 -0600 Disable snow DA tests commit 0459203 Author: David Huber <[email protected]> Date: Thu Feb 22 12:55:51 2024 -0600 Update GDASApp hash to current develop commit 5c96eb2 Author: David Huber <[email protected]> Date: Thu Feb 22 12:37:47 2024 -0600 Update GDAS hash to allow modified snow DA analysis commit 79144f2 Merge: abbb0b8 6f9afff Author: DavidHuber <[email protected]> Date: Thu Feb 22 15:14:39 2024 +0000 Merge remote-tracking branch 'origin/develop' into ss160 commit abbb0b8 Merge: 4ad837e 4529e8c Author: DavidHuber <[email protected]> Date: Thu Feb 22 15:11:03 2024 +0000 Merge remote-tracking branch 'henry/feature/gwdev_issue_2129' into ss160 commit 4ad837e Merge: 516b2a2 7ca45db Author: DavidHuber <[email protected]> Date: Thu Feb 22 15:10:24 2024 +0000 Merge remote-tracking branch 'henry/feature/gfsv17_issue_2125' into ss160 commit 516b2a2 Author: DavidHuber <[email protected]> Date: Thu Feb 22 14:19:16 2024 +0000 Updated GDAS to include rocoto/1.3.6 on Hera. commit 6f9afff Author: Jessica Meixner <[email protected]> Date: Wed Feb 21 13:09:44 2024 -0500 Add some flexibility for ocean/ice output (NOAA-EMC#2327) This adds functionality to have ocean/ice output frequency be separate from the atm model. One time was created because there's an assumption in the post that these are the same. This could be further modified to remove this assumption. Refs NOAA-EMC#1629 commit e2d88dd Merge: 3e6b1e2 a23b7f2 Author: Janet Derrico <[email protected]> Date: Tue Feb 20 16:08:46 2024 -0700 Merge branch 'NOAA-EMC:develop' into develop commit f6d3015 Author: David Huber <[email protected]> Date: Tue Feb 20 09:53:08 2024 -0600 Update GDASApp hash to include SS/1.6.0 support. commit 0bf340b Author: David Huber <[email protected]> Date: Tue Feb 20 09:07:32 2024 -0600 Construct SS paths from version variables. commit 3330cd7 Author: David Huber <[email protected]> Date: Tue Feb 20 09:06:19 2024 -0600 Removed MET/METplus 'not available' comments commit fdc638c Author: David Huber <[email protected]> Date: Tue Feb 20 08:35:15 2024 -0600 Move SS module path to version files. commit d7d28a6 Author: David Huber <[email protected]> Date: Tue Feb 20 07:53:15 2024 -0600 Update comment about METplus support. commit a812f88 Author: David Huber <[email protected]> Date: Tue Feb 20 07:45:45 2024 -0600 Update verif-global to latest WCOSS2 support. commit d81f07f Author: David Huber <[email protected]> Date: Tue Feb 20 07:41:38 2024 -0600 Clean up build_upp.sh. -Corrected whitespace (tabs instead of spaces) -Removed debug print statement -Alphebetized flags commit ae7eb19 Author: David Huber <[email protected]> Date: Fri Feb 16 16:15:40 2024 -0500 Fix whitespace in build_upp.sh. Co-authored-by: Rahul Mahajan <[email protected]> commit 48b34d0 Author: David Huber <[email protected]> Date: Fri Feb 16 20:56:55 2024 +0000 Added verif-global support back to WCOSS2. commit 4529e8c Author: henrywinterbottom-wxdev <[email protected]> Date: Fri Feb 16 11:12:01 2024 -0700 Bug fix. commit 8e4f94d Author: henrywinterbottom-wxdev <[email protected]> Date: Fri Feb 16 11:04:41 2024 -0700 Updates requested by reviewer Rahul Mahajan. commit 4624ce2 Author: henrywinterbottom-wxdev <[email protected]> Date: Fri Feb 16 10:52:11 2024 -0700 Updates requested by reviewer; testing -- DO NOT REVIEW. commit ed25bbd Author: henrywinterbottom-wxdev <[email protected]> Date: Fri Feb 16 09:33:59 2024 -0700 Linter corrections. commit 6a0b7bf Merge: f9fb64e 2415b7b Author: David Huber <[email protected]> Date: Fri Feb 16 09:50:22 2024 -0600 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit f9fb64e Merge: 777d97d a23b7f2 Author: David Huber <[email protected]> Date: Fri Feb 16 09:49:42 2024 -0600 Merge remote-tracking branch 'emc/develop' into ss160 commit 7ca45db Merge: 73bc76b a23b7f2 Author: Henry R. Winterbottom <[email protected]> Date: Fri Feb 16 07:46:35 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit eb2ed53 Merge: 9929277 a23b7f2 Author: Henry R. Winterbottom <[email protected]> Date: Fri Feb 16 07:46:24 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit a23b7f2 Author: RussTreadon-NOAA <[email protected]> Date: Fri Feb 16 09:37:58 2024 -0500 Add JEDI 3DEnVar atmosphere only CI test stub (NOAA-EMC#2309) commit cf83885 Author: Jessica Meixner <[email protected]> Date: Fri Feb 16 01:55:02 2024 -0500 Add unstructured grid for HR3/GFS (NOAA-EMC#2230) This adds the capability to use unstructured grids in the global workflow, which will be used in HR3. There are new fix files for a low-resolution 100km grid and a grid closer to our targeted GFSv17 grid which has the resolution combined from the older multi_1 and GFSv16 grids. The fix file update is here: NOAA-EMC#2229 Note: This now means that GFS tests need a new build option: `./build_all.sh -w` So that PDLIB=ON is turned on for compiling relevant UFS and WW3 codes. Resolves NOAA-EMC#1547 commit 9929277 Merge: eb8791c 094e3b8 Author: Henry R. Winterbottom <[email protected]> Date: Thu Feb 15 15:05:50 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit 094e3b8 Author: Cory Martin <[email protected]> Date: Thu Feb 15 14:43:55 2024 -0500 Move IMS remapping files from COM_OBS to FIXgdas (NOAA-EMC#2322) * Add in IMS obs fix directory and update submodule for gdas commit d465ea0 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Thu Feb 15 19:25:02 2024 +0000 Set HOMEgfs for module_setup in CI driver (NOAA-EMC#2321) Hotfixes to CI Bash system from updates with sourcing `detect_machine.sh` in `ush/module-setup.sh` using **HOMEgfs**. commit 2415b7b Author: David Huber <[email protected]> Date: Thu Feb 15 19:21:17 2024 +0000 Load default rocoto on Jet. commit eb8791c Merge: 60d5ee6 638684e Author: Henry R. Winterbottom <[email protected]> Date: Thu Feb 15 11:56:40 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit 777d97d Author: David Huber <[email protected]> Date: Thu Feb 15 12:34:59 2024 -0600 Fixed Orion cdo version. commit ef07235 Author: DavidHuber <[email protected]> Date: Thu Feb 15 16:29:32 2024 +0000 Revert UFS hash. commit 0ce8c0d Author: DavidHuber <[email protected]> Date: Thu Feb 15 14:55:48 2024 +0000 Fix git version in Hera's gwsetup module. commit 3080a34 Author: DavidHuber <[email protected]> Date: Wed Feb 14 20:52:34 2024 +0000 Fixed xarray version for SS/1.6.0. commit 49392dd Author: DavidHuber <[email protected]> Date: Wed Feb 14 20:29:41 2024 +0000 Updated GSI-Utils hash to head of develop. commit c3553f0 Merge: 4568653 638684e Author: DavidHuber <[email protected]> Date: Wed Feb 14 20:28:14 2024 +0000 Merge remote-tracking branch 'origin/develop' into ss160 commit 4568653 Author: David Huber <[email protected]> Date: Wed Feb 14 14:22:13 2024 -0600 Reupgrade Hercules to SS/1.6.0 commit 638684e Author: Kate Friedman <[email protected]> Date: Wed Feb 14 14:55:21 2024 -0500 Remove `finddate.sh` from system (NOAA-EMC#2308) * Retire finddate.sh usage from system * Update gfs-utils hash to 7a84c88 - New hash includes removal of finddate.sh Refs NOAA-EMC#2279 commit 2b160f8 Author: DavidHuber <[email protected]> Date: Wed Feb 14 18:31:28 2024 +0000 Reenable METplus jobs on Hercules. commit 8f59002 Author: DavidHuber <[email protected]> Date: Wed Feb 14 18:30:23 2024 +0000 Update GSI hashes. commit 73bc76b Author: henrywinterbottom-wxdev <[email protected]> Date: Wed Feb 14 09:27:37 2024 -0700 Updates based on user request. commit e4bc674 Author: henrywinterbottom-wxdev <[email protected]> Date: Wed Feb 14 08:03:45 2024 -0700 Corrected based on reviewer review. commit 60d5ee6 Merge: 40f2cf6 1aaef05 Author: Henry R. Winterbottom <[email protected]> Date: Tue Feb 13 18:08:33 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit 0330411 Merge: 929b903 1aaef05 Author: Henry R. Winterbottom <[email protected]> Date: Tue Feb 13 17:58:12 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit 1aaef05 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Feb 13 18:15:59 2024 -0500 Jenkins Pipeline updates for Canceling Jobs (NOAA-EMC#2307) Tuning updates for Jenkins Pipeline : - Added short circuit for all parallel runs of cases on error of any - Fixed canceling of all scheduled jobs on first case error - Added feature to save error log files to Jenkins Archive facility on fail commit 6404892 Author: Rahul Mahajan <[email protected]> Date: Tue Feb 13 14:57:37 2024 -0500 Ocean/ice product generation for GFS and GEFS (NOAA-EMC#2286) This PR does several things: 1. the model output for ocean and ice in the `COM/` directory are now named per EE2 convention for coupled model. E.g `gfs.ocean.t12z.6hr_avg.f120.nc` and `gfs.ocean.t12z.daily.f120.nc` 2. The products are generated using the `ocnicepost.fd` utility developed by @DeniseWorthen in https://github.com/NOAA-EMC/gfs-utils and converted to grib2 using example scripts provided by @GwenChen-NOAA using `wgrib2`. 3. NetCDF products on the native grid are also generated by subsetting variables from the raw model output. This is done with `xarray`. 4. updates the hash of https://github.com/NOAA-EMC/gfs-utils to include fixes in `ocnicepost.fd` 5. removes NCL related scripting that was previously used for ocean/ice interpolation and `reg2grb2` used for converting to grib2. 6. updates archive scripts to accommodate updated file names 7. removes intermediate ocean processed files such as 2D/3D/xsect data- sets 8. separate jobs are added for ocean and ice product generation. 9. removes intermediate restarts for the mediator and only saves the medi- ator restart at the end of the forecast in `COM`. 10. Increases memory for offline UPP when run at C768. The program segfaults with an OOM when memory is self allocated based on PEs by the scheduler on Hera. 11. Enables ocean/ice ensemble product generation for GEFS 12. Some minor clean-ups Fixes NOAA-EMC#935 Fixes NOAA-EMC#1317 Fixes NOAA-EMC#1864 commit 40f2cf6 Author: henrywinterbottom-wxdev <[email protected]> Date: Tue Feb 13 10:18:53 2024 -0700 Implemented ush/detect_machine.sh for host determination and removed redundant checks for expected file paths. commit 929b903 Merge: 2d08d01 3f99f70 Author: Henry R. Winterbottom <[email protected]> Date: Tue Feb 13 08:31:06 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit 3f99f70 Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Feb 13 00:57:18 2024 -0500 Add wave post jobs to GEFS (NOAA-EMC#2292) Adds the wave post jobs for gridded and points to GEFS. Boundary point jobs are added even though the current GEFS buoy file does not contain any (tested by manually subbing in the GFS buoy file). Resolves NOAA-EMC#827 commit 842adf3 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Mon Feb 12 12:50:08 2024 -0500 Added additional test cases to the pr list in Jenkins (NOAA-EMC#2306) C48mx500_3DVarAOWCDA, C96C48_hybatmDA, and C96_atmsnowDA Co-authored-by: terrance.mcguinness <[email protected]> commit bb4ca65 Author: CatherineThomas-NOAA <[email protected]> Date: Mon Feb 12 14:50:41 2024 +0000 Redo v16.3 config.base changes for DA increments (NOAA-EMC#2304) Include the additional hydrometeors to the INCREMENTS_TO_ZERO and INCVARS_ZERO_STRAT variables in config.base that were modified in v16.3. Resolves: NOAA-EMC#2303 commit 061992b Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Sat Feb 10 01:33:36 2024 -0500 Fix Jenkins success reporting (NOAA-EMC#2302) Moving the post section back outside of main Run Experiments stage. This allows the system to correctly report the **Success** status until after all tests pass. _Had originally moved them in attempts to solve "Not an SCM GitHub Job" issue and cause the reporting to misbehave._ Also ran through Jenkins linter and updated some messaging that was incorrectly reporting system build type. commit 28ccf78 Merge: b972f66 54daa31 Author: David Huber <[email protected]> Date: Fri Feb 9 14:00:43 2024 -0600 Merge remote-tracking branch 'emc/develop' into ss160 commit b972f66 Author: David Huber <[email protected]> Date: Fri Feb 9 10:47:00 2024 -0600 Fix SS versions for CI modules. commit 4b01d8e Author: David Huber <[email protected]> Date: Fri Feb 9 10:44:30 2024 -0600 Revert Hercules modules to SS/1.5.1. commit 54daa31 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Thu Feb 8 15:48:38 2024 -0500 Jenkins Declartive Pipeline for CI with gfs/gefs multibuilds (NOAA-EMC#2246) Adding top level Jenkins file for CI tests running on Jenkins Controller: - Declarative Multi-branch Pipeline (has enhanced restart capabilities on a per section bases) - Starts Pipeline from Label PR same as BASH system (for now) - Progress and restarts can me managed with CAC Login at [EPIC OAR Jenkins](https://jenkins.epic.oarcloud.noaa.gov) - Has logic for multi **gfs/gefs** system builds (arguments based on a configuration file `ci/casts/yamls/build.yaml`) - Any number of **systems** may be added by manual adding an ele- ment to the matrix in the Jenkinsfile - _It may be possible to dynamic add matrix values with a specialty plug-in_ - Currently only runs on **Orion** and **Hera** using `mterry` account Resolves NOAA-EMC#2119 Resolves NOAA-EMC#2118 commit 43429e2 Author: Rahul Mahajan <[email protected]> Date: Thu Feb 8 15:30:28 2024 -0500 Enable AO WCDA test (NOAA-EMC#1963) This PR: - adds GSI + SOCA C48 5-deg ocean 3DVar test (courtesy @guillaumevernieres) - adds a toggle to optionally disable ocnanalvrfy job. commit 2d08d01 Merge: 4745d4a f563528 Author: Henry R. Winterbottom <[email protected]> Date: Thu Feb 8 07:24:54 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit f563528 Author: Kate Friedman <[email protected]> Date: Wed Feb 7 15:09:12 2024 -0500 Update JGLOBAL_FORECAST for octal error (NOAA-EMC#2295) Add "10#" to ENSMEM value > 0 check to handle octal errors. commit 4745d4a Author: henrywinterbottom-wxdev <[email protected]> Date: Wed Feb 7 08:45:49 2024 -0700 Removed jlogfile references. commit 5894ca2 Author: henrywinterbottom-wxdev <[email protected]> Date: Wed Feb 7 08:32:16 2024 -0700 Removed dummy variable passed to perl scripts. commit dae884a Author: henrywinterbottom-wxdev <[email protected]> Date: Wed Feb 7 08:29:49 2024 -0700 Removed jlogfile and postmsg references within gempak scripts. commit 801058f Author: Henry R. Winterbottom <[email protected]> Date: Wed Feb 7 00:41:59 2024 -0700 Consolidate `npe_node_max` (NOAA-EMC#2289) - The environment variable `npe_node_max` is removed from all files beneath `global-workflow/env`; - The environment variable `npe_node_max` is removed from `parm/config/gefs/config.ufs` and `parm/config/gfs/config.ufs`; - The environment variable `npe_node_max` is maintained only within `parm/config/gefs/config.resources` and `parm/config/gfs/config.resources`. Resolves NOAA-EMC#2133 commit b0325e0 Author: Henry R. Winterbottom <[email protected]> Date: Wed Feb 7 00:40:20 2024 -0700 Removes files module loading file no longer used by the GW (NOAA-EMC#2281) Removes `module-setup.csh.inc` and `module-setup.sh.inc`. The module `ush/module-setup.sh` is updated such that it now sources `ush/detect_machine.sh` to determine which supported platform the global-workflow is being execute on. Resolves NOAA-EMC#2130 commit 3e6b1e2 Merge: f4c8e00 1ccc989 Author: Janet Derrico <[email protected]> Date: Tue Feb 6 10:43:55 2024 -0700 Merge branch 'NOAA-EMC:develop' into develop commit 1ccc989 Author: Walter Kolczynski - NOAA <[email protected]> Date: Mon Feb 5 14:16:07 2024 -0500 Remove EnKF forecast groups (NOAA-EMC#2280) Removes the grouping of EnKF forecasts so each job only runs one forecast. Member and MEMDIR are now set at the workflow manager (rocoto) level. This change makes much of the system simpler (especially dependencies) and allows the elimination of the separate efcs scripts. Metatask names of updated jobs have been updated to make them a little less opaque by using the same name name as its constituent tasks (e.g. the forecast metatask is named `enkgdasfcst`, not `enkfgdasefcs`). Metatasks that weren't updated retain the same names as before for now. Resolves NOAA-EMC#2254 commit 9f3383f Author: Henry R. Winterbottom <[email protected]> Date: Mon Feb 5 12:15:13 2024 -0700 Updated detect_machine.sh using that from UFS WM. (NOAA-EMC#2252) Updates `ush/detect_machine.sh` to match the UFS weather-model `tests/detect_machine.sh` prepared by @BrianCurtis-NOAA Resolves NOAA-EMC#2228 commit 7d68b0b Author: CatherineThomas-NOAA <[email protected]> Date: Sun Feb 4 22:02:41 2024 +0000 Update global_cycle for fractional grid (NOAA-EMC#2262) The hash for ufs_utils is updated to include the changes for fractional grid support within global_cycle. This commit also removes the hack to skip global_cycle in cycling mode with v17 physics. Resolves: NOAA-EMC#1775 Refs: ufs-community/UFS_UTILS#815 Refs: ufs-community/UFS_UTILS#891 commit ed592a6 Author: Kate Friedman <[email protected]> Date: Sat Feb 3 02:55:14 2024 -0500 Retire cycle-specific FHMAX_GFS variables (NOAA-EMC#2278) This PR retires the `FHMAX_GFS_${cyc}` variables that allowed users to specify different gfs forecast lengths for each cycle. This function is no longer supported in global-workflow. The `FHMAX_GFS_*` variables will be removed and will no longer be checked to set the final `FHMAX_GFS` variable. The same forecast length will be set for every cycle. This PR also includes a small fix to add new post parm files into the `.gitignore` file. This was intended to be included in a different PR but that PR is on hold for further testing so it is being included here to get it into `develop` sooner. Resolves NOAA-EMC#2218 commit 977e2d6 Author: Henry R. Winterbottom <[email protected]> Date: Fri Feb 2 07:49:09 2024 -0700 New GDASApp hash. (NOAA-EMC#2285) commit b5f2bd9 Merge: 4d66742 0400e1f Author: David Huber <[email protected]> Date: Tue Jan 30 13:55:00 2024 -0600 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 0400e1f Author: David Huber <[email protected]> Date: Tue Jan 30 09:57:11 2024 -0600 Fix gfs_utils Orion spack-stack env path. commit 6bbe823 Author: DWesl <[email protected]> Date: Mon Jan 29 21:15:30 2024 -0500 Use seq to generate the list of times, instead of a bash for-loop (NOAA-EMC#2264) I'm running a year-long forecast, which means I get a large portion of the log file dedicated to these loops. `seq ${START} ${STEP} ${STOP}` will generate a sequence going from START to STOP by STEP, including STOP if relevant. That seems to be the purpose of these loops. It will by default separate the list with newlines, but `seq -s ' ' ${START} ${STEP} ${STOP}` will separate them with spaces instead, more closely mimicing the previous behavior. I would like this to be two lines in the log, rather than a few hundred, and this may also be faster, though probably more for reasons of fewer writes to disk than because bash isn't designed for arithmetic. commit f4c8e00 Merge: 61975cf d5bee38 Author: Janet Derrico <[email protected]> Date: Mon Jan 29 15:38:56 2024 -0700 Merge branch 'NOAA-EMC:develop' into develop commit d5bee38 Author: Kate Friedman <[email protected]> Date: Mon Jan 29 14:35:02 2024 -0500 Correct typos in GFS config.resources (NOAA-EMC#2267) This PR corrects some typos in `parm/config/gfs/config.resources` that were introduced in PR NOAA-EMC#2216. The esfc job was failing in tests on WCOSS2 due to insufficient memory. This lead to discovering the other typos. The esfc job completes without error after its memory is set back to `80GB` from the incorrect `8GB`. Resolves NOAA-EMC#2266 commit 81557be Author: David Huber <[email protected]> Date: Mon Jan 29 12:13:31 2024 -0600 Update monitor hash to noaa-emc with SS/1.6.0 support. commit 2238dd6 Author: DavidHuber <[email protected]> Date: Mon Jan 29 13:21:30 2024 +0000 Update Orion, Hercules, S4 modulefiles. commit 6ffd94f Author: DavidHuber <[email protected]> Date: Fri Jan 26 16:01:23 2024 +0000 Update GDAS hash to include SS/1.6.0 support. commit be11f85 Merge: 56b9680 04e0772 Author: DavidHuber <[email protected]> Date: Fri Jan 26 15:34:24 2024 +0000 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 8ff3448 Author: Rahul Mahajan <[email protected]> Date: Fri Jan 26 10:12:18 2024 -0500 Add a yaml for snow DA testing. (NOAA-EMC#2199) - adds a new test yaml C96_atmsnowDA.yaml for 3DVar atmosphere with GSI and Land (Snow) DA with JEDI - moves a few yamls from platforms/ to yamls/ - adds ability to overwrite a previously created experiment as an addition to user input. --------- Co-authored-by: Cory Martin <[email protected]> commit 04e0772 Author: David Huber <[email protected]> Date: Fri Jan 26 07:16:25 2024 -0600 Update ufs_utils hash for spack-stack/1.6.0 support. commit 3d44ff3 Author: Barry Baker <[email protected]> Date: Thu Jan 25 14:33:27 2024 -0500 GOCART ExtData biogenic climatology fix (NOAA-EMC#2253) Updates the ExtData for biogenic emissions to be climatology rather than for current time. Fixes an issue which will crash by default for other years. commit 66f58b8 Author: Guillaume Vernieres <[email protected]> Date: Thu Jan 25 13:16:41 2024 -0500 Added missing container case in gfs/config.resources (NOAA-EMC#2258) fixes NOAA-EMC#2257 commit 553b4f2 Author: WenMeng-NOAA <[email protected]> Date: Thu Jan 25 13:00:45 2024 -0500 Fix post parm links (NOAA-EMC#2243) Change symbolic links under parm/post with the latest version of develop branch from UPP repository and enable MERRA2 aerosol fields. Resolves NOAA-EMC#2259 commit 4d66742 Merge: 6c05803 afa09e3 Author: David Huber <[email protected]> Date: Thu Jan 25 07:49:08 2024 -0600 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 6c05803 Author: David Huber <[email protected]> Date: Thu Jan 25 07:48:42 2024 -0600 Fix wgrib2/gfs_utils on Hercules. commit ee6f536 Author: Kate Friedman <[email protected]> Date: Thu Jan 25 07:43:13 2024 -0500 Update GFS version to v16.3.13 in index.rst (NOAA-EMC#2256) GFSv16.3.13 WAFS update was implemented Refs NOAA-EMC#2013 commit 2445d44 Author: RussTreadon-NOAA <[email protected]> Date: Thu Jan 25 06:17:11 2024 -0500 Simplify and extend load_ufsda_modules to Hercules (NOAA-EMC#2245) GDASApp jobs do not run on Hercules because `ush/load_ufsda_modules.sh` does not include logic to load the appropriate GDASApp modules on Hercules. This PR extends `load_ufsda_modules.sh` functionality to Hercules, thereby enabling GDASApp jobs to run on Hercules. Resolves NOAA-EMC#2244 commit 56b9680 Author: DavidHuber <[email protected]> Date: Wed Jan 24 19:47:34 2024 +0000 Update hashes (revert WCOSS2 modules). commit afa09e3 Author: DavidHuber <[email protected]> Date: Wed Jan 24 18:59:40 2024 +0000 New (cleaner history) gdas hash. commit a9eaec2 Author: DavidHuber <[email protected]> Date: Wed Jan 24 18:52:27 2024 +0000 Update gdasapp to include ss/1.6.0 support. commit 5ef8eb2 Merge: 4c46354 e400068 Author: DavidHuber <[email protected]> Date: Wed Jan 24 17:08:54 2024 +0000 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 4c46354 Author: DavidHuber <[email protected]> Date: Wed Jan 24 17:05:12 2024 +0000 Reenable verif-global support commit f775755 Author: DavidHuber <[email protected]> Date: Wed Jan 24 16:59:10 2024 +0000 Assign fcsthrs for awips_g2 job. commit e400068 Author: David Huber <[email protected]> Date: Mon Jan 22 15:01:07 2024 -0600 More gsi-addon path fixes. commit f663d47 Author: David Huber <[email protected]> Date: Mon Jan 22 14:41:59 2024 -0600 Fix gsi-addon paths for hercules, orion, and S4. commit e304bbe Author: DavidHuber <[email protected]> Date: Mon Jan 22 18:59:34 2024 +0000 Better optimize build jobs (more ufs jobs). commit ccc6e2d Author: DavidHuber <[email protected]> Date: Mon Jan 22 18:56:18 2024 +0000 Reenable verif-global. NOAA-EMC#2195 commit 3ef3411 Merge: 4365f63 f4d187f Author: DavidHuber <[email protected]> Date: Mon Jan 22 18:39:10 2024 +0000 Merge remote-tracking branch 'origin/develop' into ss160 commit 4365f63 Author: DavidHuber <[email protected]> Date: Mon Jan 22 18:37:25 2024 +0000 Corrected the SS env. name in the version files. NOAA-EMC#2195 commit f4d187f Author: AndrewEichmann-NOAA <[email protected]> Date: Mon Jan 22 12:28:28 2024 -0500 Converts obsproc to obsprep in prepoceanobs config file (NOAA-EMC#2236) Converts obsproc to obsprep in prepoceanobs config file as a compliment to mutually depended GDASApp PR NOAA-EMC/GDASApp#858 The motivations are explained in refs NOAA-EMC/GDASApp#857 commit 9a09d30 Author: DavidHuber <[email protected]> Date: Fri Jan 19 21:23:50 2024 +0000 Corrected gsi-addon-dev spelling. commit 21ff645 Author: DavidHuber <[email protected]> Date: Fri Jan 19 21:11:34 2024 +0000 Update modulefiles, submodules to spack-stack 1.6.0. NOAA-EMC#2195 commit d4c55d1 Author: Kate Friedman <[email protected]> Date: Fri Jan 19 15:43:37 2024 -0500 Update typing hint for WCOSS version of python (NOAA-EMC#2238) The typing hint `typing.List` was deprecated with python 3.9 in favor of using the primitive `list[str]`, but the functional version of python on WCOSS2 is <3.9, causing `setup_xml.py` to fail there. This replaces `list[str]` as a typing hint with the deprecated form until the supported version on WCOSS2 is >=3.9. commit 61975cf Merge: 1344313 4919287 Author: Janet Derrico <[email protected]> Date: Fri Jan 19 08:38:17 2024 -0700 Merge branch 'NOAA-EMC:develop' into develop commit 4919287 Author: Barry Baker <[email protected]> Date: Thu Jan 18 22:31:27 2024 -0500 GOCART Emission updates for GEFSv13 and GDAS (NOAA-EMC#2201) This PR addresses several things needed for more recent simulations using GOCART2G as well as preparing for the GEFSv13 30 year run. The main updates are: - Update CEDS to use monthly emission files instead of daily. This will drastically reduce the number of files needed. No science change - Update biogenic MEGAN inputs to use a climatology rather than the offline biogenic previously used. This is needed to deal with simulations where the current dataset is not available. - Update volcanic SO4 emissions to use degassing emissions only. This is to support the need for more recent simulations where data is not available. commit 13d25cf Author: Kate Friedman <[email protected]> Date: Thu Jan 18 22:29:43 2024 -0500 Add `POSTAMBLE_CMD` into preamble postamble (NOAA-EMC#2235) This PR adds the ability to run a command at the end of jobs via the preamble's postamble function. A new command can be set via `POSTAMBLE_CMD` and will be invoked at the end of jobs. Users can add the command to the top of an env file to have every job run it or it can be placed within a job if-block in the env file to run for just that job. Resolves NOAA-EMC#1145 commit 7759163 Author: Rahul Mahajan <[email protected]> Date: Thu Jan 18 01:13:49 2024 -0500 Add option to create WGNE atmosphere products (NOAA-EMC#2233) Adds option to create WGNE products for the atmosphere. Resolves NOAA-EMC#1951 Resolves NOAA-EMC#2226 commit d95ed85 Author: Rahul Mahajan <[email protected]> Date: Wed Jan 17 18:04:56 2024 -0500 Use ufs.configure, model_configure, MOM_input, data_table, and ice_in templates from UFS-weather-model (NOAA-EMC#2051) This PR: - links `ufs.configure.*.IN`, `model_configure.IN`, `MOM_input_${OCNRES}.in`, `MOM6_data_table.IN`, and `ice_in.IN` from ufs-weather-model into the global-workflow `parm/ufs` directory - prepares local variables for use in the templates in the respective functions for FV3, MOM6, and CICE6 - uses `atparse.bash` to render these templates into fully formed namelists - Work was performed by @DeniseWorthen in the ufs-weather-model to templatize several variables that are hard-wired in the ufs-weather-model for CICE. See ufs-community/ufs-weather-model/NOAA-EMC#2010 commit 44a66dd Author: RussTreadon-NOAA <[email protected]> Date: Wed Jan 17 13:52:09 2024 -0500 Update gdas.cd hash to use gsibec tag 1.1.3 (NOAA-EMC#2231) (NOAA-EMC#2234) commit 9046d97 Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Jan 17 10:19:18 2024 -0500 Add basic atmos products for GEFS and refactor resources (NOAA-EMC#2216) * Add basic atmos products for GEFS Adds basic atmosphere products for GEFS members (no mean or spread). To facilitate the addition of GEFS parameter lists, the existing GFS lists are renamed. They are also relocated to `parm/products/` direc tory instead of `parm/post/`. GEFS v12 uses different parameter lists for different resolutions, but for this implementation, the 0p25 lists are used for all resolutions. However, to hedge against the final con- figuration, all of the GEFS parameter lists have been added to parm. Implementation of different parameter lists for each resolution will take additional refactoring of the atmos_products job, as it currently assumes all resolutions use the same lists. The new GEFS rocoto task is implented as two loops of metatasks (made possible by PR NOAA-EMC#2189). The member is set at the rocoto level, so the setting in `config.base` had to be updated to accept a pass-through. The generation of a forecast hour list is moved up to its own function in `rocoto.tasks`, separate from the post groups which are not used. This can be used as a model for future metatasks (or refactoring of old ones). `rocoto_viewer.py` does function with the nested metatasks, though only one level of folding is available and the metatask name is that of the lower metatask (though it encompasses the entire outer metatask). Additionally, the GEFS `config.resources` had diverged from the GFS version, which included not having a section for the atm products job. This led to the refactoring of the GFS `config.resources`, including switching to using a `case` statement instead of sequential `elif`. This refactored script was then copied over to GEFS, replacing the old one, with all jobs not currently implemented for GEFS removed (except wave post, whose inclusion is immenent). New blocks can be copied over from GFS as they are added. Resolves NOAA-EMC#823 commit fbba174 Author: RussTreadon-NOAA <[email protected]> Date: Tue Jan 16 14:05:48 2024 -0500 Update GDASApp (gdas.cd) hash (NOAA-EMC#2225) GDASApp now uses gitsubmodules commit 1344313 Merge: 4b58891 dddd837 Author: Janet Derrico <[email protected]> Date: Tue Jan 16 11:13:59 2024 -0700 Merge branch 'NOAA-EMC:develop' into develop commit dddd837 Author: Rahul Mahajan <[email protected]> Date: Tue Jan 16 12:17:19 2024 -0500 Fix ocean resolution for the S2SWA test (NOAA-EMC#2223) commit 83edaf1 Author: David Huber <[email protected]> Date: Tue Jan 16 11:07:02 2024 -0500 Apply fixes to archiving jobs (NOAA-EMC#2221) Add checks for potentially missing log/data files and update log names for archiving. Missing sflux index files are also added to the products script. Resolves NOAA-EMC#2076 commit c590476 Author: Rahul Mahajan <[email protected]> Date: Fri Jan 12 19:21:02 2024 -0500 Update hash to ufs-weather-model. The noahmptable.tbl was reorganized, so update link_workflow.sh to use the same one used in UFSWM RT (NOAA-EMC#2219) commit c041968 Author: Kate Friedman <[email protected]> Date: Fri Jan 12 12:09:35 2024 -0500 Add ocean resolution to setup_expt invocation and retire/reduce COMROT/ROTDIR usage (NOAA-EMC#2214) Two series of updates: 1) Update setup scripts to now allow users to provide ocean resolution 2) Housekeeping to retire the `COMROT` variable, replacing it with other variables as needed, and reduce the `ROTDIR` variable usage. Both updates change options for the workflow setup API. Refs NOAA-EMC#2061 commit 997f978 Author: AndrewEichmann-NOAA <[email protected]> Date: Fri Jan 12 10:46:36 2024 -0500 Allow use of ocean obs prep in WCDA cycling and remove R2D2 (NOAA-EMC#2215) Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same. Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS. Replaces the current R2D2 processing. commit 12a5bb1 Merge: 4cb5802 6492c2d Author: David Huber <[email protected]> Date: Fri Jan 12 09:26:27 2024 -0500 Merge pull request NOAA-EMC#2217 from DavidHuber-NOAA/update/versions Update and clean up version and module files commit 6492c2d Author: David Huber <[email protected]> Date: Thu Jan 11 11:49:08 2024 -0600 Update orion module/version files for met/metplus NOAA-EMC#2123 commit 94c9937 Author: DavidHuber <[email protected]> Date: Thu Jan 11 17:42:53 2024 +0000 Comment met/metplus out from Hera modulefile. NOAA-EMC#2123 commit 8c32f8b Merge: a65e4c6 4cb5802 Author: David Huber <[email protected]> Date: Thu Jan 11 11:34:44 2024 -0600 Merge branch 'develop' of github.com:noaa-emc/global-workflow into develop commit a65e4c6 Author: David Huber <[email protected]> Date: Thu Jan 11 11:34:19 2024 -0600 Initial update of version/module files NOAA-EMC#2123 commit 4b58891 Merge: a75e73e 4cb5802 Author: Janet Derrico <[email protected]> Date: Wed Jan 10 10:15:48 2024 -0700 Merge branch 'NOAA-EMC:develop' into develop commit 4cb5802 Author: souopgui <[email protected]> Date: Wed Jan 10 08:30:22 2024 -0600 Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh when running MPMD tasks (NOAA-EMC#2212) Fix OpenMP over-allocation of resources running MPMD tasks Co-authored-by: Innocent Souopgui <[email protected]> commit b056b53 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Mon Jan 8 17:28:05 2024 -0500 Add Hercules as valid machine in CI scripts (NOAA-EMC#2207) Few updates to CI scripts to include names for hercules that where missed the first time. commit 6574d29 Author: Rahul Mahajan <[email protected]> Date: Mon Jan 8 17:25:47 2024 -0500 Fix invalid GH action and restart file name (NOAA-EMC#2210) Resolves a typo that leads to an invalid workflow yaml and fixes the restart filename in restart detection. Resolves NOAA-EMC#2205 commit 69605ea Author: Rahul Mahajan <[email protected]> Date: Mon Jan 8 17:00:28 2024 -0500 Stop attempting to comment link to RTD for non-PRs (NOAA-EMC#2209) Adds a check so comments with a link to documentation are only generated for PRs. commit 4e160a8 Author: Rahul Mahajan <[email protected]> Date: Mon Jan 8 13:10:15 2024 -0500 Enable UPP for GOES processing (NOAA-EMC#2203) Wnables the creation of special master grib2 files from UPP for GOES processing commit c15875b Author: David Huber <[email protected]> Date: Mon Jan 8 09:56:06 2024 -0500 Port cycling to Hercules (NOAA-EMC#2196) Adds cycled support for Hercules (excluding gsi-monitor). Partially resolves NOAA-EMC#1588 GSI monitoring is disabled on Hercules due to missing Perl modules. That will be enabled in a later PR. commit ef6827d Author: Walter Kolczynski - NOAA <[email protected]> Date: Mon Jan 8 09:43:12 2024 -0500 Refactor rocoto task XML creation (NOAA-EMC#2189) Refactors the rocoto task generation to be recursive. This will allow nested metatasks to loop over multiple variables, which is needed for GEFS product generation. As part of this refactor, there is no longer separate arguments to designate metatasks. Instead, task dicts can include a nested 'task_dict' as well as a 'var_dict' containing the variables to loop over. The nested task dict can then either have another layer, or be the innermost task. To accommodate the new recursive nature, some defaults that were previously defined in create_wf_task() had to be pushed down into the function that creates the innermost task. Also, former keywords have been absorbed by the task dict. Refs NOAA-EMC#823 Refs NOAA-EMC#827 commit 2b81cfa Author: Walter Kolczynski - NOAA <[email protected]> Date: Mon Jan 8 09:41:03 2024 -0500 Update fix versions (NOAA-EMC#2198) Updates fix versions for a few components: - Update cice and mom6 versions to support C96/1p00 marine - Update wave to change betamax setting for glo_025 waves Resolves NOAA-EMC#2004 Resolves NOAA-EMC#2107 commit a75e73e Merge: 5adc47b 9d901db Author: Janet Derrico <[email protected]> Date: Tue Jan 2 12:44:40 2024 -0700 Merge branch 'NOAA-EMC:develop' into develop commit 5adc47b Merge: a3ce9db a3c5099 Author: Janet Derrico <[email protected]> Date: Tue Dec 26 12:40:08 2023 -0700 Merge branch 'NOAA-EMC:develop' into develop commit a3ce9db Merge: 2b1a8e3 a81da33 Author: Janet Derrico <[email protected]> Date: Tue Dec 19 09:12:48 2023 -0700 Merge branch 'NOAA-EMC:develop' into develop commit 2b1a8e3 Merge: 4562dec 9505cb4 Author: Janet Derrico <[email protected]> Date: Fri Dec 15 09:50:35 2023 -0700 Merge branch 'NOAA-EMC:develop' into develop commit 4562dec Merge: 9f7eeba 29d3417 Author: Janet Derrico <[email protected]> Date: Mon Dec 11 12:10:25 2023 -0700 Merge pull request NOAA-GSL#34 from NOAA-EMC/develop Sync develop branch with EMC develop
UFS: 21Feb24, 6988662 FV3: 14Feb24, 0fe9ba3 UPP: 23Jan23, 945cb2c UFS_UTILS: 22Feb24, d805336 Squashed commit of the following: commit 732a874 Author: Rahul Mahajan <[email protected]> Date: Mon Mar 4 16:04:26 2024 -0500 Reformat snowDA templates to jinja2 (NOAA-EMC#2371) # Description This PR: - replaces use of non-jinja2 templates in the yaml templates. Specifically `$( )` in favor of pure jinja2. - uses jinja2's built-in capability to include templates within templates, thereby allowing to assemble a completely rendered template before passing it to for e.g. yaml loader. - requires updates to `wxflow` and `gdasapp` - Changes in `wxflow` in `parse_j2yaml` are **not** backwards compatible Additionally, this PR: - renames `config.base.emc.dyn` to `config.base`. Resolves NOAA-EMC#2347 commit d1fa411 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Sat Mar 2 04:54:26 2024 +0000 Reduce Jenkins messaging to GitHub (NOAA-EMC#2370) This PR updates the Jenkins Pipeline code with safeguards against the errors caused when Jenkins fails to authenticate with GitHub to message or update a label. This was achieved simply by: - Reducing the number out messages sent to the GitHub PR - Putting try blocks around most of the update label calls Co-authored-by: tmcguinness <[email protected]> commit 52fa3cb Author: Henry R. Winterbottom <[email protected]> Date: Fri Mar 1 12:36:27 2024 -0700 Adding debug option for all build scripts (NOAA-EMC#2326) This PR addresses issue NOAA-EMC#300 that allows building in `debug` mode. Co-authored-by: David Huber <[email protected]> Co-authored-by: Rahul Mahajan <[email protected]> commit 91738cb Author: DWesl <[email protected]> Date: Fri Mar 1 13:46:42 2024 -0500 Sort list of coupler restart files for restart time determination (NOAA-EMC#2360) The loop in the following conditional seems to assume the list is sorted, so make that explicit in the array construction. commit 23c2552 Author: Neil Barton <[email protected]> Date: Fri Mar 1 13:45:39 2024 -0500 Update stage IC to handle ocean perturbations (NOAA-EMC#2364) This PR adds the option to stage ocean perturbation files for ensemble forecasts. These perturbation files are used in GEFS forecasts. A new variable is introduced in config.base to use the ocean perturbation files. This PR does not include using these perturbation files. A future PR will address this. commit 8efe05f Author: Jessica Meixner <[email protected]> Date: Fri Mar 1 07:41:56 2024 -0500 Turn on C48mx500_3DVarAOWCDA test on hera (NOAA-EMC#2363) This PR activates the C48mx500_3DVarAOWCDA test on hera. This required an update of the gdas app. commit 5166593 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Thu Feb 29 20:14:41 2024 +0000 Move Jenkinsfile into ci subdirectory (NOAA-EMC#2355) Just moves the Jenkinsfile into the ci directory Co-authored-by: tmcguinness <[email protected]> commit b7af315 Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Feb 28 22:20:58 2024 +0000 Fix rocoto forecast hour determination for GEFS (NOAA-EMC#2351) The function that generates the list of forecast hours for rocoto was trying to use variables that are not defined for GEFS, causing workflow generation to fail. The function is updated to not try to load these variables before loading the ones actually used for GFS/ GEFS. Also turns GEFS CI test back on and adds an entry to stage C192 ICs (note: these have not been placed in the centralized location.) commit d3a4927 Author: Cory Martin <[email protected]> Date: Wed Feb 28 09:38:49 2024 -0500 Rename the land DA jobs to snow DA to better reflect what they are doing (NOAA-EMC#2330) This PR renames all of the land DA jobs to snow DA to better reflect that this is a JEDI-based snow analysis capability and not a more generic land surface analysis. commit 2693810 Author: Jessica Meixner <[email protected]> Date: Tue Feb 27 01:25:51 2024 -0500 Update ufs-waether-model hash (NOAA-EMC#2338) Routine update of ufs-weather-model hash. Other small updates: * removes comment referencing closed issue. * Updates the CICE diag frequency to once per day as recommend here: NOAA-EMC#1810 (comment) * Updated amount of time for C384 gdas forecast as it was running out of time * Removed unused variable wave_sys_ver commit 9608852 Author: RussTreadon-NOAA <[email protected]> Date: Mon Feb 26 14:10:01 2024 -0500 Update JEDI ATM to use .nc for obs and generalize x,y layout (NOAA-EMC#2336) # Description The changes in this PR are twofold 1. replace `.nc4` suffix for JEDI ATM observation related files with `.nc` 2. use templated variables to specify `{layout_x, layout_y}` for JEDI ATM variational and local ensemble apps The first change conforms with the Unidata recommendation that netCDF files end with the suffix `.nc`. The second change replaces hardwired JEDI ATM var and ens `{layout_x, layout_y}` in `config.resources` with a more flexible approach. Resolves NOAA-EMC#2335 commit c5c8466 Author: Kate Friedman <[email protected]> Date: Mon Feb 26 10:18:50 2024 -0500 Remove FIX* variables for fix subfolders (NOAA-EMC#2337) Remove `FIX*` variables for fix subfolders and replace them with the remaining `FIXgfs` variable and the subfolder name (e.g. `${FIXam}` -> `${FIXgfs}/am`). The UFS_UTILS and GDASApp repos were similarly updated. This PR includes a new UFS_UTILS hash. The updated GDASAPP hash was already committed within the spack-stack/1.6.0 PR NOAA-EMC#2239. Resolves NOAA-EMC#2184 commit 950c38a Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Fri Feb 23 21:15:46 2024 +0000 Fix several Jenkins issues (NOAA-EMC#2334) Jenkins Updates Resolving final kinks: - Removed all `git` shell commands and now exclusively use Software Control Manger (**scm**) plugin. - Add feature for skipping hosts per configuration specified in case yaml files. - Solved and tested false positive builds and experiments. - Tested archiving of task error log on case fail - First case fail quits pipeline and cancels all pending scheduled jobs - Duel build per yaml configuration arguments supported - All designated case files in PR directory pass on intended host (fully tested on Hera) Remaining updates: - Fist build fail short circuit when building sub-modules and archiving build error log. - Re-build/no-build built in logic for Replay and Rerunning previously failed experiments. commit c67393a Merge: 6f9afff 79d305e Author: David Huber <[email protected]> Date: Fri Feb 23 14:18:15 2024 +0000 Merge pull request NOAA-EMC#2239 from DavidHuber-NOAA/ss160 Update to spack-stack 1.6.0 Includes all submodules except the UFS, which will be updated at a later time. commit 79d305e Author: David Huber <[email protected]> Date: Thu Feb 22 14:53:57 2024 -0600 Disable snow DA tests commit 0459203 Author: David Huber <[email protected]> Date: Thu Feb 22 12:55:51 2024 -0600 Update GDASApp hash to current develop commit 5c96eb2 Author: David Huber <[email protected]> Date: Thu Feb 22 12:37:47 2024 -0600 Update GDAS hash to allow modified snow DA analysis commit 79144f2 Merge: abbb0b8 6f9afff Author: DavidHuber <[email protected]> Date: Thu Feb 22 15:14:39 2024 +0000 Merge remote-tracking branch 'origin/develop' into ss160 commit abbb0b8 Merge: 4ad837e 4529e8c Author: DavidHuber <[email protected]> Date: Thu Feb 22 15:11:03 2024 +0000 Merge remote-tracking branch 'henry/feature/gwdev_issue_2129' into ss160 commit 4ad837e Merge: 516b2a2 7ca45db Author: DavidHuber <[email protected]> Date: Thu Feb 22 15:10:24 2024 +0000 Merge remote-tracking branch 'henry/feature/gfsv17_issue_2125' into ss160 commit 516b2a2 Author: DavidHuber <[email protected]> Date: Thu Feb 22 14:19:16 2024 +0000 Updated GDAS to include rocoto/1.3.6 on Hera. commit 6f9afff Author: Jessica Meixner <[email protected]> Date: Wed Feb 21 13:09:44 2024 -0500 Add some flexibility for ocean/ice output (NOAA-EMC#2327) This adds functionality to have ocean/ice output frequency be separate from the atm model. One time was created because there's an assumption in the post that these are the same. This could be further modified to remove this assumption. Refs NOAA-EMC#1629 commit f6d3015 Author: David Huber <[email protected]> Date: Tue Feb 20 09:53:08 2024 -0600 Update GDASApp hash to include SS/1.6.0 support. commit 0bf340b Author: David Huber <[email protected]> Date: Tue Feb 20 09:07:32 2024 -0600 Construct SS paths from version variables. commit 3330cd7 Author: David Huber <[email protected]> Date: Tue Feb 20 09:06:19 2024 -0600 Removed MET/METplus 'not available' comments commit fdc638c Author: David Huber <[email protected]> Date: Tue Feb 20 08:35:15 2024 -0600 Move SS module path to version files. commit d7d28a6 Author: David Huber <[email protected]> Date: Tue Feb 20 07:53:15 2024 -0600 Update comment about METplus support. commit a812f88 Author: David Huber <[email protected]> Date: Tue Feb 20 07:45:45 2024 -0600 Update verif-global to latest WCOSS2 support. commit d81f07f Author: David Huber <[email protected]> Date: Tue Feb 20 07:41:38 2024 -0600 Clean up build_upp.sh. -Corrected whitespace (tabs instead of spaces) -Removed debug print statement -Alphebetized flags commit ae7eb19 Author: David Huber <[email protected]> Date: Fri Feb 16 16:15:40 2024 -0500 Fix whitespace in build_upp.sh. Co-authored-by: Rahul Mahajan <[email protected]> commit 48b34d0 Author: David Huber <[email protected]> Date: Fri Feb 16 20:56:55 2024 +0000 Added verif-global support back to WCOSS2. commit 4529e8c Author: henrywinterbottom-wxdev <[email protected]> Date: Fri Feb 16 11:12:01 2024 -0700 Bug fix. commit 8e4f94d Author: henrywinterbottom-wxdev <[email protected]> Date: Fri Feb 16 11:04:41 2024 -0700 Updates requested by reviewer Rahul Mahajan. commit 4624ce2 Author: henrywinterbottom-wxdev <[email protected]> Date: Fri Feb 16 10:52:11 2024 -0700 Updates requested by reviewer; testing -- DO NOT REVIEW. commit ed25bbd Author: henrywinterbottom-wxdev <[email protected]> Date: Fri Feb 16 09:33:59 2024 -0700 Linter corrections. commit 6a0b7bf Merge: f9fb64e 2415b7b Author: David Huber <[email protected]> Date: Fri Feb 16 09:50:22 2024 -0600 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit f9fb64e Merge: 777d97d a23b7f2 Author: David Huber <[email protected]> Date: Fri Feb 16 09:49:42 2024 -0600 Merge remote-tracking branch 'emc/develop' into ss160 commit 7ca45db Merge: 73bc76b a23b7f2 Author: Henry R. Winterbottom <[email protected]> Date: Fri Feb 16 07:46:35 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit eb2ed53 Merge: 9929277 a23b7f2 Author: Henry R. Winterbottom <[email protected]> Date: Fri Feb 16 07:46:24 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit a23b7f2 Author: RussTreadon-NOAA <[email protected]> Date: Fri Feb 16 09:37:58 2024 -0500 Add JEDI 3DEnVar atmosphere only CI test stub (NOAA-EMC#2309) commit cf83885 Author: Jessica Meixner <[email protected]> Date: Fri Feb 16 01:55:02 2024 -0500 Add unstructured grid for HR3/GFS (NOAA-EMC#2230) This adds the capability to use unstructured grids in the global workflow, which will be used in HR3. There are new fix files for a low-resolution 100km grid and a grid closer to our targeted GFSv17 grid which has the resolution combined from the older multi_1 and GFSv16 grids. The fix file update is here: NOAA-EMC#2229 Note: This now means that GFS tests need a new build option: `./build_all.sh -w` So that PDLIB=ON is turned on for compiling relevant UFS and WW3 codes. Resolves NOAA-EMC#1547 commit 9929277 Merge: eb8791c 094e3b8 Author: Henry R. Winterbottom <[email protected]> Date: Thu Feb 15 15:05:50 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit 094e3b8 Author: Cory Martin <[email protected]> Date: Thu Feb 15 14:43:55 2024 -0500 Move IMS remapping files from COM_OBS to FIXgdas (NOAA-EMC#2322) * Add in IMS obs fix directory and update submodule for gdas commit d465ea0 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Thu Feb 15 19:25:02 2024 +0000 Set HOMEgfs for module_setup in CI driver (NOAA-EMC#2321) Hotfixes to CI Bash system from updates with sourcing `detect_machine.sh` in `ush/module-setup.sh` using **HOMEgfs**. commit 2415b7b Author: David Huber <[email protected]> Date: Thu Feb 15 19:21:17 2024 +0000 Load default rocoto on Jet. commit eb8791c Merge: 60d5ee6 638684e Author: Henry R. Winterbottom <[email protected]> Date: Thu Feb 15 11:56:40 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit 777d97d Author: David Huber <[email protected]> Date: Thu Feb 15 12:34:59 2024 -0600 Fixed Orion cdo version. commit ef07235 Author: DavidHuber <[email protected]> Date: Thu Feb 15 16:29:32 2024 +0000 Revert UFS hash. commit 0ce8c0d Author: DavidHuber <[email protected]> Date: Thu Feb 15 14:55:48 2024 +0000 Fix git version in Hera's gwsetup module. commit 3080a34 Author: DavidHuber <[email protected]> Date: Wed Feb 14 20:52:34 2024 +0000 Fixed xarray version for SS/1.6.0. commit 49392dd Author: DavidHuber <[email protected]> Date: Wed Feb 14 20:29:41 2024 +0000 Updated GSI-Utils hash to head of develop. commit c3553f0 Merge: 4568653 638684e Author: DavidHuber <[email protected]> Date: Wed Feb 14 20:28:14 2024 +0000 Merge remote-tracking branch 'origin/develop' into ss160 commit 4568653 Author: David Huber <[email protected]> Date: Wed Feb 14 14:22:13 2024 -0600 Reupgrade Hercules to SS/1.6.0 commit 638684e Author: Kate Friedman <[email protected]> Date: Wed Feb 14 14:55:21 2024 -0500 Remove `finddate.sh` from system (NOAA-EMC#2308) * Retire finddate.sh usage from system * Update gfs-utils hash to 7a84c88 - New hash includes removal of finddate.sh Refs NOAA-EMC#2279 commit 2b160f8 Author: DavidHuber <[email protected]> Date: Wed Feb 14 18:31:28 2024 +0000 Reenable METplus jobs on Hercules. commit 8f59002 Author: DavidHuber <[email protected]> Date: Wed Feb 14 18:30:23 2024 +0000 Update GSI hashes. commit 73bc76b Author: henrywinterbottom-wxdev <[email protected]> Date: Wed Feb 14 09:27:37 2024 -0700 Updates based on user request. commit e4bc674 Author: henrywinterbottom-wxdev <[email protected]> Date: Wed Feb 14 08:03:45 2024 -0700 Corrected based on reviewer review. commit 60d5ee6 Merge: 40f2cf6 1aaef05 Author: Henry R. Winterbottom <[email protected]> Date: Tue Feb 13 18:08:33 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit 0330411 Merge: 929b903 1aaef05 Author: Henry R. Winterbottom <[email protected]> Date: Tue Feb 13 17:58:12 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit 1aaef05 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Feb 13 18:15:59 2024 -0500 Jenkins Pipeline updates for Canceling Jobs (NOAA-EMC#2307) Tuning updates for Jenkins Pipeline : - Added short circuit for all parallel runs of cases on error of any - Fixed canceling of all scheduled jobs on first case error - Added feature to save error log files to Jenkins Archive facility on fail commit 6404892 Author: Rahul Mahajan <[email protected]> Date: Tue Feb 13 14:57:37 2024 -0500 Ocean/ice product generation for GFS and GEFS (NOAA-EMC#2286) This PR does several things: 1. the model output for ocean and ice in the `COM/` directory are now named per EE2 convention for coupled model. E.g `gfs.ocean.t12z.6hr_avg.f120.nc` and `gfs.ocean.t12z.daily.f120.nc` 2. The products are generated using the `ocnicepost.fd` utility developed by @DeniseWorthen in https://github.com/NOAA-EMC/gfs-utils and converted to grib2 using example scripts provided by @GwenChen-NOAA using `wgrib2`. 3. NetCDF products on the native grid are also generated by subsetting variables from the raw model output. This is done with `xarray`. 4. updates the hash of https://github.com/NOAA-EMC/gfs-utils to include fixes in `ocnicepost.fd` 5. removes NCL related scripting that was previously used for ocean/ice interpolation and `reg2grb2` used for converting to grib2. 6. updates archive scripts to accommodate updated file names 7. removes intermediate ocean processed files such as 2D/3D/xsect data- sets 8. separate jobs are added for ocean and ice product generation. 9. removes intermediate restarts for the mediator and only saves the medi- ator restart at the end of the forecast in `COM`. 10. Increases memory for offline UPP when run at C768. The program segfaults with an OOM when memory is self allocated based on PEs by the scheduler on Hera. 11. Enables ocean/ice ensemble product generation for GEFS 12. Some minor clean-ups Fixes NOAA-EMC#935 Fixes NOAA-EMC#1317 Fixes NOAA-EMC#1864 commit 40f2cf6 Author: henrywinterbottom-wxdev <[email protected]> Date: Tue Feb 13 10:18:53 2024 -0700 Implemented ush/detect_machine.sh for host determination and removed redundant checks for expected file paths. commit 929b903 Merge: 2d08d01 3f99f70 Author: Henry R. Winterbottom <[email protected]> Date: Tue Feb 13 08:31:06 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit 3f99f70 Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Feb 13 00:57:18 2024 -0500 Add wave post jobs to GEFS (NOAA-EMC#2292) Adds the wave post jobs for gridded and points to GEFS. Boundary point jobs are added even though the current GEFS buoy file does not contain any (tested by manually subbing in the GFS buoy file). Resolves NOAA-EMC#827 commit 842adf3 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Mon Feb 12 12:50:08 2024 -0500 Added additional test cases to the pr list in Jenkins (NOAA-EMC#2306) C48mx500_3DVarAOWCDA, C96C48_hybatmDA, and C96_atmsnowDA Co-authored-by: terrance.mcguinness <[email protected]> commit bb4ca65 Author: CatherineThomas-NOAA <[email protected]> Date: Mon Feb 12 14:50:41 2024 +0000 Redo v16.3 config.base changes for DA increments (NOAA-EMC#2304) Include the additional hydrometeors to the INCREMENTS_TO_ZERO and INCVARS_ZERO_STRAT variables in config.base that were modified in v16.3. Resolves: NOAA-EMC#2303 commit 061992b Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Sat Feb 10 01:33:36 2024 -0500 Fix Jenkins success reporting (NOAA-EMC#2302) Moving the post section back outside of main Run Experiments stage. This allows the system to correctly report the **Success** status until after all tests pass. _Had originally moved them in attempts to solve "Not an SCM GitHub Job" issue and cause the reporting to misbehave._ Also ran through Jenkins linter and updated some messaging that was incorrectly reporting system build type. commit 28ccf78 Merge: b972f66 54daa31 Author: David Huber <[email protected]> Date: Fri Feb 9 14:00:43 2024 -0600 Merge remote-tracking branch 'emc/develop' into ss160 commit b972f66 Author: David Huber <[email protected]> Date: Fri Feb 9 10:47:00 2024 -0600 Fix SS versions for CI modules. commit 4b01d8e Author: David Huber <[email protected]> Date: Fri Feb 9 10:44:30 2024 -0600 Revert Hercules modules to SS/1.5.1. commit 54daa31 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Thu Feb 8 15:48:38 2024 -0500 Jenkins Declartive Pipeline for CI with gfs/gefs multibuilds (NOAA-EMC#2246) Adding top level Jenkins file for CI tests running on Jenkins Controller: - Declarative Multi-branch Pipeline (has enhanced restart capabilities on a per section bases) - Starts Pipeline from Label PR same as BASH system (for now) - Progress and restarts can me managed with CAC Login at [EPIC OAR Jenkins](https://jenkins.epic.oarcloud.noaa.gov) - Has logic for multi **gfs/gefs** system builds (arguments based on a configuration file `ci/casts/yamls/build.yaml`) - Any number of **systems** may be added by manual adding an ele- ment to the matrix in the Jenkinsfile - _It may be possible to dynamic add matrix values with a specialty plug-in_ - Currently only runs on **Orion** and **Hera** using `mterry` account Resolves NOAA-EMC#2119 Resolves NOAA-EMC#2118 commit 43429e2 Author: Rahul Mahajan <[email protected]> Date: Thu Feb 8 15:30:28 2024 -0500 Enable AO WCDA test (NOAA-EMC#1963) This PR: - adds GSI + SOCA C48 5-deg ocean 3DVar test (courtesy @guillaumevernieres) - adds a toggle to optionally disable ocnanalvrfy job. commit 2d08d01 Merge: 4745d4a f563528 Author: Henry R. Winterbottom <[email protected]> Date: Thu Feb 8 07:24:54 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit f563528 Author: Kate Friedman <[email protected]> Date: Wed Feb 7 15:09:12 2024 -0500 Update JGLOBAL_FORECAST for octal error (NOAA-EMC#2295) Add "10#" to ENSMEM value > 0 check to handle octal errors. commit 4745d4a Author: henrywinterbottom-wxdev <[email protected]> Date: Wed Feb 7 08:45:49 2024 -0700 Removed jlogfile references. commit 5894ca2 Author: henrywinterbottom-wxdev <[email protected]> Date: Wed Feb 7 08:32:16 2024 -0700 Removed dummy variable passed to perl scripts. commit dae884a Author: henrywinterbottom-wxdev <[email protected]> Date: Wed Feb 7 08:29:49 2024 -0700 Removed jlogfile and postmsg references within gempak scripts. commit 801058f Author: Henry R. Winterbottom <[email protected]> Date: Wed Feb 7 00:41:59 2024 -0700 Consolidate `npe_node_max` (NOAA-EMC#2289) - The environment variable `npe_node_max` is removed from all files beneath `global-workflow/env`; - The environment variable `npe_node_max` is removed from `parm/config/gefs/config.ufs` and `parm/config/gfs/config.ufs`; - The environment variable `npe_node_max` is maintained only within `parm/config/gefs/config.resources` and `parm/config/gfs/config.resources`. Resolves NOAA-EMC#2133 commit b0325e0 Author: Henry R. Winterbottom <[email protected]> Date: Wed Feb 7 00:40:20 2024 -0700 Removes files module loading file no longer used by the GW (NOAA-EMC#2281) Removes `module-setup.csh.inc` and `module-setup.sh.inc`. The module `ush/module-setup.sh` is updated such that it now sources `ush/detect_machine.sh` to determine which supported platform the global-workflow is being execute on. Resolves NOAA-EMC#2130 commit 1ccc989 Author: Walter Kolczynski - NOAA <[email protected]> Date: Mon Feb 5 14:16:07 2024 -0500 Remove EnKF forecast groups (NOAA-EMC#2280) Removes the grouping of EnKF forecasts so each job only runs one forecast. Member and MEMDIR are now set at the workflow manager (rocoto) level. This change makes much of the system simpler (especially dependencies) and allows the elimination of the separate efcs scripts. Metatask names of updated jobs have been updated to make them a little less opaque by using the same name name as its constituent tasks (e.g. the forecast metatask is named `enkgdasfcst`, not `enkfgdasefcs`). Metatasks that weren't updated retain the same names as before for now. Resolves NOAA-EMC#2254 commit 9f3383f Author: Henry R. Winterbottom <[email protected]> Date: Mon Feb 5 12:15:13 2024 -0700 Updated detect_machine.sh using that from UFS WM. (NOAA-EMC#2252) Updates `ush/detect_machine.sh` to match the UFS weather-model `tests/detect_machine.sh` prepared by @BrianCurtis-NOAA Resolves NOAA-EMC#2228 commit 7d68b0b Author: CatherineThomas-NOAA <[email protected]> Date: Sun Feb 4 22:02:41 2024 +0000 Update global_cycle for fractional grid (NOAA-EMC#2262) The hash for ufs_utils is updated to include the changes for fractional grid support within global_cycle. This commit also removes the hack to skip global_cycle in cycling mode with v17 physics. Resolves: NOAA-EMC#1775 Refs: ufs-community/UFS_UTILS#815 Refs: ufs-community/UFS_UTILS#891 commit ed592a6 Author: Kate Friedman <[email protected]> Date: Sat Feb 3 02:55:14 2024 -0500 Retire cycle-specific FHMAX_GFS variables (NOAA-EMC#2278) This PR retires the `FHMAX_GFS_${cyc}` variables that allowed users to specify different gfs forecast lengths for each cycle. This function is no longer supported in global-workflow. The `FHMAX_GFS_*` variables will be removed and will no longer be checked to set the final `FHMAX_GFS` variable. The same forecast length will be set for every cycle. This PR also includes a small fix to add new post parm files into the `.gitignore` file. This was intended to be included in a different PR but that PR is on hold for further testing so it is being included here to get it into `develop` sooner. Resolves NOAA-EMC#2218 commit 977e2d6 Author: Henry R. Winterbottom <[email protected]> Date: Fri Feb 2 07:49:09 2024 -0700 New GDASApp hash. (NOAA-EMC#2285) commit b5f2bd9 Merge: 4d66742 0400e1f Author: David Huber <[email protected]> Date: Tue Jan 30 13:55:00 2024 -0600 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 0400e1f Author: David Huber <[email protected]> Date: Tue Jan 30 09:57:11 2024 -0600 Fix gfs_utils Orion spack-stack env path. commit 6bbe823 Author: DWesl <[email protected]> Date: Mon Jan 29 21:15:30 2024 -0500 Use seq to generate the list of times, instead of a bash for-loop (NOAA-EMC#2264) I'm running a year-long forecast, which means I get a large portion of the log file dedicated to these loops. `seq ${START} ${STEP} ${STOP}` will generate a sequence going from START to STOP by STEP, including STOP if relevant. That seems to be the purpose of these loops. It will by default separate the list with newlines, but `seq -s ' ' ${START} ${STEP} ${STOP}` will separate them with spaces instead, more closely mimicing the previous behavior. I would like this to be two lines in the log, rather than a few hundred, and this may also be faster, though probably more for reasons of fewer writes to disk than because bash isn't designed for arithmetic. commit d5bee38 Author: Kate Friedman <[email protected]> Date: Mon Jan 29 14:35:02 2024 -0500 Correct typos in GFS config.resources (NOAA-EMC#2267) This PR corrects some typos in `parm/config/gfs/config.resources` that were introduced in PR NOAA-EMC#2216. The esfc job was failing in tests on WCOSS2 due to insufficient memory. This lead to discovering the other typos. The esfc job completes without error after its memory is set back to `80GB` from the incorrect `8GB`. Resolves NOAA-EMC#2266 commit 81557be Author: David Huber <[email protected]> Date: Mon Jan 29 12:13:31 2024 -0600 Update monitor hash to noaa-emc with SS/1.6.0 support. commit 2238dd6 Author: DavidHuber <[email protected]> Date: Mon Jan 29 13:21:30 2024 +0000 Update Orion, Hercules, S4 modulefiles. commit 6ffd94f Author: DavidHuber <[email protected]> Date: Fri Jan 26 16:01:23 2024 +0000 Update GDAS hash to include SS/1.6.0 support. commit be11f85 Merge: 56b9680 04e0772 Author: DavidHuber <[email protected]> Date: Fri Jan 26 15:34:24 2024 +0000 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 8ff3448 Author: Rahul Mahajan <[email protected]> Date: Fri Jan 26 10:12:18 2024 -0500 Add a yaml for snow DA testing. (NOAA-EMC#2199) - adds a new test yaml C96_atmsnowDA.yaml for 3DVar atmosphere with GSI and Land (Snow) DA with JEDI - moves a few yamls from platforms/ to yamls/ - adds ability to overwrite a previously created experiment as an addition to user input. --------- Co-authored-by: Cory Martin <[email protected]> commit 04e0772 Author: David Huber <[email protected]> Date: Fri Jan 26 07:16:25 2024 -0600 Update ufs_utils hash for spack-stack/1.6.0 support. commit 3d44ff3 Author: Barry Baker <[email protected]> Date: Thu Jan 25 14:33:27 2024 -0500 GOCART ExtData biogenic climatology fix (NOAA-EMC#2253) Updates the ExtData for biogenic emissions to be climatology rather than for current time. Fixes an issue which will crash by default for other years. commit 66f58b8 Author: Guillaume Vernieres <[email protected]> Date: Thu Jan 25 13:16:41 2024 -0500 Added missing container case in gfs/config.resources (NOAA-EMC#2258) fixes NOAA-EMC#2257 commit 553b4f2 Author: WenMeng-NOAA <[email protected]> Date: Thu Jan 25 13:00:45 2024 -0500 Fix post parm links (NOAA-EMC#2243) Change symbolic links under parm/post with the latest version of develop branch from UPP repository and enable MERRA2 aerosol fields. Resolves NOAA-EMC#2259 commit 4d66742 Merge: 6c05803 afa09e3 Author: David Huber <[email protected]> Date: Thu Jan 25 07:49:08 2024 -0600 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 6c05803 Author: David Huber <[email protected]> Date: Thu Jan 25 07:48:42 2024 -0600 Fix wgrib2/gfs_utils on Hercules. commit ee6f536 Author: Kate Friedman <[email protected]> Date: Thu Jan 25 07:43:13 2024 -0500 Update GFS version to v16.3.13 in index.rst (NOAA-EMC#2256) GFSv16.3.13 WAFS update was implemented Refs NOAA-EMC#2013 commit 2445d44 Author: RussTreadon-NOAA <[email protected]> Date: Thu Jan 25 06:17:11 2024 -0500 Simplify and extend load_ufsda_modules to Hercules (NOAA-EMC#2245) GDASApp jobs do not run on Hercules because `ush/load_ufsda_modules.sh` does not include logic to load the appropriate GDASApp modules on Hercules. This PR extends `load_ufsda_modules.sh` functionality to Hercules, thereby enabling GDASApp jobs to run on Hercules. Resolves NOAA-EMC#2244 commit 56b9680 Author: DavidHuber <[email protected]> Date: Wed Jan 24 19:47:34 2024 +0000 Update hashes (revert WCOSS2 modules). commit afa09e3 Author: DavidHuber <[email protected]> Date: Wed Jan 24 18:59:40 2024 +0000 New (cleaner history) gdas hash. commit a9eaec2 Author: DavidHuber <[email protected]> Date: Wed Jan 24 18:52:27 2024 +0000 Update gdasapp to include ss/1.6.0 support. commit 5ef8eb2 Merge: 4c46354 e400068 Author: DavidHuber <[email protected]> Date: Wed Jan 24 17:08:54 2024 +0000 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 4c46354 Author: DavidHuber <[email protected]> Date: Wed Jan 24 17:05:12 2024 +0000 Reenable verif-global support commit f775755 Author: DavidHuber <[email protected]> Date: Wed Jan 24 16:59:10 2024 +0000 Assign fcsthrs for awips_g2 job. commit e400068 Author: David Huber <[email protected]> Date: Mon Jan 22 15:01:07 2024 -0600 More gsi-addon path fixes. commit f663d47 Author: David Huber <[email protected]> Date: Mon Jan 22 14:41:59 2024 -0600 Fix gsi-addon paths for hercules, orion, and S4. commit e304bbe Author: DavidHuber <[email protected]> Date: Mon Jan 22 18:59:34 2024 +0000 Better optimize build jobs (more ufs jobs). commit ccc6e2d Author: DavidHuber <[email protected]> Date: Mon Jan 22 18:56:18 2024 +0000 Reenable verif-global. NOAA-EMC#2195 commit 3ef3411 Merge: 4365f63 f4d187f Author: DavidHuber <[email protected]> Date: Mon Jan 22 18:39:10 2024 +0000 Merge remote-tracking branch 'origin/develop' into ss160 commit 4365f63 Author: DavidHuber <[email protected]> Date: Mon Jan 22 18:37:25 2024 +0000 Corrected the SS env. name in the version files. NOAA-EMC#2195 commit f4d187f Author: AndrewEichmann-NOAA <[email protected]> Date: Mon Jan 22 12:28:28 2024 -0500 Converts obsproc to obsprep in prepoceanobs config file (NOAA-EMC#2236) Converts obsproc to obsprep in prepoceanobs config file as a compliment to mutually depended GDASApp PR NOAA-EMC/GDASApp#858 The motivations are explained in refs NOAA-EMC/GDASApp#857 commit 9a09d30 Author: DavidHuber <[email protected]> Date: Fri Jan 19 21:23:50 2024 +0000 Corrected gsi-addon-dev spelling. commit 21ff645 Author: DavidHuber <[email protected]> Date: Fri Jan 19 21:11:34 2024 +0000 Update modulefiles, submodules to spack-stack 1.6.0. NOAA-EMC#2195 commit d4c55d1 Author: Kate Friedman <[email protected]> Date: Fri Jan 19 15:43:37 2024 -0500 Update typing hint for WCOSS version of python (NOAA-EMC#2238) The typing hint `typing.List` was deprecated with python 3.9 in favor of using the primitive `list[str]`, but the functional version of python on WCOSS2 is <3.9, causing `setup_xml.py` to fail there. This replaces `list[str]` as a typing hint with the deprecated form until the supported version on WCOSS2 is >=3.9. commit 4919287 Author: Barry Baker <[email protected]> Date: Thu Jan 18 22:31:27 2024 -0500 GOCART Emission updates for GEFSv13 and GDAS (NOAA-EMC#2201) This PR addresses several things needed for more recent simulations using GOCART2G as well as preparing for the GEFSv13 30 year run. The main updates are: - Update CEDS to use monthly emission files instead of daily. This will drastically reduce the number of files needed. No science change - Update biogenic MEGAN inputs to use a climatology rather than the offline biogenic previously used. This is needed to deal with simulations where the current dataset is not available. - Update volcanic SO4 emissions to use degassing emissions only. This is to support the need for more recent simulations where data is not available. commit 13d25cf Author: Kate Friedman <[email protected]> Date: Thu Jan 18 22:29:43 2024 -0500 Add `POSTAMBLE_CMD` into preamble postamble (NOAA-EMC#2235) This PR adds the ability to run a command at the end of jobs via the preamble's postamble function. A new command can be set via `POSTAMBLE_CMD` and will be invoked at the end of jobs. Users can add the command to the top of an env file to have every job run it or it can be placed within a job if-block in the env file to run for just that job. Resolves NOAA-EMC#1145 commit 7759163 Author: Rahul Mahajan <[email protected]> Date: Thu Jan 18 01:13:49 2024 -0500 Add option to create WGNE atmosphere products (NOAA-EMC#2233) Adds option to create WGNE products for the atmosphere. Resolves NOAA-EMC#1951 Resolves NOAA-EMC#2226 commit d95ed85 Author: Rahul Mahajan <[email protected]> Date: Wed Jan 17 18:04:56 2024 -0500 Use ufs.configure, model_configure, MOM_input, data_table, and ice_in templates from UFS-weather-model (NOAA-EMC#2051) This PR: - links `ufs.configure.*.IN`, `model_configure.IN`, `MOM_input_${OCNRES}.in`, `MOM6_data_table.IN`, and `ice_in.IN` from ufs-weather-model into the global-workflow `parm/ufs` directory - prepares local variables for use in the templates in the respective functions for FV3, MOM6, and CICE6 - uses `atparse.bash` to render these templates into fully formed namelists - Work was performed by @DeniseWorthen in the ufs-weather-model to templatize several variables that are hard-wired in the ufs-weather-model for CICE. See ufs-community/ufs-weather-model/NOAA-EMC#2010 commit 44a66dd Author: RussTreadon-NOAA <[email protected]> Date: Wed Jan 17 13:52:09 2024 -0500 Update gdas.cd hash to use gsibec tag 1.1.3 (NOAA-EMC#2231) (NOAA-EMC#2234) commit 9046d97 Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Jan 17 10:19:18 2024 -0500 Add basic atmos products for GEFS and refactor resources (NOAA-EMC#2216) * Add basic atmos products for GEFS Adds basic atmosphere products for GEFS members (no mean or spread). To facilitate the addition of GEFS parameter lists, the existing GFS lists are renamed. They are also relocated to `parm/products/` direc tory instead of `parm/post/`. GEFS v12 uses different parameter lists for different resolutions, but for this implementation, the 0p25 lists are used for all resolutions. However, to hedge against the final con- figuration, all of the GEFS parameter lists have been added to parm. Implementation of different parameter lists for each resolution will take additional refactoring of the atmos_products job, as it currently assumes all resolutions use the same lists. The new GEFS rocoto task is implented as two loops of metatasks (made possible by PR NOAA-EMC#2189). The member is set at the rocoto level, so the setting in `config.base` had to be updated to accept a pass-through. The generation of a forecast hour list is moved up to its own function in `rocoto.tasks`, separate from the post groups which are not used. This can be used as a model for future metatasks (or refactoring of old ones). `rocoto_viewer.py` does function with the nested metatasks, though only one level of folding is available and the metatask name is that of the lower metatask (though it encompasses the entire outer metatask). Additionally, the GEFS `config.resources` had diverged from the GFS version, which included not having a section for the atm products job. This led to the refactoring of the GFS `config.resources`, including switching to using a `case` statement instead of sequential `elif`. This refactored script was then copied over to GEFS, replacing the old one, with all jobs not currently implemented for GEFS removed (except wave post, whose inclusion is immenent). New blocks can be copied over from GFS as they are added. Resolves NOAA-EMC#823 commit fbba174 Author: RussTreadon-NOAA <[email protected]> Date: Tue Jan 16 14:05:48 2024 -0500 Update GDASApp (gdas.cd) hash (NOAA-EMC#2225) GDASApp now uses gitsubmodules commit dddd837 Author: Rahul Mahajan <[email protected]> Date: Tue Jan 16 12:17:19 2024 -0500 Fix ocean resolution for the S2SWA test (NOAA-EMC#2223) commit 83edaf1 Author: David Huber <[email protected]> Date: Tue Jan 16 11:07:02 2024 -0500 Apply fixes to archiving jobs (NOAA-EMC#2221) Add checks for potentially missing log/data files and update log names for archiving. Missing sflux index files are also added to the products script. Resolves NOAA-EMC#2076 commit c590476 Author: Rahul Mahajan <[email protected]> Date: Fri Jan 12 19:21:02 2024 -0500 Update hash to ufs-weather-model. The noahmptable.tbl was reorganized, so update link_workflow.sh to use the same one used in UFSWM RT (NOAA-EMC#2219) commit c041968 Author: Kate Friedman <[email protected]> Date: Fri Jan 12 12:09:35 2024 -0500 Add ocean resolution to setup_expt invocation and retire/reduce COMROT/ROTDIR usage (NOAA-EMC#2214) Two series of updates: 1) Update setup scripts to now allow users to provide ocean resolution 2) Housekeeping to retire the `COMROT` variable, replacing it with other variables as needed, and reduce the `ROTDIR` variable usage. Both updates change options for the workflow setup API. Refs NOAA-EMC#2061 commit 997f978 Author: AndrewEichmann-NOAA <[email protected]> Date: Fri Jan 12 10:46:36 2024 -0500 Allow use of ocean obs prep in WCDA cycling and remove R2D2 (NOAA-EMC#2215) Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same. Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS. Replaces the current R2D2 processing. commit 12a5bb1 Merge: 4cb5802 6492c2d Author: David Huber <[email protected]> Date: Fri Jan 12 09:26:27 2024 -0500 Merge pull request NOAA-EMC#2217 from DavidHuber-NOAA/update/versions Update and clean up version and module files commit 6492c2d Author: David Huber <[email protected]> Date: Thu Jan 11 11:49:08 2024 -0600 Update orion module/version files for met/metplus NOAA-EMC#2123 commit 94c9937 Author: DavidHuber <[email protected]> Date: Thu Jan 11 17:42:53 2024 +0000 Comment met/metplus out from Hera modulefile. NOAA-EMC#2123 commit 8c32f8b Merge: a65e4c6 4cb5802 Author: David Huber <[email protected]> Date: Thu Jan 11 11:34:44 2024 -0600 Merge branch 'develop' of github.com:noaa-emc/global-workflow into develop commit a65e4c6 Author: David Huber <[email protected]> Date: Thu Jan 11 11:34:19 2024 -0600 Initial update of version/module files NOAA-EMC#2123 commit 4cb5802 Author: souopgui <[email protected]> Date: Wed Jan 10 08:30:22 2024 -0600 Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh when running MPMD tasks (NOAA-EMC#2212) Fix OpenMP over-allocation of resources running MPMD tasks Co-authored-by: Innocent Souopgui <[email protected]> commit b056b53 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Mon Jan 8 17:28:05 2024 -0500 Add Hercules as valid machine in CI scripts (NOAA-EMC#2207) Few updates to CI scripts to include names for hercules that where missed the first time. commit 6574d29 Author: Rahul Mahajan <[email protected]> Date: Mon Jan 8 17:25:47 2024 -0500 Fix invalid GH action and restart file name (NOAA-EMC#2210) Resolves a typo that leads to an invalid workflow yaml and fixes the restart filename in restart detection. Resolves NOAA-EMC#2205 commit 69605ea Author: Rahul Mahajan <[email protected]> Date: Mon Jan 8 17:00:28 2024 -0500 Stop attempting to comment link to RTD for non-PRs (NOAA-EMC#2209) Adds a check so comments with a link to documentation are only generated for PRs. commit 4e160a8 Author: Rahul Mahajan <[email protected]> Date: Mon Jan 8 13:10:15 2024 -0500 Enable UPP for GOES processing (NOAA-EMC#2203) Wnables the creation of special master grib2 files from UPP for GOES processing commit c15875b Author: David Huber <[email protected]> Date: Mon Jan 8 09:56:06 2024 -0500 Port cycling to Hercules (NOAA-EMC#2196) Adds cycled support for Hercules (excluding gsi-monitor). Partially resolves NOAA-EMC#1588 GSI monitoring is disabled on Hercules due to missing Perl modules. That will be enabled in a later PR. commit ef6827d Author: Walter Kolczynski - NOAA <[email protected]> Date: Mon Jan 8 09:43:12 2024 -0500 Refactor rocoto task XML creation (NOAA-EMC#2189) Refactors the rocoto task generation to be recursive. This will allow nested metatasks to loop over multiple variables, which is needed for GEFS product generation. As part of this refactor, there is no longer separate arguments to designate metatasks. Instead, task dicts can include a nested 'task_dict' as well as a 'var_dict' containing the variables to loop over. The nested task dict can then either have another layer, or be the innermost task. To accommodate the new recursive nature, some defaults that were previously defined in create_wf_task() had to be pushed down into the function that creates the innermost task. Also, former keywords have been absorbed by the task dict. Refs NOAA-EMC#823 Refs NOAA-EMC#827 commit 2b81cfa Author: Walter Kolczynski - NOAA <[email protected]> Date: Mon Jan 8 09:41:03 2024 -0500 Update fix versions (NOAA-EMC#2198) Updates fix versions for a few components: - Update cice and mom6 versions to support C96/1p00 marine - Update wave to change betamax setting for glo_025 waves Resolves NOAA-EMC#2004 Resolves NOAA-EMC#2107
Squashed commit of the following: commit c54fe98c4fe8d811907366d4ba6ff16347bf174c Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Apr 2 15:58:49 2024 -0400 Move bash utility functions out of preamble (#2447) The preamble was accumulating a bunch of utility functions. These functions are now moved to a separate file that is sourced by the preamble. The only functions remaining in the preamble are those related to script control and logging (`set_trace()`, `set_strict()`, `postamble()`). Resolves #2346 commit 4a39c8afc0555a8f2d621efb55589b9b309a416c Author: David Huber <[email protected]> Date: Tue Apr 2 18:00:21 2024 +0000 Reenable the minimization monitor on Hera (#2446) This allows the minimization monitor to run on Hera Rocky 8. A missing perl module was added (List/MoreUtils.pm), but had to be installed under the perl/5.38.0 installation, thus that module needs to be loaded. Resolves #2439 commit 0eaa53771b5e8d476d3b5feabd3181c8dc48629a Author: Travis Elless <[email protected]> Date: Tue Apr 2 00:31:14 2024 -0400 Fix rotating member bugs (#2443) When PR #2427 introduced the rotating subset of member guess states for the early-cycle EnKF, the rotating member calculation function was omitted from the DOSFCANL_ENKF if block in the enkf surface script. This PR adds this feature to this section. This PR also removes hard coded values that were included in this function and are replaced with a variable equal to the number of late cycle members. Resolves #2441 commit 39ba9d720c38ac85239a1eb1696c78df82396644 Author: CatherineThomas-NOAA <[email protected]> Date: Mon Apr 1 17:48:42 2024 -0400 Remove the reset of upper layer humidity (#2449) # Description The parameter "nudge_qv" resets the upper layer humidity to HALOE climatology when cold starting. This parameter has been set to ".true." but is no longer needed using v16+ ICs and will now be set to ".false." by default. Resolves: #2448 commit 7f6bf216566e92bbe072ebe4b64d26cc60fb53f1 Author: Jiarui Dong <[email protected]> Date: Mon Apr 1 13:08:33 2024 -0400 Archive the snow DA analysis into HPSS (#2414) This PR adds the capabilities to archive the snow analysis output into HPSS. Changes are made to archive the snow stats, letkfoi yaml file and snow analysis into HPSS. commit c1b11a2559e618f61866498b5dad503ba74d8332 Author: Neil Barton <[email protected]> Date: Mon Apr 1 13:05:57 2024 -0400 Add GEFS ENS Atmos options (#2392) This PR adds the FV3 atmos perturbation options when running GEFS. This is needed for GEFS reforecasts and GEFS operational forecasts. This PR continues to address the below issues #1720 #1921 Co-authored-by: Rahul Mahajan <[email protected]> Co-authored-by: Walter Kolczynski - NOAA <[email protected]> Co-authored-by: Bing Fu <[email protected]> commit 834ce31348a627e14d448cdbe33d4ec0dabe99e4 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Mar 29 13:17:08 2024 -0400 Refactor gempak jobs for new COM and style (#2374) Updates the gempak jobs to fit the new COM structure while also refactoring them some to improve the style. Despite these technical changes, the overall structure is left unchanged for most scripts, though some have been rewritten to make the needed changes easier. Some of these scripts had already been updated some in the original COM refactor and thus needed fewer updates. Style updates includes converting all gempak scripts to bash, making them shellcheck compliant, and removing trailing whitespace. Further refactoring to improve maintainability will be needed in the future (see #2341, #2342, #2343, #2348). The GFS gif scripts were identical except the forecast hour, so they are collapsed down into two: one for f000 and one for other forecast hours. The gempak executables have short path limits. To get around this without having the gempak module recompiled, target directories (mostly relevant for the gempak meta jobs) are symlinked into the working directory to drasticly reduce the path lengths. Part of this update includes replacing existing MPMD calls with the new standard `ush/run_mpmd.sh` script. A new function, `wait_for_file()`, is introduced to standardize waiting for a file to be available. Gempak forecast hours are often hard-coded within scripts. In addition to issues with maintainability, this causes problems for shorter forecasts, such as we typically run for testing purposes. For now, we simply check the values against the forecast length and reduce if necessary. Future work (#2348) will be needed to remove these hard-coded values with variables set in the config file (or just use update gempak products to match standard output time variables). One-degree gempak files have been updated to include `1p00` in the filename. Several gempak job dependencies are corrected. Fake gempak data for external models is being staged on tier-1 machines to allow testing. **Output has not been verified.** Future PRs will likely be needed to bring full functionality online. Resolves #2158 Resolves #2152 Resolves #2151 Resolves #2249 Resolves #2247 Refs #2157 Refs #2348 commit 20635b0639656769842218d544ec7ce2436337c5 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Fri Mar 29 08:15:29 2024 +0000 Turn GEFS CI test on for Hera (#2442) Re-enabling gefs case to test gefs system builds in Jenkins on Hera. Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]> Co-authored-by: terrance.mcguinness <[email protected]> Co-authored-by: Walter.Kolczynski <[email protected]> commit ba6a9d5fa6a079b1e3fdd424a493252bbf499c5d Author: Walter Kolczynski - NOAA <[email protected]> Date: Thu Mar 28 17:34:22 2024 -0400 Modify APP based on RUN (#2413) There is a need to change which coupled components are on depending on the current `RUN`. To facilitate this, the `APP` is modified prior to the setting of the `DO_<component>` variables based on `RUN`, turning off components as desired. This new system also replaces the `DO_<component>_ENKF` switches that were formerly used to turn components off for the ensemble. Also expands allows apps for cycled to include S2SWA. Resolves #2318 commit 3ff7a92c25564ddf984cb09cb5667ae8fafe01a0 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Thu Mar 28 17:48:00 2024 +0000 Fix post log arg check and don't create build semaphore (#2440) Two Hot Fixes to Jenkins latest updates: 1. Logic fixed in checking for mutually exclusive use of gists and repo for publishing error files 2. Removed creation of build success file semaphore forcing complete rebuild as the default behavior for rerun/restarts Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]> Co-authored-by: terrance.mcguinness <[email protected]> commit d6be3b5c3a1b8fd025a303b40e0660e2914906a7 Author: Henry R. Winterbottom <[email protected]> Date: Wed Mar 27 20:56:18 2024 -0600 Update global-workflow and subcomponents to Hera/Rocky 8 partition (#2421) This PR addresses issue #2329. The following is accomplished: - All submodule RDHPCS Hera stacks are updated to be compatible with the Rocky-8 distro spack-stack; - The global-workflow version files `versions/build.hera.ver` and `versions/run.hera.ver` are updated for Rocky-8; - All submodule hashes have been updated to be compliant with the Rocky-8 distro spack-stack (see the reference PRs below); - Update to `parm/config/config.base` is made for not yet compliant packages; - Relevant updates are made to `modulefiles/module_base.hera.lua` and `modulefiles/module_gwsetup.lua`. Resolves #2329 Refs: [#958](https://github.com/NOAA-EMC/GDASApp/issues/958) [#49](https://github.com/NOAA-EMC/gfs-utils/issues/49) [#124](https://github.com/NOAA-EMC/GSI-Monitor/issues/124) [#31](https://github.com/NOAA-EMC/GSI-utils/issues/31) [#2167](https://github.com/ufs-community/ufs-weather-model/issues/2167) [#2143](https://github.com/ufs-community/ufs-weather-model/issues/2143) [#913](https://github.com/ufs-community/UFS_UTILS/issues/913) Co-authored-by: Rahul Mahajan <[email protected]> Co-authored-by: David Huber <[email protected]> commit 47302153f13f6b23539be841b78ed78664599c08 Author: Travis Elless <[email protected]> Date: Wed Mar 27 21:14:57 2024 -0400 Add a rotating subset of members for early-cycle enkf (#2427) The early-cycle EnKF needs the ability to run with fewer members than the late-cycle due to operational resource constraints. Because of this requirement, the introduction of a rotating subset of member first-guess states used by the early-cycle ensemble is also needed in order to preserve the rotating member initial condition functionality currently used by the GEFS. Co-authored-by: Travis J Elless <[email protected]> Co-authored-by: travis elless <[email protected]> commit 94c282ef6fdcd47076e932bcadb5bdd55236aa05 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Wed Mar 27 20:28:15 2024 +0000 Uploading error logs to GitHub from Jenkins CI Runs (#2429) This PR enhances the user experience within GitHub for when errors occur during build and running of CI cases from within the PR messages. This is done by uploading the error logs to GitHub Gists and then publishing the links to them along with the full paths of the logs on disk. This PR adds the python Class **GitHubPR** in `${HOMEgfs}/ci/scripts/utils/githubpr.py` by inhearting the GitHub Class from **pyGitHub**. We use this module to introduce a helper python utility that can publish a list of log files into a GitHub Gist and/or the designated branch **error_logs** in the **emcbot** repo **ci-global-workflows** for storing error log files for review from any git configured terminal. This upload feature will also create persistence of errors over time. Also the `build_all.sh -k` script has been updated to support a "quick kill" feature (thanks David) that stops the parallel builds whenever one fails and creates an error_log file that has the paths to the error files that are also uploaded and published in the PR messages in GitHub. Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]> Co-authored-by: terrance.mcguinness <[email protected]> Co-authored-by: DavidHuber <[email protected]> Co-authored-by: Walter Kolczynski - NOAA <[email protected]> commit 6c5065e2e83a45b14505e7575aa4500482ef7452 Author: Rahul Mahajan <[email protected]> Date: Wed Mar 27 03:39:16 2024 -0400 Add option to use traditional threading in the UFS (#2384) # Description This PR: - adds the option of running the ufs-weather-model with traditional threading in addition to ESMF-managed threading. See new toggle `USE_ESMF_THREADING=YES|NO` set in `config.fcst` - does not change the current default of using ESMF-managed threading. Traditional threading use might need a little more fine tuning for the job-card specification. This will be achieved when the UFSWM RT completely switches over to traditional threading - updates the hash of the ufs-weather-model to the PR https://github.com/ufs-community/ufs-weather-model/pull/2172 Resolves #2277 In addition to the above stated objectives, this PR also addresses open issues. In particular, this PR: - adds a newline at the end of `diag_table_aod`. Fixes #2407 @zhanglikate - reserves more memory on WCOSS2 for offline UPP when running at C768. Fixes #2408 @WenMeng-NOAA Co-authored-by: David Huber <[email protected]> commit bc1c46dfd7393c5164abcdc2dfa76a9c4bc834b8 Author: RussTreadon-NOAA <[email protected]> Date: Tue Mar 26 22:27:30 2024 -0400 Correct GDASApp paths (#2435) The changes in this PR - account for changes in GDASApp directory structure - generalize how the path to the GDASApp python ioda library is specified Resolves #2434 commit f0b912be6f2cf2fac590272253f19cb082fbf5f2 Author: David Huber <[email protected]> Date: Mon Mar 25 21:46:32 2024 +0000 Fix *earc jobs where the number of members isn't a multiple of 10 (#2424) This limits the earc search for ensemble members to the maximum number of members, which prevents attempting to send non-existent members to HPSS if the number of ensemble members is not a multiple of 10. Resolves #2390s commit daeb0c855017f8ffd6f06870744b825b276097f3 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Fri Mar 22 17:40:04 2024 +0000 hotfix to update full path to error logs on CI case fail (#2425) This hotfix PR prepends the full path to the error logs on disk to be communitated correctly to the GitHub message to the PR that is being processed when there is a failure in from a case. commit 50f75526549245f2b5d984cdb44e402852e086ec Author: YaliMao-NOAA <[email protected]> Date: Thu Mar 21 16:58:25 2024 +0000 Add WAFS jobs, scripts and ush to GFS v17 workflow repository (#2412) # Description This PR adds WAFS jobs, scripts and ush to GFS v17 workflow repository --------- Co-authored-by: yali mao <[email protected]> Co-authored-by: Rahul Mahajan <[email protected]> Co-authored-by: yali mao <[email protected]> commit 03ba78ae3df589211d2776254c6e8584ecdc226f Author: David Huber <[email protected]> Date: Thu Mar 21 13:33:50 2024 +0000 Hotfix: send the correct number of build jobs for the UFS (#2423) This fixes a bug in build_ufs.sh that was causing the UFS to always build with 8 jobs (except on the cloud). commit 4d1bf5266f00b35778ea47896f438e3ef612628d Author: Kate Friedman <[email protected]> Date: Wed Mar 20 14:00:31 2024 -0400 Updates to RTD documentation (#2418) Updates to the RTD documentation include: - Textual updates - Better definition of GDA subfolder structure - Added note about GDAur having been discontinued - Adjust copyright and author information - Fix Git version table and update its contents - Add "Table of Contents" header before table of contents on front page - Add AWS ICs path to init page - Add link to UFS_UTILS gdas_init RTD documentation - Add note about bash to `gw_setup.sh` section and added a warning block Refs #2395 commit afe874ee8b28942e459796cd1005ec598458a5b7 Author: Neil Barton <[email protected]> Date: Tue Mar 19 14:35:02 2024 -0400 Add GEFS Ocean Perturbation Options (#2385) This PR adds the MOM6 ocean perturbation options when running GEFS. This is needed for GEFS reforecasts and GEFS operational forecasts. This PR continues to address the below issues https://github.com/NOAA-EMC/global-workflow/issues/1720 https://github.com/NOAA-EMC/global-workflow/issues/1921 Fixes #2403 commit fa855baa851b0cb635edd1b9ae1bfed5112d41e5 Author: Clara Draper <[email protected]> Date: Mon Mar 18 12:49:14 2024 -0600 Add initial GSI-based soil analysis capability (#2263) First set of changes for adding the new soil analysis, from the assimilation of screen-level T and q. The changes here enable the screen-level observations to be assimilated in the Hybrid (Var and EnKF) update, and the soil temperature and soil moisture updates to be made in the EnKF only. The functionality is turned on by setting GSI_SOILANAL to YES in config.base. Resolves #1479 commit e9700d84b521907ee23e1584712f80e25e60f08e Author: Jessica Meixner <[email protected]> Date: Mon Mar 18 09:32:13 2024 -0400 re-enable ci/cases/pr/C48mx500_3DVarAOWCDA.yaml (#2405) Updates to re-enable C48mx500_3DVarAOWCDA CI test after it was disabled in https://github.com/NOAA-EMC/global-workflow/pull/2371 Fixes github.com/NOAA-EMC/global-workflow/issues/2404 commit 3ccffeee120340ab580fc9d96b552970c9f42a8f Author: Rahul Mahajan <[email protected]> Date: Mon Mar 18 09:30:35 2024 -0400 Parse jediyaml only once (#2387) `JEDIYAML` was being parsed 3 times; once in `get_obs_dict`, second in `get_bias_dict` and a third time in `initialize` for the specific component analysis task. This PR: - eliminates the duplications and constructs the `jedi_config` dictionary just once. The dictionary is written out before calling the executable. - updates hash to gdasapp - updates configs for snow, aerosol, atmvar and atmens JEDI-DA to include `JEDI_FIX_YAML` and `CRTM_FIX_YAML` . This allows greater flexibility and control over the contents of these fix data sets to be copied into the run directory. - Combines snowDA and aerosolDA into a single test Co-authored-by: Cory Martin <[email protected]> Co-authored-by: David Huber <[email protected]> commit a5f24951c5bef142747c6f6cc6abd474f0b53ac2 Author: CatherineThomas-NOAA <[email protected]> Date: Fri Mar 15 14:47:54 2024 -0400 Fix ensemble archive groups to include all members (#2402) The number of groups used in the ensemble archive step (earc) needs to include a task for the ensemble stat files such as the mean and the spread, resulting in `n_groups+1` tasks for `earc`. Resolves: #2390 commit 056cfdca9e7fd7426a315fcbffc38d8ee2891212 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Fri Mar 15 18:30:23 2024 +0000 GitHub message error paths (#2401) Add feature to message paths to error logs of failed experiments to GitHub Messaging the PR from Jenkins. commit d897ee4936d62160811d936248c8555187f81b65 Author: Rahul Mahajan <[email protected]> Date: Thu Mar 14 12:37:49 2024 -0400 Missed a comma from the hotfix this AM (#2399) This PR is a hotfix to the hotfix from earlier this AM. A comma was missing. commit 906540acacf1b2ce4c0489d0d9d4913f53a4e8ad Author: Rahul Mahajan <[email protected]> Date: Thu Mar 14 10:40:03 2024 -0400 Fix KeyError issue in ocean/ice postprocessing job. (#2398) The jjob for ocean and ice pp, only defines the component specific history and grib directory. This causes an error in the exscript trying to pull keys for both ocean and ice. Fix this. Surprised this has not caused failures before today Co-authored-by: David Huber <[email protected]> commit c27f243ce24c60261718f15628f6ab30d7b09f7b Author: Rahul Mahajan <[email protected]> Date: Wed Mar 13 13:31:57 2024 -0400 Remove documentation about generating ICs using global-workflow (#2397) Removes instructions on generating ics using global-workflow and directs the user to use ufs-utils. commit 0edbdc197441582f9c402da0f3a7f144b88960c7 Author: DavidNew-NOAA <[email protected]> Date: Tue Mar 12 16:30:45 2024 -0400 Changed config.atmanl to allow non-hybrid background error yamls (#2394) # Description Makes change so that if DOHYBVAR equals "NO", then the JEDI background error yaml is set to staticb_${STATICB_TYPE}.yaml.j2 rather than hybvar_${STATICB_TYPE}.yaml.j2. This allows GDAS to run without hybvar, which may be necessary for development purposes. This is all accomplished by a simple switch in config.atmanl. commit ccb1f528489e740bb2adc4958146552323dd8709 Author: RussTreadon-NOAA <[email protected]> Date: Tue Mar 12 10:45:39 2024 -0400 Add JEDI atmosphere only CI (#2357) The PR contains a minimal set of changes to enable JEDI atmospheric DA CI testing. Prototype JEDI atmospheric cycling has begun. The JEDI atmosphere DA CI case provides an automated way to see if future PRs impact JEDI atmospheric cycling. Resolves #2294 Dependency: GDASApp PR [#937](https://github.com/NOAA-EMC/GDASApp/pull/937) commit b96f5ebbb1968bd539336652b87a2faa8ce68fd4 Author: Kate Friedman <[email protected]> Date: Tue Mar 12 07:58:40 2024 -0400 Add switch to control `debug=true` on WCOSS2 for development testing (#2388) Adds a switch (`DEBUG_POSTSCRIPT`) to control whether `debug=true` is set when submitting development rocoto jobs to PBS schedulers (currently just WCOSS2). There isn't an equivalent flag to set for SLURM on the RDHPCS. Have added this new switch to documentation. Refs #619 commit 02d650500353663d0b193ef14003897daa5dd86c Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Mon Mar 11 21:51:16 2024 +0000 Rewrote pr_list_database.py to use wxflow's SQLiteDB Class (#2376) This PR updates the `pr_list_database.py` code to use **wxflow** SQLiteDB Class - Improved code's readability - Uses better code style matching project's software culture - Better docstring standards Co-authored-by: tmcguinness <[email protected]> Co-authored-by: Rahul Mahajan <[email protected]> Co-authored-by: Walter Kolczynski - NOAA <[email protected]> commit a3374607d01fbdabbec0660afb82b5eb3677b4af Author: AndrewEichmann-NOAA <[email protected]> Date: Fri Mar 8 16:08:42 2024 -0500 Return ocnanalrun npes resource setting back to previous value (#2386) Variable `npes` in `ocnanalrun` entry of `config.resources` was erroneously changed in https://github.com/NOAA-EMC/global-workflow/pull/2299 and this PR changes it back. Resolves https://github.com/NOAA-EMC/GDASApp/issues/962 commit d7e9bde84aebe922039589bd2bcd65832c1074eb Author: BoCui-NOAA <[email protected]> Date: Thu Mar 7 16:14:28 2024 -0500 Add new BUFR table file parm/product/bufr_ij9km.txt for GFSv17 C1152 (#2383) This PR will add a new table file parm/product/bufr_ij9km.txt, and modify ush/gfs_bufr.sh to choose the different bufr table files based on the GFSv17 run resolution, i.e. use file bufr_ij9km.txt for C1152 or bufr_ij13km.txt, for C768. Resolves #2382 commit 4a525bef3bbed2ea60a71f71b3740c82df125c36 Author: AndrewEichmann-NOAA <[email protected]> Date: Thu Mar 7 16:12:31 2024 -0500 Add global-workflow infrastructure for ocean analysis recentering task (#2299) Adds jjob, rocoto script, config file, and basic `config.resources` entry for ocean analysis recentering task This PR is a dependency for further work on the associated issue within global-workflow and GDASApp Refs https://github.com/NOAA-EMC/GDASApp/issues/912 commit f83d17a937006add55241ed453e42f4fcbae50aa Author: Kate Friedman <[email protected]> Date: Thu Mar 7 09:29:14 2024 -0500 Clean out non-gfs top level variables (#2366) Clean out non-gfs top level variables that are duplicates or no longer needed. Also standardize how we set these variables in scripts. Refs #2332 commit c7b306e052497aef0022cd53550a168d2c5b6e5b Author: Guillaume Vernieres <[email protected]> Date: Wed Mar 6 16:16:08 2024 -0500 Forgotten templated DO_VRFY_OCEANDA (#2379) # Description This PR adds the possibility to use the switch for the ocean and sea-ice DA verify task from the yaml configuration. - fixes [GDASApp/issues/954](https://github.com/NOAA-EMC/GDASApp/issues/954) commit ba6a4fdf6e245b57530f2b20e6f0ccf567115720 Author: David Huber <[email protected]> Date: Tue Mar 5 19:09:48 2024 +0000 Add Hercules support for the GSI monitor (#2373) # Description This updates the GSI monitor hash and updates the modulefiles to add support for the monitor on Hercules. commit 732a874a2c6793296f136afb23545fab9869b181 Author: Rahul Mahajan <[email protected]> Date: Mon Mar 4 16:04:26 2024 -0500 Reformat snowDA templates to jinja2 (#2371) # Description This PR: - replaces use of non-jinja2 templates in the yaml templates. Specifically `$( )` in favor of pure jinja2. - uses jinja2's built-in capability to include templates within templates, thereby allowing to assemble a completely rendered template before passing it to for e.g. yaml loader. - requires updates to `wxflow` and `gdasapp` - Changes in `wxflow` in `parse_j2yaml` are **not** backwards compatible Additionally, this PR: - renames `config.base.emc.dyn` to `config.base`. Resolves #2347 commit d1fa41106e991556606b0f62a15bf45f469f4f79 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Sat Mar 2 04:54:26 2024 +0000 Reduce Jenkins messaging to GitHub (#2370) This PR updates the Jenkins Pipeline code with safeguards against the errors caused when Jenkins fails to authenticate with GitHub to message or update a label. This was achieved simply by: - Reducing the number out messages sent to the GitHub PR - Putting try blocks around most of the update label calls Co-authored-by: tmcguinness <[email protected]> commit 52fa3cb32d8b50e47f391b82ea8901435fc88aff Author: Henry R. Winterbottom <[email protected]> Date: Fri Mar 1 12:36:27 2024 -0700 Adding debug option for all build scripts (#2326) This PR addresses issue #300 that allows building in `debug` mode. Co-authored-by: David Huber <[email protected]> Co-authored-by: Rahul Mahajan <[email protected]> commit 91738cbf871d8cdce46912e2c11e304d567a2aae Author: DWesl <[email protected]> Date: Fri Mar 1 13:46:42 2024 -0500 Sort list of coupler restart files for restart time determination (#2360) The loop in the following conditional seems to assume the list is sorted, so make that explicit in the array construction. commit 23c25527ad2a62275cd9105bd103b8520a28e573 Author: Neil Barton <[email protected]> Date: Fri Mar 1 13:45:39 2024 -0500 Update stage IC to handle ocean perturbations (#2364) This PR adds the option to stage ocean perturbation files for ensemble forecasts. These perturbation files are used in GEFS forecasts. A new variable is introduced in config.base to use the ocean perturbation files. This PR does not include using these perturbation files. A future PR will address this. commit 8efe05f475b81e7cf6376745d5f1ce31987cb4eb Author: Jessica Meixner <[email protected]> Date: Fri Mar 1 07:41:56 2024 -0500 Turn on C48mx500_3DVarAOWCDA test on hera (#2363) This PR activates the C48mx500_3DVarAOWCDA test on hera. This required an update of the gdas app. commit 5166593945e9ecc04dfa3409752576c08797d09f Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Thu Feb 29 20:14:41 2024 +0000 Move Jenkinsfile into ci subdirectory (#2355) Just moves the Jenkinsfile into the ci directory Co-authored-by: tmcguinness <[email protected]> commit b7af315bb9dea77b37c6d030b71060b87bedf33e Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Feb 28 22:20:58 2024 +0000 Fix rocoto forecast hour determination for GEFS (#2351) The function that generates the list of forecast hours for rocoto was trying to use variables that are not defined for GEFS, causing workflow generation to fail. The function is updated to not try to load these variables before loading the ones actually used for GFS/ GEFS. Also turns GEFS CI test back on and adds an entry to stage C192 ICs (note: these have not been placed in the centralized location.) commit d3a49271b6c3816a9feeb7f6fb474797bacf1d7e Author: Cory Martin <[email protected]> Date: Wed Feb 28 09:38:49 2024 -0500 Rename the land DA jobs to snow DA to better reflect what they are doing (#2330) This PR renames all of the land DA jobs to snow DA to better reflect that this is a JEDI-based snow analysis capability and not a more generic land surface analysis. commit 2693810d6ea9d9b20090777ff3a98e3d072c76d7 Author: Jessica Meixner <[email protected]> Date: Tue Feb 27 01:25:51 2024 -0500 Update ufs-waether-model hash (#2338) Routine update of ufs-weather-model hash. Other small updates: * removes comment referencing closed issue. * Updates the CICE diag frequency to once per day as recommend here: https://github.com/NOAA-EMC/global-workflow/issues/1810#issuecomment-1686278925 * Updated amount of time for C384 gdas forecast as it was running out of time * Removed unused variable wave_sys_ver commit 9608852784871ebf03d92b53bde891b6dcab8684 Author: RussTreadon-NOAA <[email protected]> Date: Mon Feb 26 14:10:01 2024 -0500 Update JEDI ATM to use .nc for obs and generalize x,y layout (#2336) # Description The changes in this PR are twofold 1. replace `.nc4` suffix for JEDI ATM observation related files with `.nc` 2. use templated variables to specify `{layout_x, layout_y}` for JEDI ATM variational and local ensemble apps The first change conforms with the Unidata recommendation that netCDF files end with the suffix `.nc`. The second change replaces hardwired JEDI ATM var and ens `{layout_x, layout_y}` in `config.resources` with a more flexible approach. Resolves #2335 commit c5c84660f10f0ef9ce939231b2f7fda498b39a29 Author: Kate Friedman <[email protected]> Date: Mon Feb 26 10:18:50 2024 -0500 Remove FIX* variables for fix subfolders (#2337) Remove `FIX*` variables for fix subfolders and replace them with the remaining `FIXgfs` variable and the subfolder name (e.g. `${FIXam}` -> `${FIXgfs}/am`). The UFS_UTILS and GDASApp repos were similarly updated. This PR includes a new UFS_UTILS hash. The updated GDASAPP hash was already committed within the spack-stack/1.6.0 PR #2239. Resolves #2184 commit 950c38a093c6a4e2b67e18c76390280d8bfbaef7 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Fri Feb 23 21:15:46 2024 +0000 Fix several Jenkins issues (#2334) Jenkins Updates Resolving final kinks: - Removed all `git` shell commands and now exclusively use Software Control Manger (**scm**) plugin. - Add feature for skipping hosts per configuration specified in case yaml files. - Solved and tested false positive builds and experiments. - Tested archiving of task error log on case fail - First case fail quits pipeline and cancels all pending scheduled jobs - Duel build per yaml configuration arguments supported - All designated case files in PR directory pass on intended host (fully tested on Hera) Remaining updates: - Fist build fail short circuit when building sub-modules and archiving build error log. - Re-build/no-build built in logic for Replay and Rerunning previously failed experiments. commit c67393a203285792b852da0d83fd10fa47155669 Merge: 6f9afff07 79d305e8c Author: David Huber <[email protected]> Date: Fri Feb 23 14:18:15 2024 +0000 Merge pull request #2239 from DavidHuber-NOAA/ss160 Update to spack-stack 1.6.0 Includes all submodules except the UFS, which will be updated at a later time. commit 79d305e8cbc339208ea6fe0475ddc56af94a285b Author: David Huber <[email protected]> Date: Thu Feb 22 14:53:57 2024 -0600 Disable snow DA tests commit 0459203e97211b041520b39e93a188951396ba33 Author: David Huber <[email protected]> Date: Thu Feb 22 12:55:51 2024 -0600 Update GDASApp hash to current develop commit 5c96eb2272fe6117f9e4a4c0c790db58e4870d46 Author: David Huber <[email protected]> Date: Thu Feb 22 12:37:47 2024 -0600 Update GDAS hash to allow modified snow DA analysis commit 79144f2403a33d08140577cc3e8a61d6c4924403 Merge: abbb0b8a7 6f9afff07 Author: DavidHuber <[email protected]> Date: Thu Feb 22 15:14:39 2024 +0000 Merge remote-tracking branch 'origin/develop' into ss160 commit abbb0b8a76b39d34433802fd4e3d7973fb9f0a39 Merge: 4ad837ea1 4529e8cf3 Author: DavidHuber <[email protected]> Date: Thu Feb 22 15:11:03 2024 +0000 Merge remote-tracking branch 'henry/feature/gwdev_issue_2129' into ss160 commit 4ad837ea157b98d2bd173cb696c4d30d142e5540 Merge: 516b2a270 7ca45db8f Author: DavidHuber <[email protected]> Date: Thu Feb 22 15:10:24 2024 +0000 Merge remote-tracking branch 'henry/feature/gfsv17_issue_2125' into ss160 commit 516b2a270234bdab5714ef2705c83dd3835b134d Author: DavidHuber <[email protected]> Date: Thu Feb 22 14:19:16 2024 +0000 Updated GDAS to include rocoto/1.3.6 on Hera. commit 6f9afff073dd589096f992a3448fb7f0e62c9804 Author: Jessica Meixner <[email protected]> Date: Wed Feb 21 13:09:44 2024 -0500 Add some flexibility for ocean/ice output (#2327) This adds functionality to have ocean/ice output frequency be separate from the atm model. One time was created because there's an assumption in the post that these are the same. This could be further modified to remove this assumption. Refs #1629 commit f6d3015ab9f9fd23ce0081baa2edbc5d9f5f3e16 Author: David Huber <[email protected]> Date: Tue Feb 20 09:53:08 2024 -0600 Update GDASApp hash to include SS/1.6.0 support. commit 0bf340bce2f865c582e5305f0c5984cd3affe74e Author: David Huber <[email protected]> Date: Tue Feb 20 09:07:32 2024 -0600 Construct SS paths from version variables. commit 3330cd7310bde8090b68720c225656074676d6b2 Author: David Huber <[email protected]> Date: Tue Feb 20 09:06:19 2024 -0600 Removed MET/METplus 'not available' comments commit fdc638ca1616b347912caec77e5abc2d3e6f18af Author: David Huber <[email protected]> Date: Tue Feb 20 08:35:15 2024 -0600 Move SS module path to version files. commit d7d28a6b65b84c8d821abd2c13d0c068bd5ad6d8 Author: David Huber <[email protected]> Date: Tue Feb 20 07:53:15 2024 -0600 Update comment about METplus support. commit a812f88af3fc043d57494840e81a7527723858e4 Author: David Huber <[email protected]> Date: Tue Feb 20 07:45:45 2024 -0600 Update verif-global to latest WCOSS2 support. commit d81f07fbf53666a37ab01bd463152e10252869ae Author: David Huber <[email protected]> Date: Tue Feb 20 07:41:38 2024 -0600 Clean up build_upp.sh. -Corrected whitespace (tabs instead of spaces) -Removed debug print statement -Alphebetized flags commit ae7eb194cbe2213e564807dd7bc03a28d493eff2 Author: David Huber <[email protected]> Date: Fri Feb 16 16:15:40 2024 -0500 Fix whitespace in build_upp.sh. Co-authored-by: Rahul Mahajan <[email protected]> commit 48b34d0f388a398bb91f7c3b1e5f8338f4beb7b9 Author: David Huber <[email protected]> Date: Fri Feb 16 20:56:55 2024 +0000 Added verif-global support back to WCOSS2. commit 4529e8cf3736ffbacf615a27e99f4d1beec391aa Author: henrywinterbottom-wxdev <[email protected]> Date: Fri Feb 16 11:12:01 2024 -0700 Bug fix. commit 8e4f94d13d32849b2862a9d59aa070f4103c61ae Author: henrywinterbottom-wxdev <[email protected]> Date: Fri Feb 16 11:04:41 2024 -0700 Updates requested by reviewer Rahul Mahajan. commit 4624ce21c99ab303afa10c1dd8ddcce7b6f715ca Author: henrywinterbottom-wxdev <[email protected]> Date: Fri Feb 16 10:52:11 2024 -0700 Updates requested by reviewer; testing -- DO NOT REVIEW. commit ed25bbd0b26a893d32ce4a10b368dec2bb722424 Author: henrywinterbottom-wxdev <[email protected]> Date: Fri Feb 16 09:33:59 2024 -0700 Linter corrections. commit 6a0b7bf214815c13eec98a93bd3abe9978de04e4 Merge: f9fb64ef8 2415b7b4f Author: David Huber <[email protected]> Date: Fri Feb 16 09:50:22 2024 -0600 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit f9fb64ef802b683d7b369f8e8268d423ab581481 Merge: 777d97d3a a23b7f2fd Author: David Huber <[email protected]> Date: Fri Feb 16 09:49:42 2024 -0600 Merge remote-tracking branch 'emc/develop' into ss160 commit 7ca45db8fa32c84ef117ff2938a650822c81a786 Merge: 73bc76bfd a23b7f2fd Author: Henry R. Winterbottom <[email protected]> Date: Fri Feb 16 07:46:35 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit eb2ed53857eb3387735488a1ce5d701ff680e3db Merge: 9929277dc a23b7f2fd Author: Henry R. Winterbottom <[email protected]> Date: Fri Feb 16 07:46:24 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit a23b7f2fdca5be700d257e28052a0104f2173a0f Author: RussTreadon-NOAA <[email protected]> Date: Fri Feb 16 09:37:58 2024 -0500 Add JEDI 3DEnVar atmosphere only CI test stub (#2309) commit cf83885548bb3a6740c033f42479ce2ad283a4a9 Author: Jessica Meixner <[email protected]> Date: Fri Feb 16 01:55:02 2024 -0500 Add unstructured grid for HR3/GFS (#2230) This adds the capability to use unstructured grids in the global workflow, which will be used in HR3. There are new fix files for a low-resolution 100km grid and a grid closer to our targeted GFSv17 grid which has the resolution combined from the older multi_1 and GFSv16 grids. The fix file update is here: NOAA-EMC/global-workflow#2229 Note: This now means that GFS tests need a new build option: `./build_all.sh -w` So that PDLIB=ON is turned on for compiling relevant UFS and WW3 codes. Resolves NOAA-EMC/global-workflow#1547 commit 9929277dc7d0ad90f5366faf4b5f2278969a0aa2 Merge: eb8791ccb 094e3b86d Author: Henry R. Winterbottom <[email protected]> Date: Thu Feb 15 15:05:50 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit 094e3b86da44f1d3fc1d99f68f6fdfcd36deb09f Author: Cory Martin <[email protected]> Date: Thu Feb 15 14:43:55 2024 -0500 Move IMS remapping files from COM_OBS to FIXgdas (#2322) * Add in IMS obs fix directory and update submodule for gdas commit d465ea06e8b2a8f3a5eb1120647c1e2ce5197d66 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Thu Feb 15 19:25:02 2024 +0000 Set HOMEgfs for module_setup in CI driver (#2321) Hotfixes to CI Bash system from updates with sourcing `detect_machine.sh` in `ush/module-setup.sh` using **HOMEgfs**. commit 2415b7b4f3e6c376aca27707510001141cc9dd92 Author: David Huber <[email protected]> Date: Thu Feb 15 19:21:17 2024 +0000 Load default rocoto on Jet. commit eb8791ccbe684828dc529d0e553551969274fc22 Merge: 60d5ee64b 638684e0b Author: Henry R. Winterbottom <[email protected]> Date: Thu Feb 15 11:56:40 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit 777d97d3a1c9f5ec5e8af3ca40a41224ec7099a1 Author: David Huber <[email protected]> Date: Thu Feb 15 12:34:59 2024 -0600 Fixed Orion cdo version. commit ef0723503c72f295de93521c7102c43e75c47417 Author: DavidHuber <[email protected]> Date: Thu Feb 15 16:29:32 2024 +0000 Revert UFS hash. commit 0ce8c0dbc13227884fef1c637e93616a28c68d34 Author: DavidHuber <[email protected]> Date: Thu Feb 15 14:55:48 2024 +0000 Fix git version in Hera's gwsetup module. commit 3080a34253e8e24105bf2be72b6a872b1c072935 Author: DavidHuber <[email protected]> Date: Wed Feb 14 20:52:34 2024 +0000 Fixed xarray version for SS/1.6.0. commit 49392dd47ff84b6586052aeae6879d7d8050b746 Author: DavidHuber <[email protected]> Date: Wed Feb 14 20:29:41 2024 +0000 Updated GSI-Utils hash to head of develop. commit c3553f0d8e6a05c6234e7c14a179983aa44fd6f3 Merge: 4568653a6 638684e0b Author: DavidHuber <[email protected]> Date: Wed Feb 14 20:28:14 2024 +0000 Merge remote-tracking branch 'origin/develop' into ss160 commit 4568653a67aa37c902379db628fb10f69fe7190f Author: David Huber <[email protected]> Date: Wed Feb 14 14:22:13 2024 -0600 Reupgrade Hercules to SS/1.6.0 commit 638684e0bfcd06700cc8695f09824891a0a1eee1 Author: Kate Friedman <[email protected]> Date: Wed Feb 14 14:55:21 2024 -0500 Remove `finddate.sh` from system (#2308) * Retire finddate.sh usage from system * Update gfs-utils hash to 7a84c88 - New hash includes removal of finddate.sh Refs #2279 commit 2b160f8470bed16c513ca4a5665e2b6d4448c50e Author: DavidHuber <[email protected]> Date: Wed Feb 14 18:31:28 2024 +0000 Reenable METplus jobs on Hercules. commit 8f5900265a31e894060bbe9c89b262f4df0b1760 Author: DavidHuber <[email protected]> Date: Wed Feb 14 18:30:23 2024 +0000 Update GSI hashes. commit 73bc76bfd47f2cff54df55e15d9ed8969683367d Author: henrywinterbottom-wxdev <[email protected]> Date: Wed Feb 14 09:27:37 2024 -0700 Updates based on user request. commit e4bc674cf3b2df10e0b0dfd50a8ecb0f4f7825d8 Author: henrywinterbottom-wxdev <[email protected]> Date: Wed Feb 14 08:03:45 2024 -0700 Corrected based on reviewer review. commit 60d5ee64bda7a16c1f2dc20c8badcd7c8fc4e592 Merge: 40f2cf6cd 1aaef05d3 Author: Henry R. Winterbottom <[email protected]> Date: Tue Feb 13 18:08:33 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit 03304112347a673b7a0fcc404703bb10960bc47a Merge: 929b90330 1aaef05d3 Author: Henry R. Winterbottom <[email protected]> Date: Tue Feb 13 17:58:12 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit 1aaef05d317cd1eec548ef2b9842679c531cef8b Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Feb 13 18:15:59 2024 -0500 Jenkins Pipeline updates for Canceling Jobs (#2307) Tuning updates for Jenkins Pipeline : - Added short circuit for all parallel runs of cases on error of any - Fixed canceling of all scheduled jobs on first case error - Added feature to save error log files to Jenkins Archive facility on fail commit 64048926627f8c9edb087de286095e3b93a214c2 Author: Rahul Mahajan <[email protected]> Date: Tue Feb 13 14:57:37 2024 -0500 Ocean/ice product generation for GFS and GEFS (#2286) This PR does several things: 1. the model output for ocean and ice in the `COM/` directory are now named per EE2 convention for coupled model. E.g `gfs.ocean.t12z.6hr_avg.f120.nc` and `gfs.ocean.t12z.daily.f120.nc` 2. The products are generated using the `ocnicepost.fd` utility developed by @DeniseWorthen in https://github.com/NOAA-EMC/gfs-utils and converted to grib2 using example scripts provided by @GwenChen-NOAA using `wgrib2`. 3. NetCDF products on the native grid are also generated by subsetting variables from the raw model output. This is done with `xarray`. 4. updates the hash of https://github.com/NOAA-EMC/gfs-utils to include fixes in `ocnicepost.fd` 5. removes NCL related scripting that was previously used for ocean/ice interpolation and `reg2grb2` used for converting to grib2. 6. updates archive scripts to accommodate updated file names 7. removes intermediate ocean processed files such as 2D/3D/xsect data- sets 8. separate jobs are added for ocean and ice product generation. 9. removes intermediate restarts for the mediator and only saves the medi- ator restart at the end of the forecast in `COM`. 10. Increases memory for offline UPP when run at C768. The program segfaults with an OOM when memory is self allocated based on PEs by the scheduler on Hera. 11. Enables ocean/ice ensemble product generation for GEFS 12. Some minor clean-ups Fixes #935 Fixes #1317 Fixes #1864 commit 40f2cf6cd70ac94e01babc96982f37ae1b0c7e79 Author: henrywinterbottom-wxdev <[email protected]> Date: Tue Feb 13 10:18:53 2024 -0700 Implemented ush/detect_machine.sh for host determination and removed redundant checks for expected file paths. commit 929b90330c7eb345011c2c850915e0004ca26b11 Merge: 2d08d015a 3f99f700c Author: Henry R. Winterbottom <[email protected]> Date: Tue Feb 13 08:31:06 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit 3f99f700c987526c8eb754b3f4c7b698b3e9b1dc Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Feb 13 00:57:18 2024 -0500 Add wave post jobs to GEFS (#2292) Adds the wave post jobs for gridded and points to GEFS. Boundary point jobs are added even though the current GEFS buoy file does not contain any (tested by manually subbing in the GFS buoy file). Resolves #827 commit 842adf38087aec9f1c0bca9567e4b11d494e14c7 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Mon Feb 12 12:50:08 2024 -0500 Added additional test cases to the pr list in Jenkins (#2306) C48mx500_3DVarAOWCDA, C96C48_hybatmDA, and C96_atmsnowDA Co-authored-by: terrance.mcguinness <[email protected]> commit bb4ca65fe5524f76e40b97346339f1dda6680ce1 Author: CatherineThomas-NOAA <[email protected]> Date: Mon Feb 12 14:50:41 2024 +0000 Redo v16.3 config.base changes for DA increments (#2304) Include the additional hydrometeors to the INCREMENTS_TO_ZERO and INCVARS_ZERO_STRAT variables in config.base that were modified in v16.3. Resolves: #2303 commit 061992bb6160554430cf688adf6184f01b732098 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Sat Feb 10 01:33:36 2024 -0500 Fix Jenkins success reporting (#2302) Moving the post section back outside of main Run Experiments stage. This allows the system to correctly report the **Success** status until after all tests pass. _Had originally moved them in attempts to solve "Not an SCM GitHub Job" issue and cause the reporting to misbehave._ Also ran through Jenkins linter and updated some messaging that was incorrectly reporting system build type. commit 28ccf78073a20ba1e4d3b379d164109b54ff6708 Merge: b972f66fc 54daa31ce Author: David Huber <[email protected]> Date: Fri Feb 9 14:00:43 2024 -0600 Merge remote-tracking branch 'emc/develop' into ss160 commit b972f66fc924790c48f38d395e7141fa78ef9d90 Author: David Huber <[email protected]> Date: Fri Feb 9 10:47:00 2024 -0600 Fix SS versions for CI modules. commit 4b01d8eeca26c3b3d843a4b1e7b1618f281de68f Author: David Huber <[email protected]> Date: Fri Feb 9 10:44:30 2024 -0600 Revert Hercules modules to SS/1.5.1. commit 54daa31ce0a3c23d4d74def5e54436a39a899ed4 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Thu Feb 8 15:48:38 2024 -0500 Jenkins Declartive Pipeline for CI with gfs/gefs multibuilds (#2246) Adding top level Jenkins file for CI tests running on Jenkins Controller: - Declarative Multi-branch Pipeline (has enhanced restart capabilities on a per section bases) - Starts Pipeline from Label PR same as BASH system (for now) - Progress and restarts can me managed with CAC Login at [EPIC OAR Jenkins](https://jenkins.epic.oarcloud.noaa.gov) - Has logic for multi **gfs/gefs** system builds (arguments based on a configuration file `ci/casts/yamls/build.yaml`) - Any number of **systems** may be added by manual adding an ele- ment to the matrix in the Jenkinsfile - _It may be possible to dynamic add matrix values with a specialty plug-in_ - Currently only runs on **Orion** and **Hera** using `mterry` account Resolves #2119 Resolves #2118 commit 43429e23c12c1f2050b3a3f356abdec98dc73ea0 Author: Rahul Mahajan <[email protected]> Date: Thu Feb 8 15:30:28 2024 -0500 Enable AO WCDA test (#1963) This PR: - adds GSI + SOCA C48 5-deg ocean 3DVar test (courtesy @guillaumevernieres) - adds a toggle to optionally disable ocnanalvrfy job. commit 2d08d015afb9c850577efd9754add16b10c45ae6 Merge: 4745d4a06 f56352874 Author: Henry R. Winterbottom <[email protected]> Date: Thu Feb 8 07:24:54 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit f56352874d6dc133a4f1181f77c8f91ca38a6416 Author: Kate Friedman <[email protected]> Date: Wed Feb 7 15:09:12 2024 -0500 Update JGLOBAL_FORECAST for octal error (#2295) Add "10#" to ENSMEM value > 0 check to handle octal errors. commit 4745d4a06148cc6c702c647e12ede4875e3a5862 Author: henrywinterbottom-wxdev <[email protected]> Date: Wed Feb 7 08:45:49 2024 -0700 Removed jlogfile references. commit 5894ca2bf11e8ab7910c69781a9fbe51352a7e8c Author: henrywinterbottom-wxdev <[email protected]> Date: Wed Feb 7 08:32:16 2024 -0700 Removed dummy variable passed to perl scripts. commit dae884a7c48b4a30c1844685c3d0ef50c9b78344 Author: henrywinterbottom-wxdev <[email protected]> Date: Wed Feb 7 08:29:49 2024 -0700 Removed jlogfile and postmsg references within gempak scripts. commit 801058ffb0cbbfe101fd5b686aed79c5bf7538c1 Author: Henry R. Winterbottom <[email protected]> Date: Wed Feb 7 00:41:59 2024 -0700 Consolidate `npe_node_max` (#2289) - The environment variable `npe_node_max` is removed from all files beneath `global-workflow/env`; - The environment variable `npe_node_max` is removed from `parm/config/gefs/config.ufs` and `parm/config/gfs/config.ufs`; - The environment variable `npe_node_max` is maintained only within `parm/config/gefs/config.resources` and `parm/config/gfs/config.resources`. Resolves #2133 commit b0325e0157598702cbba6c3cc09af0120881e2b4 Author: Henry R. Winterbottom <[email protected]> Date: Wed Feb 7 00:40:20 2024 -0700 Removes files module loading file no longer used by the GW (#2281) Removes `module-setup.csh.inc` and `module-setup.sh.inc`. The module `ush/module-setup.sh` is updated such that it now sources `ush/detect_machine.sh` to determine which supported platform the global-workflow is being execute on. Resolves #2130 commit 1ccc9896b361f2aaef8e6e7592a06ae4cfb7c491 Author: Walter Kolczynski - NOAA <[email protected]> Date: Mon Feb 5 14:16:07 2024 -0500 Remove EnKF forecast groups (#2280) Removes the grouping of EnKF forecasts so each job only runs one forecast. Member and MEMDIR are now set at the workflow manager (rocoto) level. This change makes much of the system simpler (especially dependencies) and allows the elimination of the separate efcs scripts. Metatask names of updated jobs have been updated to make them a little less opaque by using the same name name as its constituent tasks (e.g. the forecast metatask is named `enkgdasfcst`, not `enkfgdasefcs`). Metatasks that weren't updated retain the same names as before for now. Resolves #2254 commit 9f3383fd8d8322428a40b94764a172a16872995e Author: Henry R. Winterbottom <[email protected]> Date: Mon Feb 5 12:15:13 2024 -0700 Updated detect_machine.sh using that from UFS WM. (#2252) Updates `ush/detect_machine.sh` to match the UFS weather-model `tests/detect_machine.sh` prepared by @BrianCurtis-NOAA Resolves #2228 commit 7d68b0b164f0ffcd56867ae4fdab67905d9589eb Author: CatherineThomas-NOAA <[email protected]> Date: Sun Feb 4 22:02:41 2024 +0000 Update global_cycle for fractional grid (#2262) The hash for ufs_utils is updated to include the changes for fractional grid support within global_cycle. This commit also removes the hack to skip global_cycle in cycling mode with v17 physics. Resolves: #1775 Refs: ufs-community/UFS_UTILS#815 Refs: ufs-community/UFS_UTILS#891 commit ed592a6ecfabc0d0b64a6e276531b7bc5ae3b8ea Author: Kate Friedman <[email protected]> Date: Sat Feb 3 02:55:14 2024 -0500 Retire cycle-specific FHMAX_GFS variables (#2278) This PR retires the `FHMAX_GFS_${cyc}` variables that allowed users to specify different gfs forecast lengths for each cycle. This function is no longer supported in global-workflow. The `FHMAX_GFS_*` variables will be removed and will no longer be checked to set the final `FHMAX_GFS` variable. The same forecast length will be set for every cycle. This PR also includes a small fix to add new post parm files into the `.gitignore` file. This was intended to be included in a different PR but that PR is on hold for further testing so it is being included here to get it into `develop` sooner. Resolves #2218 commit 977e2d67b268477321aa26fc56073dd373e4f979 Author: Henry R. Winterbottom <[email protected]> Date: Fri Feb 2 07:49:09 2024 -0700 New GDASApp hash. (#2285) commit b5f2bd9ec5632c4be43004604eed0e130dfe1735 Merge: 4d667421d 0400e1f35 Author: David Huber <[email protected]> Date: Tue Jan 30 13:55:00 2024 -0600 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 0400e1f3558be8e34c1298d32e14999c9dd46f8c Author: David Huber <[email protected]> Date: Tue Jan 30 09:57:11 2024 -0600 Fix gfs_utils Orion spack-stack env path. commit 6bbe823e729291db326d108765d3a92a99552a58 Author: DWesl <[email protected]> Date: Mon Jan 29 21:15:30 2024 -0500 Use seq to generate the list of times, instead of a bash for-loop (#2264) I'm running a year-long forecast, which means I get a large portion of the log file dedicated to these loops. `seq ${START} ${STEP} ${STOP}` will generate a sequence going from START to STOP by STEP, including STOP if relevant. That seems to be the purpose of these loops. It will by default separate the list with newlines, but `seq -s ' ' ${START} ${STEP} ${STOP}` will separate them with spaces instead, more closely mimicing the previous behavior. I would like this to be two lines in the log, rather than a few hundred, and this may also be faster, though probably more for reasons of fewer writes to disk than because bash isn't designed for arithmetic. commit d5bee38979cde547861261d1cd150f3a61601d4b Author: Kate Friedman <[email protected]> Date: Mon Jan 29 14:35:02 2024 -0500 Correct typos in GFS config.resources (#2267) This PR corrects some typos in `parm/config/gfs/config.resources` that were introduced in PR #2216. The esfc job was failing in tests on WCOSS2 due to insufficient memory. This lead to discovering the other typos. The esfc job completes without error after its memory is set back to `80GB` from the incorrect `8GB`. Resolves #2266 commit 81557beca9eecd878e7b25b3822e30a4276f4a16 Author: David Huber <[email protected]> Date: Mon Jan 29 12:13:31 2024 -0600 Update monitor hash to noaa-emc with SS/1.6.0 support. commit 2238dd6ac0094ba2ff5e1027e964ef29ad33352c Author: DavidHuber <[email protected]> Date: Mon Jan 29 13:21:30 2024 +0000 Update Orion, Hercules, S4 modulefiles. commit 6ffd94fd95f54ceb940f0c9201774ad73fbb055b Author: DavidHuber <[email protected]> Date: Fri Jan 26 16:01:23 2024 +0000 Update GDAS hash to include SS/1.6.0 support. commit be11f85f28cf832e5fbb390fdd387f1bdecb5f82 Merge: 56b968080 04e0772d9 Author: DavidHuber <[email protected]> Date: Fri Jan 26 15:34:24 2024 +0000 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 8ff344844e28c3b2d03a0356f88b14635f318c12 Author: Rahul Mahajan <[email protected]> Date: Fri Jan 26 10:12:18 2024 -0500 Add a yaml for snow DA testing. (#2199) - adds a new test yaml C96_atmsnowDA.yaml for 3DVar atmosphere with GSI and Land (Snow) DA with JEDI - moves a few yamls from platforms/ to yamls/ - adds ability to overwrite a previously created experiment as an addition to user input. --------- Co-authored-by: Cory Martin <[email protected]> commit 04e0772d9d3e77ac5a24ce4570d48cb41424a08b Author: David Huber <[email protected]> Date: Fri Jan 26 07:16:25 2024 -0600 Update ufs_utils hash for spack-stack/1.6.0 support. commit 3d44ff38c5c3324c22fc104fe3259b4ac864c6d6 Author: Barry Baker <[email protected]> Date: Thu Jan 25 14:33:27 2024 -0500 GOCART ExtData biogenic climatology fix (#2253) Updates the ExtData for biogenic emissions to be climatology rather than for current time. Fixes an issue which will crash by default for other years. commit 66f58b8ab1a9524d6be95271f27a06c2f32e5f78 Author: Guillaume Vernieres <[email protected]> Date: Thu Jan 25 13:16:41 2024 -0500 Added missing container case in gfs/config.resources (#2258) fixes #2257 commit 553b4f2e74ef610115436b75f7f6df100babd8dd Author: WenMeng-NOAA <[email protected]> Date: Thu Jan 25 13:00:45 2024 -0500 Fix post parm links (#2243) Change symbolic links under parm/post with the latest version of develop branch from UPP repository and enable MERRA2 aerosol fields. Resolves #2259 commit 4d667421d5eefea2347ea1dd8097e39e167d7201 Merge: 6c058039e afa09e356 Author: David Huber <[email protected]> Date: Thu Jan 25 07:49:08 2024 -0600 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 6c058039e209c67ea477d37d2d6f76b7a2fa68ac Author: David Huber <[email protected]> Date: Thu Jan 25 07:48:42 2024 -0600 Fix wgrib2/gfs_utils on Hercules. commit ee6f536ea0228c60f5a8bec4037cd6f7ea63b816 Author: Kate Friedman <[email protected]> Date: Thu Jan 25 07:43:13 2024 -0500 Update GFS version to v16.3.13 in index.rst (#2256) GFSv16.3.13 WAFS update was implemented Refs #2013 commit 2445d44d0d66f35512080b0bd5867501660793bb Author: RussTreadon-NOAA <[email protected]> Date: Thu Jan 25 06:17:11 2024 -0500 Simplify and extend load_ufsda_modules to Hercules (#2245) GDASApp jobs do not run on Hercules because `ush/load_ufsda_modules.sh` does not include logic to load the appropriate GDASApp modules on Hercules. This PR extends `load_ufsda_modules.sh` functionality to Hercules, thereby enabling GDASApp jobs to run on Hercules. Resolves #2244 commit 56b9680803f109720f6439276a0e5783a9c49352 Author: DavidHuber <[email protected]> Date: Wed Jan 24 19:47:34 2024 +0000 Update hashes (revert WCOSS2 modules). commit afa09e356503f1befc162df9a79dc9ce7414dc22 Author: DavidHuber <[email protected]> Date: Wed Jan 24 18:59:40 2024 +0000 New (cleaner history) gdas hash. commit a9eaec23d5103ea766342ff81d77df8e0f6d9a58 Author: DavidHuber <[email protected]> Date: Wed Jan 24 18:52:27 2024 +0000 Update gdasapp to include ss/1.6.0 support. commit 5ef8eb24eeaeaff9c9a03767d929f2114fd4840f Merge: 4c463548b e400068a2 Author: DavidHuber <[email protected]> Date: Wed Jan 24 17:08:54 2024 +0000 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 4c463548b0c38f36c13c01716fa0b1e91544e440 Author: DavidHuber <[email protected]> Date: Wed Jan 24 17:05:12 2024 +0000 Reenable verif-global support commit f775755df5f1579edfafbce9a7b47034907d023f Author: DavidHuber <[email protected]> Date: Wed Jan 24 16:59:10 2024 +0000 Assign fcsthrs for awips_g2 job. commit e400068a2951e5fa3b130369861b4a60ece01491 Author: David Huber <[email protected]> Date: Mon Jan 22 15:01:07 2024 -0600 More gsi-addon path fixes. commit f663d4786f226f8164d348d403e8d105cc3d801b Author: David Huber <[email protected]> Date: Mon Jan 22 14:41:59 2024 -0600 Fix gsi-addon paths for hercules, orion, and S4. commit e304bbeb364067e411fb50801796d000b44d9147 Author: DavidHuber <[email protected]> Date: Mon Jan 22 18:59:34 2024 +0000 Better optimize build jobs (more ufs jobs). commit ccc6e2d445d4c2e2f44fb907c7bc972b1e69f6ff Author: DavidHuber <[email protected]> Date: Mon Jan 22 18:56:18 2024 +0000 Reenable verif-global. #2195 commit 3ef3411f856b0c5a9cf51686f3a51a2252596690 Merge: 4365f63e5 f4d187f4e Author: DavidHuber <[email protected]> Date: Mon Jan 22 18:39:10 2024 +0000 Merge remote-tracking branch 'origin/develop' into ss160 commit 4365f63e54e2ddb9b88e768a6e88a92504b5d482 Author: DavidHuber <[email protected]> Date: Mon Jan 22 18:37:25 2024 +0000 Corrected the SS env. name in the version files. #2195 commit f4d187f4e45fe89583d18987d68a883490827104 Author: AndrewEichmann-NOAA <[email protected]> Date: Mon Jan 22 12:28:28 2024 -0500 Converts obsproc to obsprep in prepoceanobs config file (#2236) Converts obsproc to obsprep in prepoceanobs config file as a compliment to mutually depended GDASApp PR NOAA-EMC/GDASApp#858 The motivations are explained in refs NOAA-EMC/GDASApp#857 commit 9a09d3082208ad206cf6e7103a53bfb7c4946f4a Author: DavidHuber <[email protected]> Date: Fri Jan 19 21:23:50 2024 +0000 Corrected gsi-addon-dev spelling. commit 21ff6458aac9372b26cc223f6a114953a137067e Author: DavidHuber <[email protected]> Date: Fri Jan 19 21:11:34 2024 +0000 Update modulefiles, submodules to spack-stack 1.6.0. #2195 commit d4c55d1011f8b0385d25b62ac04710837ed8413e Author: Kate Friedman <[email protected]> Date: Fri Jan 19 15:43:37 2024 -0500 Update typing hint for WCOSS version of python (#2238) The typing hint `typing.List` was deprecated with python 3.9 in favor of using the primitive `list[str]`, but the functional version of python on WCOSS2 is <3.9, causing `setup_xml.py` to fail there. This replaces `list[str]` as a typing hint with the deprecated form until the supported version on WCOSS2 is >=3.9. commit 491928712ae1dabac62750450c9cad8f538c2a3e Author: Barry Baker <[email protected]> Date: Thu Jan 18 22:31:27 2024 -0500 GOCART Emission updates for GEFSv13 and GDAS (#2201) This PR addresses several things needed for more recent simulations using GOCART2G as well as preparing for the GEFSv13 30 year run. The main updates are: - Update CEDS to use monthly emission files instead of daily. This will drastically reduce the number of files needed. No science change - Update biogenic MEGAN inputs to use a climatology rather than the offline biogenic previously used. This is needed to deal with simulations where the current dataset is not available. - Update volcanic SO4 emissions to use degassing emissions only. This is to support the need for more recent simulations where data is not available. commit 13d25cfc3614de978bfd4b7f273d1f13cb820878 Author: Kate Friedman <[email protected]> Date: Thu Jan 18 22:29:43 2024 -0500 Add `POSTAMBLE_CMD` into preamble postamble (#2235) This PR adds the ability to run a command at the end of jobs via the preamble's postamble function. A new command can be set via `POSTAMBLE_CMD` and will be invoked at the end of jobs. Users can add the command to the top of an env file to have every job run it or it can be placed within a job if-block in the env file to run for just that job. Resolves #1145 commit 7759163c668eb6ccc11dc1ecd39c0dc5d433cdc1 Author: Rahul Mahajan <[email protected]> Date: Thu Jan 18 01:13:49 2024 -0500 Add option to…
This issue has come up for GEFS in PR #2561. In the GEFS reforecast, |
Description
Currently it's hard-coded in the diag_table that ocean output is 6 hourly: https://github.com/NOAA-EMC/global-workflow/blob/develop/parm/parm_fv3diag/diag_table#L3
However, @jiandewang found that there are currently constraints in that the ocean/ice (which must be consistent because of the currently combined grib output), must also be the same as the forecast model due to these lines in the scripts:
ush/forecast_postdet.sh:
Requirements
Ideally we can run without hard-coding the 6-> (atm time step) and have the ocean/ice model have different time steps.
Acceptance Criteria (Definition of Done)
Be able to run with 3 hourly atm time-steps and 6 hourly ocean or 3 hourly atm and ocn/ice and not have to change anything other than a config file.
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