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Merge gsl_ufs_dev from EMC develop (emc_dev_mar4_732a874a)
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
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