Add switch to control debug=true on WCOSS2 for development testing
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- When pbspro: add debug=true to native statement; similar to what already happens but now users can turn it off - When slurm: add SBATCH_DEBUG=2 (-vv, very verbose) to xml; exports SBATCH_DEBUG to environment for all jobs Refs NOAA-EMC#619
Set SBATCH_DEBUG via the envars in the xml instead of as an ENTITY at the top. The setting now exports with job submissions. Refs NOAA-EMC#619
* origin/develop: Return ocnanalrun npes resource setting back to previous value (NOAA-EMC#2386) Add new BUFR table file parm/product/bufr_ij9km.txt for GFSv17 C1152 (NOAA-EMC#2383) Add global-workflow infrastructure for ocean analysis recentering task (NOAA-EMC#2299) Clean out non-gfs top level variables (NOAA-EMC#2366) Forgotten templated DO_VRFY_OCEANDA (NOAA-EMC#2379) Add Hercules support for the GSI monitor (NOAA-EMC#2373) Reformat snowDA templates to jinja2 (NOAA-EMC#2371) Reduce Jenkins messaging to GitHub (NOAA-EMC#2370) Adding debug option for all build scripts (NOAA-EMC#2326) Sort list of coupler restart files for restart time determination (NOAA-EMC#2360) Update stage IC to handle ocean perturbations (NOAA-EMC#2364) Turn on C48mx500_3DVarAOWCDA test on hera (NOAA-EMC#2363) Move Jenkinsfile into ci subdirectory (NOAA-EMC#2355)
Removing the debug switch setting for SLURM since it doesn't work as expected. Also added notes to DEBUG setting in configs to note that it only works on WCOSS2. Refs NOAA-EMC#619
aerorahul
reviewed
Mar 11, 2024
aerorahul
approved these changes
Mar 11, 2024
- Rename DEBUG to DEBUG_SCHEDULER. - Add note that it's PBS only and that it sets debug=true. - Add switch to documentation. Refs NOAA-EMC#619
Rename variable in setup scripts Refs NOAA-EMC#619
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@KateFriedman-NOAA This looks good to me. Just a FYI, the following exists for SLURM: OPT_DebugFlags. It is more convoluted than the above, but this is more intended as a FYI and beyond the scope of this PR (and likely anything else we might need). |
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Thanks @HenryWinterbottom-NOAA ! I spoke with the Hera sysadmins about those options too but they are also meant for the admin side of the scheduler and not for users. |
@KateFriedman-NOAA That makes sense. The nerd in me has SLURM running on a small cluster here, so I forgot that it required admin permissions. Thank you for the heads up. |
Based on reviewer feedback and discussion. Refs NOAA-EMC#619
RTD sample link was not posted in updated PR. Add missing curly brackets to line. Refs NOAA-EMC#619
WalterKolczynski-NOAA
approved these changes
Mar 11, 2024
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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…
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Description
This PR adds a switch (
DEBUG_POSTSCRIPT) to control whetherdebug=trueis set when submitting development rocoto jobs to PBS schedulers (currently just WCOSS2). This switch added toconfig.basewill only work and be invoked on PBS platforms (e.g. WCOSS2). There isn't an equivalent flag to set for SLURM on the RDHPCS. Have added this new switch to documentation.The
DEBUG_POSTSCRIPTswitch inconfig.basewill be set to off/"NO"by default.This PR does not touch the
debug=truesettings in the ecf scripts, which should remain for ops per NCO requests.Resolves #619
Type of change
Change characteristics
How has this been tested?
Low res tests on Hera and WCOSS2.
Checklist