Update intel compile to Intel2022 #571
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Bring in upstream changes 9/10/2020
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@hu5970 , thank you for opening this PR. Since [email protected] is working on GSI intel2020+ and hdf5 issue, we should add him as a reviewer to this PR. Others potential reviewers include
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modulefiles/gsi_common.lua
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| @@ -6,12 +6,13 @@ local netcdf_ver=os.getenv("netcdf_ver") or "4.7.4" | |||
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| local bufr_ver=os.getenv("bufr_ver") or "11.7.0" | |||
| local bacio_ver=os.getenv("bacio_ver") or "2.4.1" | |||
| local w3emc_ver=os.getenv("w3emc_ver") or "2.9.1" | |||
| local w3emc_ver=os.getenv("w3emc_ver") or "2.9.2" | |||
| local w3nco_ver=os.getenv("w3nco_ver") or "2.4.1" | |||
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Why is is necessary to add w3nco to the list of common modules to build with intel2022?
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@RussTreadon-NOAA w3nco was loaded by nemsio versions 2.5.2 and earlier, but is no longer, so it now needs to be loaded explicitly.
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Thanks for the explanation.
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@DavidHuber-NOAA
If you are loading nemsio, 2.5.4, it depends on w3emc. You no longer need w3nco.
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@aerorahul I removed the w3nco load. Thanks! Note there is a placeholder for the new ncdiag library here which provides a local install on Hera presently. I will update this when the new ncdiag PR is merged and the new tag is installed everywhere.
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| help([[ | |||
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| prepend_path("MODULEPATH", "/scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/modulefiles/stack") | |||
| prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/miniconda3/modulefiles") | |||
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Does this prepend_path point at the official installation all UFS and EMC apps should use?
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Others should also confirm but the MODULEPATHs I see in this PR jive with the ones that ufs-weather-model moved to (ufs-community/ufs-weather-model#1465) and which global-workflow and other components are also moving to. The ufs-weather-model issue I refer to has a nice listing at the top of the various machine installs.
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The updated prepend_path and module versions all come from ufs-weather-model develop for Hera, Jet, and Orion.
I did not change setup for other machines because I cannot access them. But the ufs-weather-model develop still use intel 19 for wcoss2, which should be updated for both model and GSI.
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Let's work with g-w and others to update as many modulefiles as possible. Tagging @KateFriedman-NOAA , natalie-perlin, and @GeorgeVandenberghe-NOAA , and [email protected]. Should anyone be removed from this list? Should anyone be added?
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Looks like all of the (fully) supported R&D platforms are covered in this PR (Hera, Orion, Jet). @DavidHuber-NOAA is providing updates for S4 (low support). WCOSS2 is not considered in this PR since it's only intel 2019 still and not EPIC-maintained hpc-stacks. Will update WCOSS2 to intel 2022 at a later date (likely when we move to spack-stack but not 100% on that). Updates in this PR should not break WCOSS2 functionality.
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OK. GSI develop must use officially approved and maintained modules. It would be good to get confirmation from EMC g-w and library staff that this PR brings in the correct modules and versions.
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Paths look correct. A couple versions are ahead of where workflow is (and not in UFS), but we can update to match.
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Is this resolved, then?
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If GSI paths are ahead of g-w, will gsi.x and enkf.x run correctly in g-w?
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This will need to be resolved in the g-w. I linked this discussion into the relevant issue NOAA-EMC/global-workflow#812. I believe this conversation can be resolved.
src/gsi/screen_to_ncdiag.f90
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| @@ -0,0 +1,30 @@ | |||
| module screen_to_ncdiag | |||
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It seems this new subroutine could / should be added to the ncdiag module for use by a larger body of applications.
We build gsi.x and enkf.x using module ncdiag/1.0.0.
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@RussTreadon-NOAA I started looking into this option, but there is at least one challenge. How should missing values be defined in ncdiag? That library doesn't have an r_missing variable. We could define one for each of the data types supported, but how would we remain consistent between the GSI, EnKF, and ncdiag?
This also brings up a side note. I picked r_missing not knowing if that was the best option. I noticed several places where apparent missing values of -99999.0, -999.0, and others were used. Should <kind>_missing=-9999_<kind> be the standard?
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Good points. Let's hear what others have to say.
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@RussTreadon-NOAA After reading through this again and thinking about it, I believe the best solution is to move this subroutine to ncdiag. I've opened issue NOAA-EMC/GSI-ncdiag#1 and will have a PR opened shortly. As for the missing value, netCDF4 defines a missing value as NF90_FILL_FLOAT, which is already used when writing 2d data in nc_diag, so I will go ahead with that as the replacement for NaN.
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These functions have been moved to the ncdiag library and all of the use statements updated to include them.
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Merged current head of develop into working copy of hu5970:intel2022. Build and run global_3dvar ctest. The update stdout is significantly larger than the control stdout.
Orion-login-4:/work/noaa/stmp/rtreadon/pr571/tmpreg_global_3dvar$ ls -l global_3dvar_*/stdout
-rw-r----- 1 rtreadon stmp 4529880 Jun 12 17:17 global_3dvar_hiproc_contrl/stdout
-rw-r----- 1 rtreadon stmp 954584015 Jun 12 17:00 global_3dvar_hiproc_updat/stdout
-rw-r----- 1 rtreadon stmp 4482084 Jun 12 17:10 global_3dvar_loproc_contrl/stdout
-rw-r----- 1 rtreadon stmp 954584220 Jun 12 16:54 global_3dvar_loproc_updat/stdout
Orion-login-4:/work/noaa/stmp/rtreadon/pr571/tmpreg_global_3dvar$
Orion-login-4:/work/noaa/stmp/rtreadon/pr571/tmpreg_global_3dvar$ wc global_3dvar_*/stdout
72786 557117 4529880 global_3dvar_hiproc_contrl/stdout
16451292 131604233 954584015 global_3dvar_hiproc_updat/stdout
71349 552335 4482084 global_3dvar_loproc_contrl/stdout
16451295 131604251 954584220 global_3dvar_loproc_updat/stdout
A check of the update stdout shows thousands lines of printout containing
** WARNING: Invalid metadata operator: *. Writing FILL
** WARNING: Invalid metadata operator: *. Writing FILL
** WARNING: Invalid metadata operator: *. Writing FILL
We need to turn off or at least limit the amount of WARNING: Invalid metadata operator: *. Writing FILL printout.
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@RussTreadon-NOAA This is worrisome. These should not be getting printed out. Looking at lines 1269-1275 of ncdw_metadata.f90, * should be a valid operator, so that error should not be printed:
case("*")
if(isnan(metadata_operand_x) .or. isnan(metadata_operand_y)) then
f_metadata_value = NLAYER_FILL_FLOAT
else
f_metadata_value = &
sngl(metadata_operand_x * metadata_operand_y)
endif
I will see if I can replicate these warnings and debug.
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I see the issue. Using a string length of 2 for the input operator to the nc_diag_metadata_to_single_operator subroutine results in the second character being filled with the next byte of memory if that operator is only length 1. A character length of * should be used instead. I had caught this locally, but never committed it, which is why it worked in testing previously.
I'll make the change to ncdiag, test it, and open a PR.
src/gsi/genstats_gps.f90
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| @@ -753,6 +753,8 @@ end subroutine contents_binary_diag_ | |||
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| subroutine contents_netcdf_diag_ | |||
| use sparsearr, only: sparr2, readarray, fullarray | |||
| use constants, only: r_missing | |||
| use screen_to_ncdiag | |||
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GSI coding standards require
- All module declarations must explicitly specify which module components (variables or routines) are used within the given routine (e.g., use constants, only: zero, one, two)
To conform to this standard we need
use screen_to_ncdiag, only: screen_to_single_nc_diag_metadata
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screen_to_ncdiag no longer referenced in src/gsi
7 tasks
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Did we correct the other GSI issue(s) that were causing hangs with
hdf5/1.14.0?
…On Mon, Sep 11, 2023 at 7:07 PM arun chawla ***@***.***> wrote:
Let us complete this PR. We can have a separate one for update to netcdf
4.9,2 and hdf5 1.14.0. Yes this does not have intel 2022 on wcoss2, but it
works with intel 2022 everywhere else and does not break with intel 19 on
wcoss2. That is good progress. We can update to intel 2022 on wcoss2 when
it is available there
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Changes were committed but more extensive testing with |
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@GeorgeVandenberghe-NOAA - there are no known issues with hdf5/1.14.0 and netcdf/4.9.2 (Orion/Hercule, Hera, Jet, Gaea, Gaea C5, Cheyenne/ Derecho) |
natalie-perlin
approved these changes
Sep 12, 2023
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Thank you @natalie-perlin for the approval. I will run ctests using If anyone else on this PR can review the changes that would be appreciated. GSI code management policy requires two peer reviews and approvals plus a review and approval from a Handling Review team member. |
DavidHuber-NOAA
suggested changes
Sep 12, 2023
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| help([[ | |||
| ]]) | |||
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| prepend_path("MODULEPATH", "/scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/modulefiles/stack") | |||
| prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/miniconda3/modulefiles") | |||
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This will need to be resolved in the g-w. I linked this discussion into the relevant issue NOAA-EMC/global-workflow#812. I believe this conversation can be resolved.
DavidHuber-NOAA
approved these changes
Sep 12, 2023
…s for updat and contrl ctest jobs (NOAA-EMC#447)
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In running ctests on Hera and Orion find that apart from Therefore, replace Variable Test and confirm that the updated |
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Hera and Orion ctests 7 out of 9 tests fail on Hera due to different analysis results. Analysis differences appear to originate from numerical roundoff. 2 tests generate identical analyses but fail other checks. Details below:
5 out of 9 tests fail on Orion due to different analysis results. Analysis differences appear to originate from numerical roundoff. 4 tests yield identical analysis results but fail other checks. Details below:
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RussTreadon-NOAA
approved these changes
Sep 12, 2023
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…1882) This PR changes the module loads in g-w jobs `anal.sh`, `eobs.sh`, and `eupd.sh` to use machine specific modulefiles from `sorc/gsi_enkf.fd/modulefiles`. This is necessary because [NOAA-EMC/GSI#571](NOAA-EMC/GSI#571) updated `gsi.x` and `enkf.x` builds to intel/2022 on NOAA RDHPCS machines. Resolves #1863
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global-workflow: 02Jan24, 9d901db UFS: 21Dec23, 991d652 UPP: 07Nov23, 78f369b Squashed commit of the following: commit 4e4e50803d95566e1c7967cf4cfa575391d77f25 Author: Judy.K.Henderson <[email protected]> Date: Fri Jan 12 00:44:59 2024 +0000 Change default HPSS_PROJECT to fim Change restart_interval_gfs to -1 so no files are written ro RERUN_RESTART directory commit 791d7a27c6b12f07d9c12ce491338e3da59eb1d8 Author: Judy.K.Henderson <[email protected]> Date: Thu Jan 11 23:34:36 2024 +0000 Add namelist parameter, nord_tr, for GSL suites commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5 Author: Judy.K.Henderson <[email protected]> Date: Thu Jan 11 23:31:22 2024 +0000 Add changes for running v17p8_mynn - new field table, field_table_thompson_aero_tke_progsigma - updated namelist parameters in config.fcst commit 982a1f02e3b880be43f4ae8a3f0ffbb34c056aea Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 9 02:26:22 2024 +0000 Add experiment setup script for p8_ugwpv1 commit c5a3697d22fdbb02bb80ddffee2629dddc10c702 Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 9 02:19:13 2024 +0000 Add memory report to srun command in env/HERA.env commit ece7e516ca65ec0240899e7d84321310a6887595 Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 9 02:13:42 2024 +0000 Updated GSL-specific files under ufs_utils.fd_gsl commit 1b153fc95b93a16eb40b791be7322100fde4a3d4 Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 9 01:52:56 2024 +0000 Create new branch, gsl_ufs_dev, from dev_02jan24_9d901db Add initial GSL modifications - changes to workflow files * GSL paths, projects, entities - new FV3_GFS_v17_p8_ugwpv1_mynn suite definition file (SDF) - updated namelist parameters in ush/parsing_namelists_FV3.sh - create new GSL directories: ufs_model.fd_gsl and ufs_utils.fd_gsl * new SDFs, add instantaneous flux variables to grib2 configuration files * add Thompson tracers to initial conditions - new sync script: rsync_gsl.sh - new job files: getic.sh, makeinit_link.sh - modify build_ufs.sh to include MYNN SDF commit 9d901dbbff4d41586580316bdc094d24760119e6 Author: Henry R. Winterbottom <[email protected]> Date: Tue Jan 2 10:30:33 2024 -0700 Stop Gempak pgrb2 spec from modifying $DATA (#2147) This PR addresses issue #1224. The following is accomplished: - Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time; - Shell linter exceptions are addressed accordingly; - The respective GEMPAK tasks is added to the Rocoto mesh. Resolves #1224 commit 31ad23527802f7d07171132cc620f7135c4d8cba Author: Henry R. Winterbottom <[email protected]> Date: Tue Jan 2 10:27:30 2024 -0700 Reorganize NPOESS scripts (#2166) This PR addresses issue #1226. The following is accomplished: - Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated; - Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh` are moved accordingly; this specifically applies to the environment variable `FHOUR`, `SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`; - The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level (if necessary); - Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however, this may not be necessary (see `TODO` note within draft PR. Resolves #1226 commit 22bd82fa93b49e5ce98eb3f69123956dd5018049 Author: Kate Friedman <[email protected]> Date: Tue Jan 2 11:55:03 2024 -0500 Orog fix file reorg and fix directory variable standardization (#2181) This PR makes updates to use the newly reorganized `orog/20231027` fix file version and standardizes the fix file directory variables. Changes: 1. Update UFS_UTILS hash to ce385ce 2. Update fix file version file to use new orog timestamp: `orog_ver=20231027` 3. Add ".mx$(OCNRES)" to `oro_data` filenames in scripts 4. Remove ".mx$(ocn_res)_frac" from the directory names for atmosphere resolutions under the `/orog` folder 5. Adds fix file directory variables to `config.base`, many of which are pulled up out of lower scripts; introduce `FIXcpl` 6. Renamed/replaced the following fix file directory variables: - `FV3JEDI_FIX` --> `FIXgdas` - `FIXfv3`, `FIX_orog` and `OROFIX` --> `FIXorog` - `FIX_ugwd` and `OROFIX_ugwd` --> `FIXugwd` - `FIX_am`, `FIXgsm`, `FIXSYND` --> `FIXam` - `FIX_lut` --> `FIXlut` - `FIX_aer` --> `FIXaer` - `FIX_SFC` --> `FIXsfc` - `FIX_DIR` --> `FIXgfs` - `RTMFIX` and `FIXCRTM` --> `CRTM_FIX` (is `CRTM_FIX` in crtm module, so not using `FIXcrtm`) 7. Correct the defaults for `FIXwave` in wave JJOB scripts 8. Update variable names in `*fixed_files.yaml` files, as well as update naming convention for `oro_data` files Resolves #1984 Resolves #1981 Resolves #2175 commit 03d03bf53b43914a55c384cb33eb06f6a9a443a6 Author: Andrew Collard <[email protected]> Date: Tue Jan 2 11:53:44 2024 -0500 Remove HIRS from GSI processing (#2183) With the update to CRTM 2.4.0.1, an issue with versioning of CRTM HIRS files has been exposed. This is documented in JCSDA/crtm#42. As HIRS radiances are no longer used in the GSI, these data should be removed from processing until a suitable update to CRTM is available. Resolves #2182 commit a3c50998d35525a39a66d5592fbf327ab3569e8b Author: Jessica Meixner <[email protected]> Date: Fri Dec 22 18:07:48 2023 -0500 Update ufs-weather-model version (#2186) * update model to latest version which includes needed bugfixes for HR3 commit 774c7302e618370ef578bec3ccabc70486d6da1b Author: David Huber <[email protected]> Date: Fri Dec 22 11:34:53 2023 -0500 Fix analysis post processing's handling of 0-padded negative integers (#2187) This screens for the analysis 'forecast' hour (-001) and handles the '-' and circumvents octal issues. commit d1251360325faf75af9df0608557fcd10202a883 Author: Barry Baker <[email protected]> Date: Thu Dec 21 11:23:48 2023 -0500 Fix for restoring cycling aerosols in fo-mode post COM refactor (#2179) - Update to COM reorg aerosol initialization job - Address bug in joining paths for data dependency in this job --------- Co-authored-by: Rahul Mahajan <[email protected]> commit e55a05980709288d902ad1bd894164bfa5a18a65 Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Dec 20 22:14:01 2023 -0500 Stop calling ufs-utils link script (#2172) The `link_workflow.sh` script was calling the ufs_utils version of the same. That step is only necessary if a user is going to run one of the stand-alone ufs-utils, which is rare. commit ef3e5ad7c63be1644c82333c95853c3caf2d8995 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Dec 19 22:02:55 2023 -0500 Fix handling of excluded hosts list (#2170) This PR fixes the issue with `create_experment.py` so that the yaml configuration file can have a string of list of strings when specifying the host name to exclude from the CI tests. commit ea74a5719efc8f0fe631c5ff93426a4299a614f3 Author: AndrewEichmann-NOAA <[email protected]> Date: Tue Dec 19 16:21:41 2023 -0500 Add COMOUT_OBS to marine obs prep (#2173) Adds `COMOUT_OBS` (defined from `COM_OBS_TMPL`) to marine obs prep task to properly handle marine obs prep files. Used to keep obs after IODA conversion, QC, and other prep. Towards resolving NOAA-EMC/GDASApp#815 commit c2500feace0bb7c04ce67a90dd3182120ee67b2e Author: David Huber <[email protected]> Date: Tue Dec 19 14:55:20 2023 -0500 Return failed status if a build fails. (#2171) If any of the builds fail, this makes build_all.sh return the sum of the error codes encountered. Fixes #2168 commit 76fdd81cd84ed812181996a102379d8d964ba27a Author: Kate Friedman <[email protected]> Date: Tue Dec 19 13:24:34 2023 -0500 Update index.rst for new GFSv16.3.12 in ops (#2169) Refs #2096 commit a81da33e8fe7541a36f68e7a4f14a384cadd36c8 Author: Kate Friedman <[email protected]> Date: Tue Dec 19 10:22:21 2023 -0500 Set place=shared for shared jobs on WCOSS2 (develop) (#2156) Set job as shared when not exclusive on WCOSS2 WCOSS2 defaults to exclusive when it is not specified as either exclusive (place=exclhost) or shared (place=shared). Now set shared when job should be shared. Refs #2135 commit 89aea972f7964dac3f515e8070d7c534812c5fb4 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Dec 15 16:31:06 2023 -0500 Update gfs-utils version for Hercules (#2163) An update of gfs-utils was misssing from the previous PR that added initial Hercules support (#2128). Also includes gfs-utils update for new marine post. commit 9505cb4abc6ca2643a8ab254d14ca2000747fa44 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Thu Dec 14 16:15:31 2023 -0500 CI Updates to support Hercules (#2155) If merged, this PR will update the CI scripts so they will run on Hercules for forecast only NOTE: This is a stop gap to issue #2131 until its block on #1588 is removed. Resolves #2154 commit c5ca82f04a2efae78389dec1c46b94ef4fb5bbe5 Author: Rahul Mahajan <[email protected]> Date: Thu Dec 14 16:05:33 2023 -0500 Correct fbwind (#2161) commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a Author: Kate Friedman <[email protected]> Date: Thu Dec 14 12:06:23 2023 -0500 Add MOS jobs to rocoto mesh (#2148) Create separate jobs for GFS MOS - extracted from now-retired vrfy job Refs #2068 commit bb6151aa50c27253cb9b8f0a6601ddd58526b8b3 Author: Walter Kolczynski - NOAA <[email protected]> Date: Thu Dec 14 05:38:29 2023 -0500 Replace checkout script with submodules (#2142) Replaces the checkout script with git submodules. This change brings workflow in line with other repos and git standards. Due to these changes, the build system is updated slightly. First, the options that were formerly used with `checkout.sh` to reduce unneeded builds (`-g` for GSI and `-u` for UFSDA) are moved to `build_all.sh` instead. This is needed since build all will not be able to key off directories existing or not to determine which com- ponents to build. Second, the partial build system is removed. It was rarely, if ever, used, and parts of it were already ignored with the previous changes to base builds off whether directories exist. The manage externals file is also removed since that is also not being used. Following these changes, clones/checkout will need to either be recursive, or `git submodule update` will need to be called separately to make sure components are properly checked out (non-exhaustive list): ``` ## Checkout develop (method 1) git clone --recursive https://github.com/NOAA-EMC/global-workflow destination ## Checkout develop (method 2) git clone --jobs 8 https://github.com/NOAA-EMC/global-workflow destination cd destination git submodule update --init --recursive --jobs 8 ## Checkout existing branch some_branch (method 1) git clone --recursive --jobs 8 -b some_branch https://github.com/NOAA-EMC/global-workflow destination ## Checkout existing branch some_branch (method 2) git clone https://github.com/NOAA-EMC/global-workflow destination cd destination git checkout --recurse-submodules some_branch ## Checkout existing branch some_branch (method 3) git clone https://github.com/NOAA-EMC/global-workflow destination cd destination git checkout some_branch git submodule update --init --recursive --jobs 8 ## Checkout new branch new_branch git clone https://github.com/NOAA-EMC/global-workflow destination cd destination git checkout -b new_branch git submodule update --init --recursive --jobs 8 ``` The git ignore list had to be updated to use explicit paths as the wildcard paths pick up the ones that are now submodules. UFS creates files during the build process that are not in its ignore list, so that sub- module ignores the "dirty" state to avoid confusing users running `git status`. CI and documentation are also updated to reflect the changes. Resolves #2141 commit 1332188ce2409e012ec127d44880e49732f7f379 Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Dec 13 09:32:57 2023 -0500 Enable radar reflectivity output (#2143) Turns on radar reflectivity output from FV3. This eliminates missing values appearing in the grib2 files. commit 24d898ec0ec0c7fcbda6966988f9a986f528ed14 Author: David Huber <[email protected]> Date: Wed Dec 13 09:32:24 2023 -0500 Fix Hercules hostname (#2150) * Allow lower or upper hostname on hercules. * Add Hercules to issue template. commit 2896bb8787698be28ad20f2298589e6e95eaf9fb Author: Kate Friedman <[email protected]> Date: Tue Dec 12 09:13:06 2023 -0500 Fix module load typo (#2145) Fix typo with loading the crtm module in the UPP hack for WCOSS2 Refs #2144 commit 29d34172a67d976f910e78158ff0337e1ef099ca Author: Cory Martin <[email protected]> Date: Thu Dec 7 15:12:05 2023 -0500 Update GDAS hash to most recent stable versions (#2138) commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102 Author: Henry R. Winterbottom <[email protected]> Date: Thu Dec 7 10:41:05 2023 -0700 Corrected typo in a gempak job gempakncdcupapgif . (#2137) commit 3483f550db1ae35a680de49f7485ce5a11902dd9 Author: Cory Martin <[email protected]> Date: Thu Dec 7 12:34:56 2023 -0500 Add support for FGAT and IAU for aerosol DA (#1940) commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9 Author: David Huber <[email protected]> Date: Thu Dec 7 12:33:46 2023 -0500 Enable forecast-only experiments on Hercules (#2128) This add forecast-only support for Hercules to the global workflow. Partially satisfies #1588. Co-authored-by: Walter Kolczynski - NOAA <[email protected]> commit a29f751aed05312da3d80d396159bb5a906d6ce4 Author: Henry R. Winterbottom <[email protected]> Date: Wed Dec 6 13:45:56 2023 -0700 Adds GEMPAK and related jobs to rocoto task mesh (#2127) commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082 Author: Rahul Mahajan <[email protected]> Date: Tue Dec 5 15:47:52 2023 -0500 Separate offline UPP from interpolated grib2 product generation (#2110) This PR: - Replaces the use of `JGLOBAL_ATMOS_POST` with `JGLOBAL_ATMOS_UPP` and `JGLOBAL_ATMOS_PRODUCTS`. - Introduces `JGLOBAL_ATMOS_PRODUCTS` that is responsible for creating grib2 products from the master file produced by UPP (inline from the model, or offline by running `JGLOBAL_ATMOS_UPP`). Rocoto job `atmos_products.sh`, ex-script `exglobal_atmos_products.sh` are also added along with a `config.atmos_products`. Updates are made to the relevant `env` files as well as `config.resources` to reflect the addition of this job. - reduces the number of cores needed appropriately for forecast products when there is no offline UPP necessary. - renames older `fv3gfs_dwn_nems.sh` to `interp_atmos_master.sh` and `inter_flux.sh` to `interp_atmos_sflux.sh` - removes `fv3gfs_downstream_nems.sh` as it is absorbed into `exglobal_atmos_products.sh` - removes no longer used scripts for `gfs_post.sh`, `gfs_transfer.sh` (DBN alerts are absorbed into `exglobal_atmos_products.sh`), `post.sh`, `JGLOBAL_ATMOS_POST`, `ex${RUN}_atmos_post.sh` scripts. - Rocoto workflow related scripts are updated to add `atmos_products` as a job. When `WRITE_DOPOST` is `.false.`, `upp.sh` job to run the UPP offline is also added. Dependencies have been appropriately applied. - removes `PGB1F` option that creates 1-degree grib1 products that are no longer needed in GFSv17. The hacks from (now deleted) `post.sh` had to be reinstated in `upp.sh` to load the modules from UPP instead of `load_fv3gfs_modules.sh`. commit 44186f594aaf5f8feea0eadd4c5c3b59de3a825e Author: Kate Friedman <[email protected]> Date: Tue Dec 5 12:28:08 2023 -0500 Update index.rst for new GFSv16.3.11 version (#2121) Refs #1356 commit e62a3a73cd22701962b7bf210fdfee37f37a5474 Author: Henry R. Winterbottom <[email protected]> Date: Tue Dec 5 09:08:12 2023 -0700 Splits AWIPS jobs into seperate tasks (#2094) This PR addresses issue #1228. The following is accomplished: - Separate rocoto jobs have been created beneath `jobs/rocoto/` -- `awips_20sh` and `awips_g2sh`; these jobs replace `awips.sh` which was calling multiple J-jobs within the respective `awips.sh` scripts; - New tasks has been added to `workflow/rocoto/tasks.py` for the new AWIPS scripts; - The `gfs_cycled` and `gfs_forecast_only` modules beneath `workflow/rocoto` have been updated accordingly. Resolves #1228 commit 04d97e9aa7ab84b9754ab670074cfb19d543aa26 Author: Kate Friedman <[email protected]> Date: Mon Dec 4 13:38:30 2023 -0500 Consolidate VMINMON and cleanup monitor scripts (#2088) This PR combines the GDAS and GFS versions of the VMINMON JJOB and ex-driver scripts into single GLOBAL/global versions. Additionally: * some further cleanup of the GSI-Monitor scripts is done; variable settings in ex-driver scripts are moved up to the JJOB level * the fix symlinks are consolidated into a new `fix/mon` subfolder (formerly `fix/gdas`) and copies of the gfs monitor fix files under `fix/products` are removed Resolves #1925 commit a286a11fdcbc31c8bc6d944890bc56294bc8caf6 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Mon Dec 4 17:48:44 2023 +0000 Robust CI Restarts (#2093) Improved CI robustness for reverting back to **CI-Ready** from any given state New Features: - Improved `scancel` routine (refactored into bash "subroutine") - Improved messaging (see below) when ever a user changes state - Any and all previous build scripts and running experiments are killed as a result of reset to **Ready** Resolves #2060 commit 73621e9b20b20f85e8b21e4c1e09ed1d80ecd46f Author: David Huber <[email protected]> Date: Sun Dec 3 11:19:19 2023 -0500 Upgrade to spack-stack/1.5.1 and Intel 2022 on non-production machines (#2084) Update module files to spack-stack/1.5.1 and compilers to Intel 2022+ on all non-production machines. commit 6d548b250688861eb20a7e0dc852a0e4ba9e64f4 Author: jiandewang <[email protected]> Date: Thu Nov 30 12:00:21 2023 -0500 Add variable tob in diag_table for ocean model output(#2105) commit c19810cce252fcdb25fd9960c05b08b5f8d8b1ad Author: AndrewEichmann-NOAA <[email protected]> Date: Wed Nov 29 15:17:36 2023 -0500 Added variables to config.prepoceanobs (#2101) commit c2d78a61a224678fb804eed19f39d1f07408ae5f Author: Kate Friedman <[email protected]> Date: Wed Nov 29 12:39:08 2023 -0500 Add missing cut to VDATE setting in JGFS_ATMOS_VERIFICATION (#2098) Refs #2097 commit c1c025f91ddac73aea595cc9fa4dd0bea80575fc Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Nov 29 17:15:10 2023 +0000 Add wave init to GEFS (#2089) Adds the wave init job to GEFS. Since the output would be the same for every member, the job is only run once for the control, then links are created in each of the member directories pointing to that copy. New ww3_multi and ww3_shell templates for GEFS are copied from the GFS versions. The GEFS restart frequency is changed to not be zero, and the comment about not setting it to zero is copied from the gfs config.base. The restart interval for the GEFS perturbed members is changed to equal that of the control. Also fixes a bug where `RUNwave` was not defined for ensemble forecasts, and another bug in the GEFS stage_ic dependency. Resolves #2017 commit 64a2470ce29b7d8d5cb85ebcb4048ff82958f64e Author: Kate Friedman <[email protected]> Date: Wed Nov 29 11:26:34 2023 -0500 Adjust permissions for jobs/JGFS_ATMOS_VERIFICATION (#2095) Add execute permissions (755) commit 964b77bc6de67291973c2c70598a1f8cb72501c5 Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Nov 28 18:45:51 2023 +0000 Make proper j-job for MET+ (#2090) Creates a proper j-job for the metp job, moving much of the material from the `jobs/rocoto` script there (some of it within `jjob_header`). Also updates the old `COMIN` variable for the COM refactor (although it does not appear used in the verify scripts currently). This is a partial step towards restoring/improving metp functionality and remains untested. Refs #1575 commit 8c11eeb8556619e8db4e0efb6394ce5a2c1aae0f Author: Henry R. Winterbottom <[email protected]> Date: Thu Nov 23 10:31:32 2023 -0700 Adds FBWINDS support to global-workflow (#2082) This PR addresses issue #1221. The following was accomplished: - A new Rocoto job is added; `jobs/rocoto/fbwinds.sh`; - `workflow/applications/gfs_cycled.py` is updated to include the `fbwinds` task; - `workflow/applications/gfs_forecast_only.py` is updated to include the `fbwinds` task; - A new function is added to `workflow/rocoto/gfs_tasks.py`, `fbwinds` is added as new GFS (only) task; - `workflow/rocoto/tasks.py` is updated to include the `fbwinds` task. Resolves #1221 commit 513db190d21f9ede0724a2cd5606372b1d7605de Author: Henry R. Winterbottom <[email protected]> Date: Tue Nov 21 22:52:58 2023 -0700 Adds NPOESS support to global-workflow (#2083) This PR addresses issue #1225. The following was accomplished: - A new Rocoto job is added; `jobs/rocoto/npoess.sh`; - `workflow/applications/gfs_cycled.py` is updated to include the `npoess` task; - `workflow/applications/gfs_forecast_only.py` is updated to include the `npoess` task; - A new function is added to `workflow/rocoto/gfs_tasks.py`, `npoess` is added as new GFS (only) task; - `workflow/rocoto/tasks.py` is updated to include the `npoess` task. Resolves #1225 commit 62d8e99e77ffe44784f4c61c3f2296c6d1a72413 Author: Kate Friedman <[email protected]> Date: Fri Nov 17 20:25:50 2023 -0500 Retire vrfy job (#2080) Retires the `vrfy` job from the global-workflow system. All associated scripts, configs, and references to the job are removed. Additionally, the switches listed in RTD were updated to reflect new ones added in other PRs for issue #235. Resolves #2069 Refs #235 commit ea386abf11ecbacef407388e8d57e71b30148a35 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Nov 17 23:59:46 2023 +0000 Enable different coupled settings for ensemble (#2030) Adds the ability to turn off some coupled components for the ensemble. To enable this, many settings are moved out of `config.fcst` and into `config.ufs` so they are calculated after any overrides of `DO_*` have been made. Some settings also had to be moved out of `config.base` for the same reason. A switch to turn on gocart is added to `config.ufs`, but unlike the other switches this one takes no arguments. The name of the ufs configure template used is converted from a partial file name to the full file name. Resolves #1692 commit fe792c0c9a1c46908cbd18c7e71eb836974cf1de Author: Kate Friedman <[email protected]> Date: Fri Nov 17 17:19:16 2023 -0500 Add --cpus-per-task to srun commands for Hera and Orion (#2077) This PR adds the `--cpus-per-task` flag to non-CFP `APRUN`/srun commands in the env files for Orion and Hera. This is needed as a result of an upgrade to SLURM on Orion that no longer exported the thread value to the environment. Issue #1996 was a hotfix to add this flag for the analysis job that was suddenly running slowly after the SLURM upgrade. A similar SLURM upgrade was done on Hera but the sysadmins there implemented a workaround so this issue did not appear there. This PR adds the `--cpus-per-task` flag for both machines...needed on Orion and as a safety measure on Hera. Also included in this PR is a fix to indentations in the `scripts/exglobal_diag.sh` script that was noticed during work for this PR. Timing differences were not observed for other jobs after adding this srun flag. Job timings were of a similar variation between control and test runs. Any potential additional speedup was not observed. The test runs also reproduced the control runs with `develop`. Resolves #2044 commit 42c943be305c297a56b104bb50727938c1ba688f Author: Kate Friedman <[email protected]> Date: Fri Nov 17 15:41:34 2023 -0500 Adjust modules in post.sh for WCOSS2 (#2079) On WCOSS2 the grib_util module is named a bit different and needs the libjpeg module loaded beforehand. commit cd4e6a1987e7fd71dff06766f540b5d32c8b648d Author: Jessica Meixner <[email protected]> Date: Fri Nov 17 11:49:32 2023 -0500 Update ufs-weather-model and remove upp hack (#2071) Updates the model to the most recent commit of ufs-weather-model. This should allow for the removal of the UPP hack that was added in PR #2042 This required changing nems.configure -> ufs.configure. Resolves #1942 commit 5a2d97e142aa4999b122fd5a130c63e59ea9f8e2 Author: Walter Kolczynski - NOAA <[email protected]> Date: Thu Nov 16 22:15:53 2023 +0000 Fix check for existence of preamble functions (#2066) A few of the setup scripts were checking for the existence of functions set by the preamble before calling them so they could also be used stand-alone. However, the `type` command returns `1` if the function name does not exist, which will cause the script to die is `set -e` is on. Now the `type` command fails over to an empty string. commit ed2ee7c2b1457b71b271a2c40f0dfa356e0f52f8 Author: WenMeng-NOAA <[email protected]> Date: Thu Nov 16 16:38:11 2023 -0500 Update UPP products for GFS v17 (#1973) Updates of generating GFS V17 UPP products to support HR3: - Update g2tmpl to 1.0.12 - Add changes to launch cfp on WCOSS2 to generate pgrb2/pgrb2b files - Changes for generating new products (MERRA2, six winter weather variables, 1km HLCY, SDEN) in pgrb2 files Resolves #1965 Resolves #1994 commit 635c4719e603538ce7cccf9ea6b31f3f84f20849 Author: Walter Kolczynski - NOAA <[email protected]> Date: Thu Nov 16 20:35:30 2023 +0000 Fix some rocoto dependencies (#2074) A few small errors/cleanup in the dependencies, mostly in fcst: A few small errors/cleanup have crept into the dependencies with recent changes, mostly in fcst: - Fixed the offset, as it would yield a string rocoto doesn't recognize when the interval was 24+ hrs - Removed the duplicate wave dependency. When `waveprep` is included, it depends on `waveinit` so there is no need to add a `waveinit` dependency. - Converted an interval in the archive job that was missed in #2039 Resolves #2075 commit d4c7508260975c6b94fc92fd085f39d4faf3f027 Author: Rahul Mahajan <[email protected]> Date: Wed Nov 15 16:44:03 2023 -0500 Fix missing _PREV in ocean restart file location (#2070) commit 255616d37505c785bdddd5d3e39e8399110b626e Author: mdtoyNOAA <[email protected]> Date: Wed Nov 15 12:02:09 2023 -0700 Update functionality for Prototype HR3 UGWP (#1987) This PR adds/modifies namelist options and activates new 'ccpp' suite definition files for the updated Unified Gravity Wave Physics (UGWP) in the ufs-weather- model recently updated for HR3. The changes to UGWP are the use of the GSL drag suite for orographic gravity wave drag (GWD) and blocking, as well as the new UGWP Version 1 non-stationary GWD. See ufs-community/ufs-weather-model#1923 for details. Resolves #1986 commit be9085e62aae147e3c74602e2f82a99b374fc783 Author: Guillaume Vernieres <[email protected]> Date: Wed Nov 15 13:48:58 2023 -0500 Save the required CICE history for the sea-ice DA (#2062) The hist_avg setting of CICE was changed to be an array. commit 85f1f5131ffd70061231304ea477bde0559eb67b Author: Guoqing Ge <[email protected]> Date: Wed Nov 15 11:47:21 2023 -0700 Use assim_freq to configure "offset" in dependencies (#2039) Use the assim_freq from config.base to configure "offset" in dependencies instead of hard-coding them. Resolves #2038 commit 4e3d82ba3a1fa7cdd4443bcd4cf83b2f8835137c Author: Kate Friedman <[email protected]> Date: Wed Nov 15 13:39:14 2023 -0500 Resolve ENKF archive script bugs (#2065) Fix two bugs in the exgdas_enkf_earc.sh script: 1) Replace ARCH_LIST with DATA to match changes done in PR #2000 and update path to generated archive list files. 2) Add status check and exit after script attempts to make tarball on HPSS. Refs #2064 commit 42d7f2f0c48fab898b764e09cfbbd7a9fabbae08 Author: Kate Friedman <[email protected]> Date: Tue Nov 14 17:54:29 2023 -0500 Separate tracker and genesis jobs from vrfy job (#2058) This PR creates new individual jobs for the tracker and genesis jobs that are being pulled out of the `vrfy` job (issue #235). The `tracker` and `genesis` jobs will be on by default while the `genesis_fsu` job will be off by default. This mimics the current settings in the `vrfy` job. No enhancements or upgrades are made to the jobs themselves in this PR, only to separate them from the `vrfy` job. However, one change compared to how they currently run in the `vrfy` job is to no longer run the `tracker` in the gdas suite. This mimics how the `ens_tracker` package is run in operations (gfs only). Changes in this PR: 1. Create rocoto job scripts for tracker/genesis jobs. 2. Create configs for tracker/genesis jobs, as well as `config.tropcy` for shared settings. 3. Add tracker/genesis jobs to `config.resources`; use resources from the ecf scripts for `ens_tracker` jobs in operations 4. Add tracker/genesis jobs to rocoto setup for both cycled and forecast-only modes. 5. Update arguments for `jjob_header.sh` script in tracker/genesis JJOB scripts to use specific job names and configs instead of vrfy. 6. Rename `tracker_ver` to `ens_tracker_ver` in version files to mimic variable within tracker package. 7. Rename and move tracker/genesis switches to `config.base`. 8. Remove tracker/genesis jobs from `vrfy` job (`jobs/rocoto/vrfy` and `config.vrfy`). 9. Reduce vrfy job resources to accommodate tasks having been removed. Refs #235 Resolves #1988 Resolves #2048 commit 0a0d6984e094d2a551d5d8331102142e7db13fc2 Author: Rahul Mahajan <[email protected]> Date: Tue Nov 14 14:08:26 2023 -0500 Enable warm starting of the model for forecast-only mode (#2031) This PR: - adds an option to warm|cold start the ufs-weather-model when setting up an experiment for GFS/GEFS - adds the capability to stage FV3 restarts when the atmosphere is warm started from FV3 restarts. This would be used in the GEFS free-forecast for part of the reforecast capability. - If a coupled model is warm started for the atmosphere, also check if mediator restarts are present. If so, stage mediator restarts to allow restarting the coupled model. Fixes #2016 commit 2cd6a589305a9ac9d3a9a0d2136e66e42f09d3bf Author: Henry R. Winterbottom <[email protected]> Date: Tue Nov 14 12:05:20 2023 -0700 Moves UFS WM configuration files to `COM_CONF` (#2054) The UFS weather-model (WM) files are place in the COM_CONF path rather than the respective component model COM history paths. Resolves #2015 commit 6f1693081662f241fafc930b1afc88125f7f5aff Author: Kate Friedman <[email protected]> Date: Tue Nov 14 11:15:02 2023 -0500 Refine fit2obs job in rocoto mesh (#2047) This PR adjusts the `fit2obs` job in the rocoto mesh to better define when it exists and how the archive job dependencies accommodate it not being in the first half cycle. Changes in PR: 1. Remove the `fit2obs` job from the first half cycle `cycledef`. 2. Adjust the archive job dependencies to now include the `fit2obs` job in the new logic check added in PR #1983. The `gdasarch` job in the first half cycle will check if `gdasfit2obs` is complete OR no prior cycle exists. Also cleaned up this new logic check block some to make it a tad simpler. 3. Also, fix the addition of the `fit2obs` config to the config list in setup scripts. Now tied to whether `fit2obs` job is on instead of always adding the config to the list. Resolves #2043 commit 5730a71fa5d311e49d9bb11528b500f27f33d69d Author: Henry R. Winterbottom <[email protected]> Date: Tue Nov 14 09:13:11 2023 -0700 Add `waveinit` and `waveprep` to half-cycle. (#2037) This PR addresses issue #1444. The `waveinit` and `waveprep` tasks have been added to the GDAS have cycle. The downstream dependencies for the respective GFS and GDAS forecast tasks have been removed. Resolves #1444 commit 28d2e93c3857de95b0309a089cd7dac736ccaded Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Nov 14 16:11:47 2023 +0000 Update wave IC source for C384 (#2055) The default wave grid for C384 has changed since P8, so a single wave IC on the new grid is available under a different IC name. commit 81dd2d9855091315611106a5afbdaeaa15e6e4ae Author: Walter Kolczynski - NOAA <[email protected]> Date: Thu Nov 9 17:19:57 2023 +0000 Fix analysis and post on Orion (#2046) Fixes a couple things to get workflow to work on Orion again: First, while #2042 allowed post to be built, the `upp.x` executable would fail due to a missing library. Now post jobs (temporarily) uses the UPP modules (plus others needed for runtime) instead of the normal workflow runtime module. This should actually fix #2041. This hack can likely be removed once we move to spack-stack. Second, the launcher command for the analysis jobs on Orion are updated to specify the number of CPUs per task. This was necessary as a recent slurm update on Orion discontinued reading that value from the scheduler. Other jobs will be handled later (see #2044). Additionally, a change is made to `module-setup.sh` that will eliminate the annoyance of `gw_setup.sh` breaking tab completion because undefined variable checking was turned on for the script but not back off. Resolves #1996 Resolves #2041 Refs #2044 commit 13d06ded4155cba2d08ef2a2cd553024c5abe29d Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Nov 8 18:25:47 2023 +0000 Hack UPP version (#2042) The stack UPP was using on Orion was recently deleted, leaving us unable to build the UFS verison of UPP there. UPP has an updated version using spack-stack that works, so the checkout script is modified to check out that version of UPP after UFS has been checked out. This temporary hack can be removed once we move to a UFS version that advances the UPP version to or beyond 78f369b. Resolves #2041 commit 20f6eceb8ff58f84174a27eb849c1d74566a3e03 Author: jiandewang <[email protected]> Date: Wed Nov 8 11:14:55 2023 -0500 Add basic C1152 settings (#2020) Adding C1152 setting in host.yaml, config.base and config.stage_ic so that can run C1152 S2SW. Resolves #2019 commit 5183c43bbbd07285869feacb49d8680afe85929a Author: Barry Baker <[email protected]> Date: Tue Nov 7 01:14:40 2023 -0500 Update UFS for dust fix and remove nitrates by default (#1989) This PR updates the `ufs-weather-model` to the latest hash that included the dust fix (PR #1922). Along with this I removed the nitrates by default in support of the GEFSv13 EP4 and EP5 experiments. Removed unneeded inputs that should help with speed improvements. commit 34a73cf2ed5afefc776d9cc73b6ebf439122a1bb Author: David Huber <[email protected]> Date: Mon Nov 6 14:00:51 2023 -0500 Reduce gdas builds to 8 #2029 (#2036) Reduce the default number of build jobs for the GDASApp to 8 from 16. This is needed for Orion as the build crashes during a linking step. Though not verified, it appears this may be caused by using too much memory with 16 builds. The issue disappears when using 8 build jobs. Resolves #2029 commit 75269e4bb9764b81589efc7d703825b80e74c8f5 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Mon Nov 6 17:34:47 2023 +0000 Streamline CI reporting to PRs (#2026) Cleaned up the logs for CI PRs sent to the GitHub Messages: - Eliminates redundant accumulative reporting - Reports on all created or skipped experiment instantiations in a single message - Gives one line report once for each experiment completion - Single final report completion of CI See some examples in forked [PR 195](https://github.com/TerrenceMcGuinness-NOAA/global-workflow/pull/195) Resolves #2007 commit 8d55126bb0b27c79c8bee7f72b014abd34950ff9 Author: Guillaume Vernieres <[email protected]> Date: Fri Nov 3 17:06:09 2023 -0400 Implement IAU Cycling Type with Marine Data Assimilation Enabled (#1944) Allows cycling in IAU mode with the S2S UFS model, soca and the GSI. Most of the work related to making IAU work was done by @JessicaMeixner-NOAA . Thanks @JessicaMeixner-NOAA ! Resolves #1943 Refs #1776 commit 2563806821d4ae3b57120bc61aa0575139a708f0 Author: jiandewang <[email protected]> Date: Fri Nov 3 11:49:37 2023 -0400 Add two ucx modules in load_ufswm_modules.sh to solve C768 and C1152 S2SW job hanging issue on WCOSS2 (#2021) commit cbdc09711a83493f363a737d1e3e46c48a09719d Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Nov 3 04:09:33 2023 +0000 Fix staging of MOM data (#2028) During the update to stage_ic, the copying of the additional res_N files for 0p25 was omitted. These are now properly copied. Resolves #2027 commit bd4c56d99c23c5c41f0bd5f8a980ef99ee160888 Author: AndrewEichmann-NOAA <[email protected]> Date: Thu Nov 2 16:09:59 2023 -0400 changed optional script name vars for ocean analysis (#2025) commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6 Author: Kate Friedman <[email protected]> Date: Thu Nov 2 16:01:18 2023 -0400 Create separate GSI monitor jobs and remove from vrfy job (#1983) This PR will move the GSI monitor tasks from the `vrfy` job into their own separate jobs in the rocoto mesh. This takes care of part of issue #235. Changes in this PR: 1. Create new individual GSI monitor jobs in the rocoto mesh to match how it is done in operations. The new jobs are: `gdasverfozn`, `gdasverfrad`, `gdasvminmon`, and `gfsvminmon`. The names correspond to the names in operations and the ecf script names. The jobs are only added to cycled mode, none of the jobs are run in forecast-only mode. 2. Updates to GSI monitor scripts: * Update `ush/jjob_header.sh` arguments in JJOB scripts to call new individual job names and configs. * Introduce `COM_*` variables and use of the `generate_com` utility. This results in the outputs landing in `COM` subfolders, like occurs in operations, instead of landing in the online archive. * Some variable cleanup in JJOB and ush scripts, includes cleaning up usage of `DATA` variable and its removal at the end of the jobs. * Add missing exit statements to `JGFS_ATMOS_VMINMON` and `JGDAS_ATMOS_VERFRAD`. 3. Create new rocoto job scripts for the new individual GSI monitor jobs. 4. Create new configs for the new individual GSI monitor jobs. 5. Add new individual GSI monitor jobs to resource configuration, using the same resources as in operations. 6. Move and rename GSI monitor job switches from `config.vrfy` to `config.base`. Also add switches to setup system. New switches to control each job being added to the rocoto mesh are: `DO_VERFOZN`, `DO_VERFRAD`, `DO_VMINMON` 7. Add GSI monitor job output to archival job and into resulting HPSS tarballs or local tarballs. This now matches what is done in operations. 8. Remove the GSI monitor tasks from the rocoto `vrfy` job and associated `config.vrfy`. Example output locations and files (not showing contents of oznmon/horiz or oznmon/time for brevity, see archival script for full list of output files): ``` kate.friedman@dlogin09:/lfs/h2/emc/ptmp/kate.friedman/comrot/testmonitor2> ll gdas.20211221/00/products/atmos/*mon gdas.20211221/00/products/atmos/minmon: total 112 -rw-r--r-- 1 kate.friedman emc 14030 Oct 25 15:00 2021122100.costs.txt -rw-r--r-- 1 kate.friedman emc 84932 Oct 25 15:00 2021122100.cost_terms.txt -rw-r--r-- 1 kate.friedman emc 808 Oct 25 15:00 2021122100.gnorms.ieee_d -rw-r--r-- 1 kate.friedman emc 808 Oct 25 15:00 2021122100.reduction.ieee_d -rw-r--r-- 1 kate.friedman emc 80 Oct 25 15:00 gnorm_data.txt gdas.20211221/00/products/atmos/oznmon: total 8 drwxr-sr-x 2 kate.friedman emc 4096 Oct 25 15:05 horiz drwxr-sr-x 2 kate.friedman emc 4096 Oct 25 15:05 time gdas.20211221/00/products/atmos/radmon: total 21036 -rw-r--r-- 1 kate.friedman emc 231 Oct 25 15:12 bad_diag.2021122100 -rw-r--r-- 1 kate.friedman emc 9035 Oct 25 15:12 bad_pen.2021122100 -rw-r--r-- 1 kate.friedman emc 1449 Oct 25 15:12 low_count.2021122100 -rw-r--r-- 1 kate.friedman emc 20523403 Oct 25 15:07 radmon_angle.tar.gz -rw-r--r-- 1 kate.friedman emc 217272 Oct 25 15:08 radmon_bcoef.tar.gz -rw-r--r-- 1 kate.friedman emc 502151 Oct 25 15:10 radmon_bcor.tar.gz -rw-r--r-- 1 kate.friedman emc 264480 Oct 25 15:12 radmon_time.tar.gz -rw-r--r-- 1 kate.friedman emc 684 Oct 25 15:12 warning.2021122100 kate.friedman@dlogin09:/lfs/h2/emc/ptmp/kate.friedman/comrot/testmonitor2> ll gfs.20211221/00/products/atmos/minmon/ total 88 -rw-r--r-- 1 kate.friedman emc 10530 Oct 25 14:55 2021122100.costs.txt -rw-r--r-- 1 kate.friedman emc 63882 Oct 25 14:55 2021122100.cost_terms.txt -rw-r--r-- 1 kate.friedman emc 808 Oct 25 14:55 2021122100.gnorms.ieee_d -rw-r--r-- 1 kate.friedman emc 608 Oct 25 14:55 2021122100.reduction.ieee_d -rw-r--r-- 1 kate.friedman emc 80 Oct 25 14:55 gnorm_data.txt ``` Lingering work and considerations: 1. Issue #1925 2. Consider not hardcoding the list of types in archival and perhaps tie it to something reliable or configurable (maybe into `config.verfozn`?): `subtyplist="gome_metop-b omi_aura ompslp_npp ompsnp_n20 ompsnp_npp ompstc8_n20 ompstc8_npp sbuv2_n19"` Resolves #1908 commit 31b05a99b77d0f6eaa8b116485a41a43867d20e1 Author: Henry R. Winterbottom <[email protected]> Date: Thu Nov 2 12:23:32 2023 -0600 Move analysis post to new stand-alone task (#1979) This PR addresses issue #1130. A new task `postanl.sh` has been added such that the `anl` post-processing is not it's own task within the Rocoto workflow. This change prevents the GDAS experiment from breaking due to failures caused by the `anl` not being available for the first cycle. Resolves #1130 commit 247cdf8c7e10e6c98f782799fc51c069b6474e70 Author: Henry R. Winterbottom <[email protected]> Date: Thu Nov 2 11:18:53 2023 -0600 Corrects missing local variable reference (#2023) Fixes missing `$` in variable reference in archive job. Resolves #2022 commit 241742b246da1794646b68e41c3d6fe00b95dd07 Author: AndrewEichmann-NOAA <[email protected]> Date: Wed Nov 1 14:19:55 2023 -0400 Updates to prep ocean obs task (#1870) commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd Author: Henry R. Winterbottom <[email protected]> Date: Wed Nov 1 12:09:33 2023 -0600 No longer write archive lists COM (#2000) Changes the respective `.txt` files used for the HPSS archive to the `DATA` path. Each defined text file has been updated to explicitly write to `DATA` rather than `COM` such that the files are deleted rather than being archived. Resolves #760 commit 517b92f9c20c9e44abba3183325e35a95a7334a5 Author: David Huber <[email protected]> Date: Tue Oct 31 16:33:11 2023 -0400 Parallelize the build scripts (#1998) Optimized/parallelized build scripts. A few notes: 1) The default number of build jobs is 20, but one could argue for using 40. When researching this, I looked up what the SRW is compiling with. That system uses 40 cores, which seems a little excessive, but on testing the global workflow, the actual number of cores being used at any given time rarely exceeds 16 when running with 40 cores. This is because the builds tend to use multiple threads in the beginning when compiling low-level modules while the higher-level modules are more or less serial AND because the GDASApp takes several minutes to initialize all of its subrepositories by which time the smaller builds are complete. 2) I also updated checkout.sh so that all checkouts are simultaneous. The CPU load for `git submodule` is quite low, so running 16 instead of 8 jobs at once is not much more expensive. 3) To make this work, I had to add `-j` options to most of the build scripts. The only exception is build_upp, for which the build script within the UPP is hard coded to use 6 cores. 4) I fixed a few small bugs in the build scripts along the way. 5) Lastly, this reduce the total build time from ~2.5 hours for the entire system (including GDAS and GSI in the same build) to ~40 minutes when running with `-j 40`. Resolves #1978 commit 67c050c201f92e855d09211e41a5f51ee1cb5230 Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Oct 31 19:00:47 2023 +0000 Add missing export for rCDUMP in stage_ic (#2009) rCDUMP is needed by the exscript but was never exported by the jjob. commit 872068cb5ea78b311f7a77e97ee1428ae027cb61 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Oct 31 14:37:55 2023 +0000 Add output error log to user for create_experiment.py on fail in CI (#1974) Small changes to driver CI bash scripts to recapture error log from `create_experment.py` logger Fixes #1939 commit b2e4a2e9d269842acbb1b37dd563ee5dee2adf0f Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Oct 31 13:57:02 2023 +0000 Allow CI case to exclude running on certain platforms (#2001) commit 7cc137116f1619bf1e5a12eaacb98d17da97c223 Author: Jeff Whitaker <[email protected]> Date: Tue Oct 31 07:54:24 2023 -0600 Add initial C96/1 deg coupled model support (#1991) commit 7086ddc4bece6fb2a8c1c2e6090800d4293e410e Author: AndrewEichmann-NOAA <[email protected]> Date: Mon Oct 30 19:58:43 2023 -0400 Add ocean analysis files to HPSS archiving task (#1985) This PR adds the files under `analysis/ocean` (except those in `bump` and `vrfy`) to the HPSS archiving job, in `gdasocean_analysis.tar`, which were previously not archived. Resolves NOAA-EMC/GDASApp/issues/693 commit eabc82ad30c118645c0e6e216162d823882a8139 Author: Guillaume Vernieres <[email protected]> Date: Mon Oct 30 10:31:27 2023 -0400 Make the early cycle work with the coupled UFS configured as S2S (#1954) commit aff6ca7ae559e424dae128d6cfd5da4a4e3049e7 Author: Anil Kumar <[email protected]> Date: Fri Oct 27 14:11:55 2023 -0400 GEFS Staging in exglobal_stage_ic (#1892) Adjusts source paths for forecast-only ICs in support of extension to ensembles. New paths omit the resolution (that is captured by the IC id name) and allow for a member level. Directories with the reorganized ICs have been added to the three tier-1 machines under glopara space. Building on this, also adds capability to stage GEFS ICs. Resolves #911 commit 77c1ff2bfa26b341b01f41e50ee0ecb31cc4f661 Author: RussTreadon-NOAA <[email protected]> Date: Thu Oct 26 23:44:27 2023 -0400 Update GDASApp hash (#1975) Update GDASApp hash to bring recent UFSDA development into g-w. Resolves #1972 commit 962368884991670d3a1ee1c5a065d5bce4b7561a Author: David Huber <[email protected]> Date: Thu Oct 26 16:10:23 2023 -0400 Test tarballs for rstprod before calling chgrp (#1967) Certain tarballs may or may not contain `rstprod` data. For instance, the first half cycle gdas and enkfgdas tarballs will not contain `rstprod`, while future cycles likely will. Also, some systems do not have `rstprod` on them. This will test the contents of the tarballs first before attempting to change the group to rstprod. Resolves #1460 commit c02e118c0ac5485109c9bd33472ff42db309cd9b Author: Jessica Meixner <[email protected]> Date: Thu Oct 26 15:05:05 2023 -0400 Update ufs model to version from 10-12-23 (#1933) This updates the ufs-weather-model to the commit hash from 10-12-23 from the HR2 tag. The diffs can be seen here: https://github.com/ufs-community/ufs-weather-model/compare/GFSv17.HR2...68050e58589a82ab509aaefaafdc2a6b90f34e48 Resolves #1811 commit 8556541daa79b0180fde48a58a8dcfb2f8c56ea5 Author: Rahul Mahajan <[email protected]> Date: Wed Oct 25 16:15:28 2023 -0400 Fix incorrect usage of CFP on WCOSS2 (#1977) commit 0b5cf9b67a8146d9d4815ea6545f7f2524120d83 Author: Kate Friedman <[email protected]> Date: Wed Oct 25 13:17:28 2023 -0400 Update GFS version in index.rst to v16.3.10 (#1976) Update the "State of operations" GFS version number to new v16.3.10 (Annual CO2 fix file update in operations). Refs #1924 commit e817f5dd38c26a88f76d90eb71124f1acbfc5a8f Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Oct 25 02:03:14 2023 +0000 Fix path for marine products (#1966) When PR #1823 was merged, the name of the marine product template was not updated in ocnpost, leading the products to be placed in the wrong location and missed by the archive job. Resolves #1902 commit 7cdfad4eaa7abe0769ff13396c54e6d93afebf8f Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Oct 24 22:19:46 2023 +0000 Build GDASapp for CI tests (#1964) * added -u to global checkout so CI test builds tests for GDASapps * Update check_ci.sh needed more quotes --------- Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]> commit c58deae0cf078d1ee093529064d74f60482aa3f4 Author: Henry R. Winterbottom <[email protected]> Date: Tue Oct 24 16:19:04 2023 -0600 Updates for NOAA CSP AWS global-workflow related file paths. (#1970) Co-authored-by: henrywinterbottom-wxdev <[email protected]> commit 1b00224e18842cd873eb1779be08f96687e49e1f Author: Kate Friedman <[email protected]> Date: Tue Oct 24 14:48:24 2023 -0400 Set SENDCOM=YES for tracker/genesis tasks (#1971) Set SENDCOM to YES in config.vrfy to get outputs copied back to COM. Will reevaluate the need for SENDCOM when moving the tracker/genesis jobs out of the vrfy job with issue #235 work. Refs #1947 commit e2c624d8904cd988394c73d0edb22fa593229d3f Author: RussTreadon-NOAA <[email protected]> Date: Tue Oct 24 13:32:52 2023 -0400 Refactor UFSDA ATM var and ens layout (#1945) commit 8940adddfe9d21189740e71487603fb2acee2336 Author: David Huber <[email protected]> Date: Tue Oct 24 11:02:29 2023 -0400 Optimize the checkout script (#1956) * Multithread the checkout script #1953 commit 4b5cd0bc435fc158258ca38c3d5f44add6b60469 Author: Rahul Mahajan <[email protected]> Date: Mon Oct 23 12:04:26 2023 -0400 Fix nth_eupd in gfs/config.resources. remove sections of jobs not run as part of gefs from gefs/config.resources (#1952) commit 08ce4f8d3ed8e07b4d488a80b5054c6206b04404 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Oct 20 16:14:53 2023 +0000 Fix enkfgfs cleanup dependency (#1941) When #1906 was merged, the dependency for enkf cycles was hard-coded to use the enkfgdas archive instead of depending on the `RUN`. commit 1a5d0b51642eb70f71e693355e86212d3607b7b3 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Oct 20 15:54:33 2023 +0000 Split clean-up into separate job (#1906) Moves the clean-up that was previously done in the archive jobs into their own separate job. The clean-up is also streamlined considerably by using only `COM_TOP` instead of going through every template. There is also additional streamlining/corrections in the function that does the actual removing. Some settings used by both jobs were elevated to `config.base`. Others only needed for cleanup were moved to the new config for that job. Also corrects a small error encountered when attempting to rerun an ensemble forecast. Resolves #583 Resolves #1872 commit 3de102c28daf9eb50ce65e0afe911f5a416ce861 Author: Rahul Mahajan <[email protected]> Date: Tue Oct 17 09:30:18 2023 -0400 Updates to CI to clarify HOMEgfs (#1931) * replace HOMEgfs_PR with HOMEgfs, and HOMEgfs with ROOT_DIR. ROOT_DIR is the location where the ci scripts live * update type to system in case yamls * move create_experiment.py to workflow/ * detect HOMEgfs in create_experiment.py based on location. update to use jinja templates in the cases * remove export of HOMEgfs from driver.sh commit bfea2594207a477ea00e3b7fef95c2d7befd492b Author: Henry R. Winterbottom <[email protected]> Date: Sun Oct 15 23:27:47 2023 -0600 Remove SENDCOM (#1929) This PR addresses issue #1501. All instances of `SENDCOM` gates have been removed. The workflow was inconsistent in its use of `SENDCOM` to gate movement of files to `COM` and have been removed based on NCO guidelines. Resolves #1501. commit 9a8911a0b30f0367d061facfb3b835480728081d Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Fri Oct 13 14:21:01 2023 +0000 update nth_eupd to 8 for Orion because of out of memmory errors (#1927) Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]> commit ea4dfa5800b5cb529478cc64d329f567393fa37d Author: Guillaume Vernieres <[email protected]> Date: Thu Oct 12 21:29:19 2023 -0400 Marine DA configuration updates (#1922) Minor updates the configuration related to running the marine DA and the coupled UFS. What's proposed in this PR: - Memory increased for the marine DA analysis step - The coupled UFS is (was?) running out of memory without the changes in `config.ufs`. - Updates to the IAU section of MOM_input to allow for a current increment. commit c2d112b40a926c9f33a653cfbb832cb811a60352 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Thu Oct 12 23:52:43 2023 +0000 Fix missing pipe in check_ci (#1926) Bugfix: left out pipe to word count` | wc -l` after updating: `num_platforms=$(ls ../platforms/config.* | wc -l)` to `num_platforms=$(find ../platforms -type f -name "config.*")` when it was flagged by the BASH linter. commit 51d93e15eb30382017aaf72813d34f7010f47948 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Oct 10 19:09:26 2023 +0000 Updated cron bash ci script to remove weekly CI test PR on success (#1915) This PR updates the check CI bash script in cron to remove the PR that is created by the weekly CI test driver when all the tests has passed on all the platforms. This is done by the script checking if all other labels for all the platforms for the PR that has currently been flagged to have run to a successful completion by the check ci bash script. commit 2d64b74a0b0407d01d6f657efa6af9637a131448 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Wed Oct 4 22:33:25 2023 +0000 CI driver_weekly bugfix deleting new branch if is already on repo (#1899) Bugfix and updates to weekly CI test that deletes the new modified branch if it is already on the repo but now also makes sure that the intermediary branch that creates the PR is coming from emcbot. commit e4a6c35ae020253f07921ca34a17f19e928b0b6c Author: Rahul Mahajan <[email protected]> Date: Wed Oct 4 09:42:12 2023 -0400 Fix typo in cice history filename commit d50938bc4f6705b722338bbea03f925614f953ed Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Oct 3 23:37:39 2023 -0400 Change metp dependency (#1900) MET+ jobs rely on files already having been placed in the local archive directory, but the job only depended on post, resulting in the job prematurely firing. The dependency is now updated to be on the archive job instead. Resolves #1756 commit 836642bb201cd2e5e205eda2ae4a28993623355d Author: Rahul Mahajan <[email protected]> Date: Tue Oct 3 14:45:57 2023 -0400 Use deterministic marine resolutions for ensemble (#1894) This PR determines the ensemble resolution for ocean, ice and waves based on the deterministic configuration as there is no dual-resolution capability requested for these model components. For cycled DA, if the deterministic uses a coupled model, the ensemble will also be a coupled model. This can be turned off manually via adding `DO_AERO_ENKF`, `DO_OCN_ENKF`, `DO_ICE_ENKF` and `DO_WAVE_ENKF` flags set in `config.base` or `config.efcs`. This is currently handled manually and will be automated when a requirement arises for this flexibility. Fixes #1730 commit 48ba775909870f0d27275128bd07ec134b92c356 Author: Kate Friedman <[email protected]> Date: Mon Oct 2 13:34:02 2023 -0400 Update vrfy.sh to only run MINMON in cycled mode (#1901) Update MINMON if-block in jobs/rocoto/vrfy.sh to only invoke this section when MODE is cycled. Refs #1076 commit e65162f3083c34b639854e3216e2355ff6fccc0b Author: RussTreadon-NOAA <[email protected]> Date: Fri Sep 29 19:18:07 2023 -0400 Update module loads to intel/2022 for jobs running gsi.x and enkf.x (#1882) This PR changes the module loads in g-w jobs `anal.sh`, `eobs.sh`, and `eupd.sh` to use machine specific modulefiles from `sorc/gsi_enkf.fd/modulefiles`. This is necessary because [NOAA-EMC/GSI#571](https://github.com/NOAA-EMC/GSI/pull/571) updated `gsi.x` and `enkf.x` builds to intel/2022 on NOAA RDHPCS machines. Resolves #1863 commit cd439d0bf2ae5fb57139fcb9983aa2755fdc9b2c Author: Rahul Mahajan <[email protected]> Date: Fri Sep 29 15:35:54 2023 -0400 Add coupled forecast-only tests for S2S and S2SW (#1895) This PR: - replaces the PR C48 S2S forecast-only test with a S2SW configuration - adds a weekly C384 S2SWA forecast-only test. The C384 S2SWA is a weekly test and will not be triggered/tested in this PR, but will be tested on Friday. See notes on Orion below in the testing section. @JessicaMeixner-NOAA kindly provided the details in https://github.com/NOAA-EMC/global-workflow/issues/1794#issuecomment-1740768751 commit 02787fe9ba9e5a6881e5ccf9a9e352545eeadb9d Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Fri Sep 29 18:03:23 2023 +0000 Ci rename platform scripts (#1896) Simply renaming the platform config files in ${HOMEgfs}/ci/platforms to config.${MACHINE} so wxflow can read them too in support of up and coming functional testing. commit bb5a58541d6514d16901dca240dfbbc810bd31c8 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Sep 29 13:28:39 2023 -0400 Merge S2S defaults config back into other configs (#1876) When the prototype S2S was first added, we placed some settings in a `config.defaults.s2sw` file to avoid interference with existing settings. Now that we are moving towards v17 and run S2S regularly, it is time to merge these settings back into the other config files. The wave output frequency settings are updated to the coarser fre- quency as that is more suitable for development. The prior (ops) settings are noted as comments. There are a couple of settings that control ice fields within FV3. These are placed in `config.ice`, so when the ice model is on those settings are still used. Changes the output frequency from 3 to 6. While we may leave this setting as the default for development, it is required right now because the ocean frequency is hard-coded to 6 but links are created based on `$FHOUT_GFS`. Resolving #1629 should correct this limitation. "Gaussian" archive is updated to the former override values. Resolves #1606 Refs #1629 commit 49dc315c1ef6c5f4952a06b0ba70c36e771f128e Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Sep 29 13:25:58 2023 -0400 Move product functions to separate script (#1891) PR #1822 converted some formerly stand-alone scripts and moved them inside one of the standard product scripts. However, `trim_rh.sh` is also used by gempak and AWIPS, so this change caused those jobs to start failing (they are not yet tested by CI). Those functions have now been moved into a separate product functions script that can be sourced by all the scripts that need the functions. A third similar script was also eliminated and converted into a function. Additionally fixes a base bug in AWIPS and updates some scripts to satisfy (or at least mostly satisfy) the linter. **AWIPS still failing when creating GRIB1 products.** That will be addressed in a future PR (and may need a subject-matter expert). Resolves #1890 commit 3e750d10be577106fb269a78e18765b8d2b8030d Author: Rahul Mahajan <[email protected]> Date: Thu Sep 28 16:21:52 2023 -0400 Fix a few bugs reported by devs (#1893) This PR fixes a few bugs that were reported by developers: - a namelist section is unclosed in `parsing_namelists_FV3.sh` - resolution is not being properly cut from `CASE` - date should be in UTC to properly go back and forth around DST dates. Resolves #1796 commit e886e8aef633389d65e23cc42456827e1db2a771 Author: Kate Friedman <[email protected]> Date: Tue Sep 26 13:01:17 2023 -0400 Fix wavepostbndpntbll data dependency (#1888) Update the data dependency path for the wavepostbndpntbll job to use the ATMOS/atmos subfolder instead of WAVE/wave for the atm.logf file it needs to fire off. Refs #1887 commit bb1e561c6a519b9b1cf3fb3ac724e2d240bc3b5b Author: Andy Tangborn <[email protected]> Date: Tue Sep 26 11:08:49 2023 -0400 Update aero analysis for new bump files and archive aero diags (#1886) This PR updates the global workflow so that it can handle the latest version of the JEDI aero staticb, and also archives the aerosol diagnostic files. commit 3d2b72ecd395585f650b2801b2ec3471bd938d63 Author: David Huber <[email protected]> Date: Tue …
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Jan 29, 2024
Squashed commit of the following: commit 3c0c126a376af31866a93aef4cdd0b4145150c58 Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 16 17:32:25 2024 +0000 Add script for remapping 1/4 degree grib2 grids to other domains commit f217d4ed9a500e9a1bdcc17548729d972a1763ac Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 16 16:46:25 2024 +0000 Update link script for ufs_utils.fd commit 5b21b31900955013b4e8106d3ae906b9da93b361 Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 16 16:45:25 2024 +0000 Add GSL archive scripts for initial conditions commit abb88baf9dd536a3b2ea1e24eaa99cbfe85af799 Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 16 16:42:17 2024 +0000 Move configuration files for getic and init from jobs/rocoto to parm/config/gfs commit 45b235180719ab79d2514f0317207fbebfb8aedd Author: Judy.K.Henderson <[email protected]> Date: Sun Jan 14 03:21:15 2024 +0000 Add suite definition file for v17p8_ugwpv1_c3 to sorc/ufs_model.fd_gsl commit 147b1fce99254dcb602c333cc559feaa9a396e81 Author: Judy.K.Henderson <[email protected]> Date: Sun Jan 14 01:57:22 2024 +0000 Add getic and init tasks to workflow to create initial conditions in realtime commit 4e4e50803d95566e1c7967cf4cfa575391d77f25 Author: Judy.K.Henderson <[email protected]> Date: Fri Jan 12 00:44:59 2024 +0000 Change default HPSS_PROJECT to fim Change restart_interval_gfs to -1 so no files are written ro RERUN_RESTART directory commit 791d7a27c6b12f07d9c12ce491338e3da59eb1d8 Author: Judy.K.Henderson <[email protected]> Date: Thu Jan 11 23:34:36 2024 +0000 Add namelist parameter, nord_tr, for GSL suites commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5 Author: Judy.K.Henderson <[email protected]> Date: Thu Jan 11 23:31:22 2024 +0000 Add changes for running v17p8_mynn - new field table, field_table_thompson_aero_tke_progsigma - updated namelist parameters in config.fcst commit 982a1f02e3b880be43f4ae8a3f0ffbb34c056aea Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 9 02:26:22 2024 +0000 Add experiment setup script for p8_ugwpv1 commit c5a3697d22fdbb02bb80ddffee2629dddc10c702 Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 9 02:19:13 2024 +0000 Add memory report to srun command in env/HERA.env commit ece7e516ca65ec0240899e7d84321310a6887595 Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 9 02:13:42 2024 +0000 Updated GSL-specific files under ufs_utils.fd_gsl commit 1b153fc95b93a16eb40b791be7322100fde4a3d4 Author: Judy.K.Henderson <[email protected]> Date: Tue Jan 9 01:52:56 2024 +0000 Create new branch, gsl_ufs_dev, from dev_02jan24_9d901db Add initial GSL modifications - changes to workflow files * GSL paths, projects, entities - new FV3_GFS_v17_p8_ugwpv1_mynn suite definition file (SDF) - updated namelist parameters in ush/parsing_namelists_FV3.sh - create new GSL directories: ufs_model.fd_gsl and ufs_utils.fd_gsl * new SDFs, add instantaneous flux variables to grib2 configuration files * add Thompson tracers to initial conditions - new sync script: rsync_gsl.sh - new job files: getic.sh, makeinit_link.sh - modify build_ufs.sh to include MYNN SDF commit 9d901dbbff4d41586580316bdc094d24760119e6 Author: Henry R. Winterbottom <[email protected]> Date: Tue Jan 2 10:30:33 2024 -0700 Stop Gempak pgrb2 spec from modifying $DATA (#2147) This PR addresses issue #1224. The following is accomplished: - Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time; - Shell linter exceptions are addressed accordingly; - The respective GEMPAK tasks is added to the Rocoto mesh. Resolves #1224 commit 31ad23527802f7d07171132cc620f7135c4d8cba Author: Henry R. Winterbottom <[email protected]> Date: Tue Jan 2 10:27:30 2024 -0700 Reorganize NPOESS scripts (#2166) This PR addresses issue #1226. The following is accomplished: - Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated; - Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh` are moved accordingly; this specifically applies to the environment variable `FHOUR`, `SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`; - The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level (if necessary); - Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however, this may not be necessary (see `TODO` note within draft PR. Resolves #1226 commit 22bd82fa93b49e5ce98eb3f69123956dd5018049 Author: Kate Friedman <[email protected]> Date: Tue Jan 2 11:55:03 2024 -0500 Orog fix file reorg and fix directory variable standardization (#2181) This PR makes updates to use the newly reorganized `orog/20231027` fix file version and standardizes the fix file directory variables. Changes: 1. Update UFS_UTILS hash to ce385ce 2. Update fix file version file to use new orog timestamp: `orog_ver=20231027` 3. Add ".mx$(OCNRES)" to `oro_data` filenames in scripts 4. Remove ".mx$(ocn_res)_frac" from the directory names for atmosphere resolutions under the `/orog` folder 5. Adds fix file directory variables to `config.base`, many of which are pulled up out of lower scripts; introduce `FIXcpl` 6. Renamed/replaced the following fix file directory variables: - `FV3JEDI_FIX` --> `FIXgdas` - `FIXfv3`, `FIX_orog` and `OROFIX` --> `FIXorog` - `FIX_ugwd` and `OROFIX_ugwd` --> `FIXugwd` - `FIX_am`, `FIXgsm`, `FIXSYND` --> `FIXam` - `FIX_lut` --> `FIXlut` - `FIX_aer` --> `FIXaer` - `FIX_SFC` --> `FIXsfc` - `FIX_DIR` --> `FIXgfs` - `RTMFIX` and `FIXCRTM` --> `CRTM_FIX` (is `CRTM_FIX` in crtm module, so not using `FIXcrtm`) 7. Correct the defaults for `FIXwave` in wave JJOB scripts 8. Update variable names in `*fixed_files.yaml` files, as well as update naming convention for `oro_data` files Resolves #1984 Resolves #1981 Resolves #2175 commit 03d03bf53b43914a55c384cb33eb06f6a9a443a6 Author: Andrew Collard <[email protected]> Date: Tue Jan 2 11:53:44 2024 -0500 Remove HIRS from GSI processing (#2183) With the update to CRTM 2.4.0.1, an issue with versioning of CRTM HIRS files has been exposed. This is documented in JCSDA/crtm#42. As HIRS radiances are no longer used in the GSI, these data should be removed from processing until a suitable update to CRTM is available. Resolves #2182 commit a3c50998d35525a39a66d5592fbf327ab3569e8b Author: Jessica Meixner <[email protected]> Date: Fri Dec 22 18:07:48 2023 -0500 Update ufs-weather-model version (#2186) * update model to latest version which includes needed bugfixes for HR3 commit 774c7302e618370ef578bec3ccabc70486d6da1b Author: David Huber <[email protected]> Date: Fri Dec 22 11:34:53 2023 -0500 Fix analysis post processing's handling of 0-padded negative integers (#2187) This screens for the analysis 'forecast' hour (-001) and handles the '-' and circumvents octal issues. commit d1251360325faf75af9df0608557fcd10202a883 Author: Barry Baker <[email protected]> Date: Thu Dec 21 11:23:48 2023 -0500 Fix for restoring cycling aerosols in fo-mode post COM refactor (#2179) - Update to COM reorg aerosol initialization job - Address bug in joining paths for data dependency in this job --------- Co-authored-by: Rahul Mahajan <[email protected]> commit e55a05980709288d902ad1bd894164bfa5a18a65 Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Dec 20 22:14:01 2023 -0500 Stop calling ufs-utils link script (#2172) The `link_workflow.sh` script was calling the ufs_utils version of the same. That step is only necessary if a user is going to run one of the stand-alone ufs-utils, which is rare. commit ef3e5ad7c63be1644c82333c95853c3caf2d8995 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Dec 19 22:02:55 2023 -0500 Fix handling of excluded hosts list (#2170) This PR fixes the issue with `create_experment.py` so that the yaml configuration file can have a string of list of strings when specifying the host name to exclude from the CI tests. commit ea74a5719efc8f0fe631c5ff93426a4299a614f3 Author: AndrewEichmann-NOAA <[email protected]> Date: Tue Dec 19 16:21:41 2023 -0500 Add COMOUT_OBS to marine obs prep (#2173) Adds `COMOUT_OBS` (defined from `COM_OBS_TMPL`) to marine obs prep task to properly handle marine obs prep files. Used to keep obs after IODA conversion, QC, and other prep. Towards resolving NOAA-EMC/GDASApp#815 commit c2500feace0bb7c04ce67a90dd3182120ee67b2e Author: David Huber <[email protected]> Date: Tue Dec 19 14:55:20 2023 -0500 Return failed status if a build fails. (#2171) If any of the builds fail, this makes build_all.sh return the sum of the error codes encountered. Fixes #2168 commit 76fdd81cd84ed812181996a102379d8d964ba27a Author: Kate Friedman <[email protected]> Date: Tue Dec 19 13:24:34 2023 -0500 Update index.rst for new GFSv16.3.12 in ops (#2169) Refs #2096 commit a81da33e8fe7541a36f68e7a4f14a384cadd36c8 Author: Kate Friedman <[email protected]> Date: Tue Dec 19 10:22:21 2023 -0500 Set place=shared for shared jobs on WCOSS2 (develop) (#2156) Set job as shared when not exclusive on WCOSS2 WCOSS2 defaults to exclusive when it is not specified as either exclusive (place=exclhost) or shared (place=shared). Now set shared when job should be shared. Refs #2135 commit 89aea972f7964dac3f515e8070d7c534812c5fb4 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Dec 15 16:31:06 2023 -0500 Update gfs-utils version for Hercules (#2163) An update of gfs-utils was misssing from the previous PR that added initial Hercules support (#2128). Also includes gfs-utils update for new marine post. commit 9505cb4abc6ca2643a8ab254d14ca2000747fa44 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Thu Dec 14 16:15:31 2023 -0500 CI Updates to support Hercules (#2155) If merged, this PR will update the CI scripts so they will run on Hercules for forecast only NOTE: This is a stop gap to issue #2131 until its block on #1588 is removed. Resolves #2154 commit c5ca82f04a2efae78389dec1c46b94ef4fb5bbe5 Author: Rahul Mahajan <[email protected]> Date: Thu Dec 14 16:05:33 2023 -0500 Correct fbwind (#2161) commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a Author: Kate Friedman <[email protected]> Date: Thu Dec 14 12:06:23 2023 -0500 Add MOS jobs to rocoto mesh (#2148) Create separate jobs for GFS MOS - extracted from now-retired vrfy job Refs #2068 commit bb6151aa50c27253cb9b8f0a6601ddd58526b8b3 Author: Walter Kolczynski - NOAA <[email protected]> Date: Thu Dec 14 05:38:29 2023 -0500 Replace checkout script with submodules (#2142) Replaces the checkout script with git submodules. This change brings workflow in line with other repos and git standards. Due to these changes, the build system is updated slightly. First, the options that were formerly used with `checkout.sh` to reduce unneeded builds (`-g` for GSI and `-u` for UFSDA) are moved to `build_all.sh` instead. This is needed since build all will not be able to key off directories existing or not to determine which com- ponents to build. Second, the partial build system is removed. It was rarely, if ever, used, and parts of it were already ignored with the previous changes to base builds off whether directories exist. The manage externals file is also removed since that is also not being used. Following these changes, clones/checkout will need to either be recursive, or `git submodule update` will need to be called separately to make sure components are properly checked out (non-exhaustive list): ``` ## Checkout develop (method 1) git clone --recursive https://github.com/NOAA-EMC/global-workflow destination ## Checkout develop (method 2) git clone --jobs 8 https://github.com/NOAA-EMC/global-workflow destination cd destination git submodule update --init --recursive --jobs 8 ## Checkout existing branch some_branch (method 1) git clone --recursive --jobs 8 -b some_branch https://github.com/NOAA-EMC/global-workflow destination ## Checkout existing branch some_branch (method 2) git clone https://github.com/NOAA-EMC/global-workflow destination cd destination git checkout --recurse-submodules some_branch ## Checkout existing branch some_branch (method 3) git clone https://github.com/NOAA-EMC/global-workflow destination cd destination git checkout some_branch git submodule update --init --recursive --jobs 8 ## Checkout new branch new_branch git clone https://github.com/NOAA-EMC/global-workflow destination cd destination git checkout -b new_branch git submodule update --init --recursive --jobs 8 ``` The git ignore list had to be updated to use explicit paths as the wildcard paths pick up the ones that are now submodules. UFS creates files during the build process that are not in its ignore list, so that sub- module ignores the "dirty" state to avoid confusing users running `git status`. CI and documentation are also updated to reflect the changes. Resolves #2141 commit 1332188ce2409e012ec127d44880e49732f7f379 Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Dec 13 09:32:57 2023 -0500 Enable radar reflectivity output (#2143) Turns on radar reflectivity output from FV3. This eliminates missing values appearing in the grib2 files. commit 24d898ec0ec0c7fcbda6966988f9a986f528ed14 Author: David Huber <[email protected]> Date: Wed Dec 13 09:32:24 2023 -0500 Fix Hercules hostname (#2150) * Allow lower or upper hostname on hercules. * Add Hercules to issue template. commit 2896bb8787698be28ad20f2298589e6e95eaf9fb Author: Kate Friedman <[email protected]> Date: Tue Dec 12 09:13:06 2023 -0500 Fix module load typo (#2145) Fix typo with loading the crtm module in the UPP hack for WCOSS2 Refs #2144 commit 29d34172a67d976f910e78158ff0337e1ef099ca Author: Cory Martin <[email protected]> Date: Thu Dec 7 15:12:05 2023 -0500 Update GDAS hash to most recent stable versions (#2138) commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102 Author: Henry R. Winterbottom <[email protected]> Date: Thu Dec 7 10:41:05 2023 -0700 Corrected typo in a gempak job gempakncdcupapgif . (#2137) commit 3483f550db1ae35a680de49f7485ce5a11902dd9 Author: Cory Martin <[email protected]> Date: Thu Dec 7 12:34:56 2023 -0500 Add support for FGAT and IAU for aerosol DA (#1940) commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9 Author: David Huber <[email protected]> Date: Thu Dec 7 12:33:46 2023 -0500 Enable forecast-only experiments on Hercules (#2128) This add forecast-only support for Hercules to the global workflow. Partially satisfies #1588. Co-authored-by: Walter Kolczynski - NOAA <[email protected]> commit a29f751aed05312da3d80d396159bb5a906d6ce4 Author: Henry R. Winterbottom <[email protected]> Date: Wed Dec 6 13:45:56 2023 -0700 Adds GEMPAK and related jobs to rocoto task mesh (#2127) commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082 Author: Rahul Mahajan <[email protected]> Date: Tue Dec 5 15:47:52 2023 -0500 Separate offline UPP from interpolated grib2 product generation (#2110) This PR: - Replaces the use of `JGLOBAL_ATMOS_POST` with `JGLOBAL_ATMOS_UPP` and `JGLOBAL_ATMOS_PRODUCTS`. - Introduces `JGLOBAL_ATMOS_PRODUCTS` that is responsible for creating grib2 products from the master file produced by UPP (inline from the model, or offline by running `JGLOBAL_ATMOS_UPP`). Rocoto job `atmos_products.sh`, ex-script `exglobal_atmos_products.sh` are also added along with a `config.atmos_products`. Updates are made to the relevant `env` files as well as `config.resources` to reflect the addition of this job. - reduces the number of cores needed appropriately for forecast products when there is no offline UPP necessary. - renames older `fv3gfs_dwn_nems.sh` to `interp_atmos_master.sh` and `inter_flux.sh` to `interp_atmos_sflux.sh` - removes `fv3gfs_downstream_nems.sh` as it is absorbed into `exglobal_atmos_products.sh` - removes no longer used scripts for `gfs_post.sh`, `gfs_transfer.sh` (DBN alerts are absorbed into `exglobal_atmos_products.sh`), `post.sh`, `JGLOBAL_ATMOS_POST`, `ex${RUN}_atmos_post.sh` scripts. - Rocoto workflow related scripts are updated to add `atmos_products` as a job. When `WRITE_DOPOST` is `.false.`, `upp.sh` job to run the UPP offline is also added. Dependencies have been appropriately applied. - removes `PGB1F` option that creates 1-degree grib1 products that are no longer needed in GFSv17. The hacks from (now deleted) `post.sh` had to be reinstated in `upp.sh` to load the modules from UPP instead of `load_fv3gfs_modules.sh`. commit 44186f594aaf5f8feea0eadd4c5c3b59de3a825e Author: Kate Friedman <[email protected]> Date: Tue Dec 5 12:28:08 2023 -0500 Update index.rst for new GFSv16.3.11 version (#2121) Refs #1356 commit e62a3a73cd22701962b7bf210fdfee37f37a5474 Author: Henry R. Winterbottom <[email protected]> Date: Tue Dec 5 09:08:12 2023 -0700 Splits AWIPS jobs into seperate tasks (#2094) This PR addresses issue #1228. The following is accomplished: - Separate rocoto jobs have been created beneath `jobs/rocoto/` -- `awips_20sh` and `awips_g2sh`; these jobs replace `awips.sh` which was calling multiple J-jobs within the respective `awips.sh` scripts; - New tasks has been added to `workflow/rocoto/tasks.py` for the new AWIPS scripts; - The `gfs_cycled` and `gfs_forecast_only` modules beneath `workflow/rocoto` have been updated accordingly. Resolves #1228 commit 04d97e9aa7ab84b9754ab670074cfb19d543aa26 Author: Kate Friedman <[email protected]> Date: Mon Dec 4 13:38:30 2023 -0500 Consolidate VMINMON and cleanup monitor scripts (#2088) This PR combines the GDAS and GFS versions of the VMINMON JJOB and ex-driver scripts into single GLOBAL/global versions. Additionally: * some further cleanup of the GSI-Monitor scripts is done; variable settings in ex-driver scripts are moved up to the JJOB level * the fix symlinks are consolidated into a new `fix/mon` subfolder (formerly `fix/gdas`) and copies of the gfs monitor fix files under `fix/products` are removed Resolves #1925 commit a286a11fdcbc31c8bc6d944890bc56294bc8caf6 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Mon Dec 4 17:48:44 2023 +0000 Robust CI Restarts (#2093) Improved CI robustness for reverting back to **CI-Ready** from any given state New Features: - Improved `scancel` routine (refactored into bash "subroutine") - Improved messaging (see below) when ever a user changes state - Any and all previous build scripts and running experiments are killed as a result of reset to **Ready** Resolves #2060 commit 73621e9b20b20f85e8b21e4c1e09ed1d80ecd46f Author: David Huber <[email protected]> Date: Sun Dec 3 11:19:19 2023 -0500 Upgrade to spack-stack/1.5.1 and Intel 2022 on non-production machines (#2084) Update module files to spack-stack/1.5.1 and compilers to Intel 2022+ on all non-production machines. commit 6d548b250688861eb20a7e0dc852a0e4ba9e64f4 Author: jiandewang <[email protected]> Date: Thu Nov 30 12:00:21 2023 -0500 Add variable tob in diag_table for ocean model output(#2105) commit c19810cce252fcdb25fd9960c05b08b5f8d8b1ad Author: AndrewEichmann-NOAA <[email protected]> Date: Wed Nov 29 15:17:36 2023 -0500 Added variables to config.prepoceanobs (#2101) commit c2d78a61a224678fb804eed19f39d1f07408ae5f Author: Kate Friedman <[email protected]> Date: Wed Nov 29 12:39:08 2023 -0500 Add missing cut to VDATE setting in JGFS_ATMOS_VERIFICATION (#2098) Refs #2097 commit c1c025f91ddac73aea595cc9fa4dd0bea80575fc Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Nov 29 17:15:10 2023 +0000 Add wave init to GEFS (#2089) Adds the wave init job to GEFS. Since the output would be the same for every member, the job is only run once for the control, then links are created in each of the member directories pointing to that copy. New ww3_multi and ww3_shell templates for GEFS are copied from the GFS versions. The GEFS restart frequency is changed to not be zero, and the comment about not setting it to zero is copied from the gfs config.base. The restart interval for the GEFS perturbed members is changed to equal that of the control. Also fixes a bug where `RUNwave` was not defined for ensemble forecasts, and another bug in the GEFS stage_ic dependency. Resolves #2017 commit 64a2470ce29b7d8d5cb85ebcb4048ff82958f64e Author: Kate Friedman <[email protected]> Date: Wed Nov 29 11:26:34 2023 -0500 Adjust permissions for jobs/JGFS_ATMOS_VERIFICATION (#2095) Add execute permissions (755) commit 964b77bc6de67291973c2c70598a1f8cb72501c5 Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Nov 28 18:45:51 2023 +0000 Make proper j-job for MET+ (#2090) Creates a proper j-job for the metp job, moving much of the material from the `jobs/rocoto` script there (some of it within `jjob_header`). Also updates the old `COMIN` variable for the COM refactor (although it does not appear used in the verify scripts currently). This is a partial step towards restoring/improving metp functionality and remains untested. Refs #1575 commit 8c11eeb8556619e8db4e0efb6394ce5a2c1aae0f Author: Henry R. Winterbottom <[email protected]> Date: Thu Nov 23 10:31:32 2023 -0700 Adds FBWINDS support to global-workflow (#2082) This PR addresses issue #1221. The following was accomplished: - A new Rocoto job is added; `jobs/rocoto/fbwinds.sh`; - `workflow/applications/gfs_cycled.py` is updated to include the `fbwinds` task; - `workflow/applications/gfs_forecast_only.py` is updated to include the `fbwinds` task; - A new function is added to `workflow/rocoto/gfs_tasks.py`, `fbwinds` is added as new GFS (only) task; - `workflow/rocoto/tasks.py` is updated to include the `fbwinds` task. Resolves #1221 commit 513db190d21f9ede0724a2cd5606372b1d7605de Author: Henry R. Winterbottom <[email protected]> Date: Tue Nov 21 22:52:58 2023 -0700 Adds NPOESS support to global-workflow (#2083) This PR addresses issue #1225. The following was accomplished: - A new Rocoto job is added; `jobs/rocoto/npoess.sh`; - `workflow/applications/gfs_cycled.py` is updated to include the `npoess` task; - `workflow/applications/gfs_forecast_only.py` is updated to include the `npoess` task; - A new function is added to `workflow/rocoto/gfs_tasks.py`, `npoess` is added as new GFS (only) task; - `workflow/rocoto/tasks.py` is updated to include the `npoess` task. Resolves #1225 commit 62d8e99e77ffe44784f4c61c3f2296c6d1a72413 Author: Kate Friedman <[email protected]> Date: Fri Nov 17 20:25:50 2023 -0500 Retire vrfy job (#2080) Retires the `vrfy` job from the global-workflow system. All associated scripts, configs, and references to the job are removed. Additionally, the switches listed in RTD were updated to reflect new ones added in other PRs for issue #235. Resolves #2069 Refs #235 commit ea386abf11ecbacef407388e8d57e71b30148a35 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Nov 17 23:59:46 2023 +0000 Enable different coupled settings for ensemble (#2030) Adds the ability to turn off some coupled components for the ensemble. To enable this, many settings are moved out of `config.fcst` and into `config.ufs` so they are calculated after any overrides of `DO_*` have been made. Some settings also had to be moved out of `config.base` for the same reason. A switch to turn on gocart is added to `config.ufs`, but unlike the other switches this one takes no arguments. The name of the ufs configure template used is converted from a partial file name to the full file name. Resolves #1692 commit fe792c0c9a1c46908cbd18c7e71eb836974cf1de Author: Kate Friedman <[email protected]> Date: Fri Nov 17 17:19:16 2023 -0500 Add --cpus-per-task to srun commands for Hera and Orion (#2077) This PR adds the `--cpus-per-task` flag to non-CFP `APRUN`/srun commands in the env files for Orion and Hera. This is needed as a result of an upgrade to SLURM on Orion that no longer exported the thread value to the environment. Issue #1996 was a hotfix to add this flag for the analysis job that was suddenly running slowly after the SLURM upgrade. A similar SLURM upgrade was done on Hera but the sysadmins there implemented a workaround so this issue did not appear there. This PR adds the `--cpus-per-task` flag for both machines...needed on Orion and as a safety measure on Hera. Also included in this PR is a fix to indentations in the `scripts/exglobal_diag.sh` script that was noticed during work for this PR. Timing differences were not observed for other jobs after adding this srun flag. Job timings were of a similar variation between control and test runs. Any potential additional speedup was not observed. The test runs also reproduced the control runs with `develop`. Resolves #2044 commit 42c943be305c297a56b104bb50727938c1ba688f Author: Kate Friedman <[email protected]> Date: Fri Nov 17 15:41:34 2023 -0500 Adjust modules in post.sh for WCOSS2 (#2079) On WCOSS2 the grib_util module is named a bit different and needs the libjpeg module loaded beforehand. commit cd4e6a1987e7fd71dff06766f540b5d32c8b648d Author: Jessica Meixner <[email protected]> Date: Fri Nov 17 11:49:32 2023 -0500 Update ufs-weather-model and remove upp hack (#2071) Updates the model to the most recent commit of ufs-weather-model. This should allow for the removal of the UPP hack that was added in PR #2042 This required changing nems.configure -> ufs.configure. Resolves #1942 commit 5a2d97e142aa4999b122fd5a130c63e59ea9f8e2 Author: Walter Kolczynski - NOAA <[email protected]> Date: Thu Nov 16 22:15:53 2023 +0000 Fix check for existence of preamble functions (#2066) A few of the setup scripts were checking for the existence of functions set by the preamble before calling them so they could also be used stand-alone. However, the `type` command returns `1` if the function name does not exist, which will cause the script to die is `set -e` is on. Now the `type` command fails over to an empty string. commit ed2ee7c2b1457b71b271a2c40f0dfa356e0f52f8 Author: WenMeng-NOAA <[email protected]> Date: Thu Nov 16 16:38:11 2023 -0500 Update UPP products for GFS v17 (#1973) Updates of generating GFS V17 UPP products to support HR3: - Update g2tmpl to 1.0.12 - Add changes to launch cfp on WCOSS2 to generate pgrb2/pgrb2b files - Changes for generating new products (MERRA2, six winter weather variables, 1km HLCY, SDEN) in pgrb2 files Resolves #1965 Resolves #1994 commit 635c4719e603538ce7cccf9ea6b31f3f84f20849 Author: Walter Kolczynski - NOAA <[email protected]> Date: Thu Nov 16 20:35:30 2023 +0000 Fix some rocoto dependencies (#2074) A few small errors/cleanup in the dependencies, mostly in fcst: A few small errors/cleanup have crept into the dependencies with recent changes, mostly in fcst: - Fixed the offset, as it would yield a string rocoto doesn't recognize when the interval was 24+ hrs - Removed the duplicate wave dependency. When `waveprep` is included, it depends on `waveinit` so there is no need to add a `waveinit` dependency. - Converted an interval in the archive job that was missed in #2039 Resolves #2075 commit d4c7508260975c6b94fc92fd085f39d4faf3f027 Author: Rahul Mahajan <[email protected]> Date: Wed Nov 15 16:44:03 2023 -0500 Fix missing _PREV in ocean restart file location (#2070) commit 255616d37505c785bdddd5d3e39e8399110b626e Author: mdtoyNOAA <[email protected]> Date: Wed Nov 15 12:02:09 2023 -0700 Update functionality for Prototype HR3 UGWP (#1987) This PR adds/modifies namelist options and activates new 'ccpp' suite definition files for the updated Unified Gravity Wave Physics (UGWP) in the ufs-weather- model recently updated for HR3. The changes to UGWP are the use of the GSL drag suite for orographic gravity wave drag (GWD) and blocking, as well as the new UGWP Version 1 non-stationary GWD. See ufs-community/ufs-weather-model#1923 for details. Resolves #1986 commit be9085e62aae147e3c74602e2f82a99b374fc783 Author: Guillaume Vernieres <[email protected]> Date: Wed Nov 15 13:48:58 2023 -0500 Save the required CICE history for the sea-ice DA (#2062) The hist_avg setting of CICE was changed to be an array. commit 85f1f5131ffd70061231304ea477bde0559eb67b Author: Guoqing Ge <[email protected]> Date: Wed Nov 15 11:47:21 2023 -0700 Use assim_freq to configure "offset" in dependencies (#2039) Use the assim_freq from config.base to configure "offset" in dependencies instead of hard-coding them. Resolves #2038 commit 4e3d82ba3a1fa7cdd4443bcd4cf83b2f8835137c Author: Kate Friedman <[email protected]> Date: Wed Nov 15 13:39:14 2023 -0500 Resolve ENKF archive script bugs (#2065) Fix two bugs in the exgdas_enkf_earc.sh script: 1) Replace ARCH_LIST with DATA to match changes done in PR #2000 and update path to generated archive list files. 2) Add status check and exit after script attempts to make tarball on HPSS. Refs #2064 commit 42d7f2f0c48fab898b764e09cfbbd7a9fabbae08 Author: Kate Friedman <[email protected]> Date: Tue Nov 14 17:54:29 2023 -0500 Separate tracker and genesis jobs from vrfy job (#2058) This PR creates new individual jobs for the tracker and genesis jobs that are being pulled out of the `vrfy` job (issue #235). The `tracker` and `genesis` jobs will be on by default while the `genesis_fsu` job will be off by default. This mimics the current settings in the `vrfy` job. No enhancements or upgrades are made to the jobs themselves in this PR, only to separate them from the `vrfy` job. However, one change compared to how they currently run in the `vrfy` job is to no longer run the `tracker` in the gdas suite. This mimics how the `ens_tracker` package is run in operations (gfs only). Changes in this PR: 1. Create rocoto job scripts for tracker/genesis jobs. 2. Create configs for tracker/genesis jobs, as well as `config.tropcy` for shared settings. 3. Add tracker/genesis jobs to `config.resources`; use resources from the ecf scripts for `ens_tracker` jobs in operations 4. Add tracker/genesis jobs to rocoto setup for both cycled and forecast-only modes. 5. Update arguments for `jjob_header.sh` script in tracker/genesis JJOB scripts to use specific job names and configs instead of vrfy. 6. Rename `tracker_ver` to `ens_tracker_ver` in version files to mimic variable within tracker package. 7. Rename and move tracker/genesis switches to `config.base`. 8. Remove tracker/genesis jobs from `vrfy` job (`jobs/rocoto/vrfy` and `config.vrfy`). 9. Reduce vrfy job resources to accommodate tasks having been removed. Refs #235 Resolves #1988 Resolves #2048 commit 0a0d6984e094d2a551d5d8331102142e7db13fc2 Author: Rahul Mahajan <[email protected]> Date: Tue Nov 14 14:08:26 2023 -0500 Enable warm starting of the model for forecast-only mode (#2031) This PR: - adds an option to warm|cold start the ufs-weather-model when setting up an experiment for GFS/GEFS - adds the capability to stage FV3 restarts when the atmosphere is warm started from FV3 restarts. This would be used in the GEFS free-forecast for part of the reforecast capability. - If a coupled model is warm started for the atmosphere, also check if mediator restarts are present. If so, stage mediator restarts to allow restarting the coupled model. Fixes #2016 commit 2cd6a589305a9ac9d3a9a0d2136e66e42f09d3bf Author: Henry R. Winterbottom <[email protected]> Date: Tue Nov 14 12:05:20 2023 -0700 Moves UFS WM configuration files to `COM_CONF` (#2054) The UFS weather-model (WM) files are place in the COM_CONF path rather than the respective component model COM history paths. Resolves #2015 commit 6f1693081662f241fafc930b1afc88125f7f5aff Author: Kate Friedman <[email protected]> Date: Tue Nov 14 11:15:02 2023 -0500 Refine fit2obs job in rocoto mesh (#2047) This PR adjusts the `fit2obs` job in the rocoto mesh to better define when it exists and how the archive job dependencies accommodate it not being in the first half cycle. Changes in PR: 1. Remove the `fit2obs` job from the first half cycle `cycledef`. 2. Adjust the archive job dependencies to now include the `fit2obs` job in the new logic check added in PR #1983. The `gdasarch` job in the first half cycle will check if `gdasfit2obs` is complete OR no prior cycle exists. Also cleaned up this new logic check block some to make it a tad simpler. 3. Also, fix the addition of the `fit2obs` config to the config list in setup scripts. Now tied to whether `fit2obs` job is on instead of always adding the config to the list. Resolves #2043 commit 5730a71fa5d311e49d9bb11528b500f27f33d69d Author: Henry R. Winterbottom <[email protected]> Date: Tue Nov 14 09:13:11 2023 -0700 Add `waveinit` and `waveprep` to half-cycle. (#2037) This PR addresses issue #1444. The `waveinit` and `waveprep` tasks have been added to the GDAS have cycle. The downstream dependencies for the respective GFS and GDAS forecast tasks have been removed. Resolves #1444 commit 28d2e93c3857de95b0309a089cd7dac736ccaded Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Nov 14 16:11:47 2023 +0000 Update wave IC source for C384 (#2055) The default wave grid for C384 has changed since P8, so a single wave IC on the new grid is available under a different IC name. commit 81dd2d9855091315611106a5afbdaeaa15e6e4ae Author: Walter Kolczynski - NOAA <[email protected]> Date: Thu Nov 9 17:19:57 2023 +0000 Fix analysis and post on Orion (#2046) Fixes a couple things to get workflow to work on Orion again: First, while #2042 allowed post to be built, the `upp.x` executable would fail due to a missing library. Now post jobs (temporarily) uses the UPP modules (plus others needed for runtime) instead of the normal workflow runtime module. This should actually fix #2041. This hack can likely be removed once we move to spack-stack. Second, the launcher command for the analysis jobs on Orion are updated to specify the number of CPUs per task. This was necessary as a recent slurm update on Orion discontinued reading that value from the scheduler. Other jobs will be handled later (see #2044). Additionally, a change is made to `module-setup.sh` that will eliminate the annoyance of `gw_setup.sh` breaking tab completion because undefined variable checking was turned on for the script but not back off. Resolves #1996 Resolves #2041 Refs #2044 commit 13d06ded4155cba2d08ef2a2cd553024c5abe29d Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Nov 8 18:25:47 2023 +0000 Hack UPP version (#2042) The stack UPP was using on Orion was recently deleted, leaving us unable to build the UFS verison of UPP there. UPP has an updated version using spack-stack that works, so the checkout script is modified to check out that version of UPP after UFS has been checked out. This temporary hack can be removed once we move to a UFS version that advances the UPP version to or beyond 78f369b. Resolves #2041 commit 20f6eceb8ff58f84174a27eb849c1d74566a3e03 Author: jiandewang <[email protected]> Date: Wed Nov 8 11:14:55 2023 -0500 Add basic C1152 settings (#2020) Adding C1152 setting in host.yaml, config.base and config.stage_ic so that can run C1152 S2SW. Resolves #2019 commit 5183c43bbbd07285869feacb49d8680afe85929a Author: Barry Baker <[email protected]> Date: Tue Nov 7 01:14:40 2023 -0500 Update UFS for dust fix and remove nitrates by default (#1989) This PR updates the `ufs-weather-model` to the latest hash that included the dust fix (PR #1922). Along with this I removed the nitrates by default in support of the GEFSv13 EP4 and EP5 experiments. Removed unneeded inputs that should help with speed improvements. commit 34a73cf2ed5afefc776d9cc73b6ebf439122a1bb Author: David Huber <[email protected]> Date: Mon Nov 6 14:00:51 2023 -0500 Reduce gdas builds to 8 #2029 (#2036) Reduce the default number of build jobs for the GDASApp to 8 from 16. This is needed for Orion as the build crashes during a linking step. Though not verified, it appears this may be caused by using too much memory with 16 builds. The issue disappears when using 8 build jobs. Resolves #2029 commit 75269e4bb9764b81589efc7d703825b80e74c8f5 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Mon Nov 6 17:34:47 2023 +0000 Streamline CI reporting to PRs (#2026) Cleaned up the logs for CI PRs sent to the GitHub Messages: - Eliminates redundant accumulative reporting - Reports on all created or skipped experiment instantiations in a single message - Gives one line report once for each experiment completion - Single final report completion of CI See some examples in forked [PR 195](https://github.com/TerrenceMcGuinness-NOAA/global-workflow/pull/195) Resolves #2007 commit 8d55126bb0b27c79c8bee7f72b014abd34950ff9 Author: Guillaume Vernieres <[email protected]> Date: Fri Nov 3 17:06:09 2023 -0400 Implement IAU Cycling Type with Marine Data Assimilation Enabled (#1944) Allows cycling in IAU mode with the S2S UFS model, soca and the GSI. Most of the work related to making IAU work was done by @JessicaMeixner-NOAA . Thanks @JessicaMeixner-NOAA ! Resolves #1943 Refs #1776 commit 2563806821d4ae3b57120bc61aa0575139a708f0 Author: jiandewang <[email protected]> Date: Fri Nov 3 11:49:37 2023 -0400 Add two ucx modules in load_ufswm_modules.sh to solve C768 and C1152 S2SW job hanging issue on WCOSS2 (#2021) commit cbdc09711a83493f363a737d1e3e46c48a09719d Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Nov 3 04:09:33 2023 +0000 Fix staging of MOM data (#2028) During the update to stage_ic, the copying of the additional res_N files for 0p25 was omitted. These are now properly copied. Resolves #2027 commit bd4c56d99c23c5c41f0bd5f8a980ef99ee160888 Author: AndrewEichmann-NOAA <[email protected]> Date: Thu Nov 2 16:09:59 2023 -0400 changed optional script name vars for ocean analysis (#2025) commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6 Author: Kate Friedman <[email protected]> Date: Thu Nov 2 16:01:18 2023 -0400 Create separate GSI monitor jobs and remove from vrfy job (#1983) This PR will move the GSI monitor tasks from the `vrfy` job into their own separate jobs in the rocoto mesh. This takes care of part of issue #235. Changes in this PR: 1. Create new individual GSI monitor jobs in the rocoto mesh to match how it is done in operations. The new jobs are: `gdasverfozn`, `gdasverfrad`, `gdasvminmon`, and `gfsvminmon`. The names correspond to the names in operations and the ecf script names. The jobs are only added to cycled mode, none of the jobs are run in forecast-only mode. 2. Updates to GSI monitor scripts: * Update `ush/jjob_header.sh` arguments in JJOB scripts to call new individual job names and configs. * Introduce `COM_*` variables and use of the `generate_com` utility. This results in the outputs landing in `COM` subfolders, like occurs in operations, instead of landing in the online archive. * Some variable cleanup in JJOB and ush scripts, includes cleaning up usage of `DATA` variable and its removal at the end of the jobs. * Add missing exit statements to `JGFS_ATMOS_VMINMON` and `JGDAS_ATMOS_VERFRAD`. 3. Create new rocoto job scripts for the new individual GSI monitor jobs. 4. Create new configs for the new individual GSI monitor jobs. 5. Add new individual GSI monitor jobs to resource configuration, using the same resources as in operations. 6. Move and rename GSI monitor job switches from `config.vrfy` to `config.base`. Also add switches to setup system. New switches to control each job being added to the rocoto mesh are: `DO_VERFOZN`, `DO_VERFRAD`, `DO_VMINMON` 7. Add GSI monitor job output to archival job and into resulting HPSS tarballs or local tarballs. This now matches what is done in operations. 8. Remove the GSI monitor tasks from the rocoto `vrfy` job and associated `config.vrfy`. Example output locations and files (not showing contents of oznmon/horiz or oznmon/time for brevity, see archival script for full list of output files): ``` kate.friedman@dlogin09:/lfs/h2/emc/ptmp/kate.friedman/comrot/testmonitor2> ll gdas.20211221/00/products/atmos/*mon gdas.20211221/00/products/atmos/minmon: total 112 -rw-r--r-- 1 kate.friedman emc 14030 Oct 25 15:00 2021122100.costs.txt -rw-r--r-- 1 kate.friedman emc 84932 Oct 25 15:00 2021122100.cost_terms.txt -rw-r--r-- 1 kate.friedman emc 808 Oct 25 15:00 2021122100.gnorms.ieee_d -rw-r--r-- 1 kate.friedman emc 808 Oct 25 15:00 2021122100.reduction.ieee_d -rw-r--r-- 1 kate.friedman emc 80 Oct 25 15:00 gnorm_data.txt gdas.20211221/00/products/atmos/oznmon: total 8 drwxr-sr-x 2 kate.friedman emc 4096 Oct 25 15:05 horiz drwxr-sr-x 2 kate.friedman emc 4096 Oct 25 15:05 time gdas.20211221/00/products/atmos/radmon: total 21036 -rw-r--r-- 1 kate.friedman emc 231 Oct 25 15:12 bad_diag.2021122100 -rw-r--r-- 1 kate.friedman emc 9035 Oct 25 15:12 bad_pen.2021122100 -rw-r--r-- 1 kate.friedman emc 1449 Oct 25 15:12 low_count.2021122100 -rw-r--r-- 1 kate.friedman emc 20523403 Oct 25 15:07 radmon_angle.tar.gz -rw-r--r-- 1 kate.friedman emc 217272 Oct 25 15:08 radmon_bcoef.tar.gz -rw-r--r-- 1 kate.friedman emc 502151 Oct 25 15:10 radmon_bcor.tar.gz -rw-r--r-- 1 kate.friedman emc 264480 Oct 25 15:12 radmon_time.tar.gz -rw-r--r-- 1 kate.friedman emc 684 Oct 25 15:12 warning.2021122100 kate.friedman@dlogin09:/lfs/h2/emc/ptmp/kate.friedman/comrot/testmonitor2> ll gfs.20211221/00/products/atmos/minmon/ total 88 -rw-r--r-- 1 kate.friedman emc 10530 Oct 25 14:55 2021122100.costs.txt -rw-r--r-- 1 kate.friedman emc 63882 Oct 25 14:55 2021122100.cost_terms.txt -rw-r--r-- 1 kate.friedman emc 808 Oct 25 14:55 2021122100.gnorms.ieee_d -rw-r--r-- 1 kate.friedman emc 608 Oct 25 14:55 2021122100.reduction.ieee_d -rw-r--r-- 1 kate.friedman emc 80 Oct 25 14:55 gnorm_data.txt ``` Lingering work and considerations: 1. Issue #1925 2. Consider not hardcoding the list of types in archival and perhaps tie it to something reliable or configurable (maybe into `config.verfozn`?): `subtyplist="gome_metop-b omi_aura ompslp_npp ompsnp_n20 ompsnp_npp ompstc8_n20 ompstc8_npp sbuv2_n19"` Resolves #1908 commit 31b05a99b77d0f6eaa8b116485a41a43867d20e1 Author: Henry R. Winterbottom <[email protected]> Date: Thu Nov 2 12:23:32 2023 -0600 Move analysis post to new stand-alone task (#1979) This PR addresses issue #1130. A new task `postanl.sh` has been added such that the `anl` post-processing is not it's own task within the Rocoto workflow. This change prevents the GDAS experiment from breaking due to failures caused by the `anl` not being available for the first cycle. Resolves #1130 commit 247cdf8c7e10e6c98f782799fc51c069b6474e70 Author: Henry R. Winterbottom <[email protected]> Date: Thu Nov 2 11:18:53 2023 -0600 Corrects missing local variable reference (#2023) Fixes missing `$` in variable reference in archive job. Resolves #2022 commit 241742b246da1794646b68e41c3d6fe00b95dd07 Author: AndrewEichmann-NOAA <[email protected]> Date: Wed Nov 1 14:19:55 2023 -0400 Updates to prep ocean obs task (#1870) commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd Author: Henry R. Winterbottom <[email protected]> Date: Wed Nov 1 12:09:33 2023 -0600 No longer write archive lists COM (#2000) Changes the respective `.txt` files used for the HPSS archive to the `DATA` path. Each defined text file has been updated to explicitly write to `DATA` rather than `COM` such that the files are deleted rather than being archived. Resolves #760 commit 517b92f9c20c9e44abba3183325e35a95a7334a5 Author: David Huber <[email protected]> Date: Tue Oct 31 16:33:11 2023 -0400 Parallelize the build scripts (#1998) Optimized/parallelized build scripts. A few notes: 1) The default number of build jobs is 20, but one could argue for using 40. When researching this, I looked up what the SRW is compiling with. That system uses 40 cores, which seems a little excessive, but on testing the global workflow, the actual number of cores being used at any given time rarely exceeds 16 when running with 40 cores. This is because the builds tend to use multiple threads in the beginning when compiling low-level modules while the higher-level modules are more or less serial AND because the GDASApp takes several minutes to initialize all of its subrepositories by which time the smaller builds are complete. 2) I also updated checkout.sh so that all checkouts are simultaneous. The CPU load for `git submodule` is quite low, so running 16 instead of 8 jobs at once is not much more expensive. 3) To make this work, I had to add `-j` options to most of the build scripts. The only exception is build_upp, for which the build script within the UPP is hard coded to use 6 cores. 4) I fixed a few small bugs in the build scripts along the way. 5) Lastly, this reduce the total build time from ~2.5 hours for the entire system (including GDAS and GSI in the same build) to ~40 minutes when running with `-j 40`. Resolves #1978 commit 67c050c201f92e855d09211e41a5f51ee1cb5230 Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Oct 31 19:00:47 2023 +0000 Add missing export for rCDUMP in stage_ic (#2009) rCDUMP is needed by the exscript but was never exported by the jjob. commit 872068cb5ea78b311f7a77e97ee1428ae027cb61 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Oct 31 14:37:55 2023 +0000 Add output error log to user for create_experiment.py on fail in CI (#1974) Small changes to driver CI bash scripts to recapture error log from `create_experment.py` logger Fixes #1939 commit b2e4a2e9d269842acbb1b37dd563ee5dee2adf0f Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Oct 31 13:57:02 2023 +0000 Allow CI case to exclude running on certain platforms (#2001) commit 7cc137116f1619bf1e5a12eaacb98d17da97c223 Author: Jeff Whitaker <[email protected]> Date: Tue Oct 31 07:54:24 2023 -0600 Add initial C96/1 deg coupled model support (#1991) commit 7086ddc4bece6fb2a8c1c2e6090800d4293e410e Author: AndrewEichmann-NOAA <[email protected]> Date: Mon Oct 30 19:58:43 2023 -0400 Add ocean analysis files to HPSS archiving task (#1985) This PR adds the files under `analysis/ocean` (except those in `bump` and `vrfy`) to the HPSS archiving job, in `gdasocean_analysis.tar`, which were previously not archived. Resolves NOAA-EMC/GDASApp/issues/693 commit eabc82ad30c118645c0e6e216162d823882a8139 Author: Guillaume Vernieres <[email protected]> Date: Mon Oct 30 10:31:27 2023 -0400 Make the early cycle work with the coupled UFS configured as S2S (#1954) commit aff6ca7ae559e424dae128d6cfd5da4a4e3049e7 Author: Anil Kumar <[email protected]> Date: Fri Oct 27 14:11:55 2023 -0400 GEFS Staging in exglobal_stage_ic (#1892) Adjusts source paths for forecast-only ICs in support of extension to ensembles. New paths omit the resolution (that is captured by the IC id name) and allow for a member level. Directories with the reorganized ICs have been added to the three tier-1 machines under glopara space. Building on this, also adds capability to stage GEFS ICs. Resolves #911 commit 77c1ff2bfa26b341b01f41e50ee0ecb31cc4f661 Author: RussTreadon-NOAA <[email protected]> Date: Thu Oct 26 23:44:27 2023 -0400 Update GDASApp hash (#1975) Update GDASApp hash to bring recent UFSDA development into g-w. Resolves #1972 commit 962368884991670d3a1ee1c5a065d5bce4b7561a Author: David Huber <[email protected]> Date: Thu Oct 26 16:10:23 2023 -0400 Test tarballs for rstprod before calling chgrp (#1967) Certain tarballs may or may not contain `rstprod` data. For instance, the first half cycle gdas and enkfgdas tarballs will not contain `rstprod`, while future cycles likely will. Also, some systems do not have `rstprod` on them. This will test the contents of the tarballs first before attempting to change the group to rstprod. Resolves #1460 commit c02e118c0ac5485109c9bd33472ff42db309cd9b Author: Jessica Meixner <[email protected]> Date: Thu Oct 26 15:05:05 2023 -0400 Update ufs model to version from 10-12-23 (#1933) This updates the ufs-weather-model to the commit hash from 10-12-23 from the HR2 tag. The diffs can be seen here: https://github.com/ufs-community/ufs-weather-model/compare/GFSv17.HR2...68050e58589a82ab509aaefaafdc2a6b90f34e48 Resolves #1811 commit 8556541daa79b0180fde48a58a8dcfb2f8c56ea5 Author: Rahul Mahajan <[email protected]> Date: Wed Oct 25 16:15:28 2023 -0400 Fix incorrect usage of CFP on WCOSS2 (#1977) commit 0b5cf9b67a8146d9d4815ea6545f7f2524120d83 Author: Kate Friedman <[email protected]> Date: Wed Oct 25 13:17:28 2023 -0400 Update GFS version in index.rst to v16.3.10 (#1976) Update the "State of operations" GFS version number to new v16.3.10 (Annual CO2 fix file update in operations). Refs #1924 commit e817f5dd38c26a88f76d90eb71124f1acbfc5a8f Author: Walter Kolczynski - NOAA <[email protected]> Date: Wed Oct 25 02:03:14 2023 +0000 Fix path for marine products (#1966) When PR #1823 was merged, the name of the marine product template was not updated in ocnpost, leading the products to be placed in the wrong location and missed by the archive job. Resolves #1902 commit 7cdfad4eaa7abe0769ff13396c54e6d93afebf8f Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Oct 24 22:19:46 2023 +0000 Build GDASapp for CI tests (#1964) * added -u to global checkout so CI test builds tests for GDASapps * Update check_ci.sh needed more quotes --------- Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]> commit c58deae0cf078d1ee093529064d74f60482aa3f4 Author: Henry R. Winterbottom <[email protected]> Date: Tue Oct 24 16:19:04 2023 -0600 Updates for NOAA CSP AWS global-workflow related file paths. (#1970) Co-authored-by: henrywinterbottom-wxdev <[email protected]> commit 1b00224e18842cd873eb1779be08f96687e49e1f Author: Kate Friedman <[email protected]> Date: Tue Oct 24 14:48:24 2023 -0400 Set SENDCOM=YES for tracker/genesis tasks (#1971) Set SENDCOM to YES in config.vrfy to get outputs copied back to COM. Will reevaluate the need for SENDCOM when moving the tracker/genesis jobs out of the vrfy job with issue #235 work. Refs #1947 commit e2c624d8904cd988394c73d0edb22fa593229d3f Author: RussTreadon-NOAA <[email protected]> Date: Tue Oct 24 13:32:52 2023 -0400 Refactor UFSDA ATM var and ens layout (#1945) commit 8940adddfe9d21189740e71487603fb2acee2336 Author: David Huber <[email protected]> Date: Tue Oct 24 11:02:29 2023 -0400 Optimize the checkout script (#1956) * Multithread the checkout script #1953 commit 4b5cd0bc435fc158258ca38c3d5f44add6b60469 Author: Rahul Mahajan <[email protected]> Date: Mon Oct 23 12:04:26 2023 -0400 Fix nth_eupd in gfs/config.resources. remove sections of jobs not run as part of gefs from gefs/config.resources (#1952) commit 08ce4f8d3ed8e07b4d488a80b5054c6206b04404 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Oct 20 16:14:53 2023 +0000 Fix enkfgfs cleanup dependency (#1941) When #1906 was merged, the dependency for enkf cycles was hard-coded to use the enkfgdas archive instead of depending on the `RUN`. commit 1a5d0b51642eb70f71e693355e86212d3607b7b3 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Oct 20 15:54:33 2023 +0000 Split clean-up into separate job (#1906) Moves the clean-up that was previously done in the archive jobs into their own separate job. The clean-up is also streamlined considerably by using only `COM_TOP` instead of going through every template. There is also additional streamlining/corrections in the function that does the actual removing. Some settings used by both jobs were elevated to `config.base`. Others only needed for cleanup were moved to the new config for that job. Also corrects a small error encountered when attempting to rerun an ensemble forecast. Resolves #583 Resolves #1872 commit 3de102c28daf9eb50ce65e0afe911f5a416ce861 Author: Rahul Mahajan <[email protected]> Date: Tue Oct 17 09:30:18 2023 -0400 Updates to CI to clarify HOMEgfs (#1931) * replace HOMEgfs_PR with HOMEgfs, and HOMEgfs with ROOT_DIR. ROOT_DIR is the location where the ci scripts live * update type to system in case yamls * move create_experiment.py to workflow/ * detect HOMEgfs in create_experiment.py based on location. update to use jinja templates in the cases * remove export of HOMEgfs from driver.sh commit bfea2594207a477ea00e3b7fef95c2d7befd492b Author: Henry R. Winterbottom <[email protected]> Date: Sun Oct 15 23:27:47 2023 -0600 Remove SENDCOM (#1929) This PR addresses issue #1501. All instances of `SENDCOM` gates have been removed. The workflow was inconsistent in its use of `SENDCOM` to gate movement of files to `COM` and have been removed based on NCO guidelines. Resolves #1501. commit 9a8911a0b30f0367d061facfb3b835480728081d Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Fri Oct 13 14:21:01 2023 +0000 update nth_eupd to 8 for Orion because of out of memmory errors (#1927) Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]> commit ea4dfa5800b5cb529478cc64d329f567393fa37d Author: Guillaume Vernieres <[email protected]> Date: Thu Oct 12 21:29:19 2023 -0400 Marine DA configuration updates (#1922) Minor updates the configuration related to running the marine DA and the coupled UFS. What's proposed in this PR: - Memory increased for the marine DA analysis step - The coupled UFS is (was?) running out of memory without the changes in `config.ufs`. - Updates to the IAU section of MOM_input to allow for a current increment. commit c2d112b40a926c9f33a653cfbb832cb811a60352 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Thu Oct 12 23:52:43 2023 +0000 Fix missing pipe in check_ci (#1926) Bugfix: left out pipe to word count` | wc -l` after updating: `num_platforms=$(ls ../platforms/config.* | wc -l)` to `num_platforms=$(find ../platforms -type f -name "config.*")` when it was flagged by the BASH linter. commit 51d93e15eb30382017aaf72813d34f7010f47948 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Tue Oct 10 19:09:26 2023 +0000 Updated cron bash ci script to remove weekly CI test PR on success (#1915) This PR updates the check CI bash script in cron to remove the PR that is created by the weekly CI test driver when all the tests has passed on all the platforms. This is done by the script checking if all other labels for all the platforms for the PR that has currently been flagged to have run to a successful completion by the check ci bash script. commit 2d64b74a0b0407d01d6f657efa6af9637a131448 Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Wed Oct 4 22:33:25 2023 +0000 CI driver_weekly bugfix deleting new branch if is already on repo (#1899) Bugfix and updates to weekly CI test that deletes the new modified branch if it is already on the repo but now also makes sure that the intermediary branch that creates the PR is coming from emcbot. commit e4a6c35ae020253f07921ca34a17f19e928b0b6c Author: Rahul Mahajan <[email protected]> Date: Wed Oct 4 09:42:12 2023 -0400 Fix typo in cice history filename commit d50938bc4f6705b722338bbea03f925614f953ed Author: Walter Kolczynski - NOAA <[email protected]> Date: Tue Oct 3 23:37:39 2023 -0400 Change metp dependency (#1900) MET+ jobs rely on files already having been placed in the local archive directory, but the job only depended on post, resulting in the job prematurely firing. The dependency is now updated to be on the archive job instead. Resolves #1756 commit 836642bb201cd2e5e205eda2ae4a28993623355d Author: Rahul Mahajan <[email protected]> Date: Tue Oct 3 14:45:57 2023 -0400 Use deterministic marine resolutions for ensemble (#1894) This PR determines the ensemble resolution for ocean, ice and waves based on the deterministic configuration as there is no dual-resolution capability requested for these model components. For cycled DA, if the deterministic uses a coupled model, the ensemble will also be a coupled model. This can be turned off manually via adding `DO_AERO_ENKF`, `DO_OCN_ENKF`, `DO_ICE_ENKF` and `DO_WAVE_ENKF` flags set in `config.base` or `config.efcs`. This is currently handled manually and will be automated when a requirement arises for this flexibility. Fixes #1730 commit 48ba775909870f0d27275128bd07ec134b92c356 Author: Kate Friedman <[email protected]> Date: Mon Oct 2 13:34:02 2023 -0400 Update vrfy.sh to only run MINMON in cycled mode (#1901) Update MINMON if-block in jobs/rocoto/vrfy.sh to only invoke this section when MODE is cycled. Refs #1076 commit e65162f3083c34b639854e3216e2355ff6fccc0b Author: RussTreadon-NOAA <[email protected]> Date: Fri Sep 29 19:18:07 2023 -0400 Update module loads to intel/2022 for jobs running gsi.x and enkf.x (#1882) This PR changes the module loads in g-w jobs `anal.sh`, `eobs.sh`, and `eupd.sh` to use machine specific modulefiles from `sorc/gsi_enkf.fd/modulefiles`. This is necessary because [NOAA-EMC/GSI#571](https://github.com/NOAA-EMC/GSI/pull/571) updated `gsi.x` and `enkf.x` builds to intel/2022 on NOAA RDHPCS machines. Resolves #1863 commit cd439d0bf2ae5fb57139fcb9983aa2755fdc9b2c Author: Rahul Mahajan <[email protected]> Date: Fri Sep 29 15:35:54 2023 -0400 Add coupled forecast-only tests for S2S and S2SW (#1895) This PR: - replaces the PR C48 S2S forecast-only test with a S2SW configuration - adds a weekly C384 S2SWA forecast-only test. The C384 S2SWA is a weekly test and will not be triggered/tested in this PR, but will be tested on Friday. See notes on Orion below in the testing section. @JessicaMeixner-NOAA kindly provided the details in https://github.com/NOAA-EMC/global-workflow/issues/1794#issuecomment-1740768751 commit 02787fe9ba9e5a6881e5ccf9a9e352545eeadb9d Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Fri Sep 29 18:03:23 2023 +0000 Ci rename platform scripts (#1896) Simply renaming the platform config files in ${HOMEgfs}/ci/platforms to config.${MACHINE} so wxflow can read them too in support of up and coming functional testing. commit bb5a58541d6514d16901dca240dfbbc810bd31c8 Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Sep 29 13:28:39 2023 -0400 Merge S2S defaults config back into other configs (#1876) When the prototype S2S was first added, we placed some settings in a `config.defaults.s2sw` file to avoid interference with existing settings. Now that we are moving towards v17 and run S2S regularly, it is time to merge these settings back into the other config files. The wave output frequency settings are updated to the coarser fre- quency as that is more suitable for development. The prior (ops) settings are noted as comments. There are a couple of settings that control ice fields within FV3. These are placed in `config.ice`, so when the ice model is on those settings are still used. Changes the output frequency from 3 to 6. While we may leave this setting as the default for development, it is required right now because the ocean frequency is hard-coded to 6 but links are created based on `$FHOUT_GFS`. Resolving #1629 should correct this limitation. "Gaussian" archive is updated to the former override values. Resolves #1606 Refs #1629 commit 49dc315c1ef6c5f4952a06b0ba70c36e771f128e Author: Walter Kolczynski - NOAA <[email protected]> Date: Fri Sep 29 13:25:58 2023 -0400 Move product functions to separate script (#1891) PR #1822 converted some formerly stand-alone scripts and moved them inside one of the standard product scripts. However, `trim_rh.sh` is also used by gempak and AWIPS, so this change caused those jobs to start failing (they are not yet tested by CI). Those functions have now been moved into a separate product functions script that can be sourced by all the scripts that need the functions. A third similar script was also eliminated and converted into a function. Additionally fixes a base bug in AWIPS and updates some scripts to satisfy (or at least mostly satisfy) the linter. **AWIPS still failing when creating GRIB1 products.** That will be addressed in a future PR (and may need a subject-matter expert). Resolves #1890 commit 3e750d10be577106fb269a78e18765b8d2b8030d Author: Rahul Mahajan <[email protected]> Date: Thu Sep 28 16:21:52 2023 -0400 Fix a few bugs reported by devs (#1893) This PR fixes a …
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Description:
This PR commit the code fixes for compiling GSI and EnKF using Intel 2022 and the hpc-stack built Intel 2022 libraries.
Fixes: #447 GSI fails to run using newer Intel compilers (i.e, Intel 2022)
How Has This Been Tested?
The code was compiled successfully with new intel 2022 compiler on Hera, Jet, and Orion.
The regression test suite was run and all 9 cases were run through without crashes. But all 9 test cases failed because the memory usage of the code with intel 2022 is increased and the results of the analysis with radiance data are slightly different from the code compiled with intel 18.
The GSI hybrid analysis for conus 3km RRFS was also used as test case. The new code produced identical results if there are no satellite radiance data. The new code with satellite radiance data produced slightly difference results comparing to current RRFS GSI analysis. Those differences are tiny and should not impact scientific results.
DUE DATE for merger of this PR into develop is 6/21/2023 (six weeks after PR creation).